CA 02591930 2007-03-30
DEMANDES OU BREVETS VOLUMINEUX
LA PRESENTE PARTIE DE CETTE DEMANDE OU CE BREVETS
COMPREND PLUS D'UN TOME.
CECI EST LE TOME 1 DE 2
NOTE: Pour les tomes additionels, veillez contacter le Bureau Canadien des
Brevets.
JUMBO APPLICATIONS / PATENTS
THIS SECTION OF THE APPLICATION / PATENT CONTAINS MORE
THAN ONE VOLUME.
THIS IS VOLUME I OF 2
NOTE: For additional volumes please contact the Canadian Patent Office.
CA 02591930 2007-03-30
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SECRETED AND TRANSMEMBYtANE POLYPEP'lTDES AND NUCLEIC ACIDS ENCODING THE
SAME
FISLD OF THE INVENTION
The present invention relates generally to the identification and isolation of
novel DNA and to the
recombinant production of novel polypeptides.
BACKGjLOUND OF THE INVENTION
Extracellular proteins play impartant roles m, among other things, the
formation, differentiation and
maintenance of multicellular organisms. The fate of many individual cells,
e.g., proli,feration, migration,
differentiation, or interaction with other cells, is typically governed by
information received fcam other cells
and/or the immediate environment. This information is often transmitted by
secreted polypeptides (for instance,
mitogenic factors, survival factors, cytotoxic factors, differentiation
factors, neuropeptides, and hormones) which
are, in turn, received and interpreted by diverse cell receptors or membrane-
bound proteins. These secreted
polypeptides or signaling molecules normally pass through the cellular
secretory pathway to reach their site of
action in the extraeelhtlar environment.
Secreted proteins have various industrial applications, including as
pharmaceuticals, diagnostics,
biosensors and bioreactors. Most protein drugs available at present, such as
thrombolytic agents, interferons,
interleukins, erythropoietins, colony stimulatutg factors, and various other
cytokines, are secretozy proteins.
Their receptors, which are membrane proteins, also have potential as
therapeutic or diagnostic agents. Efforts
are being undertal4en by both industry and academia to identify new, native
secreted proteins. Many efforts are
focused on the screening of mammalian recombinant DNA libraries to identify
the coding sequences for novel
secreted proteins. Examples of screening methods and techniques are described
in the literature [see, for
example, Klein et al., Proc. Natl. Acad. Sci. 93:7108-7113 (1996); U.S. Patent
No. 5,536,637)].
Membrane-bound proteins and receptors can play important roles in, among other
things, the formation,
differentiation and maintenance of muiticellular organisms. The fate of many
individual cells, e.g., proliferation,
migration, differentiation, or interaction with other cells, is typically
governedby information reoeived from other
cells and/or the immediate environment. This information is often transmitted
by secreted polypeptides (for
instance, mitogenic factors, survival factors, cytotoxic factors,
differentiation factors, neuropeptides, and
hormones) which are, in turn, received and interpreted by diverse cell
receptors or membrane-bound proteins.
Such membrane-bou.nd proteins and cell receptors include, but are not limited
to, cytoldne receptors, receptor
ldnases, receptor phosphatases, receptors involved in cell-cell interaetions,
and celluiar adhesin molecules like
selectins and integrins. For instance, transduction of signals that regulate
cell growth and differentiation is
regalated in part by phosphorylation of various ceiluiar proteins. Protein
tyrosine IUnases, enzymes that cataiyze
that process, can also act as growth factor receptors. Examples include
fibroblast growth factor receptor and
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nerve growth factor receptor.
Membrane-bound proteins and receptor molecules have various industrial
applications, including as
pharmaceutical and diagnostic agents. Receptor immunoadhesins, for instance,
can be employed as therapeutic
agents to block receptor-ligand interactions. The membrane-bound proteins can
also be employed for screening
of potential peptide or small molecule inhibitors of the relevant
receptor/ligand interaction.
Efforts are being undertaken by both industry and academia to identify new,
native receptor or
membrane-bound proteins. Many efforts are focused on the screening of
mammalian recombinant DNA libraries
to identify the coding sequences for novel receptor or membrane-bound
proteins.
SUMMARY OFTHE INVENTION
In one embodiment, the invention provides an isolated nucleic acid molecule
comprising a nucleotide
sequence that encodes a PRO polypeptide.
In one aspect, the isolated n.ucleic acid molecule comprises a nucleotide
sequence having at least about
80% nucleic acid sequence identity, alternatively at least about 81 % nucleic
acid sequence identity, alternatively
at least about 82 % nucleic acid sequence identity, alternatively at least
about 83 % nucleic acid sequence identity,
alternatively at least about 84% nucleic acid sequence identity, alternatively
at least about 85% micleic acid
sequence identity, alternatively at least about 86 % nucleic acid sequence
identity, alternatively at least about 87 %
nucleic acid sequence identity, alternatively at least about 88 % micleic acid
sequence identity, alternatively at least
about 89% nucleic acid sequence identity, alternatively at least about 90%
nucleic acid sequence identity,
alternatively at least about 91% nucleic acid sequence identity, alternatively
at least about 92% nucleic acid
sequence identity, alternatively at least about 93 % micleic acid sequence
identity, alternatively at least about 94%
nucleic acid sequence identity, alternatively at least about 95 % nucleic
acidsequence identity, alternatively at least
about 96% nucleic acid sequence identity, alternatively at least about 97%
nucleic acid sequence identity,
alternatively at least about 98% nucleic acid sequence identity and
alternatively at least aliout 99% nucleic acid
sequence identity to (a) a DNA molecule encoding a PRO polypeptide having a
full length amino acid sequence
as disclosed herein, an amino acid sequence lacldng the signal peptide as
disclosed herein, an extracellular domain
of a tranamembrane protein, with or without the signal peptide, as disclosed
herein or any other specifically
defined fragment of the full-length amino acid sequence as disclosed herein,
or (b) the complement of the DNA
molecule of (a).
In other aspects, the isolated nucleic acid molecule comprises a nucleotide
sequence having at least about
80% nucleic acid sequemce identity, alternatively at least about 81 % nucleic
acid sequence identity, altenoatively
at least about 82% nucleic acid sequence identity, alternatively at least
about 83 % nucleic acid sequence identity,
alternatively at least about 84% nucleic acid sequence identity, alternatively
at least about 85% nucleic acid
sequence identity, alternatively at least about 86 % nucleic acid sequence
identity, alternatively at least about 87 %
nucleic acid sequence identity, alternatively at least about 88 % nucleic acid
sequence identity, alternatively at least
about 89% nucleic acid sequence identity, aiternatively at least about 90%
nucleic acid sequence identity,
alternatively at least about 91% nucleic acid sequence identity, alternatively
at least about 92% nucleic acid
sequence identity, alternatively at least about 93 % nucleic acid sequence
identity, alternatively at least about 94%
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nucleic acid sequence identlty, alternadvely at least about 95 9b nucleic acid
sequence identity, alternatively at least
about 96% nucleic acid sequence identity, alternatively at least about 97%
nucleic acid sequence identity,
alternatively at least about 9896 micleic acid sequence identity and
alternatively at least about 99% nucleic acid
sequence identity to (a) a DNA molecule comprising the coding sequence of a
full-length PRO polypeptide cDNA
as disolased herein, the coding sequence of a PRO polypeptide lacking the
signal peptide as disclosed herein, the
coding sequence of an extracellutar domain of a transmembrane PRO polypeptide,
with or without the signal
peptide, as disclosed herein or the coding sequence of any other specifically
defmed fragment of the full-length
amino acid sequence as disclosed herein, or (b) the complement of the DNA
molecule of (a).
In a further aspect, the invention concerns an isolated nucleic acid molecule
comprising a nucleotide
sequence having at least about 80% nucleic accid sequence idendty,
alternatively at least about 8196 nucleic acid
sequence identity, alternatively at least about 82% nucleic acid sequence
identity, alternatively at least about 83 %
nucleic acid sequence identity, alternatively at least about 84% nucleic acid
sequence identity, alternatively at least
about 85% nucleic acid sequence identity, alternatively at least about 86%
nucleic acid sequence identity,
alternatively at least about 87% nucleic acid sequence identity, alternatively
at least about 889b nucleic acid
sequence identity, alternatively at least about 89% nucleic acid sequence
identity, alternatively at least about 90%
nucleic acid sequence identity, alternatively at least about 9196 nucleic acid
sequence identity, alternatively at least
about 92% nucleic acid sequence identity, alternatively at least about 93%
nucleic acid sequence identity,
alternatively at least about 94% nucleic acid sequence identity, alternatively
at least about 95% nucleic acid
sequence identity, altesnatively at least about 9696 mieleic acid sequence
identity, altetnatively at least about 9796
nucleic acid sequence identity, alternatively at least about 98 96 nucleic
acid sequence identity and alternatively
at least about 9996 nucleic acid seqnence identity to (a) a DNA molecule that
encodes the same mature polypeptide
encoded by any of the human protein cDNAs deposited with the ATCC as disclosed
herein, or (b) the complement
of the DNA molecule of (a).
Another aspect the inventionprovides an isolated nucleic acid molecule
c:omprising a nucleotide sequence
encoding a PRO polypeptide which is either transmembrane domain-deleted or
transmembrane domain-inactivated,
or is complementary to such encoding nucleotide sequence, wherein the
transmembrane domain(s) of sueh
polypeptide are disclosed herein. Therefore, soluble extracellular domains of
the herein described PRO
polypeptides are contemplated.
Another embodiment is directed to fragments of a PRO polypeptide coding
sequence, or the complement
thereof, that may find use as, for example, hybridization probes, for encoding
fragments of a PRO polypeptide
that may optionally encode a polypeptide comprising a bindmg sfte for an anti-
PRO antibody or as antisense
oligonucleotide probes. Such nucleic acid fragments are usually at least about
10 nucleotides in length,
alternatively at least about 15 nncleotides in length, alternatively at least
about 20 nucleotides in length,
alternatively at least about 30 nucleotides in length, alternatively at least
about 40 nucleotides in length,
alternatively at least about 50 nucleotides in length, alternatively at least
about 60 nucleotides in length,
alternatively at least about 70 nucleotides in length, alternatively at least
about 80 flucleotides in length,
alternatively at least about 90 nucleotides in length, alternatively at least
about 100 nucleotides in length,
alternatively at least about 110 nucleotides in length, alternatively at least
about 120 nucleotides in length,
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alternatively at least about 130 nucleotides in length, altematively at least
about 140 nucleotides in length,
alternatively at least about 150 nucleotides in length, aiternatively at least
about 160 nucleotides in length,
altematively at least about 170 nucleotides in length, altematively at least
about 180 nucleotides in length,
alternatively at least about 190 nucleotides in length, alternatively at least
about 200 nucleotides in length,
alternatively at least about 250 nucleotides in length, alternatively at least
about 300 nucleotides in length,
alternatively at least about 350 nucleotides in length, altemaiively at least
about 400 nucleotides in length,
alternatively at least about 450 nucleotides in length, alternatively at least
about 500 nucleotides in length,
alternatively at least about 600 nucleotides in length, altematively at least
about 700 nncleotides in length,
alternatively at least about 800 nucleotides in length, alternatively at least
about 900 nucleotides in length and
alternatively at least about 1000 nucleotides in length, wherein in this
context the term "about" means the
referencxd aucleotide sequence length plus or minos 10% of that referenced
length. It is noted that novel
fragments of a PRO polypeptide-encoding nucleotide sequence may be determined
in a routine manner by aligning
the PRO polypeptide-encoding nucleotide sequence with other known nucleotide
sequences using any of a number
of well known sequence alignment programs and determining which PRO
polypeptide-encoding nucleotide
sequence fragment(s) are novel. All of such PRO polypeptide-encoding
nucleotide sequences are contemplated
herein. Also contemplated are the PRO polypeptide fragments encoded by these
nucleotide molecule fragments,
preferably those PRO polypeptide fragments that comprise a binding site for an
anti-PRO antibody.
In another embodiment, the invention provides isolated PRO polypeptide encoded
by any of the isolated
nucleic acid sequences hereinabove identified.
In a certain aspect, the invention concerns an isolated PRO polypeptide,
comprising an amino acid
sequence having at least about 80% amino acid sequence identity, alternatively
at least about 81% amino acid
sequence idemtity, alternatively at least about 82% amino acid sequence
identity, alternatively at least about 83 %
amino acid sequence ident.ity, altiernatively at least about 84 % amino acid
sequence identity, alternatively at least
about 85% amino acid sequence identity, alternatively at least about 86% amino
acid sequence identity,
altematively at least about 87% amino acid sequence identity, alternatively at
least about 88% amino acid
sequence identity, alternatively at least about 89% amino acid sequence
identity, altematively at least about 90 %
amino acid sequence identity, alternatively at least about 91 % amino acid
sequence identity, alternatively at least
about 92% amino acid sequence identity, alternatively at least about 93% amino
acid sequence identity,
alternatively at least about 94% amino acid sequence identity, altematively at
least about 95% amino acid
sequence identity, alternatively at least about 96% amino acid seqnence
identity, alternatively at least about 97%
amino acid sequence identity, alternatively at least about 98 % amino acid
sequence identity and alternatively at
least about 99% amino acid sequence identity to a PRO polypeptide having a
full-length amino acid sequence as
disclosed herein, an amino acid sequence lacking the signal peptide as
disclosed herein, an extraoellular domain
of a transmembrane protein, with or without the signal peptide, as disclosed
herein or any other specifically
de5ned fragment of the full-length amino acid sequence as disclosed herein.
In a fiirther aspect, the invention concerns an isolated PRO polypeptide
comprising an amino acid
sequence having at least about 80 % amino acid sequenoe identity,
alternatively at least about 81 % amino acid
sequence identity, alternatively at least about 82% amino acid sequence
identity, alternatively at least about 83 96
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amino acid sequence identity, altematively at least about 84 % amino acid
sequence identity, alternatively at least
about 85% amino acid sequence identity, altematively at least about 86% amino
acid sequence identity,
altematively at least about 87% amino acid sequence identity, alternatively at
least about 88% amino acid
sequence identity, alternatively at least about 89% amino acid sequence
identity, alternatively at least about 904'0
amino acid sequence identity, alternatively at least about 91 ',6 amino acid
sequence identity, alternatively at least
about 92% amino acid sequence identity, alternatively at least about 93% amino
acid sequence identity,
altematively at least about 94% amino acid sequence identity, alternatively at
least about 95% amino acid
sequence identity, alternatively at least about 96% amino acid sequence
identity, alternatively at least about 97%
amino acid sequence identity, alternatively at least about 98 % amino acid
sequence identity and alternatively at
least about 99% amino acid sequence identity to an amino acid sequence encoded
by any of the human protein
cDNAs deposited with the ATCC as disclosed herein.
In a specific aspect, the invention provides an isolated PRO polypeptide
without the N-terminal signal
sequence and/or the initiating methionine and is encoded by a nucleotide
sequence that encodes such an amino acid
sequence as hereinbefore descrn'bed. Processes for producing the same are also
herein described, wherein those
processes comprise culturing a host cell comprising a vector which comprises
the appropriate encoding nucleic
acid molecule under conditions suitable for expression of the PRO polypeptide
and recovering the PRO
polypeptide from the cell culture.
Another aspect the invention provides an isolated PRO polypeptide which is
either transmembrane
domain-deleted or transmembrane domain-inactivated. Processes for producing
the same are also herein
described, wherein those processes comprise culturing a host cell comprising a
vector which comprises the
appropriate encoding nucleic acid molecule under conditions suitable for
expression of the PRO polypeptide and
recovering the PRO polypeptide from the cell culture.
In yet another embodiment, the invention concerns agonists and antagonists of
a native PRO polypeptide
as defined herein. In a particular embodiment, the agonist or antagonist is an
anti-PRO antibody or a small
molecule.
In a further embodiment, the invention concerns a method of identifying
agonists or antagonists to a PRO
polypeptide which comprise contacting the PRO polypeptide with a candidate
molecule and monitoring abiological
activity mediated by said PRO polypeptide. Preferably, the PRO polypeptide is
a native PRO polypeptide.
In a still further embodiment, the invention concerns a composition of matter
comprising a PRO
polypeptide, or an agonist or antagonist of a PRO polypeptide as herein
described, or an anti-PRO antibody, in
combination with a carrier. Optionally, the carrier is a pharmaceutically
acceptable carrier.
Another embodiment of the present invention is directed to the use of a PRO
polypeptide, or an agonist
or antagonist thereof as hereinbefore described, or an anti-PRO antibody, for
the preparation of a medicament
useful in the treatment of a condition which is responsive to the PRO
polypeptide, an agonist or antagonist thereof
or an anti-PRO antibody.
In other embodiments of the present invention, the invention provides vectors
comprising DNA encoding
any of the herein described polypeptides. Host cell comprising any such vector
are also provided. By way of
example, the host cells may be CHO cells, E. colf, or yeast. A process for
producing any of the herein described
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polypeptides is fiulher provided and comprises cultnring host cells under
conditions suitable for expression of the
desired polypeptide and recovering the desired polypeptide from the cell
culture.
In other embodiments, the invention provides chimeric molecules comprising any
of the herein described
polypeptides fused to a heterologous polypeptide or amino acid sequence.
Example of such chimeric molecules
comprise any of the herein described polypeptides fused to an epitope tag
sequence or a Fc region of an
immunoglobulin.
In another embodiment, the invention provides an antibody which binds,
preferably specifically, to any
of the above or below described polypeptides. Optionally, the antibody is a
monoclonal antibody, humanized
antibody, antibody fragment or single-chain antibody.
In yet other embodiments, the invention provides oligonucleotide probes which
may be usefal for
isolating genomic and cDNA nucleotide sequences, measuring or detecting
expression of an associated gene or
as antisense probes, wherein those probes may be derived from any of the above
or below described nucleotide
sequences. Preferred probe lengths are described above.
In yet other embodiments, the present invention is directed to methods of
using the PRO polypeptides
of the present invention for a variety of uses based upon the ftnctional
biological assay data presented in the
Examples below.
BRIEF DESCRIPTION OF THE DRAWINGS
Figures lA-lB show a nucleotide sequence (SEQ ID NO:1) of a native sequence
PR06004 cDNA,
wherein SEQ ID NO:1 is a clone designated herein as "DNA92259".
Figure 2 shows the amino acid sequence (SEQ ID NO:2) derived from the coding
sequence of SEQ ID
NO:1 shown in Figures 1A-1B.
Figure 3 shows a nucleotide sequence (SEQ ID NO:3) of a native sequence
PR04981 cDNA, wherein
SEQ ID NO:3 is a clone designated herein as "DNA94849-2960".
Figure 4 shows the amino acid sequence (SEQ ID NO:4) derived from the coding
sequence of SEQ ID
NO:3 shown in Figure 3.
Figure 5 shows a nucleotide sequence (SEQ ID NO:5) of a native sequence
PR07174 cDNA, wherein
SEQ ID NO:5 is a clone designated herein as "DNA96883-2745".
Figure 6 shows the amino acid sequence (SEQ ID NO:6) derived from the coding
sequence of SEQ ID
NO:5 shown in Figure 5.
Figure 7 shows a nucleotide sequence (SEQ II) NO:7) of a native sequence
PRO5778 cDNA, wherein
SEQ ID NO:7 is a clone designated herein as "DNA96894-2675".
Figure 8 shows the amino acid sequence (SEQ ID NO:8) derived from the coding
sequence of SEQ ID
NO:7 shown in Figure 7.
Figure 9 shows a nucleotide sequence (SEQ ID NO:9) of a native sequence
PR04332 cDNA, wherein
SEQ ID NO:9 is a clone designated herein as "DNA100272-2969".
Figure 10 shows the amino acid sequence (SEQ ID NO: 10) derived from the
coding sequence of SEQ
ID NO:9 shown in Figure 9.
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Figure 11 shows a nucleotide sequence (SEQ ID NO: 11) of a native sequence
PRO9799 cDNA, wherein
SEQ ID NO: 11 is a clone designated herein as "DNA108696-2966".
Figure 12 shows the amino acid sequence (SEQ ID NO: 12) derived from the
coding sequence of SEQ
ID NO:11 shown in Figure 11.
Figure 13 shows a nucleotide sequence (SEQ ID NO: 13) of a native sequence
PR09909 eDNA, wherein
SEQ ID NO:13 is a clone designated herein as "DNA117935-2801".
Figure 14 shows the amino acid sequence (SEQ ID NO: 14) derived from the
coding sequence of SEQ
ID NO:13 shown in Figure 13.
Figure 15 shows a nucleotide sequence (SEQ ID NO: 15) of a native sequence
PR09917 cDNA, wherein
SEQ ID NO: 15 is a clone designated herein as "DNA119474-2803".
Figure 16 shows the amino acid sequence (SEQ ID NO: 16) derived from the
coding sequence of SEQ
ID NO:15 shown in Figure 15.
Figure 17 shows a nucleotide sequence (SEQ ID NO: 17) of a native sequence
PRO9771 cDNA, wherein
SEQ ID NO:17 is a clone designated herein as "DNA119498-2965".
Figure 18 shows the amino acid sequence (SEQ ID NO:18) derived from the coding
sequence of SEQ
ID NO:17 shown in Figure 17.
Figure 19 shows a nucleotide sequence (SEQ ID NO: 19) of a native sequence
PR09877 cDNA, wherein
SEQ ID NO:19 is a clone designated herein as "DNA119502-2789".
Figure 20 shows the amino acid sequence (SEQ ID NO:20) derived from the coding
sequence of SEQ
ID NO:19 shown in Figure 19.
Figure 21 shows a nucleotide sequence (SEQ ID NO:21) of a native sequence
PR09903 cDNA, wherein
SEQ ID NO:21 is a clone designated herein as "DNA119516-2797".
Figure 22 shows the amino acid sequence (SEQ ID NO:22) derived from the coding
sequence of SEQ
ID NO:21 shown in Figure 21.
Figure 23 shows a nucleotide sequence (SEQ ID NO:23) of a native sequence
PR09830 cDNA, wherein
SEQ ID NO:23 is a clone designated herein as "DNA119530-2968".
Figure 24 shows the amino acid sequence (SEQ ID NO:24) derived from the coding
sequence of SEQ
ID NO:23 shown in Figure 23.
Figure 25 shows a nucleotide sequence (SEQ ID NO:25) of a native sequence
PR07155 cDNA, wherein
SEQ ID NO:25 is a clone designated herein as "DNA121772-2741".
Figure 26 shows the amino acid sequence (SEQ ID NO:26) derived from the coding
sequence of SEQ
ID NO:25 shown in Figure 25.
Figure 27 shows a nucleotide sequence (SEQ ID NO:27) of a native sequence
PR09862 cDNA, wherein
SEQ ID NO:27 is a clone designated herein as "DNA125148-2782".
Figure 28 shows the amino acid sequence (SEQ ID NO:28) derived from the coding
sequence of SEQ
ID NO:27 shown in Fignre 27.
Figure 29 shows a nucleotide sequence (SEQ ID NO:29) of a native sequence
PR09882 cDNA, wherein
SEQ ID NO:29 is a clone designated herein as "DNA125150-2793".
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Figure 30 shows the amino acid sequence (SEQ ID NO:30) derived from the coding
sequence of SEQ
ID NO:29 shown in Fignre 29.
Figure 31 shows a micleotide sequence (SEQ ID NO:31) of a native sequence
PR09864 cDNA, wherein
SEQ ID NO:31 is a clone designated herein as "DNA125151-2784".
Figure 32 shows the amino acid sequence (SEQ ID NO:32) derived from the coding
sequence of SEQ
ID NO:31 shown in Figure 31.
Figure 33 shows a nubleotide sequence (SEQ ID NO:33) of a native sequence
PRO10013 cDNA, wherein
SEQ ID NO:33 is a clone designated herein as "DNA125181-2804".
Figure 34 shows the amino acid sequence (SEQ ID NO:34) derived from the coding
sequence of SEQ
ID NO:33 shown in Figure 33.
Figure 35 shows a nucleotide sequence (SEQ ID NO:35) of a native sequence
PR09885 cDNA, wherein
SEQ ID NO:35 is a clone designated herein as "DNA125192-2794".
Figure 36 shows the amino acid sequence (SEQ ID N0:36) derived from the coding
sequence of SEQ
ID NO:35 shown in Figure 35.
Figure 37 shows a micleotide sequence (SBQ ID N0:37) of a native sequence
PR09879 cDNA, wherein
SEQ ID N0:37 is a clone designated herein as "DNA125196-2792'.
Figure 38 shows the amino acid sequence (SEQ ID NO:38) derived from the coding
sequence of SEQ
ID N0:37 shown in Figure 37.
Figure 39 shows anucleotide sequence (SEQ ID N0:39) of anative sequence
PRO10111 cDNA, wherein
SEQ ID N0:39 is a clone designated herein as "DNA125200-2810".
Figure 40 shows the amino acid sequence (SEQ ID NO:40) derived from the coding
sequence of SEQ
ID NO:39 shown in Figure 39.
Figure 41 shows a nucleotide sequence (SEQ ID N0:41) of a native sequence
PR09925 cDNA, wherein
SEQ ID NO:41 is a clone designated herein as "DNA125214-2814".
Figure 42 shows the aminp acid sequenee (SEQ ID N0:42) derived from the coding
seqnence of SEQ
ID NO:41 shown in Figure 41.
Figure 43 shows a nucleotide sequence (SEQ ID N0:43) of a native sequence
PR09905 cDNA, wherein
SEQ ID N0:43 is a clone designated herein as "DNA125219-2799". -
Figure 44 shows the amino acid sequence (SEQ ID N0:44) derived from the coding
sequence of SEQ
ID N0:43 shown in Figure 43.
Figure 45 shows a nucleotide sequence (SBQ ID NO:45) of a native sequence
PRO10276 cDNA, wherein
SEQ ID N0:45 is a clone designated herein as "DNA128309-2825".
Figure 46 shows the amino acid sequence (SEQ ID N0:46) derived from the coding
sequence of SEQ
ID NO:45 shown in Figure 45.
Figure 47 shows a nucleotide sequersce (SEQ ID N0:47) of a native sequence
PR09898 eDNA, wherein
SEQ ID NO:47 is a clone designated herein as "DNA129535-2796".
Figure 48 shows the amino acid sequence (SEQ ID NO:48) derived from the coding
sequence of SEQ
ID NO:47 shown in Figure 47.
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Figure 49 shows a nucleotide sequence (SEQ ID NO:49) of a native sequence
PR09904 cDNA, wherein
SEQ ID NO:49 is a clone designated herein as "DNA129549-2798".
Figure 50 shows the amino acid sequence (SEQ ID NO:50) derived from the coding
sequence of SEQ
ID NO:49 shown in Figure 49.
Figure 51 shows a nucleotide sequence (SEQ ID NO:51) of a native sequence PRO
19632 cDNA, wherein
SEQ ID NO:51 is a clone designated herein as "DNA129580-2863".
Figure 52 shows the amino acid sequence (SEQ ID NO:52) derived from the coding
sequence of SEQ
ID NO:51 shown in Figure 51.
Figure 53 shows anucleotide sequence (SEQ ID NO:53) of a native sequence
PR019672 cDNA, wherein
SEQ ID NO:53 is a clone designated herein as "DNA129794-2967".
Figure 54 shows the amino acid sequence (SEQ ID NO:54) derived from the coding
sequence of SEQ
ID NO:53 shown in Figure 53.
Figure 55 shows a nucleotide sequence (SEQ ID NO:55) of a native sequence
PR09783 cDNA, wherein
SEQ ID NO:55 is a clone designated herein as "DNA131590-2962".
Figure 56 shows the amino acid sequence (SEQ ID NO:56) derived from the coding
sequence of SEQ
ID NO:55 shown in Figure 55.
Figure 57 shows anucleotide sequence (SEQ ID NO:57) of a native sequence PRO
10112 cDNA, wherein
SEQ ID NO:57 is a clone designated herein as "DNA135173-2811".
Figure 58 shows the amino acid sequence (SEQ ID NO:58) derived from the coding
sequence of SEQ
ID NO:57 shown in Figure 57.
Figures 59A-59B show a nucleotide sequence (SEQ ID NO:59) of a native sequence
PRO10284 eDNA,
wherein SEQ ID NO:59 is a clone designated herein as "DNA138039-2828".
Figure 60 shows the amino acid sequence (SEQ ID NO:60) derived from the coding
sequence of SEQ
ID NO:59 shown in Figures 59A-59B.
Figure 61 shows a nucleotide sequence (SEQ ID NO:61) of a native sequence
PRO10100 cDNA, wherein
SEQ ID NO:61 is a clone designated herein as "DNA139540-2807".
Figure 62 shows the amino acid sequence (SEQ ID NO:62) derived from the coding
sequence of SEQ
ID NO:61 shown in Figure 61.
Figure 63 shows a nucleotide sequence (SEQ ID NO:63) of a native sequence
PR019628 cDNA, wherein
SEQ ID NO:63 is a clone designated herein as "DNA139602-2859".
Figure 64 shows the amino acid sequence (SEQ ID NO:64) derived from the coding
sequence of SEQ
ID NO:63 shown in Figure 63.
Figure 65 shows a nucleotide sequence (SEQ ID NO:65) of a native sequence
PRO19684 cDNA, wherein
SEQ I.T) NO:65 is a clone designated herein as "DNA139632-2880".
Figure 66 shows the amino acid sequence (SEQ ID NO:66) derived from the coding
sequence of SEQ
ID NO:65 shown in Figure 65.
Figure 67 shows a nucleotide sequence (SEQ ID NO:67) of a native sequence PRO
10274 cDNA, wherein
SEQ ID NO:67 is a clone designated herein as "DNA139686-2823".
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Figure 68 shows the amino acid sequence (SEQ ID NO:68) derived from the coding
sequence of SEQ
ID N0:67 shown in Figure 67.
Figure 69 shows a nucleotide sequence (SEQ ID NO:69) of a native sequence
PR09907 cDNA, wherein
SEQ ID NO:69 is a clone designated herein as "DNA142392-2800".
Figure 70 shows the amino acid sequence (SEQ ID NO:70) derived from the coding
sequence of SEQ
ID NO:69 shown in Figure 69.
Figure 71 shows a nucleotide sequence (SEQ ID NO:71) of a native sequence
PR09873 cDNA, wherein
SEQ ID NO:71 is a clone designated herein as "DNA143076-2787".
Figure 72 shows the amino acid sequence (SEQ ID NO:72) derived from the coding
sequence of SEQ
ID NO:71 shown in Figure 71.
Figure 73 shows a nucleotide sequence (SEQ ID NO:73) of a native sequence
PRO10201 cDNA, wherein
SEQ ID NO:73 is a clone designated herein as "DNA143294-2818".
Figure 74 shows the amino acid sequence (SEQ ID NO:74) derived from the coding
sequence of SEQ
ID NO:73 shown in Figure 73.
Figure 75 shows a nucleotide sequence (SEQ ID NO:75) of a native sequence
PRO10200 cDNA, wherein
SEQ ID NO:75 is a clone designated herein as "DNA143514-2817".
Figure 76 shows the amino acid sequence (SEQ ID NO:76) derived from the coding
sequence of SEQ
ID NO:75 shown in Figure 75.
Figure 77 shows anucleotide sequence (SEQ ID NO:77) of a native sequence
PRO10196 cDNA, wherein
SEQ ID NO:77 is a clone designated herein as "DNA144841-2816".
Figure 78 shows the amino acid sequence (SEQ ID NO:78) derived from the coding
sequence of SEQ
ID NO:77 shown in Figure 77.
Figure 79 shows anucleotide sequence (SEQ ID NO:79) of a native sequence PRO
10282 cDNA, wherein
SEQ ID NO:79 is a clone designated herein as "DNA148380-2827".
Figure 80 shows the amino acid sequence (SEQ ID NO:80) derived from the coding
sequence of SEQ
ID NO:79 shown in Figure 79.
Figure 81 shows anucleotide sequence (SEQ ID NO:81) of a native sequence PRO
19650 cDNA, wherein
SEQ ID NO:81 is a clone designated herein as "DNA149995-2871".
Figure 82 shows the amino acid sequence (SEQ ID NO:82) derived from the coding
sequence of SEQ
ID NO:81 shown in Figure 81.
Figure 83 shows anucleotide sequence (SEQ ID NO:83) of a native sequence
PR021184 cDNA, wherein
SEQ ID NO:83 is a clone designated herein as "DNA167678-2963".
Figure 84 shows the amino acid sequence (SEQ ID NO:84) derived from the coding
sequence of SEQ
ID NO:83 shown in Figure 83.
Figure 85 shows a nucleotide sequence (SEQ ID NO:85) of a native sequence
PR021201 eDNA, wherein
SEQ ID NO:85 is a clone designated herein as "DNA168028-2956".
Figure 86 shows the amino acid sequence (SEQ ID NO:86) derived from the coding
sequence of SEQ
ID NO:85 shown in Figure 85.
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Figure 87 shows anucleotide sequence (SEQ ID NO:87) of anative sequence
PRO21175 cDNA, wherein
SEQ ID NO:87 is a clone designated herein as "DNA173894-2947".
Figure 88 shows the amino acid sequence (SBQ ID NO:88) derived from the coding
sequence of SEQ
ID NO:87 shown in Figure 87.
Figare 89 shows a micleotide sequence (SEQ ID N0:89) of a native sequence
PRO21340 cDNA, wherein
SEQ ID NO:89 is a clone designated herein as "DNA176775-2957".
Figure 90 shows the amino acid sequence (SEQ ID NO:90) derived from the coding
sequence of SEQ
ID NO:89 shown in Figure 89.
Figure 91 shows a nucleotide sequence (SEQ ID N0:91) of a native sequence
PRO21384 cDNA, wherein
SEQ ID N0:91 is a clone designated herein as "DNA177313-29820.
Figure 92 shows the amino acid sequence (SEQ ID NO:92) derived from the coding
sequence of SEQ
ID NO:91 shown in Figure 91.
Figure 93 shows a nucleotide sequence (SEQ ID NO:93) of a native sequence
PR0982 cDNA, wherein
SEQ ID NO:93 is a clone designated herein as "DNA57700-1408".
Figure 94 shows the amino acid sequence (SEQ ID NO:94) derived from the coding
sequence of SEQ
ID NO:93 shown in Figure 93.
Figure 95 shows a nucleotide sequence (SEQ ID NO:95) of a native sequence
PRO1160 cDNA, wherein
SEQ ID NO:95 is a clone designated herein as "DNA62872-1509".
Figure 96 shows the amino acid sequence (SEQ ID NO:96) derived from the coding
sequence of SEQ
ID NO:95 shown in Figure 95.
Figure 97 shows a nucleotide sequence (SEQ ID NO:97) of a native sequence
PRO1187 cDNA, wherein
SEQ ID NO:97 is a clone designated herein as "DNA62876-1517".
Figure 98 shows the amino acid sequence (SEQ ID NO:98) derived from the coding
sequence of SEQ
ID NO:97 shown in Figure 97.
Figure 99 shows a nucleotide sequence (SEQ ID NO:99) of a native sequence
PR01329 cDNA, wherein
SEQ ID NO:99 is a clone designated herein as "DNA66660-1585".
Figure 100 shows the amino acid sequence (SBQ ID NO: 100) derived from the
coding sequence of SEQ
ID NO:99 shown in Figure 99.
Figure 101 shows anucleotide sequence (SEQ ID NO: 101) of a native sequence
PR0231 cDNA, wherein
SEQ ID NO: 101 is a clone designated herein as "DNA34434-1139".
Figure 102 shows the amino acid sequence (SEQ ID NO:102) derived from the
coding sequence of SEQ
ID NO:101 shown in Figure 101.
Figure 103 shows a nucleotide sequence (SEQ ID NO: 103) of a native sequence
PR0357 cDNA, wherein
SEQ ID NO:103 is a clone designated herein as "DNA44804-1248".
Figure 104 shows the amino acid sequence (SEQ ID NO: 104) derived from the
coding sequence of SEQ
ID NO:103 shown in Figure 103.
Figure 105 shows a nucleotide sequence (SEQ ID NO: 105) of a native sequence
PRO725 cDNA, wherein
SEQ ID NO: 105 is a clone designated herein as "DNA52758-1399".
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Figure 106 shows the amino acid sequence (SEQ ID N0:106) derived from the
coding sequence of SEQ
ID NO:105 shown in Figure 105.
Figure 107 shows a nucleotide sequence (SEQ ID NO: 107) of a native sequence
PRO1155 cDNA,
wherein SEQ ID NO:107 is a clone designated herein as "DNA59849-1504".
Figure 108 shows the amino acid sequence (SEQ ID N0:108) derived from the
coding sequence of SEQ
ID NO:107 shown in Figure 107.
Figure 109 shows a nucleotide sequence (SEQ ID NO:109) of a native sequence
PR01306 cDNA,
wherein SEQ ID N0:109 is a clone designated herein as "DNA65410-1569".
Figure 110 shows the amino acid sequence (SEQ ID NO: 110) derived from the
coding sequence of SEQ
ID NO: 109 shown in Figure 109.
Figure 111 shows a nucleotide sequence (SEQ ID NO:111) of a native sequence
PR01419 cDNA,
wherein SEQ ID NO: 111 is a clone designated herein as "DNA71290-1630".
Figure 112 shows the amino acid sequence (SEQ ID NO: 112) derived from the
coding sequence of SEQ
ID NO:111 shown in Figure 111.
Figure 113 shows a nucleotide sequence (SEQ ID NO:113) of a native sequence
PR0229 cDNA, wherein
SEQ ID NO:113 is a clone designated herein as "DNA33100-1159".
Figure 114 shows the amino acid sequence (SEQ ID NO: 114) derived from the
coding sequence of SEQ
ID NO:113 shown in Figure 113.
Figure 115 shows a nucleotide sequence (SEQ ID NO: 115) of a native sequence
PRO1272 cDNA,
wherein SEQ ID NO:115 is a clone designated herein as "DNA64896-1539".
Figure 116 shows the amino acid sequence (SEQ ID N0:116) derived from the
coding sequence of SEQ
ID NO:115 shown in Figure 115.
Figure 117 shows a nucleotide sequence (SEQ ID NO:117) of a native sequence
PR04405 cDNA,
wherein SEQ ID NO:117 is a clone designated herein as "DNA84920-2614".
Figure 118 shows the amino acid sequence (SEQ ID N0:118) derived from the
coding sequence of SEQ
ID NO:117 shown in Figure 117.
Figure 119 shows a nucleotide sequence (SEQ ID NO: 119) of a native sequence
PRO181 eDNA, wherein
SEQ ID NO: 119 is a clone designated herein as "DNA23330-1390".
Figure 120 shows the amino acid sequence (SEQ ID NO: 120) derived from the
coding sequence of SEQ
ID NO:119 shown in Figure 119.
Figure 121 shows a nucleotide sequence (SEQ ID NO: 121) of a native sequence
PR0214 cDNA, wherein
SEQ ID NO: 121 is a clone designated herein as "DNA32286-1191".
Figure 122 shows the amino acid sequence (SEQ ID NO: 122) derived from the
coding sequence of SEQ
ID NO:121 shown in Figure 121.
Figure 123 shows a nucleotide sequence (SEQ ID NO: 123) of a native sequence
PR0247 cDNA, wherein
SEQ ID NO: 123 is a clone designated herein as "DNA35673-1201".
Figure 124 shows the amino acid sequence (SEQ ID NO: 124) derived from the
coding sequence of SEQ
ID NO:123 shown in Figure 123.
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Figare 125 shows a nucleotide sequence (SEQ ID NO:125) of a native sequence
PR0337 cDNA, wherein
SEQ ID NO: 125 is a clone designated herein as "DNA43316-1237".
Figure 126 shows the amino acid sequence (SEQ ID NO: 126) derived from the
coding sequence of SEQ
ID NO:125 shown in Figure 125.
Figure 127 shows a nucleotide sequence (SEQ ID NO: 127) of a native sequence
PR0526 eDNA, wherein
SEQ ID NO: 127 is a clone designated herein as "DNA44184-1319".
Figure 128 shows the amino acid sequence (SEQ ID NO: 128) derived from the
coding sequence of SEQ
ID NO:127 shown in Figure 127.
Figure 129 shows a nucleotide sequence (SEQ ID NO: 129) of a native sequence
PR0363 cDNA, wherein
SEQ ID NO:129 is a clone designated herein as "DNA45419-1252".
Figare 130 shows the amino acid sequence (SEQ ID NO: 130) derived from the
coding sequence of SEQ
ID NO: 129 shown in Figure 129.
Figure 131 shows a nucleotide,sequence (SEQ ID NO:131) of a native sequence
PR0531 cDNA, wherein
SEQ ID NO: 131 is a clone designated herein as "DNA48314-1320".
Figure 132 shows the amino acid sequence (SEQ ID NO: 132) derived from the
coding sequence of SEQ
ID NO:131 shown in Figure 131.
Figure 133 shows a nucleotide sequence (SEQ ID NO:133) of a native sequence
PR01083 cDNA,
wherein SEQ ID NO: 133 is a clone designated herein as "DNA50921-1458".
Figure 134 shows the amino acid sequence (SEQ ID NO: 134) derived from the
coding sequence of SEQ
ID NO: 133 shown in Figure 133.
Figure 135 shows a nucleotide sequence (SEQ ID NO: 135) of a native sequence
PR0840 cDNA, wherein
SEQ ID NO: 135 is a clone designated herein as "DNA53987".
Figure 136 shows the amino acid sequence (SEQ ID NO: 136) derived from the
coding sequence of SEQ
ID NO: 135 shown in Figure 135.
Figure 137 shows a nucleotide sequence (SEQ ID NO: 137) of a native sequence
PRO 1080 cDNA,
wherein SEQ ID NO: 137 is a clone designated herein as "DNA56047-1456".
Figure 138 shows the amino acid sequence (SEQ ID NO: 138) derived from the
coding sequence of SEQ
ID NO:137 shown in Figure 137.
Figure 139 shows a micleotide sequence (SEQ ID NO: 139) of a native sequence
PR0788 cDNA, wherein
SEQ ID NO: 139 is a clone designated herein as "DNA56405-1357".
Figure 140 shows the amino acid sequence (SEQ ID NO: 140) derived from the
coding sequence of SEQ
ID NO:139 shown in Figure 139.
Figure 141 shows a nucleotide sequence (SEQ ID NO:141) of a native sequence
PR01478 cDNA,
wherein SEQ ID NO:141 is a clone designated herein as "DNA56531-1648".
Figure 142 shows the amino acid sequence (SEQ II) NO:142) derived from the
coding sequence of SEQ
ID NO:141 shown in Figure 141.
Figure 143 shows a nucleotide sequence (SEQ ID NO: 143) of a native sequence
PRO1134 cDNA,
wherein SEQ ID NO: 143 is a clone designated herein as "DNA56865-1491".
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Figure 144 shows the amino acid sequence (SEQ ID N0:144) derived from the
coding sequence of SEQ
ID NO:143 shown in Figure 143.
Figure 145 shows a nucleotide sequence (SEQ ID NO: 145) of a native sequence
PR0826 cDNA, wherein
SEQ ID NO: 145 is a clone designated herein as "DNA57694-1341".
Figure 146 shows the amino acid sequence (SEQ ID NO: 146) derived from the
coding sequence of SEQ
ID NO:145 shown in Figure 145.
Figure 147 shows a nucleotide sequence (SEQ ID NO: 147) of a native sequence
PRO 1005 cDNA,
wherein SEQ ID NO: 147 is a clone designated herein as "DNA57708-1411".
Figure 148 shows the amino acid sequence (SEQ ID NO: 148) derived from the
coding sequence of SEQ
ID NO: 147 shown in Figure 147.
Figare 149 shows a nucleotide sequence (SEQ ID NO: 149) of a native sequence
PR0809 cDNA, wherein
SEQ ID NO: 149 is a clone designated herein as "DNA57836-1338".
Figure 150 shows the amino acid sequence (SEQ ID NO: 150) derived from the
coding sequence of SEQ
ID NO:149 shown in Figure 149.
Figure 151 shows a nucleotide sequence (SEQ ID NO: 151) of a native sequence
PRO1194 cDNA,
wherein SEQ ID NO: 151 is a clone designated herein as "DNA57841-1522".
Figure 152 shows the amino acid sequence (SEQ ID NO: 152) derived from the
coding sequence of SEQ
ID NO:151 shown in Figure 151.
Figure 153 shows a nucleotide sequence (SEQ ID NO: 153) of a native sequence
PRO 1071 cDNA,
wherein SEQ ID NO: 153 is a clone designated herein as "DNA58847-1383".
Figure 154 shows the amino acid sequence (SEQ ID N0:154) derived from the
coding sequence of SEQ
ID NO: 153 shown in Figure 153.
Figure 155 shows a nucleotide sequence (SEQ ID NO: 155) of a native sequence
PRO1411 cDNA,
wherein SEQ ID NO: 155 is a clone designated herein as "DNA59212-1627".
Figure 156 shows the amino acid sequence (SEQ ID NO: 156) derived from the
coding sequence of SEQ
ID NO: 155 shown in Figure 155.
Figure 157 shows a nucleotide sequence (SEQ ID NO:157) of a native sequence
PR01309 cDNA,
wherein SEQ ID NO: 157 is a clone designated herein as "DNA59588-1571".
Figure 158 shows the amino acid sequence (SEQ ID NO: 158) derived from the
coding sequence of SEQ
ID NO:157 shown in Figure 157.
Figure 159 shows a nucleotide sequence (SEQ ID NO: 159) of a native sequence
PRO1025 cDNA,
wherein SEQ ID NO: 159 is a clone designated herein as "DNA59622-1334".
Figure 160 shows the amino acid sequence (SEQ ID NO: 160) derived from the
coding sequence of SEQ
ID NO:159 shown in Figure 159.
Figure 161 shows a nucleotide sequence (SEQ ID NO: 161) of a native sequence
PRO1181 cDNA,
wherein SEQ ID NO:161 is a clone designated herein as "DNA59847-2510".
Figure 162 shows the amino acid sequence (SEQ ID NO:162) derived from the
coding sequence of SEQ
ID NO:161 shown in Figure 161.
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Figure 163 shows a nucleotide sequence (SEQ ID NO: 163) of a native sequence
PROI126 cDNA,
wherein SEQ ID NO: 163 is a clone designated herein as "DNA60615-1483".
Figure 164 shows the amino acid sequence (SEQ ID NO:164) derived from the
coding sequence of SEQ
ID NO:163 shown in Figure 163.
Figure 165 shows a nucleotide sequence (SEQ ID NO: 165) of a native sequence
PRO1186 cDNA,
wherein SEQ ID NO: 165 is a clone designated herein as "DNA60621-1516".
Figure 166 shows the amino acid sequence (SEQ ID NO:166) derived from the
coding sequence of SEQ
ID NO:165 shown in Figure 165.
Figure 167 shows a nucleotide sequence (SEQ ID NO: 167) of a native sequence
PRO1192 eDNA,
wherein SEQ ID NO: 167 is a clone designated herein as "DNA62814-1521".
Figure 168 shows the amino acid sequence (SEQ ID NO: 168) derived from the
coding sequence of SEQ
ID NO:167 shown in Figure 167.
Figure 169 shows a nucleotide sequence (SEQ ID NO: 169) of a native sequence
PRO 1244 cDNA,
wherein SEQ ID NO: 169 is a clone designated herein as "DNA64883-1526".
Figure 170 shows the amino acid sequence (SEQ ID NO: 170) derived from the
coding sequence of SEQ
ID NO:169 shown in Figure 169.
Figure 171 shows a nucleotide sequence (SEQ ID NO: 171) of a native sequence
PR01274 cDNA,
wherein SEQ ID NO: 171 is a clone designated herein as "DNA64889-1541".
Figure 172 shows the amino acid sequence (SEQ ID NO: 172) derived from the
coding sequence of SEQ
ID NO:171 shown in Figure 171.
Figure 173 shows a nucleotide sequence (SEQ ID NO: 173) of a native sequence
PRO 1412 cDNA,
wherein SEQ ID NO: 173 is a clone designated herein as "DNA64897-1628".
Figure 174 shows the amino acid sequence (SEQ ID NO: 174) derived from the
coding sequence of SEQ
ID NO:173 shown in Figure 173.
Figure 175 shows a nucleotide sequence (SEQ ID NO: 175) of a native sequence
PR01286 cDNA,
wherein SEQ ID NO:175 is a clone designated herein as "DNA64903-1553".
Figure 176 shows the amino acid sequence (SEQ ID NO: 176) derived from the
coding sequence of SEQ
ID NO: 175 shown in Figure 175.
Figure 177 shows a nucleotide sequence (SEQ ID NO:177) of a native sequence
PR01330 cDNA,
wherein SEQ ID NO:177 is a clone designated herein as "DNA64907-1163-1 ".
Figure 178 shows the amino acid sequence (SEQ ID NO:178) derived from the
coding sequence of SEQ
ID NO:177 shown in Figure 177.
Figure 179 shows a nucleotide sequence (SEQ ID NO:179) of a native sequence
PRO1347 cDNA,
wherein SEQ ID NO: 179 is a clone designated herein as "DNA64950-1590".
Figure 180 shows the amino acid sequence (SEQ ID NO: 180) derived from the
coding sequence of SEQ
ID NO: 179 shown in Figure 179.
Figure 181 shows a nucleotide sequence (SEQ ID NO:181) of a native sequence
PR01305 eDNA,
wherein SEQ ID NO:181 is a clone designated herein as "DNA64952-1568".
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Figure 182 shows the amino acid sequence (SEQ ID NO: 182) derived from the
coding sequence of SEQ
ID NO:181 shown in Figure 181.
Figure 183 shows a nucleotide sequence (SEQ ID NO:183) of a native sequence
PR01273 cDNA,
wherein SEQ ID NO:183 is a clone designated herein as "DNA65402-1540".
Figure 184 shows the amino acid sequence (SEQ ID NO: 184) derived from the
coding sequence of SEQ
ID NO:183 shown in Figure 183.
Figure 185 shows a nucleotide sequence (SEQ ID NO: 185) of a native sequence
PRO1279 cDNA,
wherein SEQ ID NO:185 is a clone designated herein as "DNA65405-1547".
Figure 186 shows the amino acid sequence (SEQ ID NO:186) derived from the
coding sequence of SEQ
II) NO:185 shown in Figure 185.
Figure 187 shows a nucleotide sequence (SEQ II) NO:187) of a native sequence
PR01340 cDNA,
wherein SEQ ID NO: 187 is a clone designated herein as "DNA66663-1598".
Figure 188 shows the amino acid sequence (SEQ ID NO: 188) derived from the
coding sequence of SEQ
ID NO: 187 shown in Figure 187.
Figure 189 shows a nucleotide sequence (SEQ ID NO: 189) of a native sequence
PRO 1338 cDNA,
wherein SEQ ID NO:189 is a clone designated herein as "DNA66667".
Figure 190 shows the amino acid sequence (SEQ ID NO: 190) derived from the
coding sequence of SEQ
ID NO:189 shown in Figure 189.
Figure 191 shows a nucleotide sequence (SEQ ID NO:191) of a native sequence
PR01343 cDNA,
wherein SEQ ID NO: 191 is a clone designated herein as "DNA66675-1587".
Figure 192 shows the amino acid sequence (SEQ ID NO: 192) derived from the
coding sequence of SEQ
ID NO: 191 shown in Figure 191.
Figure 193 shows a nucleotide sequence (SEQ ID NO:193) of a native sequence
PR01376 cDNA,
wherein SEQ ID NO: 193 is a clone designated herein as "DNA67300-1605".
Figure 194 shows the amino acid sequence (SEQ ID NO: 194) derived from the
coding sequence of SEQ
ID NO: 193 shown in Figure 193.
Figure 195 shows a nucleotide sequence (SEQ ID NO: 195) of a native sequence
PRO1387 cDNA,
wherein SEQ ID NO: 195 is a clone designated herein as "DNA68872-1620".
Figure 196 shows the amino acid sequence (SEQ ID NO: 196) derived from the
coding sequence of SEQ
ID NO:195 shown in Figure 195.
Figure 197 shows a nucleotide sequence (SEQ ID N0:197) of a native sequence
PRO 1409 cDNA,
wherein SEQ ID NO:197 is a clone designated herein as "DNA71269-1621".
Figure 198 shows the amino acid sequence (SEQ ID NO: 198) derived from the
coding sequence of SEQ
ID NO: 197 shown in Figure 197.
Figure 199 shows a nucleotide sequence (SEQ ID NO: 199) of a native sequence
PRO1488 cDNA,
wherein SEQ ID NO: 199 is a clone designated herein as "DNA73736-1657".
Figure 200 shows the amino acid sequence (SEQ ID NO:200) derived from the
coding sequence of SEQ
ID NO: 199 shown in Figure 199.
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Figure 201 shows a nucleotide sequence (SEQ ID NO:201) of a native sequence
PRO1474 cDNA,
wherein SEQ ID NO:201 is a clone designated herein as "DNA73739-1645".
Figure 202 shows the amino acid sequence (SEQ ID NO:202) derived from the
coding sequence of SEQ
ID NO:201 shown in Figure 201.
Figure 203 shows a nucleoride sequence (SEQ ID NO:203) of a native sequence
PRO1917 cDNA,
wherein SEQ ID NO:203 is a clone designated herein as "DNA76400-2528".
Figure 204 shows the amino acid sequence (SEQ ID NO:204) derived from the
coding sequence of SEQ
ID NO:203 shown in Figure 203.
Figure 205 shows a nucleotide sequence (SEQ ID NO:205) of a native seqnence
PR01760 cDNA,
wherein SEQ ID NO:205 is a clone designated herein as "DNA76532-1702".
Figure 206 shows the amino acid sequence (SEQ ID NO:206) derived from the
coding sequence of SEQ
ID NO:205 shown in Figure 205.
Figure 207 shows a nucleotide sequence (SEQ ID N0:207) of a native sequence
PRO 1567 cDNA,
wherein SEQ ID NO:207 is a clone designated herein as "DNA76541-1675".
Figure 208 shows the amino acid sequence (SEQ ID NO:208) derived fmm the
coding sequence of SEQ
ID NO:207 shown in Figure 207.
Figure 209 shows a nucleotide sequence (SEQ ID NO:209) of a native sequence
PRO1887 cDNA,
wherein SEQ ID NO:209 is a clone designated herein as "DNA79862-2522".
Figure 210 shows the amino acid sequence (SEQ ID NO:210) derived from the
coding sequence of SEQ
ID NO:209 shown in Figure 209.
Figure 211 shows a nucleotide sequence (SEQ ID NO:211) of a native sequence
PR01928 cDNA,
wherein SEQ ID N0:211 is a clone designated herein as "DNA81754-2532".
Figure 212 shows the amino acid sequence (SEQ ID NO:212) derived from the
coding sequence of SEQ
ID NO:211 shown in Figure 211.
Figure 213 shows a nucleotide sequence (SEQ ID NO:213) of a native sequence
PR04341 cDNA,
wherein SEQ ID NO:213 is a clone designated herein as "DNA81761-2583".
Figure 214 shows the amino acid sequence (SEQ ID NO:214) derived from the
coding sequence of SEQ
ID NO:213 shown in Figure 213.
Figure 215 shows a nucleotide sequence (SEQ ID NO:215) of a native sequence
PR05723 cDNA,
wherein SEQ ID NO:215 is a clone designated herein as "DNA82361".
Figure 216 shows the amino acid sequence (SEQ ID NO:216) derived from the
coding sequence of SEQ
ID NO:215 shown in Figure 215.
Figure 217 shows a nucleotide sequence (SEQ ID NO:217) of a native sequence
PRO1801 cDNA,
wherein SEQ ID NO:217 is a clone designated herein as "DNA83500-2506".
Figure 218 shows the amino acid sequence (SEQ ID NO:218) derived from the
coding sequence of SEQ
ID NO:217 shown in Figure 217.
Figure 219 shows a nucleotide sequence (SEQ ID NO:219) of a native sequence
PR04333 cDNA,
wherein SEQ ID NO:219 is a clone designated herein as "DNA84210-2576".
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Figure 220 shows the amino acid sequence (SEQ ID NO:220) derived from the
coding sequence of SEQ
ID NO:219 shown in Figure 219.
Figure 221 shows a nucleotide sequence (SEQ ID NO:221) of a native sequence
PR03543 cDNA,
wherein SEQ ID NO:221 is a clone designated herein as "DNA86571-2551".
Figure 222 shows the amino acid sequence (SEQ ID NO:222) derived from the
coding sequence of SEQ
ID NO:221 shown in Figure 221.
Figure 223 shows a nucleotide sequence (SEQ ID NO:223) of a native sequence
PR03444 cDNA,
wherein SEQ ID NO:223 is a clone designated herein as "DNA87997".
Figure 224 shows the amino acid sequence (SEQ ID NO:224) derived from the
coding sequence of SEQ
ID NO:223 shown in Figure 223.
Figure 225 shows a nucleotide sequence (SEQ ID NO:225) of a native sequence
PR04302 cDNA,
wherein SEQ ID NO:225 is a clone designated herein as "DNA92218-2554".
Figure 226 shows the amino acid sequence (SEQ ID NO:226) derived from the
coding sequence of SEQ
ID NO:225 shown in Figure 225.
Figure 227 shows a nucleotide sequence (SEQ ID NO:227) of a native sequence
PR04322 eDNA,
wherein SEQ ID NO:227 is a clone designated herein as "DNA92223-2567".
Figure 228 shows the amino acid sequence (SEQ ID NO:228) derived from the
coding sequence of SEQ
ID NO:227 shown in Figure 227.
Figure 229 shows a nucleotide sequence (SEQ ID NO:229) of a native sequence
PR05725 cDNA,
wherein SEQ ID NO:229 is a clone designated herein as "DNA92265-2669".
Figure 230 shows the amino acid sequence (SEQ ID NO:230) derived from the
coding sequence of SEQ
ID NO:229 shown in Figure 229.
Figure 231 shows a nucleotide sequence (SEQ ID NO:231) of a native sequence
PR04408 cDNA,
wherein SEQ ID NO:231 is a clone designated herein as "DNA92274-2617".
Figure 232 shows the amino acid sequence (SEQ ID NO:232) derived from the
coding sequence of SEQ
ID NO:231 shown in Figure 231.
Figure 233 shows a nucleotide sequence (SEQ ID NO:233) of a native sequence
PR09940 cDNA,
wherein SEQ ID NO:223 is a clone designated herein as "DNA92282".
Figure 234 shows the amino acid sequence (SEQ ID NO:234) derived from the
coding sequence of SEQ
ID NO:233 shown in Figure 233.
Figure 235 shows a nucleotide sequence (SEQ ID NO:235) of a native sequence
PR07154 cDNA,
wherein SEQ ID NO:235 is a clone designated herein as "DNA108760-2740".
Figure 236 shows the amino acid sequence (SEQ ID NO:236) derived from the
coding sequence of SEQ
ID NO:235 shown in Figure 235.
Figure 237 shows a nucleotide sequence (SEQ ID NO:237) of a native sequence
PR07425 cDNA,
wherein SEQ ID NO:237 is a clone designated herein as "DNA108792-2753".
Figure 238 shows the amino acid sequence (SEQ ID NO:238) derived from the
coding sequence of SEQ
ID NO:237 shown in Figure 237.
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Figure 239 shows a nucleotide sequence (SEQ ID NO:239) of a native sequence
PR06079 cDNA,
wherein SEQ ID NO:239 is a clone designated herein as "DNA111750-2706".
Figare 240 shows the amino acid sequence (SEQ ID NO:240) derived from the
coding sequence of SEQ
ID NO:239 shown in Figure 239.
Figure 241 shows a nucleotide sequence (SEQ ID NO:241) of a native sequence
PR09836 cDNA,
wherein SEQ ID NO:241 is a clone designated herein as "DNA119514-2772".
Figure 242 shows the amino acid sequence (SEQ ID NO:242) derived from the
coding sequence of SEQ
ID NO:241 shown in Figure 241.
Figure 243 shows a nucleotide sequence (SEQ ID NO:243) of a native sequence
PR010096 cDNA,
wherein SEQ ID NO:243 is a clone designated herein as "DNA125185-2806".
Figure 244 shows the amino acid sequence (SEQ ID NO:244) derived from the
coding sequence of SEQ
ID NO:243 shown in Figure 243.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
I. Defmitions
The terms "PRO polypeptide" and "PRO" as used herein and when immediately
followed by a mmnerical
designation refer to various polypeptides, wherein the complete designation
(i. e. , PRO/number) refers to specific
polypeptide sequences as described herein. The terms "PRO/naimber polypeptide"
and "PRO/number" wherein
the term "number" is provided as an actual numerical designation as used
herein encompass native sequence
polypeptides and polypeptide variants (which are further defined herein). The
PRO polypeptides described herein
may be isolated from a variety of sources, such as from human tissue types or
from another source, or prepared
by recombinant or synthetic methods. The term "PRO polypeptide" refers to each
individual PRO/number
polypeptide disclosed herein. All disclosures in this specification which
refer to the "PRO polypeptide" refer to
each of the polypeptides individually as well as jointly. For example,
descriptions of the preparation of,
purification of, derivation of, formation of antibodies to or against,
administration of, compositions containing,
treatment of a disease with, etc., pertain to each polypeptide of the
invention individually. The term "PRO
polypeptide" also includes variants of the PRO/number polypeptides disclosed
herein.
A "native sequence PRO polypeptide" comprises a polypeptide having the same
amino acid sequence as
the corresponding PRO polypeptide derived from nature. Such native sequence
PRO polypeptides can be isolated
from nature or can be produced by recombinant or synthetic means. The term
"native sequence PRO polypeptide"
specifically encompasses naturally-occurring truncated or secreted forms of
the specific PRO polypeptide (e. g. ,
an extracellular domain sequence), naturally-occurring variant forms (e.g.,
alternatively spliced forms) and
naturally-occurring allelic variants of the polypeptide. In various
embodiments of the invention, the native
sequence PRO polypeptides disclosed herein are mature or full-length native
sequence polypeptides comprising
the full-Iength amino acids sequences shown in the accompanying figures. Start
and stop codons are shown in
bold font and underlined in the figures. However, while the PRO polypeptide
disclosed in the accompanying
figures are shown to begin with methionine residues designated herein as amino
acid position 1 in the figures, it
is conceivable and possible that other methionine residues located either
upstream or downstream from the amino
19
CA 02591930 2007-03-30
WO 01/093983 PCT/US01/17800
acid position 1 in the figures may be employed as the starting amino acid
residue for the PRO polypeptides.
The PRO polypeptide "extracellular domain" or "ECD" refers to a form of the
PRO polypeptide which
is essent9ally free of the transmembrane and cytoplasmic domains. Ordinarily,
a PRO polypeptide ECD will have
less than 1% of such transmembrane and/or cytoplasmic domains and preferably,
will have less than 0.5 % of such
domains. It will be understood that any transmembrane domains idendfied for
the PRO polypeptides of the
present invention are identified pursuant to criteria routinely employed in
the art for identifying that type of
hydrophobic domain. The exact boundaries of a transmembrane domain may vary
but most likely by no more
than about 5 amino acids at either end of the domain as initially identified
herein. Optionally, therefore, an
extracellular domain of a PRO polypeptide may contain from about 5 or fewer
amino acids on either side of the
transmembrane domain/extracellular domana boundary as identified in the
Examples or specification and such
polypeptides, with or without the associated signal peptide, and nucleic acid
encoding them, are comtemplated
by the present invention.
The approximate location of the "signal peptides" of the various PRO
polypeptides disclosed herein are
shown in the present speciRcation and/or the accompanying figures. It is
noted, however, that the C-terminal
boundary of a signal peptide may vary, but most likely by no more than about 5
amino acids on either side of the
signal peptide C-termmal boundary as initially identified herein, wherein the
C-terminal boundary of the signal
peptide may be identified pursuant to criteria routinely employed in the art
for identifying that type of amino acid
sequence element (e.g., Nielsen et al., Prot. Ea~. 10:1-6 (1997) and von
Heinje et al., Nucl. Acids. Res.
14:4683-4690 (1986)). Moreover, it is also recognized that, in some cases,
cleavage of a signal sequence from
a secreted polypeptide is not entirely uniform, resulting in more than one
secreted species. These mature
polypeptides, where the signal peptide is cleaved within no more than about 5
amino acids on either side of the
C-terminal boundary of the signal peptide as identified herein, and the
polynucleotides encoding them, are
contemplated by the present inve,ntion.
"PRO polypeptide variant" means an active PRO polypeptide as defmed above or
below having at least
about 80 % ami.no acid sequence identity with a fall-length native sequence
PRO polypeptide sequence as disclosed
herein, a PRO polypeptide sequence laclQng the signal peptide as disclosed
herein, an extracellular domain of a
PRO polypeptide, with or widtout the signal peptide, as disclosed herein or
any other fragment of a full-length
PRO polypeptide sequence as disclosed herein. Such PRO polypeptide variants
include, for instance, PRO
polypeptides wherein one or more amino acid residues are added, or deleted, at
the N- or C-Lerminus of the full-
length native amino acid sequence. Ordinarily, a PRO polypeptide variant will
have at least about 80% amino
acid sequence ideutity, alternatively at least about 81 % amino acid sequence
identity, alternatively at least about
82% amino acid sequence identity, alternatively at least about 83% amino acid
sequence identity, alternatively
at least about 84% amino acid sequence identity, alternatively at least about
85% amino acid sequence identity,
alternatively at least about 86% amino acid sequence identity, alternatively
at least about 87% amino acid
sequence identity, alternatively at least about 88 % amino acid sequence
identity, altern.atively at least about 89 %
amino acid sequence identity, alternatively at least about 90% amino acid
sequence identity, alternatively at least
about 91 % amino acid sequence identity, alternatively at least about 92%
amino acid sequence identity,
alternatively at least about 93% amino acid sequence identity, alternatively
at least about 94% amino acid
CA 02591930 2007-03-30
WO 01/093983 PCT/USUV17800
sequence ideatity, alteaaatively at least about 95 % amino acid sequetu,e
identity, alternatively at least aboau 96 %
amino acid sequence identity, alternatively at least about 97% amino acid
sequence identity, altemtively at least
about 98% amino acid sequence Identity and altornatively at least about 99%
amino acid seqoent7e identity to a
fall-length aative sequence PRO polypeptide sequence as disclosed herein, a
PRO polypeptide sequence lacldng
the signal Peptide as disclosed herein, an extracellular domain of a PRO
polypeptide, with or without the signal
peptide, as disclosed herein or any other specifically defined fragment of a
full-length PRO polypeptide sequence
as disolosed hereia. Ordiaarily, PRO variant polypeptides are at least about
10 amino acids in length,
altematively at Ieast about 20 amino acids in length, alternatively at least
about 30 amino acids in length,
alteraatively at least about 40 amino acids in length, albetnativaly at least
about 50 amiao acids in length,
alftmatively at Ieast about 60 amino acids in length, alternatively at least
about 70 amino acids in length,
alternatively at least about 80 amino acids in length, altecnadvely at least
about 90 atnino acids ILn length,
alternatively at least about 100 amino acids in length, alternatively at least
about 150 amino acids in length,
alternaiively at least about 200 amino acids in length, alteraatively at least
about 300 amino acids in length, or
more.
"Peseent (%) amino acid sequeaoe identity" with respect to the PRO polypoptide
sequGaces identified
herein is defined as the percentage of amino actd residues in a candidate
sequence that are identical with tlu amino
acid residues fn the specific PRO pol,ypeptfde saqaence, afber alignin,g the
aequeaces aad introducing gaps, if
necessaty, to achieve the maximum perceoi sequence identity, and not
considaring any conservative substitations
as part of the sequence identity. Alignment for putposes of determining
percent amino arad sequenee ideattty can
be aohieved in various ways that are within the s1o71 in ft art, for instance,
using publicly available computer
software such as BI.AST, BLAST-2, ALiGN or Megalign (DNASTAR) soltware. Those
slrilled in the art can
determiae appropriate paratneDers for moastuing aligament, including atry
algoritmms needed to acitieve maumal
alignment over the fall length of the sequtenoes being compared. For purposes
herein, however, % am.ino acid
sequence identity vatues ara generaoed using ft sequence coanparfsoa
cottrputer progtam ALIGN'-2, whereia the
complete source code for ft ALIGN-2 pcogram is provided in Table 1 below. ~Ibe
AUGN-2 sequence
eompatison oonnpuDer program was aut>sorecl by Genentech, Inc. and the source
code shown in Table 1 below has
beea SAed with user documemWan in the U.S. Copyright Office, Washtngtan D.C.,
20559, where it is registered
under U.S. Copyright Registration No. TXU510067. 'Tho ALION-2 program is
publicly available throagh
Genentech, Inc., South San Fraacisco, Califomia or may be compiled from the
source code provided In Table
1 below. The ALIGN-2 progiam should be compiled ibr use on a UNIX opemting
system, preferably digital
UNIX V4.0D. All seqnentloe comparisrnt parameters are set by the ALdGN-2
program and do not vary.
In situatimm where ALdGN-2 is eaployed for amino acid sequence comparlsoAs,
tlhe % amino acid
sequence identity of a given amino acid seqmaoe A to, with, or agaiast a given
amino acid sequence B (which
cam altarnatively be phrased as a given amino aoid wqmnce A fltat h s or
eamprises a cxrtaia % amino acid
sequettx identtty to, with, or agaiast a given amino acid sequence B) is
calculated as follows:
loo times the firaetfon X1Y
*-trademark 21
1
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WO 01/093983 PCT/US01/17800
where X is the mtmber of amino acid residues scored as Idet-tieal matches by
the sequence alignment program
AUGN-2 in that program's aligumeat of A and B. awd where Y is the total mumber
of amino acid residues in B.
It will be apprecismad that where the lengt of amino acid eequence A is not
equal to the length of amino acid
aequenoe B, the % amino aoid sequence identity of A to B will not equal the %
amino acid sequence identity of
B to A. As examples of % amino anid sequence identity caiailations using this
metbod, Tables 2 and 3
damonstrate how to calctilate >>re % amino aaid sequence identity of ft amino
acid seqtbence designated
"Comparison Protein" to the amino acid sequence designated "PRO", wherein
"PRO" represents the amino acid
sequence of a hypothetical PRO polypeptide of interest, "Comparison Protein"
represents the amino acid sequence
of a polypeptide against which the "PRO" polypeptide of interest is being
compared, and "X, "Y" and "Z" each
represent different hypothetioal amino acid residues.
Unless speci8cally stated othenr/ise, all % amino acid sequenee identity
values used herein are obtained
as desczibed In the immediatei)r preceding paragxaphts;ing the AIIaN-2
compuoer program. However. % amino
acid sequeace identity values may aiso be obtained as described below by using
the WU-BLAST-2 computer
program (Ahachnl et al., Methods in Bnzvmoloev 266:460480 (1996)). Most of the
WU-BLAST-2 search
parameters are set to the default values. Thow not set to default values,
i.e., the adjustable parameters, are set
with the following values: overlap span - 1, overlap fraction = 0.125, word
threshold (T) = 11, and scoring
matrix = BLOSUM62. When WU-BLAST-2 is employed, a % amino acid sequence
identity value is determined
by dividiqg (a) the mmber of matching ideatical amino acid residues betvveen
the atnitto acid sequenae of the PRO
polypeptide of interest having a seque,nce derived from the native PRO
polypeptide and the comparison amino acid
sequence of interest (i.e., ft sequence against which the PRO polypeptide of
ioterest is being compared which
may be a PRO varias polypeptide) as determined by WU BI.AST 2 by (b) the total
number of amino aoid
residues of the PRO polypeptide of interost. For example, in tha statement "a
polypeptide comprising an the
amino acid aequeace A which has or having at least 80% amino acid sequence
identity to the amino acid sequence
B", the amino acid sequence A is the compar3aon amino acid sequenc:e of
iuerest and the amino acid sequenoe
B is the amino acid sequeatce of the PRO polypeptide of interest.
Percent amino acid eequewe identity may also be determined using the sequence
eomparison program
NCBI BLASI'2 (Ahschd et al., Nncleic Aeids Res. 25:3389-3402 (1997)). The NCBI-
BI,AS"I'2 sequenoe
oomparison program may be = obtaiaed from the
National Insdtuto of Health, Betb.osda, MD. NCBI-BLAST2 uses several search
parameters, where9n all of those
search parameters ans sat to defunlt va[oas including, for example, uumask =
yes, strand = aU. expected
oecnrrences = 10, minimum low complexity length = 1515, multi-pass e-value =
0.01, constattt for multi-pass
= 25, dropoff for fiaal gapped alignment = 25 and scoring matrix = BLOSUM62.
In situatlam where NCBI-BI.AST2 is amployed for amua acid seqaenoe eompari
sona, the % amiro acid
sequeace identity of a given amino acid seqmw A to, with, or against a given
amino acid sequence B(which
can alternadvely be phrased as a given amiao acid sequence A that has or
comprises a certain % amino acid
seqoence kimdty ta" wiBi, or againat a given ammo acid seqaeaca B) is
calculated as foIIows:
10o times the fraction X/Y
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WO 01/093983 PCT/US01/17800
where X is the number of amino acid residues scored as identical matches by
the sequence aligmnent program
NCBI-BLAST2 in that program's alignment of A and B, and where Y is the total
number of amino acid residues
in B. It will be appreciated that where the length of amino acid sequence A is
not equal to the length of amino
acid sequence B, the % amino acid sequence identity of A to B will not equal
the % amino acid sequence identity
of B to A.
"PRO variant polynucleotide" or 'PRO variant micleic acid sequence" means a
nucleic acid molecule
which encodes an aative PRO polypeptide as defined below and which has at
least about 80% nucleic acid
sequence identity with a nucleotide acid sequence encoding a full-length
native sequence PRO polypeptide
sequence as disclosed herein, a full-length native sequence PRO polypeptide
sequence lacldng the signal peptide
as disclosed herein, an eatracellular domain of a PRO polypeptide, with or
without the signal peptide, as disclosed
herein or any other fragment of a full-length PRO polypeptide sequence as
disclosed herein. Ordinarily, a PRO
variant polynucleotide will have at least about 8096 nucleic acid sequenee
identity, alternatively at least about 81 %
nucleic acid sequence identity, alternatively at least about 829b nucleic acid
sequence identity, alternatively at least
about 83% nucleic acid sequence identity, alternatively at least about 84%
nucleic acid sequence identity,
alternatively at least about 85% micleic acid sequence identity, alternatively
at least about 86% nucleic acid
sequence identity, alternatively at least about 87% nucleic acid sequence
identity, alternatively at least about 88%
nucleic acid sequence identity, alternatively at least about 89 % nucleic acid
sequence identity, alternatively at least
about 90 % nncleic acid sequence identity, alternatively at least about 91 %
nucleic acid sequence identity,
alternatively at least about 9296 nucleic acid sequence identity,
alternatively at least about 9396 nucleic acid
sequence identity, alternatively at least about 949G nucleic acid sequence
identity, alternatively at least about 95 %
nucleic acid sequence identity, alternatively at least about 96 96 nucleic
acid sequence identaty, alternatively at least
about 97% nucieic acid sequence identity, alternatively at least about 98%
mtcleic acid sequence identity and
aiternatively at least about 99 % nucleic acid sequence identity with a
nucleic acid sequence encoding a full-length
native sequence PRO polypeptide sequence as disclosed herein, a full length
native sequence PRO polypeptide
sequence lacking the signal peptide as disclosed herein, an extracellular
domain of a PRO polypeptide, with or
without the signal sequence, as disclosed herein or any other fragment of a
iiill-length PRO polypeptide sequence
as disclosed herein. Variants do not encompass the native nucleotide sequence.
Ordinarily, PRO variant polynucleotides are at least about 30 nucleotides in
length, alternatively at least
about 60 nucleotides in length, alternatively at least about 90 nucleotides in
length, alternatively at least about 120
nucleotides in length, alternatively at least about 150 nucleotides in length,
alternatively at least about 180
nmmleotides in length, alternatively at least about 210 nucleotldes in length,
alternatively at least about 240
nucleotides in length, alternatively at least about 270 nucleotides in length,
alternatively at least about 300
nucleotides in length, alternatively at least about 450 nucleotides in length,
alternatively at least about 600
nncleotides in length, alternatively at least about 900 micleotides in length,
or more.
"Percent (%) nucleic acid sequence identity" with respect to PRO-encoding
nucleic acid sequences
identffied herein is detiaed as the percentage of nucleotides in a candidate
sequence that are identical with the
micleotides in the PRO micleic acid sequenoe of interest, after aligning the
sequences and inirodacing gaps, if
necessary, to achieve the maidmum percent sequence identity. Alignment for
purposes of determining percent
23
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WO 01/093983 PCT/US01/17800
nucleic acid sequenne identity can be achieved in various ways that are within
the sklll in the art, for instance,
using publicly available computer software such as BLAST, BLAST-2, ALIGN or
Megalign (DNASTAR)
software. For purposes herein, however, % nucleic acid sequence identity
values are generated using the
sequence comparison computer program ALIGN-2, wherein the complete source code
for the ALIGN-2 program
is provided in Table 1 below. The ALIGN-2 sequence comparison computer program
was authored by
Genentech, Inc. and tbe source code shown in Table 1 below has been filed with
user documentation in the U.S.
Copyright Office, Washington D.C., 20559, where it is registered under U.S.
Copyright Registration No.
TXU510087. The ALIGN-2 program is publicly available through Genentech, Inc.,
South San Francisco,
California or may be oompiled from the source code provided in Table I below.
The ALIGN 2 program should
be compiled for use on a UNIX operating system, preferably digital UNIX V4.0D.
All sequence comparison
parameters are set by the ALIGN-2 program and do not vary.
In situations where ALIGN-2 is employed for nucleic acid sequence comparisons,
the % nucleic acid
sequence identity of a given micleic acid sequence C to, with, or against a
given nucleic acid sequence D (which
can alternatively be phrased as a given nucleic acid sequence, C that has or
comprises a certain % nucleic acid
sequence identity to, with, or against a given nucleic acid sequence D) is
calculated as follows:
100 times the fraction W/Z
where W is the number of nucleotides scored as identical matches by the
seqnence alignment program ALIGN-2
in that program's alignment of C and D, and where Z is the total number of
nucleotides in D. It will be
appreciated that where the length of nucleic acid sequence C is not equal to
the length of nucleic acid sequence
D, the % nucleic acid sequence identity of C to D will not equal the % nucleic
acid sequence identity of D to C.
As examples of % nucleic acid sequence identity calculations, Tables 4 and 5,
demonstrate how to calculate the
% nucleic acid sequence identity of the nucleic acid sequence designated
"Comparison DNA" to the nucleic acid
sequence designated "PRO-DNA", wherein "PRO-DNA" represents a hypothetical PRO-
encoding nucleic acid
sequence of interest, "Comparison DNA" represents the nucleotide sequence of a
nucleic acid molecule against
which the "PRO-DNA" nucleic acid molecule of interest is being compared, and
"N", "L" and "V" each represent
dif6erent hypothetical nucleotides.
Unless specifically stated otherwise, all % nucleic acid sequence identity
values used herein are obtained
as described in the immediately preceding paragraph using the ALIGN-2 computer
program. However, % nucleic
acid seqaence identity values may also be obtained as described below by using
the WU-BLAST-2 computer
program (Altschul et a1., Methods in Enzvmology 266:460-480 (1996)). Most of
the WU-BLAST-2 search
parameters are set to the default values. Those not set to default values,
i.e., the adjustable parameters, are set
with the following values: overlap span = 1, overlap fraction = 0.125, word
threshold (T) = 11, and scoring
matrix = BLOSUM62. When WU-BI.AST-2 is employed, a % nucleic acid sequence
identity value is determined
by dividing (a) the number of matching identical nucleotides between the
nucleic acid sequence of the PRO
polypeptide-encodang nucleic acid molecule of inberest having a sequence
derived from the native sequence PRO
polypeptide-encoding nucleic acid and the comparison nucleic acid molecule of
interest (i.e., the sequence against
24
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WO 01/093983 PCT/US01/17800
which the PRO polypeptide-eacodiag nucleic add molecule of interest is being
compared which may be a variant
PRO polynucleotide) as determined by WU-BLAST-2 by (b) the total number of
nucleotides of the PRO
polypeptide-encoding nucleic acid molecule of interest. For example, in the
statement "an isolated nucleic acid
molecule comprising a nucleic acid sequenoe A which has or having at least 80%
nucleic acid sequenee identity
to the nucleic acid sequence B", the nuckic acid sequence A is the comparison
nucleic acid molecule of interest
and the nucleic acid sequence B is the nucleic acid sequence of the PRO
polypeptide-encoding nucleic acid
molecule of interest.
Percent nucleic acid sequence identity may also be determined using the
sequence comparison program
NCBI-BLAST2 (Altschul et al., Nucleic Acids Res. 25:3389-3402 (1997)). The
NCBI-BLAST2 sequence
comparison program may be obtained from the
National Institute of Health, Bethesda, MD. NCBI-BLA.ST2 uses several search
parameters, wherein all of those
search parameters are set to default values including, for example, unmask =
yes, strand = all, expected
occurreixes = 10, minimum low complexity length = 155, multi-pass e-vahx =
0.01, constant for multi-pass
= 25, dropoff for fmal gapped alignment = 25 and scoring matrix = BLOSUM62.
In situations where NCBI-BLAST2 is employed for sequence comparisona, the %
nucleic acid seqeence
identity of a given nucleic acid sequence C to, with, or against a given
nucleic acid sequence D (which can
alternatively be phrased as a given nucleic acid sequence C that has or
comprises a certain % nucleic acid
sequence identity to, with, or agaiast a given nucleic acid sequence D) is
calculated as follows:
100 times the fraction W/Z
where W is the number of aucleotides scored as identical matches by the
aequence afigament program NCBI-
BLAST2 in that program's alignment of C and D. and where Z is the total number
of nucleotides in D. It will
be appreciated that where the length of nucleic acid sequence C is not equal
to the length of nucleic acid seqnence
D, the % nucleic acid sequence identity of C to D will not equal tbe % nucleic
acid sequence identity of D to C.
In other embodiments, PRO variant polynacleotides are nucleic acid molecules
that enoode an active PRO
polypeptide and wbich are capable of hybridizing, preferably under stringent
hybridization and wash conditions,
to nucleotide sequences encoding a fbIl-length PRO polypeptide as disclosed
herein. PRO variant polypeptides
may be those that are encoded by a PRO variant polynucleotide.
"Isolated," when used to describe the various polypeptides disclosed herein,
means polypeptide that has
been identified and separated and/or reoovered from a componeat of its natural
environment. Contam9nant
components of its natural envirwrment are materials that would typically
interfere with diagnostic or therapeutic
uses for the polypeptide, and may include eazymes, hormones, and other
proteinaceous or non proteiaaceous
solutes. In preferred embodiments, the polypepdde will be purified (1) to a
degree suicient to obtain at least
15 residues of N-terminal or=iateraal amino acid sequence by use of a spinning
cup sequenator, or (2) to
hosnoge,neity by SDS-PAGE under non-reducing or reducing conditions using
Covmagsie blue or, preferably,
silver stain. Isolated polypeptide includes polypeptide in silu within
recombinant cells, since at least one
component of the PRO polypeptide natural enviromaeat will nut be present.
Ordinarily, however, isolated
CA 02591930 2007-03-30
WO 01/093983 PCT/US01/17800
polypeptide will be prepared by at least one purification step.
An "isolated" PRO polypeptide-encoding nucleic acid or other polypeptide-
encoding nucleic acid is a
nucleic acid molecule that is identified and separated from at least one
contaminant nucleic acid molecule with
which it is ordinarily associated in the natural source of the polypeptide-
encoding nucleic acid. An isolated
polypeptide-encoding nucleic acid molecule is other than in the form or
setting in which it is found in nature.
Isolated polypeptide-encoding nucleic acid molecules therefore are
distinguished from the specific polypeptide-
encoding nucleic acid molecule as it exists in natural cells. However, an
isolated polypeptide-encoding nucleic
acid molecule includes polypeptide-encoding nucleic acid molecules contained
in cells that ordinarily express the
polypeptide where, for example, the nucleic acid molecule is in a chromosomal
location different from that of
natural cells.
The term "control sequences" refers to DNA sequences necessary for the
expression of an operably
linked coding sequence in a particular host organism. The control sequences
that are suitable for prokaryotes,
for example, include a promoter, optionally an operator sequence, and a
ribosome binding site. Eukaryotic cells
are known to utilize promoters, polyadenylation signals, and enhancers.
Nucleic acid is "operably linloed" when it is placed into a fanctional
relationship with another nucleic acid
sequence. For example, DNA for a presequence or secretory leader is operably
linked to DNA for a polypeptide
if it is expressed as a preprotein that participates in the secretion of the
polypeptide; a promoter or enhancer is
operably linked to a coding sequence if it affects the transcription of the
sequence; or a ribosome binding site is
operably linked to a coding sequence if it is positioned so as to facilitate
translation. Generally, "operably linked"
means that the DNA sequences being linked are contiguous, and, in the case of
a secretory leader, contiguous and
in reading phase. However, enhancers do not have to be contiguous. Linking is
accomplished by ligation at
convenient restriction sites. If such sites do not exist, the synthetic
oligonucleotide adaptors or linkers are used
in accordance with conventional practice.
The term "antibody" is used in the broadest sense and specifically covers, for
example, single anti-PRO
monoclonal antibodies (including agonist, antagonist, and neutralizing
antibodies), anti-PRO antibody compositions
with polyepitopic specificity, single chain anti-PRO antibodies, and fragments
of anti-PRO antibodies (see below).
The term "monoclonal antibody" as used herein refers to an antibody obtained
from a population of substantially
homogeneous antibodies, i.e., the individual antibodies comprising the
population are identical except for possible
naturally-occurring mutations that may be present in minor amounts.
"Stringency" of hybridization reactions is readily determinable by one of
ordinary sldll in the art, and
generally is an empirical calculation dependent upon probe length, washing
temperature, and salt concentration.
In general, longer probes require higher temperatures for proper annealing,
while shorter probes need lower
temperatures. Hybridization generally depends on the ability of denatured DNA
to reanneal when complementary
strands are present in an environment below their melting temperature. The
higher the degree of desired
homology between the probe and hybridizable sequence, the higher the relative
temperature which can be used.
As a result, it follows that higher relative temperatures would tend to make
the reaction conditions more stringent,
while lower temperatures less so. For additional details and explan.ation of
stringency of hybridization reactions,
see Ausubel et al., Current Protocols in Molecular Biology, Wiley Interscience
Publishers, (1995).
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WO 01/093983 PCT/US01/17800
"Stringent conditions" or "high stringency conditions", as defined herein, may
be identified by those that:
(1) employ low ionic strength and high temperature for washing, for example
0.015 M sodium chloride/0.0015
M sodium citrate/0.1 % sodium dodecyl sulfate at 50 C; (2) employ during
hybridization a denaturing agent, such
as formamide, for example, 50% (v/v) formamide with 0.1% bovine serum
albumin/0.1 % Ficoll/0.1 %
polyvinylpyrrolidone/50mM sodium phosphate buffer at pH 6.5 with 750 mM sodium
chloride, 75 mM sodium
citrate at 42 C; or (3) employ 50% formamide, 5 x SSC (0.75 M NaC1, 0.075 M
sodium citrate), 50 mM sodium
phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5 x Denhardt's solution,
sonicated-sahnon sperm DNA (50
g/ml), 0.14b SDS, and 10% dextran sulfate at 42 C, with washes at 42 C in 0.2
x SSC (sodium chloride/sodium
citrate) and 50% formamide at 55 C, followed by a high-stringency wash
consisting of 0.1 x SSC containing
EDTA at 55 C.
"Moderately stringent conditions" maybe identified as described by Sambrooket
al., Molecular Cloning:
A Laboratory Manual, New York: Cold Spring Harbor Press, 1989, and include the
use of washing solution and
hybridization conditions (e.g., temperature, ionic strength and %SDS) less
stringent that those described above.
An example of moderately strin.gent conditions is overnight incubation at 37 C
in a solution comprising: 20%
formamide, 5 x SSC (150 mM NaCI, 15 mM trisodium citrate), 50 mM sodium
phosphate (pH 7.6), 5 x
Denhardt's solution, 10% dextran sulfate, and 20 mg/ml denatured sheared
salmon sperm DNA, followed by
washing the filters in 1 x SSC at about 37-50 C. The skilled artisan will
recognize how to adjust the temperature,
ionic strength, etc. as necessary to accommodate factors such as probe length
and the like.
The term "epitope tagged" when used herein refers to a chimeric polypeptide
comprising a PRO
polypeptide fused to a "tag polypeptide". The tag polypeptide has enough
residues to provide an epitope against
which an antibody can be made, yet is short enough such that it does not
interfere with activity of the polypeptide
to which it is fused. The tag polypeptide preferably also is fairly unique so
that the antibody does not substantially
cross-react with other epitopes. Suitable tag polypeptides generally have at
least six amino acid residues and
usually between about 8 and 50 amino acid residues (preferably, between about
10 and 20 amino acid residues).
As usedherein, the term "immunoadhesin" designates antibody-like molecules
which combine the binding
specificity of a heterologous protein (an "adhesin") with the effector
functions of immunoglobulin constant
domains. Structurally, the immunoadhesins comprise a fusion of an amino acid
sequence with the desired binding
specificity which is other than the antigen recognition and binding site of an
antibody (i.e., is "heterologous"),
and an immunoglobulin constant domain sequence. The adhesin part of an
immunoadhesin molecule typically is
a contiguous amino acid sequence comprising at least the binding site of a
receptor or a ligand. The
immunoglobulin constant domain sequence in the immunoadhesin may be obtained
from any immunoglobulin,
such as IgG-1, IgG-2, IgG-3, or IgG-4 subtypes, IgA (including IgA-1 and IgA-
2), IgE, IgD or IgM.
"Active" or "activity" for the purposes herein refers to form(s) of a PRO
polypeptide which retain a
biological and/or an immunological activity of native or naturally-occurring
PRO, wherein "biological" activity
refers to a biological function (either inhibitory or stimulatory) caused by a
native or naturally-occurring PRO
other than the ability to induce the production of an antibody against an
antigenic epitope possessed by a native
or naturally-occurring PRO and an "immunological" activity refers to the
ability to induce the production of an
antibody against an antigenic epitope possessed by a native or naturally-
occurring PRO.
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The term "antagonist" is used in the broadest sense, and includes any molecule
that partially or fully
blocks, inhibits, or neutralizes a biological activity of a native PRO
polypeptide disclosed herein. In a similar
manner, the term "agonist" is used in the broadest sense and includes any
molecule that mimics a biological
activity of a native PRO polypeptide disclosed herein. Suitable agonist or
antagonist molecules specifically
include agonist or antagonist antibodies or antibody fragments, fragments or
amino acid sequence variants of
native PRO polypeptides, peptides, antisense oligonucleotides, small organic
molecules, etc. Methods for
identifying agonists or antagonists of a PRO polypeptide may comprise
contacting a PRO polypeptide with a
candidate agonist or antagonist molecule and measuring a detectable change in
one or more biological activities
normally associated with the PRO polypeptide.
"Treatment" refers to both therapeutic treatment and prophylactic or
preventative measures, wherein the
object is to prevent or slow down (Iessen) the targeted pathologic condition
or disorder. Those in need of
treatment include those already with the disorder as well as those prone to
have the disorder or those in whom
the disorder is to be prevented.
"Chronic" administration refers to administration of the agent(s) in a
continuous mode as opposed to an
acute mode, so as to maintain the initial therapeutic effect (activity) for an
extended period of time. "Intermittent"
administration is treatnient that is not consecutively done without
interruption, but rather is cyclic in nature.
"Mammal" for purposes of treatment refers to any animal classified as a
mammal, including humans,
domestic and farm animals, and zoo, sports, or pet animals, such as dogs,
cats, cattle, horses, sheep, pigs, goats,
rabbits, etc. Preferably, the mammal is human.
Administration "in combination with" one or more fiuther therapeutic agents
includes simultaneous
(concurrent) and consecutive administration in any order.
"Carriers" as used herein include pharmaceutically acceptable carriers,
excipients, or stabilizers which
are nontoxic to the cell or mammal being exposed thereto at the dosages and
concentrations employed. Often the
physiologically acceptable carrier is an aqueous pH buffered solution.
Examples of physiologically acceptable
carriers include buffers such as phosphate, citrate, and other organic acids;
antioxidants including ascorbic acid;
low molecular weight (less than about 10 residues) polypeptide; proteins, such
as serum albumin, gelatin, or
immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino
acids such as glycine, glutamine,
asparagine, arginine or lysine; monosaccharides, disaccharides, and other
carbohydrates including glucose,
mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as
mannitol or sorbitol; salt-forming
counterions such as sodium; and/or nonionic surfactants such as TWEENT"',
polyethylene glycol (PEG), and
PLURONICSTm.
"Antibody fragments" comprise a portion of an intact antibody, preferably the
antigen binding or variable
region of the intact antibody. Examples of antibody fragments include Fab,
Fab', F(ab')Z, and Pv fragments;
diabodies; linear antibodies (Zapata et al., Protein Eng. 8(10): 1057-1062
[1995]); single-chain antibody
molecules; and multispecific antibodies formed from antibody fragments.
Papain digestion of antibodies produces two identical antigen-binding
fragments, called "Fab" fragments,
each with a single antigen-binding site, and a residual "Fc" fragment, a
designation reflecting the ability to
crystallize readily. Pepsin treatment yields an F(ab')2 fragment that has two
antigen-combining sites and is still
28
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capable of cross-linidng antigen.
"Fv" is the minimum antibody fragment which contains a complete antigen-
recognition and -binding site.
This region consists of a dimer of one heavy- and one light-chain variable
domain in tight, non-covalent
association. It is in this configuration that the three CDRs of each variable
domain interact to define an antigen-
binding site on the surface of the VH V, dimer. Collectively, the six CDRs
confer antigen-binding specificity to
the antibody. However, even a single variable domain (or half of an Fv
comprising only three CDRs specific for
an antigen) has the ability to recognize and bind antigen, although at a lower
affinity than the entire binding site.
The Fab fragment also contains the constant domain of the light chain and the
first constant domain
(CH1) of the heavy chain. Fab fragments differ from Fab' fragments by the
addition of a few residues at the
carboxy terminus of the heavy chain CH1 domain including one or more cysteines
from the antibody hinge region.
Fab'-SH is the designation herein for Fab' in which the cysteine residue(s) of
the constant domains bear a free
thiol group. F(ab')2 antibody fragments originally were produced as pairs of
Fab' fragments which have hinge
cysteines between them. Other chemical couplings of antibody fragments are
also known.
The "light chains" of antibodies (immunoglobulins) from any vertebrate species
can be assigned to one
of two clearly distinct types, called kappa and lambda, based on the amino
acid sequences of their constant
domains.
Depending on the amino acid sequence of the constant domain of their heavy
chains, immunoglobulins
can be assigned to different classes. There are five major classes of
immunoglobulins: IgA, IgD, IgE, IgG, and
IgM, and several of these may be further divided into subclasses (isotypes),
e.g., IgGl, IgG2, IgG3, IgG4, IgA,
and IgA2.
"Single-chain Fv" or "sFv" antibody fragments comprise the VH and VL domains
of antibody, wherein
these domains are present in a single polypeptide chain. Preferably, the Fv
polypeptide further comprises a
polypeptide linker between the VH and VL domains which enables the sFv to form
the desired structure for antigen
binding. For a review of sFv, see Pluckthun in The Pharm.acology of Monoclonal
Antibodies, vol. 113,
Rosenburg and Moore eds., Springer-Verlag, New York, pp. 269-315 (1994).
The term "diabodies" refers to small antiWy fragments with two antigen-binding
sites, which fragments
comprise a heavy-chain variable domain (V,.,) comiected to a light-chain
variable domain (V,) in the same
polypeptide chain (VH-V1,). By using a linker that is too short to allow
pairing between the two domains on the
same chain, the domains are forced to pair with the complementary domains of
another chain and create two
antigen-binding sites. Diabodies are described more fully in, for example, EP
404,097; WO 93/11161; and
Hollinger et al., Proc. Nat1. Acad. Sci. USA, 90:6444-6448 (1993).
An "isolated" antibody is one which has been identified and separated and/or
recovered from a
component of its natural environment. Contaminant components of its natural
environment are materials which
would interfere with diagnostic or therapeutic uses for the antibody, and may
include enzymes, hormones, and
other proteinaceous or nonproteinaceous solutes. In preferred embodiments, the
antibody will be purified (1) to
greater than 95 % by weight of antibody as determined by the Lowry method, and
most preferably more than 99 %
by weight, (2) to a degree sufficient to obtain at least 15 residues of N-
terminal or internal amino acid sequence
by use of a spinning cup sequenator, or (3) to homogeneity by SDS-PAGE under
reducing or nonreducing
29
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conditions using Coomassie blue or, preferably, silver stain. Isolated
antibody includes the antibody in situ within
recombinant celis since at least one component of the antibody's. natural
environment will not be present.
Ordinarily, however, isolated antibody will be prepared by at least one
purification step.
An antibody that "specifically binds to" or is "specific for" a particular
polypeptide or an epitope on a
particular polypeptide is one that binds to that particular polypeptide or
epitope on a particular polypeptide without
substantially binding to any other polypeptide or polypeptide epitope.
The word "label" when used herein refers to a detectable compound or
composition which is conjugated
directly or indirectly to the antibody so as to generate a "labeled" antibody.
The label may be detectable by itself
(e.g. radioisotope labels or fluorescent labels) or, in the case of an
enzymatic label, may catalyze chemical
alteration of a substrate compound or composition which is detectable.
By "solid phase" is meant a non-aqueous matrix to which the antibody of the
present invention can
adhere. Examples of solid phases encompassed herein include those formed
partially or entirely of glass (e.g.,
controlled pore glass), polysaccharides (e.g., agarose), polyacrylamides,
polystyrene, polyvinyl alcohol and
silicones. In certain embodiments, depending on the context, the solid phase
can comprise the well of an assay
plate; in others it is a purification column (e.g., an affinity chromatography
column). This term also includes a
discontinuous solid phase of discrete particles, such as those described in
U.S. Patent No. 4,275,149.
A "liposome" is a small vesicle composed of various types of lipids,
phospholipids and/or surfactant
which is useful for delivery of a drug (such as a PRO polypeptide or antibody
thereto) to a mammal. The
components of the liposome are commonly arranged in a bilayer formation,
similar to the lipid arrangement of
biological membranes.
A"small molecule" is defined herein to have a molecular weight below about 500
Daltons.
An "effective amount" of a polypeptide disclosed herein or an agonist or
antagonist thereof is an amount
sufficient to carry out a specifically stated purpose. An "effective amount"
may be determined empirically and
in a routine manner, in relation to the stated purpose.
CA 02591930 2007-03-30
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Table 1
*
* C-C increased from 12 to 15
* Z is average of EQ
*BisaverageofPlD
* match with stop is _M; stop-stop = 0; J(jolmr) match = 0
*1
#deffne M -8 /* value of a match with a stop
int aay[26][26] = {
1* AB CDBFGHIJKLMNOPQRSTUV WXYZ*/
/* A*/ { 2, 0, 2, 0, 0,-4, 0; 1, 2,-1, 0_M, 1, 0,-2, 1, 1, 0, 0,-6, 0,-3, 0),
/* B*/ { 0, 3,-4, 3, 2,-5, 0, 1,-2, 0, 0, 3, 2, 2, M,-1, 1, 0, 0, 0, 0,-2,-5,
0,-3, 1),
/* C{-2,-4,15, 5, 5,-4,-3,-3, 2, 0; 5,-6,-5,-4 _M,-3,-5,-4, 0,-2, 0,-2,-8, 0,
0,-5},
/* D*/ { 0, 3,-5, 4, 3,-6, 1, 1,-2, 0, 0,-4,-3, 2, M; 1, 2,-1, 0, 0, 0, 2, 7,
0,-4, 21,
/* B*/ { 0, 2,-5, 3, 4, 5, 0, 1, 2, 0, 0, 3,-2, 1,M,-1, 2; 1, 0, 0, 0,-2,-7,
0,-4, 3),
/* F{-4,-5,-4,-6; 5, 9; 5, 2, 1, 0,-5, 2, 0,-4, M,-5; 5,-4; 3, 3, 0; 1, 0, 0,
7,-5},
I* G*/ { 1, 0,-3, 1, 0,-5, 5,-2,-3, 0,-2,-4,-3, 0_M; 1,-1,-3, 1, 0, 0,-1,-7,
0,-5, 0),
/* H*/ {-1, 1,-3, 1, 1,-2,-2, 6,-2, 0, 0,-2,-2, 2,_M, 0, 3, 2,-1,-1, 0,-2,-3,
0, 0, 2),
/* I*/ {-1, 2, 2,-2,-2, 1,-3,-2, 5, 0,-2, 2, 2,-2 _M,-2, 2,-2,-1, 0, 0, 4,-5,
0,-1, 2},
/*J*/ {0,0,0,0,0,0,0,0,0,0,0,0,0,0, M,0,0,0,0,0,0,0,0,0,0,0},
/* K*/ {-1, 0,-5, 0, 0, 5, 2, 0,-2, 0, 5,-3, 0, 1, 3, 0, 0, 0,-2,-3, 0,-4, 0),
I* L {-2,-3,-6,-4,-3, 2,-4,-2, 2, 0,-3, 6, 4,-3,_M,-3,-2,-3; 3,-1, 0, 2,-2, 0,-
1, 2},
/* M{-1,-2,-5,-3, 2, 0,-3,-2, 2, 0, 0, 4, 6,-2,_M,-2,-1, 0,-2,-1, 0, 2,-4, 0,
2,-1},
I* N*1 { 0, 2,4, 2, 1,-4, 0, 2,-2, 0, 1,-3,-2, 2_M,-1, 1, 0, 1, 0, 0,-2,-4, 0,-
2, 1),
/* 0*/
/* P*/ { 0, 2, 0,-1,-3, 2,-1,M, 6, 0, 0, 1, 0, 0,-1,-6, 0,-5, 0),
/* Q{ 0, 1,-5, 2, 2,-5,-1, 3,-2, 0, 1, 2,-1, 1,M, 0, 4, 1,-1,-1, 0, 2,-5, 0,-
4, 31,
/* R {-2, 0,-4,-1,-1,-4,-3, 2,-2, 0, 3,-3, 0, 0,_M, 0, 1, 6, 0,-1, 0,-2, 2, 0,-
4, 0),
/* S*/ { 1, 0, 0, 0, 0,-3, 0, 0,-3,-2, 1_M, 1,-1, 0, 2, 1, 0,-1,-2, 0,-3, 0),
/* T*! { 1, 0, 2, 0, 0,-3, 0; 1, 0, 0, 0; 1,-1, 0, M, 0,-1; 1, 1, 3, 0, 0; 5,
0; 3, 01,
/*U*/ {0,0,0,0,0,0,0,0,0,0,0,0,0,0, M,0,0,0,0,0,0,0,0,0,0,0},
!* V*/ { 0, 2; 2, 2, 2,-1; 1,-2, 4, 0, 2, 2, 2, 2,M; 1; 2, 2,-1, 0, 0, 4,-6,
0, 2, 2},
/* W{-6,-5,-8,-7, 7, 0,-7,-3,-5, 0,-3, 2,-4,-4 _M,-6,-5, 2,-2,-5, 0,-6,17, 0,
0,-6},
/*x*1 {o,o,o,o,o,o,o,o,o,o,o,o,o,o,M,o,o,o,o,o,o,o,o,o,o,o},
/* Y*/ {-3,-3, 0,-4,-4, 7,-5, 0; 1, 0,-4,-1,-2; 2,M,-5,-4,-4,-3; 3, 0,-2, 0,
0,10,-4},
/* Z*/ { 0, 1,-5, 2, 3; 5, 0, 2, 2, 0, 0,-2,-1,1,_M, 0, 3, 0, 0, 0, 0,-2,-6,
0,-4, 4}
50
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Table 1 (cont')
#include <stdio.h>
#indude <ctype.h>
#de5ne MAXJMP 16 /* max jumps in a diag
#define MAXGAP 24 /* don't continue to penalize gaps larger than this */
#de6ne JMPS 1024 /* max jmps in an path */
#define MX 4 /* save if there's at least MX 1 bases since last jmp
#deflue DMAT 3 /* value of matcbing bases */
#define DMIS 0 /* penalty for mismatched bases */
#det9ne DINSO 8 /* penalty for a gap
#define DINS1 1 /* penalty per base
#define PINSO 8 /* penalty for a gap
#define PINS1 4 /* penalty per residue
struct jmp {
short n[MAX7MP]; /* size of jmp (neg for dely)
unsigned short x[MAXrMPJ; /* base no. of jmp in seq x
}; /* limits seq to 2' 16 -1
strnct diag {
int score; /* score at last imp
*!
long offset; /* offset of prev block
short ijmp; /* current imp index
sfruct jmp jp; J* list of jmps
,30 struct path {
int spc; /* number of leading spaces
short n[]MPSJ; /* size of jmp (gap) */
int x[JMPS]; /* loc of jmp (last elem before gap) */
};
char *ofile; /* output file name
c6sr *namex[2]; /* seq names: getseqs0
char *prog; !* prog name for err msgs
char *seqx[2]; /* aeqs: getseqs()
int dmax; /* best diag: nw0
int dmaxO; /* final diag */
int dna; /* set if dna: main0
9nt endgaps; /* set if penalizing end gaps
int gapx, gapy; /* total gaps in seqs
int len0, lenl; /* seq lens */
int ngapx, ngapy; /* total size of gaps
int smax; /* max score: nwO int *xbm; /* bitmap for matching */
long offset; /* current offset in jmp file
struat diag *dx; /* holds diagonals */
struct path pp[21; /* holds path for seqs
char *cailoc0, *malloc0, *index0, *strcpYO;
char *getseq0, *g_ca11oc0;
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Table 1 (cont')
/* Needleman-Wunsch alignment program
*
* usage: progs filel file2
* where filel and file2 are two dna or two protein sequences.
* The sequences can be in upper- or lowercase an may contam ambiguity
* Any lines beginning with ';', '>' or '<' are ignored
* Max fiie length is 65535 (limited by unsigned short x in the jmp struct)
* A sequence with 1/3 or more of its elements ACGTU is assumed to be DNA
* Output is in the file "align.out'
*
* The program may create a tmp file in /tmp to hold info about traceback.
* Original version developed under BSD 4.3 on a vax 8650
#inc[ude "nw.h"
/tumclude "day.h"
static dbval[26]
1,14,2,13,0,0,4,11,0,0,12,0,3,15,0,0,0,5,6,8,8,7,9,0,10,0
}'
static _pbval[26] = {
1, 21(1 < <('D'-'A'))1(1< <('N'-'A')), 4, 8, 16, 32, 64,
128,256,0xFFFFFFF, 1<<10, 1<<11, 1<<12, 1<<13, 1<<14,
1 15, 1 16, 1 17, 1 18, 1 19, 1 20, 1 21, 1 22,
1 < <23, 1 < <24, 1 < <251(1 < <('B'-'A'))'(1 < <('Q'-'A'))
};
main(ac, av) main
int ac;
char *avp;
{
prog = av[0];
if(acl=3){
fprintf(stderr,"usage: %s filel fi1e2\n", prog);
fprintt(stderr,"where filel and file2 are two dna or two protein
sequences.\n");
fprintf(stderr, "The sequences can be in upper- or lower-case\n");
fprintf(stderr,"Any lines beginning with';' or '<' are ignored\n");
fprintf(stderr,"Output is in the file \"align.out\"\n");
exit(1);
}
namex[0] = av[1];
namex[ll = av[2];
seqx[0] = getseq(namex[0], Mea);
seqx[l] = getseq(namex[1], &,lenl);
xbm = (dna)? dbval : -pbva1;
endgaps = 0; /* 1 to penalize endgaps *!
ofile = "align.out"; /* output file */
nwo; /* fill in the matrix, get the possible jmps
readjmps0; /* get the actual jmps */
printQ; /* print stats, alignment */
} cleanup(0); /* unlink any tmp files */
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Table 1(cont')
/* do the alignment, return best score: mainQ
* dna: vatues in Fitch and Smith, PNAS, 80, 1382-1386, 1983
* pro: PAM 250 values
* When scores are equal, we prefer mismatches to any gap, prefer
* a new gap to extending an ongoing gap, and prefer a gap in seqx
*toagapinseqy
*1
nwo nw
{
char' *px, *py; /* seqs and ptrs
int *ndely, *dely; /* keep track of dely
>nt ndelx, delx; /* keep track of delx */
int *tmp; /* for swapping rowO, rowl
int mis; /* score for each type */
mt inso, ins1; /* insertion penalties
*/
register id; /* diagonal index */
register ij; /* jmp index */
register *co10, *coll; /* score for curr, last row
register xx, yy; /* index into seqs */
dx =(strnet diag *)g_calloc("to get diags", len0+len1+1, sizeof(struct diag));
ndely =(int *)g calloc('to get ndely", len1+1, sizeoF(int));
dely =(fiit *)g_calloc("to get dely", len1+1, sizeof(mt));
colO =(int *)g calloc("to get co10", lenl+l, sfzeof(int));
coil =(int *)g_calloc("to get col l", lenl + 1, sizeof(mt));
insO = (dna)? DINSO : PINSO;
insl = (dna)? DINS1 : PINS1;
smax = -10000;
if (endgaps) {
for (co10[0] = dely[0] =-ins0, yy = 1; yy <= 1en1; yy+-t-) {
colO[yy] = dely[yy] $ col0[yy-1] - insl;
ndely[yyl = yy;
}
colo[o] = o; /* Watemian Bull Math Biol 84 */
}
else
for (yy = 1; yy <= lenl; yy++)
dely[yy] = -insO;
/* fiIl in match matrix
for (px = seqx[0], xx = 1; xx <= lenO; px++, xx++) {
/* initialize tirst entry in col
if (endgaps) {
if(xx==1)
coll[0] = delx = {ins0+ins1);
else
coll[0] = delx = co10[0] - insl;
ndelx = xx;
}
else {
coll[0] = 0;
delx = -ins0;
ndelx = 0;
}
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Table 1 (cont')
...nW
for (py = seqx[1], yy = 1; yy <= lenl; py++, yy++) {
mis = colo[yy-1];
K (dna)
mis + = (xbm[*px-'A']8cabm[*py-'A'])? DMAT : DMIS;
else
mis + = daY[ px-Wl['PY-'A'l;
/* update penalty for del in x seq;
* favor new del over ongong del
* ignore MAXGAP if weighting endgaps
if (ezidgaps I I ndely[Yy] < MAXGAP) {
if (colO[yy] - insO > = dely[yy]) {
dely[yy] = col0[yy] - (inso+insi);
ndely[YY] = 1;
} else {
dely[Yyl -= insl;
ndely[yy]++;
}
}e>se{
if (col0[yy] - (ins0+ins1) > = dely[yy])
{
dely[yy] = col0[}ry] - (ins0+ins1);
dse nmyCvY] = 1;
}
ndely[yy]++;
}
/* update penalty for del in y seq;
* favor new del over ongong del
if (endgaps ndelx < MAXGAP) {
if (coll[yy-1] - ins0 > = delx) {
delx = coll[yy-1] - (ins0+ins1);
ndelx = 1;
}else{
delx -= insl;
ndelx++;
}else{ }
if (coll[yy-1] - (ins0+ins1) > = delx) {
delx = coll[yy-1] - (ins0+ins1);
ndelx = 1;
e]se
ndelx++;
}
/* pick the maximnm score; we're favoring
* mis over any del and delx over dely
55
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Table 1(cont')
...nw
id=xx-yy+lenl-1;
if (mis >= delx 8c8c mis >= dely[yy])
coll[yy] = mis;
else if (delx > = dely[yy]) {
colljyy] = delx;
ij = dx[id].ijmp;
if (dx[id].jp.n[0] && (ldna (ndelx > = MAXJMP
&& xx > dx[id].jp.x[ijj+MX) mis > dx[idl.score+DINSO)) {
dx[idj.ijmp++;
if (++ij > = MAXJMP) {
writejmps(id);
ij = dx[id].ijmp = 0;
dx[idl.offset = offset;
offset += sizeof(strvct jmp) + sizeof(offset);
}
}
dx[id]=jp=n[ij] = ndelx;
dx[id].jp.x[ij] = xx;
dx[id].score = delx;
}
eJse {
coll[yyj = dely[yy];
ij = dx[idj.ijmp;
if (dx[id].jp=n[O] && (!dna I (ndely[yy] > = A4AXTMP
&& xx > dx[id].jp.x[ij]+MX) I I mis > dx[id].score+DINSO)) {
dx[id].ijmp+-h;
if (++ij > = MAXJMP) {
writejmps(id);
ij = dx[id].ijmp = 0;
dx[id].ofi'set = offset;
offset += sizeof(sbrack jmp) + sizeof(offset);
}
}
dx[id7=jp=n[ijl = -ndely[yy];
dx[id].jp.x[ij] = xx;
dx[id].score = dely[yy];
}
if (xx = =1en0 && yy < leni) {
/* last coI
if (eadgaps)
coll[yy] -= ins0+ins1*(leni-yy);
if (coll[yy] > smax) {
smax = co11[yy];
dmax = id;
}
}
}
if (endgaps && xx < IenO)
coll[yy-1] -= ins0+ins1*(len0-xx);
if (coll[yy-i] > smax) {
smax = coll[yy-1];
dmax -id'
}
tmp = co10; coIO = cotl; coll = tmp;
}
(void) free((cbar *)ndely);
(void) ifee((chaz *)ciely);
(void) free((dzar *)colO);
(void) &ee((cbar *)coll); }
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Table 1(cont')
*
* print0 - only routine visible outside this module
*
* static:
* getcnat() -- trace back best path, count matches: printQ
* pr align0 -- print alignment of described in array p0: print0
* dumpblock0 -- dump a block of lines with numbers, stars: pr align0
* nums0 - put out a number line: dumpblock0
* putline() - put out a line (name, [num], seq, [num]): dumpblock()
* starsO - -put a line of stars: dumpblock()
* stripname0 - strip any path and prefix from a seqname
#include "nw.h"
#cle&ne SPC 3
#define P I.INE 256 /* maximum output line */
#define P SPC 3 /* space between name or num and seq
extern _dayCZ6][261;
int olen; 1* set output line length *1
FILE *fx; /* output file */
printp print
{
nit lx, ly, firstgap, lastgap; /* overlap */
if ((fx = fopen(ofile, "w")) = = 0) {
fprintf(stderr,"%s: can't write %s\n", prog, ofile);
cleanup(l);
}
fprintf(fx, "<ffrst sequence: %s (length = %d)\n', namex[O], len0);
fprintf(fa, "<second sequence: %s (length = %d)\n", namex[1], lenl);
olen = 60;
lx = 1en0;
ly = lenl;
firstgap = lastgap = 0;
if (dmax < lenl - 1) { /* leading gap nn x
pp[0].spc =fustgap g lenl - dmax - 1;
ly -= PP[0]=spc;
}
else if (dmax > lenl - 1) { /* leading gap in y *1
pp[i]=spo = firstgap = dmax - (lenl - 1);
Ix -= pp[1]-spc;
}
if (dmax0 < len0 - 1) { /* trailing gap in x*/
lastgap = lenO - dmaxO -1;
Ix -= lastgap;
}
else ff (dmax0 > len0 - 1) {/* trailing gap in y
lastgap = dmax0 - (len0 - 1);
ly -=lastgap;
getmat(lx, ly, firstgap, lutpp);
pr align0;
}
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Table 1 (cont')
* trace back the best path, count matches
*1
static
getmat(lx, ly, firstgap, lastgap) gehnat
int lx, ly; /* "core" (mim endgaps)
int fustgap, lastgap; /* leading trailing overlap
{
int nm, i0, il, siz0, sizl;
char ontx[32];
double pct;
rqoster n0. n1;
register cbar *p0, "Pl;
1* get total matches, score
i0=i1 =siz0=sizl =0;
p0 = seqx[Ol + pp[1].spc;
pl = seqx[1] + pp[0].spc;
n0 = pp[l7.spc + 1;
nl = pp[0].spc + 1;
nm=0;
wlu7e ( *pO && *pl ) {
if (sizo) {
pl++;
nl++;
siz0--;
}
else if (sizl) {
po++;
no++;
sizl-;
}
dse {
If (xbm[*p0-'A'I&xba-[*p1-'A'])
1IIn++;
9i (n0++ == pp[01.x[iO])
siz0 = pp[03.n(i0++);
if (nl++ _= pp[1].x[il])
sizl = pp[1].n[il++];
p0++;
pl++;
} }
/* pct hasnology:
* if penalizing eadgaps, base is the shorter seq
* else, lawck off overhangs and take shorter core
if (endgaps)
lx = (len0 < 1en1)? len0 : lenl;
else
lx = (lx < ly)? lx :1y;
pct = 100. *(double)am!(double)lx;
fprintf(fx, "\n");
fprintfl(fx, "<%d match%s in an overlap of %d: %.2f percent similarityW,
nm, (nm =- 1)? "eS"f 1x, pct);
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Table 1 (cont')
fprintf(fx, "<gaps in first sequence: %d", gapx); ...getmat
if (gapx) {
(void) sprintf(outx, " (%d %s%s)",
ngapx, (dna)? "base":"residue", (ngapx = = 1)? "":"s");
fprintf(fx,"9os", outx);
fprintf(fx, ", gaps in second sequence: %d", gapy);
if (gapy) {
(void) sprintf(outx, " (%d %s%s)",
ngapy, (dna)? "base":"residue", (ngapy = = 1)? "":"s");
fprintf(fx, " %s", outx);
}
if (dna)
fprintf(&,
"\n<score: %d (match = %d, mismatch = %d, gap penalty = %d + %d per base)\n",
smax, DMAT, DMIS, DINSO, DINS1);
else
fprintf(&,
"1n<score: %d (DayhofPPAM 250 matrix, gap penalty = %d + %d per residue)1n",
smax, PINSO, PINS1);
if (endgaps)
fprintf(&,
"<endgaps penalized. left endgap: %d %s%s, right endgap: %d %s%s\n",
firstgap, (dna)? "base" : "resldue", (firstgap == 1)? "n : s",
lastgap, (dna)? "base" : "residue", (lastgap == 1)? "" : "s");
else
fprintf(fx, <endgaps not penalizedln");
}
static in; /* matches in core -- for checking */
static lmax; /* lengths of stripped file names
static ij[2]; /* jmp index for a path */
static nc[2]; /* number at start of current line */
static ni[2]; /* current elem mmmber -- for gapping
static siz[2];
static char *ps[2]; /* ptr to current element
static char *po[21; /* ptr to next output char slot */
statfic char out[2][P LINB]; /* output line */
static dtar star[P_IIN&]; /* set by stars0
* print alignment of described in stract path ppo
static
pr align() pr align
{
int nn; /* char count
int more;
register i;
for(i= 0,imax=0;i <2;i++){
nn = stripname(namex[ilk
if (nn > lmax)
lmax = nn;
nc[71;
ni[i] - 1;
siz[i] = ij[i] = 0;
ps[il = seqx[i];
po[i] = out[il; }
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Table 1(co>i{')
for (nn = nm = 0, more = 1; more; ) ( ...pr_align
for(i=more=0;i<2;i++){
!*
* do we bave more of this sequence?
*1
it (1 *Ps[i])
. contmae;
more++;
If (PPU7-spo) { p" 2eading space */
"Po[i]++
PP[il=sPc--;
}
ease 9f (siz[i]) { /* in a gap *!
"Po[il++
aiz[i]--,
else { /* we're putting a seq element
"po[il = '"psCl;
if (islower(*ps[i]))
~[i] = touPP~(*Ps[iD;
po[il+ +;
ps[i]++;
~ are we at next gap for this seq?
/
if (n[i] P07=4011) {
* we need to merge all gaps
* at this looation
*/
BizC] = pp1i]=n[ij[7++];
while (ni[i] _= PP[7=R[iji7])
siz[i] += pp[i].n[ij[i]++];
m[i]++;
}
}
if (++nn == olen ~ ~[nuore 8c& nn) {
dnunpblock0;
for(i = 0; i< 2; i++)
po[il = out[7;
ffi=0;
}
} }
* dump a block of lines, inc,lndiog numbers, stars: pr align0
*!
static
;urapbloc0 dumpblock
register i;
for (i = 0; i< 2; i++)
'"iw[i]-- _ '\o';
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Table 1 (cont')
...dumpblock
(void) putc('\n', fx);
for(i=0;i<2;i++){
if (*out[i] && (*ont[i] ! I *(Po[i])1= ' ')) {
if(i==0)
nums(i);
3f (i = = 0 8c& *out[1])
stars0;
pntline(i);
if (i 0 8c& *ovt[1])
tprintt(fx, star);
if(i==1)
mums(i);
}
}
}
* put out a number line: dampblockQ
*!
static
nums(ix) nums
int ix; /* index in outp holding seq line
{
char nline[P_LINL];
registex i, j;
register char *pn, *px, *py;
for (pn = nline, i= 0; i< Imax+P SPC; i++, pn++)
*pn _õ
for (i = ncGx], py =out[ix]; *py; pY++, pn++) {
if("PY =_" II *pY
*Pn = ";
else {
if(i%10==0(i==18a&nc[ix]1=1)){
j = (i < 0)? -i : i;
for (px = pn; j; j / = 10, px-)
if (i < 0) *px = j'K10 + '0';
*px
}
else
*pn
i++;
}
}
*pn'\0';
nc[ix] = i;
for (pn = nline; *pn; pn++)
(void) putc(*pn, fx);
(void) putc('\n', fx);
}
/*
* put out a line (name, [aum], seq, [num]): dumpblock()
static
putline(ix) putline
int ix; {
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Table 1(cont')
...putline
int i;
register char *px;
for (px = namex[ix], i = 0; *px &dt *px ! px++, i++)
(void) putc(*px, fx);
for (; i< lmax+P SPC; i++)
(void) putc(, " fx);
/* these count from 1:
* nip is current element (from 1)
* ncp is number at start of current line
for (px = oatGx); *px; px+ +)
(void) putc(*px&0x7F, fx);
(void) putc('\n', fx);
}
* put a line of stars (seqs always in out[0], out[l]): dumpblock()
static
starsp StaPS
{
int i;
register char *pO, *p1, cx, *px;
if (t*out[o] I I (*out[Ol == ' ' && *(po[ol) == ' ') I I
!*out[l] I I (*oUt[1] == && *(Po[ll) == ' '))
retum;
px = star;
for (i = imax+P_SPC; i; i-)
*px++ _ ,
for (p0 = out[0], p1 = out[1]; *p0 &,8c *pl; p0++, pi++) {
if (isalpha(*p0) && isalpha("'pt)) {
if (xbm[*p0-'A']8rxbm[*pl-'A']) {
cx=x';
nm++;
}
else if (ldna && day[*p0-'A'][*pl-'A'] > 0)
cx =
else
cx = "
}
else
cx
*px++ = cx;
}
*px++ = '1n';
1 *px='\0;
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Table 1(cont')* strip path or prefix from pn, return len: pr align0
static
stripname(pn) stripname
char *pn; /* file name (may be path) */
{
register cbar *px, *py;
py=0;
for (px = pn; *px; px+ +)
ft (*px == '/')
py=px+1;
if (py)
(void) strcpy(pn, py);
return(strlen(pn));
}
25
35
45
55
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Table 1(cont')
* cleanup() -- cleamip any tmp file
* getseq0 -- read in seq, set dna, len, maxlen
* g callocQ -- calloc() with error checkin
* readjmpsQ - get the good jmps, from tmp file if necessary
* writejmps0 - write a filled array of jmps to a tmp file: nwQ
/!'induide "nw.h"
#inclnde <sys/file.h>
char *jname ="/tmp/homgXXXXXV; /* tmp file for jmps
FII,E *fj;
int cleanupO; /* cleanup tmp file */
long IseekQ;
* remove any tmp 5le if we blow
cteannp(i) cleanup
int i;
{
if (f7)
(void) u.nlink(jname);
exit(i);
}
* read, return ptr to seq, set dna, len, maxien
* sldp lines starting with ';,, '<', or '>'
* seq in upper or lower case
char *
getseq(file, len) getseq
char *file; /* 51e name
int *len; /* seq len */
{
char line[1024], *pseq;
register char *px, *pY;
int natgc, den;
FII,E *fp;
if ((fp = fopen(61e, "r")) = = 0) {
fprintt(stderr,"%s: can't read %s\n", prog, file);
exit(l);
}
tien = natgc = 0;
white (fgets(line, 1024, fp)) {
if(*ine ==';' I I *line=='<' *Rne
contm,ne;
for (px = line; *px 1= '\n'; px++)
if (isupper(*px) I I islower('"px))
t1en++;
}
if ((pseq = mauoc((ansigned)(flen+6))) == 0) {
fprWstderr,"%s: malloc() failed to get %d bytes for %s\n", prog, tlen+6,
file);
exit(l);
}
pseq[0] = pseq[i1 = pseq[2] = pseq[3] ='\0'
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Table 1 (cont')
. .getseq
py = pseq + 4;
*len = tlen;
rewind(fp);
while (fgets(line, 1024, fp)) {
if (*line==';' I l *fine__'<' *1ine=='>')
continue;
for (px = line; *px != '\n'; px++) {
if (isupper(*px))
*py++ = *px;
else if (islower(*px))
*py++ = toupper(*px);
if (index("ATGCU",*(py-1)))
natgc++;
}
}
*py++ _ '\0';
*py = '\0';
(void) folose(fp);
dna = natgc > (tlen/3);
return(pseq+4);
}
char *
g calloc(msg, nx, sz) g_calloc
char *msg; /* program, calling routine int nx, sz; /* number and size of
elements */
{ char *px,*callocp;
if ((px = calloc((imsigned)nx, (unsigned)sz)) 0) {
if ("'msg) {
fprintf(stderr, "%s: g_calloc() failed %s (n=%d, sz=%d)1n", prog, msg, nx,
sz);
exit(1);
}
}
retum(px);
}
* get fiaal jmps from dxo or tmp file, set pp[], reset dmax: main0
readjmpsQ readjmps
{
int fd = -1;
int siz, i0, il;
register i, j, xx;
ie (f'j) {
(void) fclose(fj);
if ((fd = open(jname, O RDONLY, 0)) < 0) {
fprintf(stderr, "%s: can't open0 %s1n", prog, jname);
cleanup(1);
}
}
for(i=i0=i1 =0,dmax0=dmax,xx=len0;;i++){
wW7e (1) {
for (j = dx[dmax]=ijmp; j>= 0 && dx[dmax].jp.x[j] > xx; j-)
f)0
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Table 1 (cont')
...readjmps
if (j < 0 && dx[dmax].offset && fj) {
(void) lseek(fd, dx[dmax].offset, 0);
(void) read(fd, (char *)&dx[dmaxl=jp, sizeot(struct jmP));
(void) read(fd, (char *)&dx[dmax].offset, sizeo((dx[dmax].offset));
dx[dmax].ijmp = MAXJMP-1;
}
else
break;
}
if (i > = JMPS) {
fprintf(stderr, "%s: too many gaps in alignment\n", prog);
cleanup(1);
}
if0 >= 0) {
siz = dx[dmax].jP=nUl;
xx = dx[dmaxlJp.x[i];
dmax + = siz;
if (siz < 0) { /* gap in second seq */
pp[1].n[il] = -siz;
xx += siz;
/*id=xx-yy+lenl-1
pp[1].x[il] = xx - dmax + lenl - 1;
gapy++;
ngapy -= siz;
/* ignore MAXGAP when doing endgaps */
siz =(-siz < MAXGAP endgaps)? -siz MAXGAP;
il++;
}
else if (siz > 0) {/* gap in first seq
pp[Ol.n[i0] = siz;
PP[0].x[i0] = xx;
gapx+ +;
ngapx += siz;
/* ignore MAXGAP wben doing endgaps *1
siz =(siz < MAXGAP endgaps)? siz : MAXGAP;
i0++;
}
}
else
break;
}
/* reverse the order of jmps
for (j = 0, i0--; j< i0; j++, i0--) {
i= PP[Ol=nL1]; PP[0]=n[i] = PP[014i0]; Pp[0].n[i0] = i;
i= PP[Ol=x[il; Pp[Ol=xUl = PP[0]=x[i0]; Pp[0].x[io] = i;
}
for(i =0,i1-;j <ii;j++, il-) {
i = PP[1]=nU]; Pp[ll=n[)] = Pp[Il=n[ill; pp[1].n[ill = i;
i= pp[1].x[j]; pp[1].x(j] = pp[1].x1ill; pp[1].x[il] = i;
if(fd>=0)
(void) close(fd);
;f (6) {
(void) unlink(jname);
fj = 0;
offset = 0;
} }
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Table 1 (cont')
i*
* write a filled jmp struct offset of the prev one (if any): nwO
writejmps(ix) wl'itejl-rips
int ix;
{
dmr *mktempO;
;f (tq) {
if (mktemp(jname) < 0) {
fprintf(stderr, "%s: can'tnilctempQ % s\n", prog, jname);
cleanup(1);
if ((fj = fopen(jname. "w")) 0) {
fprintf(stderr, "%s: can't write Un", prog, jname);
exit(1);
}
}
(void) fwrite{(dtar *)&dx[ixl=jP, sizeof(straa jmp), 1, fj);
(void) fwrite((char'")&dx[ix].offset, sizeof(dx[ix].offset), 1, fj);
}
30
40
50
60
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Table 2
PRO (Length = 15 amino acids)
Comparison Protein XXXXXYYYYYYY (Length = 12 amino acids)
% amino acid sequence identity =
(the number of identically matching amino acid residues between the two
polypeptide sequences as determined
by ALIGN-2) divided by (the total number of amino acid residues of the PRO
polypeptide) _
5 divided by 15 = 33.3 %
Table 3
PRO (Length = 10 amino acids)
Comparison Protein XXXXXYYYYYYZZYZ (Length = 15 amino acids)
% amino acid sequence identity =
(the number of identically matching amino acid residues between the two
polypeptide sequences as determined
by ALIGN-2) divided by (the total number of amino acid residues of the 'PRO
polypeptide)
5 divided by 10 = 50%
Table 4
PRO-DNA NNNNNNNNNNNNNN (Length = 14 nucleotides)
Comparison DNA NNNNNNLLLLLLLLLL (Length = 16 nucleotides)
% nucleic acid sequence identity =
(the number of identically matching nucleotides between the two nucleic acid
sequences as determined by ALIGN-
2) divided by (the total number of nucleotides of the PRO-DNA nucleic acid
sequence) _
6 divided by 14 = 42.9%
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Table 5
PRO-DNA NNNNNNNNNNNN (Length = 12 nucleotides)
Comparison DNA NNNNLLLVV (Length = 9 nucleotides)
% nucleic acid sequence identity =
(the number of identically matching nucleotides between the two nucleic acid
sequences as determined by ALIGN-
2) divided by (the total number of nucleotides of the PRO-DNA nucleic acid
sequence) _
4 divided by 12 = 33.3 %
II. Comnositions and Methods of the Invention
A. Full-Length PRO Polypggdm
The present invention provides newly identified and isolated nucleotide
sequences encoding polypeptides
referred to in the present application as PRO polypeptides. In particular,
cDNAs encoding various PRO
polypeptides have been identified and isolated, as disclosed in farther detail
in the Examples below. It is noted
that proteins produced in separate expression rounds may be given different
PRO numbers but the UNQ number
is unique for any given DNA and the encoded protein, and will not be changed.
However, for sake of simplicity,
in the present specification the protein encoded by the full length native
nucleic acid molecules disclosed herein
as well as all further native homologues and variants included in the
foregoing definition of PRO, will be referred
to as "PRO/number", regardless of their origin or mode of preparation.
As disclosed in the Examples below, various cDNA clones have been deposited
with the ATCC. The
actual nucleotide sequences of those clones can readily be determined by the
sldlled artisan by sequencing of the
deposited clone using routine methods in the art. The predicted amino acid
sequence can be determined from the
nucleotide sequence using routine sldll. For the PRO polypeptides and encoding
nucleic acids described herein,
Applicants have identified what is believed to be the reading frame best
identifiable with the sequence information
available at the time.
B. PRO Polypentide Variants
In addition to the full-length native sequence PRO polypeptides described
herein, it is contemplated that
PRO variants can be prepared. PRO variants can be prepared by introducing
appropriate nucleotide changes into
the PRO DNA, and/or by synthesis of the desired PRO polypeptide. Those sldlled
in the art will appreciate that
amino acid changes may alter post-translational processes of the PRO, such as
changing the number or position
of glycosylation sites or altering the membrane anchoring characteristics.
Variations in the native full-length sequence PRO or in various domains of the
PRO described herein,
can be made, for example, using any of the techniques and guidelines for
conservative and non-conservative
49
CA 02591930 2007-03-30
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mutations set forth, for instance, in U.S. Patent No. 5,364,934. Variations
may be a substitution, deletion or
insertion of one or more codons encoding the PRO that results in a change in
the amino acid sequence of the PRO
as compared with the native sequence PRO. Optionally the variation is by
substitution of at least one amin.o acid
with any other amino acid in one or more of the domains of the PRO. Guidance
in determining which amino acid
residue may be inserted, substituted or deleted without adversely affecting
the desired activity may be found by
comparing the sequence of the PRO with that of homologous known protein
molecules and *n+*~I ++I~+ng the number
of amino acid sequence changes made in regions of high homology. Amino acid
substitutions can be the result
of replacing one amino acid with another amino acid having simil.ar structural
and/or chemical properties, such
as the replacement of a leucine with a serine, i.e., conservative amino acid
replacements. Insertions or deletions
may optionally be in the range of about I to 5 amino acids. The variation
allowed may be determined by
systematically making insertions, deletions or substitutions of amino acids in
the sequence and testing the resulting
variants for activity eshlited by the full-length or matare native sequence.
PRO polypeptide fragments are provided herein. Such fragments may be truncated
at the N-terminus
or C-terminus, or may lack internal residues, for example, when compared with
a fnll length native protein.
Certain fragments lar.k amino acid residues that are not essential for a
desired biological activity of the PRO
polypeptide.
PRO fragments may be prepared by any of a number of conventional techniques.
Desired peptide
fragments may be chemically synthesized. An alternative approach involves
generating PRO fragments by
enzymatic digestion, e.g., by treating the protein with an enzyme known to
cleave proteins at sites defined by
particular amino acid residues, or by digesting the DNA with saitable
restriction enzymes and isolating the desired
fragment. Yet another suitable technique involves isolating and amplifying a
DNA fragment encoding a desired
polypeptide fragment, by polymerase chain reaction (PCR). Oligonncleotides
that define the desired termini of
the DNA fragment are employed at the 5' and 3' primers in the PCR. Preferably,
PRO polypeptide fragments
share at least one biological and/or immunological activity with the native
PRO polypeptide disclosed herein.
In particalar embodiments, conservative substitutions of interest are shown in
Table 6 under the heading
of preferred substitutions. If such substitutions result in a change in
biological activity, then more substantial
changes, denominated exemplary substitutions in Table 6, or as further
described below in reference to amino acid
classes, are introduced and the products screened.
CA 02591930 2007-03-30
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Table 6
Original Exemplary Preferred
R esidue Substitutions Substitutions
Ala (A) val; leu; ile val
Arg (R) lys; gh-; asn lys
Asn (N) gin; his; lys; arg gln
Asp (D) glu glu
Cys (C) ser ser
Gln (Q) asn asn
Glu (E) asp asp
Gly (G) pro; ala ala
His (H) asn; gln; lys; arg arg
lle (I) leu; val; met; ala; phe;
norleucine leu
Leu (L) norleucine; ile; val;
met; ala; phe ile
Lys (K) arg; gln; asn arg
Met (M) leu; phe; ile leu
Phe (F) leu; val; iie; ala; tyr leu
Pro (P) ala ala
Ser (S) thr thr
Thr (T) ser ser
Trp (W) tyr; phe tyr
Tyr (Y) trp; phe; thr; ser phe
Val (V) ile; leu; met; phe;
ala; norleucine leu
Substantial modifications in function or kmmunological identity of the PRO
polypeptide are accomplished
by selecting substitutions that differ significantly in their effect on
maintaining (a) the structure of the polypeptide
backbone in the area of the substitution, for example, as a sheet or helical
conformation, (b) the charge or
hydrophobicity of the molecule at the target site, or (c) the bulk of the side
chain. Naturally occurring residues
are divided into groups based on common side-chain properties:
(1) hydrophobic: norleucine, met, ala, val, ieu, ile;
(2) neutral hydrophilic: cys, ser, thr;
(3) acidic: asp, glu;
(4) basic: asn, gln, his, lys, arg;
(5) residues that influence chain orientation: gly, pro; and
(6) aromatic: trp, tyr, phe.
Non-conservative substitutions vvill entail exchanging a member of one of
these classes for another class.
Such substituted residues also may be introduced into the conservative
substitution sites or, more preferably, into
the remaining (non-conserved) sites.
The variations can be made using methods ]mown in the art such as
oligonucleotide-mediated (site-
directed) mutagenesis, alanine scanning, and PCR mutagenesis. Site-directed
mutagenesis [Carter et al., Nucl.
Acids Res., 13:4331(1986); Zoller et al., Nucl. Acids Res., 10:6487 (1987)],
cassette mutagenesis [Wells et al.,
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Gene, 34:315 (1985)], restriction selection mutagenesis [Wells et al., Philos.
Trans. R. Soc. London SerA,
317:415 (1986)] or other known techniques can be performed on the cloned DNA
to produce the PRO variant
DNA.
Scanning amino aaid analysis can also be employed to identify one or more
amino acids along a
contiguous sequence. Among the preferred scanning amino acids are relatively
small, neutral amino acids. Such
amino acids include alanine, glyycine, serine, and cysteine. Alanine is
typicatly a preferred scanning amino acid
among this group because it eliminates the side-chain beyond the beta-carbon
and is less likely to alter the main-
chain conformation of the variant [Cunningham and Wells, Science, 244: 1081-
1085 (1989)]. Alanine is also
typically preferred because it is the most common amino acid. Farther, it is
frequently found in both buried and
exposed positions [Creighton, The Prateins, (W.H. Freeman & Co., N.Y.);
Chothia, J. Mol. Biol., 150:1
(1976)]. If alanine substitution does not yield adequate amounts of variant,
an isoteric amino acid can be used.
C. Modifications of PRO
Covalent modifications of PRO are included within the scope of this invention.
One type of covalent
modification includes reacting targeted amino acid residues of a PRO
polypeptide with an organic derivatizing
agent that is capable of reacting with selected side chains or the N- or C-
terminal residues of the PRO.
Derivatization with bifaactional agents is useful, for instance, for
crosslink9ng PRO to a water-insoluble support
matrix or surface for use in the method for purifying anti-PRO antibodies, and
vico-versa. Commonly used
crosslinking agents include, e.g., 1,1-bis(diazoacetyl)-2-phenylethane,
glutaraldehyde, N-hydroxysuccinimide
esters, for example, esters with 4-azidosalicylic acid, homobifunctional
imidoesters, including disuccinimidyl
esters such as 3,3'-dithiobis(sixx:inimidylpropionate), bifuncfional
maleimides such as bis-N-maleimido-1,8-octane
and agents such as methyl-3-[(p-azidophenyl)dithio]propioimidate.
Other modifications include deamidation of glutaminyl and asparaginyl residnes
to the corresponding
glutamyl and aspartyl residues, respectively, hydroxylation of proline and
lysine, phosphorylation of hydroxyl
groups of seryl or threonyl residues, methylation of the a-amino groups of
lysine, arginine, and histidine side
chains [T.B. Creighton, Proteins: Structure and Molecular Prooerties W.H.
Freeman & Co., San Francisco,
pp. 79-86 (1983)], acetylation of the N-terminal amine, and amidation of any C-
terminal carboxyl group.
Another type of oovalent modification of the PRO polypeptide included within
the scope of this invention
comprises altering the native glycosylation pattern of the polypeptide.
"Altering the native glycosylation pattem"
is intended for purposes herein to mean deleting one or more carbohydrate
moieties found in native sequenoe PRO
(either by removing the underlying glycosylation site or by deleting the
glycosylation by chemieal and/or
enzymatic means), and/or adding one or more glycosylation sites that are not
present in the native sequence PRO.
In addition, the phrase includes qualitative changes in the glyccrsylation of
the native proteins, involving a change
in the natare and proportions of the various carbohydrate moieties present.
Addition of glycosylation sites to the PRO polypeptide may be accomplished by
altering the amino acid
seyuence. The alteration may be made, for eaample, by the addition of, or
substitution by, one or more serine
or threonine residues to the native sequence PRO (for 0-linlfled glycosylation
sites). The PRO amino acid
sequence may optionally be altered through chau4$es at the DNA level,
particularly by mutating the DNA encoding
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the PRO polypeptide at preselected bases such that codons are generated that
will translate into the desired amino
acids.
Another means of increasing the number of carbohydrate moieties on the PRO
polypeptide is by chemical
or enzymatic coupling of glycosides to the polypeptide. Such methods are
described in the art, e.g., in WO
87/05330 published 11 September 1987, and in Aplin and Wriston, CRC Crit. Rev.
Biochem., pp. 259-306
(1981).
Removal of carbohydrate moieties present on the PRO polypeptide may be
accomplished chemically or
enzymatically or by mutational substitution of codons encoding for amino acid
residues that serve as targets for
glycosylation. Chemical deglycosylation techniques are known in the art and
described, for instance, by
Hakimuddin, et ai., Arch. Biochem. Bionhvs., M:52 (1987) and by Edge et al.,
Anal. Biochem., 118:131
(1981). Enzymatic cleavage of carbohydrate moieties on polypeptides can be
achieved by the use of a variety of
endo- and exo-glycosidases as described by Thotakura et al., Meth. Enzvmol.,
L38:350 (1987).
Another type of covalent modification of PRO comprises linldng the PRO
polypeptide to one of a variety
of nonproteinaceous polymers, e.g., polyethylene glycol (PEG), polypropylene
glycol, or polyoxyalkylenes, in
the mamier set forth in U.S. Patent Nos. 4,640,835; 4,496,689; 4,301,144;
4,670,417; 4,791,192 or 4,179,337.
The PRO of the present invention may also be modified in a way to form a
chimeric molecule comprising
PRO fused to another, heterologous polypeptide or amino acid sequence.
In one embodiment, such a chimeric molecule comprises a fusion of the PRO with
a tag polypeptide
which provides an epitope to which an anti-tag antibody can selectively bind.
The epitope tag is generally placed
at the amino- or carboxyl- terminus of the PRO. The presence of such epitope-
tagged forms of the PRO can be
detected using an antibody against the tag polypeptide. Also, provision of the
epitope tag enables the PRO to be
readily purified by affmity purification using an anti-tag antibody or another
type of affinity matrix that binds to
the epitope tag. Various tag polypeptides and their respective antibodies are
well Imown in the art. Examples
include poly-histidine (poly-his) or poly-histidine-glycine (poly-his-gly)
tags; the flu HA tag polypeptide and its
antibody 12CA5 [Field et al., Mol. Cell. Biol., g:2159-2165 (1988)]; the c-myc
tag and the 8F9, 3C7, 6E10, G4,
B7 and 9E10 antibodies thereto [Evan et al., Molecular and Cellular Biology,
5:3610-3616 (1985)1; and the
Herpes Simplex virus glycoprotein D (gD) tag and its antibody [Paborsky et
al., Protein EngW6e_e_riug, 3(6):547-
553 (1990)]. Other tag polypeptides include the Flag-peptide [Hopp et al.,
BioTechnoloev, 6:1204-1210 (1988)];
the KT3 epitope peptide [Martin et al., Science, 215:192-194 (1992)]; an a-
tabulin epitope peptide [Skinner et
al., J. Biol. Chem., 266:15163-15166 (1991)]; and the T7 gene 10 protein
peptide tag [Lutz-Freyermuth et al.,
Proc. Natl. Acad. Sci. USA, 87:6393-6397 (1990)].
In an alternative embodiment, the chimeric molecule may comprise a fusion of
the PRO with an
immunoglobulin or a particular region of an immunoglobulin. For a bivalent
form of the chimeric molecule (also
referred to as an "immunoadhesin"), such a fusion could be to the Fc region of
an IgG molecule. The Ig fusions
preferably include the substitution of a soluble (transmembrane domain deleted
or inactivated) form of a PRO
polypeptide inplace of at least one variable region within an Tg molecule. In
a particularly preferred embodiment,
the immunoglobulin fusion includes the hinge, CH2 and CH3, or the hinge, CH1,
CH2 and CH3 regions of an
IgGi molecule. For the production of immunoglobulin fusions see also US Patent
No. 5,428,130 issued June 27,
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1995.
D. Prevaration of PRO
The description below relates primarily to production of PRO by culturing
cells transformed or
transfected with a vector containing PRO nucleic acid. It is, of course,
contemplated that alternative methods,
which are well known in the art, may be employed to prepare PRO. For instance,
the PRO sequence, or portions
thereof, may be produced by direct peptide synthesis using solid-phase
techniques [see, e.g., Stewart et al., Solid-
Phase Peptide Synthesis, W.H. Freeman Co., San Francisco, CA (1969);
Merrif'ield, J. Am. Chem. Soc.,
85:2149-2154 (1963)]. In vftro protein synthesis may be performed using manual
techniques or by automation.
Automated synthesis may be accomplished, for instance, using an Applied
Biosystems Peptide Synthesizer (Foster
City, CA) using manufacturer's instructions. Various portions of the PRO may
be chemically synthesized
separately and combined using chemical or enzymatic methods to produce the
full-length PRO.
1. Isolation of DNA Encoding PRO
DNA encoding PRO may be obtained from a cDNA h'brary prepared from tissue
believed to possess the
PRO mRNA and to express it at a detectable level. Accordingly, human PRO DNA
can be conveniently obtained
from a cDNA library prepared from human tissue, such as described in the
Examples. The PRO-encoding gene
may also be obtained from a genomic library or by known synthetic procedures
(e.g., automated nucleic acid
synthesis).
Libraries can be screened with probes (such as antibodies to the PRO or
oligonucleotides of at least about
20-80 bases) designed to identify the gene of interest or the protein encoded
by it. Screening the cDNA or
genomic library with the selected probe may be conducted using standard
procedures, such as described in
Sambrook et al., Molecular Cloning: A Laboratory Manual (New York: Cold Spring
Harbor Laboratory Press,
1989). An alternative means to isolate the gene encoding PRO is to use PCR
methodology [Sambrook et al.,
supra; Dieffenbach et al., PCR Primer: A Laboratoa Manual (Cold Spring Harbor
Laboratory Press, 1995)].
The Examples below describe techniques for screening a cDNA library. The
oligonucleotide sequences
selected as probes should be of sufficient length and sufficiently unambiguous
that false positives are m;nimi~ed,
The oligonucleotide is preferably labeled such that it can be detected upon
hybridization to DNA in the library
being screened. Methods of labeling are wetl known in the art, and include the
use of radiolabels like 32P labeled
ATP, biotinylation or enzyme labeling. Hybridization conditions, including
moderate stringency and high
stringency, are provided in Sambrook et al., suDra.
Sequences identified in such library screening methods can be compared and
aligned to other known
sequences deposited and available in public databases such as GenBank or other
private sequence databases.
Sequence identity (at either the amino acid or nucleotide level) within
defined regions of the molecule or across
the full-length sequence can be determined using methods known in the art and
as described herein.
Nucleic acid having protein coding sequence may be obtained by screening
selected cDNA or genomic
libraries using the deduced amino acid sequence disclosed herein for the first
time, and, if necessary, using
conventional primer extension procedures as described in Sambrook et 21.,
supra, to detect precursors and
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processing intermediates of mRNA that may not have been reverse-transcribed
into cDNA.
2. Selection and Transformation of Host Cells
Host cells are transfected or transformed with expression or cloning vectors
described herein for PRO
production and cultured in conventional nutrient media modified as appropriate
for inducing promoters, selecting
transformants, or amplifying the genes encoding the desired sequences. The
culture conditions, such as media,
temperature, pH and the like, can be selected by the skilled artisan without
undue experimentation. In general,
principles, protocols, and practical techniques for maximizing the
productivity of cell cultures can be found in
Mammalian Cell Biotechnologgy: a Practical Anproach, M. Butler, ed. (IItL
Press, 1991) and Sambrook et al.,
s ra.
Methods of eukaryoflc cell transfection and prokaryotic cell transformation
are known to the ordinarily
skilled artisan, for example, CaC4, CaPOõ liposome-mediated and
electroporation. Depending on the host cell
used, transformation is performed using standard techniques appropriate to
such cells. The calcium treatment
employing calcium chloride, as described in Sambrook et al., su ra, or
electroporation is generally used for
prokaryotes. Infection with Agrobacterium tumefaciens is used for
transformation of certain plant cells, as
described by Shaw et al., Gene. 23:315 (1983) and WO 89/05859 published 29
June 1989. For mammalian cells
without such cell walls, the calcium phosphate precipitation method of Graham
and van der Eb, Viroloav, 52:456-
457 (1978) can be employed. General aspects of mammalian cell host system
transfections have been described
in U.S. Patent No. 4,399,216. Transformations into yeast are typically carried
out according to the method of
Van Solingen et al., J. Bact., 130:946 (1977) and Hsiao et al., Proc. Nati.
Acad. Sci. (USA) , 76:3829 (1979).
However, other methods for introducing DNA into cells, such as by nuclear
microinjection, electroporation,
bacterial protoplast fusion with intact cells, or polycations, e.g.,
polybrene, polyornithine, may also be used. For
various techniques for transforming mammalian cells, see Keown et al., Methods
in EnzymoloQV, 185:527-537
(1990) and Mansour et al., Nature, 336:348-352 (1988).
Suitable host cells for cloning or expressing the DNA in the vectors herein
include prokaryote, yeast,
or higher eukaryote cells. Suitable prokaryotes include but are not limited to
cubacteria, such as Gram-negative
or Gram-positive organisms, for example, Enterobacteriaceae such as E. coli.
Various E. coli strains are publicly
available, such as E. coli K12 strain MM294 (ATCC 31,446); E. coli X1776 (ATCC
31,537); E. coli strain
W3110 (ATCC 27,325) and K5 772 (ATCC 53,635). Other suitable prokaryotic host
cells include
Enterobacteriaceae such as Escherichia, e.g., E. coli, Enterobacter, Erwinfa,
Klebsiella, Proteus, Salmonella,
e.g., Salmonella typhimurium, Serratia, e.g., Serratia marcescans, and
Sfiigella, as well as Bacilli such as B.
subtilis and B. licheniformfs (e.g., B. licheniformis 41P disclosed in DD
266,710 published 12 April,1989),
Pseudornonccs such as P. aeruginosa, and Streptomyces. These examples are
illustrative rather than limiting.
Strain W3110 is one particularly preferred host or parent host because it is a
common host strain for recombinant
DNA product fermentations. Preferably, the host cell secretes minimai amounts
of proteolytic enzymes. For
example, strain W31 10 may be modified to effect a genetic mutation in the
genes encoding proteins endogenous
to the host, with examples of such hosts including E. coli W31 10 strain IA2,
which has the complete genotype
tonA ; E. coli W31 10 strain 9E4, which has the complete genotype tonA ptr3;
E. coli W31 10 strain 27C7 (ATCC
CA 02591930 2007-03-30
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55,244), which has the complete genotype tonA ptr3 phoA E15 (argF-lac)169 degP
ompT kan'; E. coli W31 10
strain 37D6, which has the complete genotype tonA ptr3 phoA E15 (argF-lac)169
degP on1pT rbs7 ilvG kanr;
E. coli W3110 strain 40B4, which is strain 37D6 with a non-kanamyc'vn
resistant degP deletion mutation; and an
E. codi strain having mutant periplasmic protease disclosed in U.S. Patent No.
4,946,783 issued 7 August 1990.
Alternatively, in vitro methods of cloning, e.g., PCR or other nucleic acid
polymerase reactions, are suitable.
In addition to prokaryotes, eukaryotic microbes such as filamentous fangi or
yeast are saitable cloning
or expression hosts for PRO-encoding vectors. Saccharomyces cerevisiae is a
commonly used lower eukaryotic
host microorganism. Others include Schizosaccharonryces pombe (Beach and
Nurse, Nature, 290: 140 [1981];
EP 139,383 published 2 May 1985); Kluyveromyces hosts (U.S. Patent No.
4,943,529; Fleer et al.,
Bio/TechnoloQV, 9:968-975 (1991)) such as, e.g., K. lactis (MW98-8C, CBS683,
CBS4574; Louvencourt et al.,
J. Bacteriol., 154(2):737-742 [1983]), K. fragilis (ATCC 12,424), K.
bulgaricus (ATCC 16,045), K. wickera ui
(ATCC 24,178), K. waltii (ATCC 56,500), K. drosophilarum (ATCC 36,906; Van den
Berg et al.,
Bio/Technology, 8:135 (1990)), K. thermotolerans, and K. marxianus; yarrowia
(EP 402,226); Pichia pastoris
(EP 183,070; Sreekrishna et al., J. Basic Microbiol., 28:265-278 [1988]);
Candida; Trichoderma reesia (EP
244,234); Neurospora crassa (Case et al., Proc. Natl. Acad. Sci. USA, 76:5259-
5263 [1979]); Schwanniomyces
such as Schwanniomyces occidentalis (EP 394,538 published 31 October 1990);
and filamentous fungi such as,
e.g., Neurospora, Penicillium, Tolypocladium (WO 91/00357 published 10 January
1991), andAspergillus hosts
such as A. nidulmrs (Ballance et al., Biochem. Biophys. Res. Commun., 112:284-
289 [1983]; Tilburn et al.,
Gene, 26:205-221 [1983]; Yelton et al., Proc. Natl. Acad. Sci. USA. 81: 1470-
1474 [1984]) and A. niger (Kelly
and Hynes, EMBO 1., 4:475-479 [1985]). Methylotropic yeasts are suitable
herein and include, but are not
limited to, yeast capable of growth on methanol selected from the genera
consisting of Hansenula, Candida,
Kloeckera, Plchia, Saccharonryces, Torulopsis, and Rhodotorula. A list of
specific species that are exemplary
of this class of yeasts may be found in C. Anthony, The Biochemistrv of
Methvlotrophs, 269 (1982).
Suitable host cells for the expression of glycosylated PRO are derived from
multicellular organisms.
Examples of invertebrate cells include insect cells such as Drosophila S2 and
Spodoptera Sf9, as well as plant
cells. Examples of useful mammalian host cell lines include Chinese hamster
ovary (CHO) and COS cells. More
specific examples include monkey kldney CV1 line transformed by SV40 (COS-7,
ATCC CRL 1651); human
embryonic Iddney line (293 or 293 cells subcloned for growth in suspension
culture, Graham et al., J. Gen Virol.,
36:59 (1977)); Chinese hamster ovary cells/-DHFR (CHO, Urlaub and Chasin,
Proc. Nati. Acad. Sci. USA,
77:4216 (1980)); mouse sertoli cells (TM4, Mather, Biol. Reprod., 23:243-
251(1980)); human lung cells (W138,
ATCC CCL 75); human liver cells (Hep G2, HB 8065); and mouse mammary tumor
(MMT 060562, ATCC
CCL51). The selection of the appropriate host cell is deemed to be within the
sicill in the art.
3. Selection and Use of a Reglicable Vector
The nucleic acid (e.g., cDNA or genomic DNA) encoding PRO may be inserted into
a replicable vector
for cloning (amplification of the DNA) or for expression. Various vectors are
publicly available. The vector
may, for example, be in the form of a plasmid, cosmid, viral particle, or
phage. The appropriate nucleic acid
sequence may be inserted into the vector by a variety of procedures. In
general, DNA is inserted into an
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appropriate restriction endonuclease site(s) using techniques lmown in the
art. Vector components generally
include, but are not limited to, one or more of a signal sequence, an origin
of replication, one or more marker
genes, an enhancer element, a promoter, and a transcription termination
sequence. Construction of suitable
vectors containing one or more of these components employs standard ligation
techniques which are lmown to the
skilled artisan.
The PRO may be produced recombinantly not only directly, but also as a fusion
polypeptide with a
heterologous polypeptide, which may be a signal sequence or other polypeptide
having a specific cleavage site
at the N-terminus of the mature protein or polypeptide. In general, the signal
sequence may be a component of
the vector, or it may be a part of the PRO-encoding DNA that is inserted into
the vector. The signal sequence
may be a prokaryotic signal sequence selected, for example, from the group of
the alkaline phosphatase,
penicillinase, lpp, or heat-stable enterotoxin II leaders. For yeast secretion
the signal sequence may be, e.g., the
yeast invertase leader, alpha factor leader (including Saccharomyces and
Kluyveromyces a-factor leaders, the latter
described in U.S. Patent No. 5,010,182), or acid phosphatase leader, the C.
albicans glucoamylase leader (EP
362,179 published 4 April 1990), or the signal described in WO 90/13646
published 15 November 1990. In
mammalian cell expression, mammatian signal sequences may be used to direct
secretion of the protein, such as
signal sequences from secreted polypeptides of the same or related species, as
well as viral secretory leaders.
Both expression and cloning vectors contain a nucleic acid sequence that
enables the vector to replicate
in one or more selected host cells. Such sequences are well known for a
variety of bacteria, yeast, and viruses.
The origin of replication from the plasmid pBR322 is suitable for most Gram-
negative bacteria, the 21z plasmid
origin is suitable for yeast, and various viral origins (SV40, polyoma,
adenovirus, VSV or BPV) are useful for
cloning vectors in mammatian cells.
Expression and cloning vectors will typically contain a selection gene, also
termed a selectable marker.
Typical selection genes encode proteins that (a) confer resistance to
antibiotics or other toxins, e.g., ampicillin,
neomycin, methotrexate, or tetracycline, (b) complement auxotrophic
deficiencies, or (c) supply critical nutrients
not available from complex media, e.g., the gene encoding D-alanine racemase
for Bacilli.
An example of suitable selectable markers for mammalian cells are those that
enable the identification
of cells competent to take up the PRO-encoding nucleic acid, such as DHFR or
thymidine ldnase. An appropriate
host cell when wild-type DHFR is employed is the CHO cell line deficient in
DHFR activity, prepared and
propagated as described by Urlaub et al., Proc. Natl. Acad. Sci. USA, 77:4216
(1980). A suitable selection gene
for use in yeast is the trpl gene present in the yeast plasmid YRp7
[Stinchcomb et al., Nature, 282:39 (1979);
Kingsman et al., en , 7:141 (1979); Tschemper et al., Gene, 10:157 (1980)].
The t7p1 gene provides a
selection marker for a mutant strain of yeast lacldng the ability to grow in
tryptophan, for example, ATCC No.
44076 or PEP4-1 [Jones, Genetics, 85:12 (1977)].
Expression and cloning vectors usually contain a promoter operably linked to
the PRO-encoding nucleic
acid sequence to direct mRNA synthesis. Promoters recognized by a variety of
potential host cells are well
known. Promoters suitable for use with prokaryotic hosts include the P-
lactamase and lactose promoter systems
[Chang et al., Nature, 275:615 (1978); Goeddel et al., Nature, 281:544
(1979)], alkaiine phosphatase, a
tryptophan (trp) promoter system [Goeddel, Nucleic Acids Res., 8:4057 (1980);
EP 36,776], and hybrid
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promoters such as the tac promoter [deBoer et al., Proc. Natl. Acad. Sci. USA,
80:21-25 (1983)]. Promoters
for use in bacterial systems aiso will contain a Shine-Dalgarno (S.D.)
sequence operably linked to the DNA
encoding PRO.
Examples of suitable promoting sequences for use with yeast hosts include the
promoters for 3-
phosphoglycerate kinase [Aitzeman et al., J. Biol. Chem., 255:2073 (1980)] or
other glqcolytic enzymes [Hess
et al., J. Adv. Enzvme Regõ 7:149 (1968); Holland, Biochemistry, 17:4900
(1978)], such as enolase,
glyceraldehyde-3-phosphate dehydrogenase, hexolonase, pyruvate decarboxylase,
phosphofructoldnase, glucose-6-
phosphate isomerase, 3-phosphoglycerate mt<tase, pyravate kinase,
triosephosphate isomerase, phosphoglucose
isomerase, and glucokinase.
Other yeast promoters, which are inducible promoters having the additional
advantage of transcription
controlled by growth conditions, are the promoter regions for alcohol
dehydrogenase 2, isocyrochrome C, acid
phosphatase, degradative enzymes associated with nitrogen metabolism,
metallothionein, glyceraldehyde-3-
phosphate dehydrogenase, and enzymes responsible for maltose and galactose
utilization. Suitable vectors and
promoters for use in yeast expression are further described in EP 73,657.
PRO transcription from vectors in mammalian host cells is controlled, for
example, by promoters
obtained from the genomes of viruses such as polyoma virus, fowipox virus (UK
2,211,504 published 5 July
1989), adenovirns (such as Adenovirus 2), bovine papilloma viras, avian
sarcoma virus, cytomegalovirus, a
retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), from heterologous
mammalian promoters, e.g., the
actin promoter or an immunoglobulin promoter, and from heat-shock promotrs,
provided such promoters are
compatible with the host cell systems.
Transcription of a DNA encoding the PRO by higher eukaryotes may be increased
by inserting an
enhancer sequence into the vector. Bnbancers are eis-acting elements of DNA,
usually about from 10 to 300 bp,
that act on a promoter to inerease its transcription. Many enhancer sequences
are now known from mammalian
genes (globin, elastase, albumin, a-Eetoprotein, and insulin). Typically,
however, one will use an enhancer from
a eukaryotic cell virus. Examples inchide the SV40 enhancer on the late side
of the replication origin (bp 100-
270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the
late side of the replication
origin, and adenovirus enhancers. The enhancer may be splioed into the vector
at a position 5' or 3' to the PRO
coding sequence, but is preferably located at a site 5' from the promoter.
Expression vectors used in eukaryotic host cells (yeast, fhngi, insect, plant,
animal, human, or nucleated
cells from other multicelhular organisms) will also contain sequences
necessary for the termination of transcription
and for stabilizing the mRNA. Such sequences are commonly available from the
5' and, occasionally 3',
untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions
contain nucleotide segments
transcnbed as polyadenylated fragments in the unhmlated portion of the mRNA
encoding PRO.
Still other methods, vectors, and host ceIIs suitable for adaptation to the
synthesis of PRO in recombinant
vertebrate cell cultare are described in Getbing et al., Nature, 293:620-625
(1981); Mantei et al., N'ature. 281:40-
46 (1979); EP 117,060; and EP 117,058.
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4. Det.ectingGene Amnlification/Exaression
Gene amplification and/or expression may be measured in a sample directly, for
example, by
conventional Southern blotting, Northern blotting to quantitate the
transcription of mRNA [Thomas, Proc. Nati.
Acad. Sci. USA, 77:5201-5205 (1980)], dot blotting (DNA analysis), or in situ
hybridization, using an
appropriately labeled probe, based on the sequences provided herein.
Alternatively, antibodies may be employed
that can recognize specific duplexes, including DNA duplexes, RNA duplexes,
and DNA-RNA hybrid duplexes
or DNA-protein duplexes. The antibodies in turn may be labeled and the assay
may be carried out where the
duplex is bound to a surface, so that upon the formation of duplex on the
surface, the presence of antibody bound
to the duplex can be detected.
Gene expression, alternatively, may be measured by immunological methods, such
as
immunohistochemical staining of cells or tissue sections and assay of cell
culture or body fluids, to quantitate
directly the expression of gene product. Antibodies useful for
immunohistochemical staining and/or assay of
sample fluids may be either monoclonal or polyclonal, and may be prepared in
any mammal. Conveniently, the
antibodies may be prepared against a native sequence PRO polypeptide or
against a synthetic peptide based on
the DNA sequences provided herein or against exogenous sequence fused to PRO
DNA and encoding a specific
antibody epitope.
5. Purification of Polvnentide
Forms of PRO may be recovered from culture medium or from host cell lysates.
If membrane-bound,
it can be released from the membrane using a suitable detergent solution (e.g.
Triton-X 100) or by enzymatic
cleavage. Cells employed in expression of PRO can be disrnpted by various
physical or chemical means, such
as freeze-thaw cycling, sonication, mechanical disruption, or cell lysing
agents.
It may be desired to purify PRO from recombinant ceIl proteins or
polypeptides. The following
procedures are exemplary of suitable purification procedures: by fractionation
on an ion-exchange column; ethanol
precipitation; reverse phase HPLC; chromatography on silica or on a cation-
exchange resin such as DEAE;
chromatofocusing; SDS-PAGE; ammonium sulfate precipitation; gel filtration
using, for example, Sephadex G-75;
protein A Sepharose columns to remove contaminants such as IgG; and metal
chelating columns to bind epitope-
tagged forms of the PRO. Various methods of protein purification may be
employed and such methods are known
in the art and descn'bed for example in Deutscher, Methods in Enzvmology, 182
(1990); Scopes, Protein
Purification: Principles and Practice. Springer-Verlag, New York (1982). The
purification step(s) selected will
depend, for example, on the nature of the production process used and the
particular PRO produced.
E. Uses for PRO
Nucleotide sequences (or their complement) encoding PRO have various
applications in the art of
molecular biology, including uses as hybridization probes, in chromosome and
gene mapping and in the generation
of anti-sense RNA and DNA. PRO nucleic acid will also be useful for the
preparation of PRO polypeptides by
the recombinant techniques described herein.
The full-length native sequence PRO gene, or portions thereof, may be used as
hybridization, probes for
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a cDNA h'brary to isolate the full-length PRO cDNA or to isolate still other
cDNAs(for instance, those encoding
naturally-occurring variants of PRO or PRO from other species) which have a
desired sequence identity to the
native PRO sequence disclosed herein. Optionally, the length of the probes
will be about 20 to about 50 bases.
The hybridization probes may be derived from at least partially novel regions
of the full length native nucleotide
sequence wherein those regions may be determined without undue experimentation
or from genomic sequences
including promoters, enhancer elements and introns of native sequence PRO. By
way of example, a screening
method wiIl comprise isolating the coding region of the PRO gene using the
known DNA sequence to synthesize
a selected probe of about 40 bases. Hybridization probes may be labeled by a
variety of labels, including
radionucleotides such as 32P or 35S, or enzymatic labels such as alkaline
phosphatase coupled to the probe via
avidin/biotin coupling systems. Labeled probes having a sequence complementary
to that of the PRO gene of the
present invention can be used to screen libraries of human cDNA, genomic DNA
or mRNA to determine which
members of such libraries the probe hybridizes to. Hybridization techniques
are described in further detail in the
Examples below.
Any EST sequences disclosed in the present application may similarly be
employed as probes, using the
methods disclosed herein.
Other useful fragments of the PRO nucleic acids include antisense or sense
oligonucleotides comprising
a singe-stranded nucleic acid sequence (either RNA or DNA) capable of binding
to target PRO mRNA (sense)
or PRO DNA (antisense) sequences. Antisense or sense oligonucleotides,
according to the present invention,
comprise a fragment of the coding region of PRO DNA. Such a fragment generally
comprises at least about 14
nucleotides, preferably from about 14 to 30 nucleotides. The ability to derive
an antisense or a sense
oligonucleotide, based upon a cDNA sequence encoding a given protein is
described in, for example, Stein and
Cohen (Cancer Res. 48:2659, 1988) and van der Krol et al. (BioTechniques
6:958, 1988).
Binding of antisense or sense oligonucleotides to target nucleic acid
sequences results in the formation
of duplexes that block transcription or translation of the target sequence by
one of several means, including
enhanced degradation of the duplexes, premature termination of transcription
or translation, or by other means.
The antisense oligonucleotides thus may be used to block expression of PRO
proteins. Antisense or sense
oligonucleotides further comprise oligonucleotides having modified sugar-
phosphodiester backbones (or other
sugar linkages, such as those described in WO 91/06629) and wherein such sugar
linkages are resistant to
endogenous nucleases. Such oligonucleotides with resistant sugar linkages are
stable in vivo (i.e., capable of
resisting enzymatic degradation) but retain sequence specificity to be able to
bind to target nucleotide sequences.
Other examples of sense or antisense oligonucleotides include those
oligonucleotides which are covalently
linked to organic moieties, such as those descn'bed in WO 90/10048, and other
moieties that increases affinity
of the oligonucleotide for a target nucleic acid sequence, such as poly-(L-
lysine). Further still, intercalating
agents, such as ellipticine, and alkylating agents or metal complexes may be
attached to sense or antisense
oligonucleotides to modify binding specificities of the antisense or sense
oligonucleotide for the target nucleotide
sequence.
Antisense or sense oligonucleotides may be introduced into a cell containing
the target nucleic acid
sequence by any gene transfer method, including, for example, CaP04 mediated
DNA transfection,
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electroporation, or by using gene transfer vectors such as Epstein-Barr viras.
In a preferred procedure, an
antisense or sense oligonucleotide is inserted into a suitable retroviral
vector. A cell containing the target nucleic
acid sequence is contacted with the recombinant retroviral vector, either in
vivo or ex vivo. Suitable retroviral
vectors include, but are not limited to, those derived from the murine
retrovirus M-MuLV, N2 (a retrovirus
derived from M-MuLV), or the double copy vectors designated DCTSA, DCT5B and
DCT5C (see WO
90/13641).
Sense or antisense oligonucleotides also may be introduced into a cell
containing the target nucleotide
sequence by formation of a conjugate with a ligand binding molecule, as
described in WO 91/04753. Suitable
ligand binding molecules include, but are not limited to, cell surface
receptors, growth factors, other cytokines,
or other ligands that bind to cell surface receptors. Preferably, conjugation
of the ligand binding molecule does
not substantially interfere with the ability of the ligand binding molecule to
bind to its corresponding molecule or
receptor, or block entry of the sense or antisense oligonucleotide or its
conjugated version into the cell.
Alternatively, a sense or an antisense oligonucleotide may be introduced into
a cell containing the target
nucleic acid sequence by formation of an oligonucleotide-lipid complex, as
described in WO 90/10448. The sense
or antisense oligonucleotide-lipid complex is preferably dissociated within
the cell by an endogenous lipase.
Antisense or sense RNA or DNA molecules are generally at least about 5 bases
in length, about 10 bases
in length, about 15 bases in length, about 20 bases in length, about 25 bases
in length, about 30 bases in length,
about 35 bases in length, about 40 bases in length, about 45 bases in length,
about 50 bases in length, about 55
bases in length, about 60 bases in length, about 65 bases in length, about 70
bases in length, about 75 bases in
length, about 80 bases in length, about 85 bases in length, about 90 bases in
length, about 95 bases in length,
about 100 bases in length, or more.
The probes may also be employed in PCR techniques to generate a pool of
sequences for identification
of closely related PRO coding sequences.
Nucleotide sequences encoding a PRO can also be used to construct
hybridization probes for mapping
the gene which encodes that PRO and for the genetic analysis of individuals
with genetic disorders. The
nucleotide sequences provided herein may be mapped to a chromosome and
specific regions of a chromosome
using kuown techniques, such as in situ hybridization, linkage analysis
against known chromosomal markers, and
hybridization screening with libraries.
When the coding sequences for PRO encode a protein which binds to another
protein (example, where
the PRO is a receptor), the PRO can be used in assays to identify the other
proteins or molecules involved in the
binding interaction. By such methods, inhibitors of the receptor/ligand
binding interaction can be identified.
Proteins involved in such binding interactions can also be used to screen for
peptide or small molecule inhibitors
or agonists of the binding interaction. Also, the receptor PRO can be used to
isolate correlative ligand(s).
Screening assays can be designed to find lead compounds that mimic the
biological activity of a native PRO or
a receptor for PRO. Such screening assays will include assays amenable to high-
throughput screening of chemi.cal
libraries, making them particularly suitable for identifying small molecule
drug candidates. Small molecules
contemplated include synthetic organic or inorganic compounds. The assays can
be performed in a variety of
formats, including protein protein binding assays, biochemical screening
assays, immunoassays and cell based
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assays, which are well characterized in the art.
Nucleic acids which encode PRO or its modified forms can also be used to
generate either transgenic
animals or "knock out" animals which, in turn, are useful in the development
and screening of therapeutically
useful reagents. A transgenic animal (e.g., a mouse or rat) is an animal
having cells that contain a transgene,
which transgene was introduced into the animal or an ancestor of the animal at
a prenatal, e.g., an embryonic
stage. A transgene is a DNA which is integrated into the genome of a cell from
which a transgenic animal
develops. In one embodiment, cDNA encoding PRO can be used to clone genomic
DNA encoding PRO in
accordance with establishedtechniques and the genomic sequences usedtu
generate transgenic animals that contain
cells which express DNA encoding PRO. Methods for generating transgenic
animals, particularly animals such
as mice or rats, have become conventional in the art and are described, for
example, in U.S. Patent Nos.
4,736,866 and 4,870,009. Typically, particular cells would be targeted for PRO
transgene incorporation with
tissue-specific enhancers. Transgenic animals that include a copy of a
transgene encoding PRO introduced into
the germ line of the animal at an embryonic stage can be used to examine the
effect of increased expression of
DNA encoding PRO. Such animals can be used as tester animals for reagents
thought to confer protection fiom,
for example, pathological conditions associated with its overexpression. In
accordance with this facet of the
invention, an animal is treated with the reagent and a reduced incidence of
the pathological condition, compared
to untreated animals bearing the transgene, would indicate a potential
ttberapeutic intervention for the pathological
condition.
Alternatively, non-human homologues of PRO can be used to construct a PRO
"knock out" animal which
has a defective or altered gene encoding PRO as a result of homologous
recombination between the endogenous
gene encoding PRO and altered genomic DNA encoding PRO introduced into an
embryonic stem cell of the
animal. For example, cDNA encoding PRO can be used to clone genomic DNA
encoding PRO in accordance
with established tecbniques. A portion of the genomic DNA encoding PRO can be
deleted or replaced with
another gene, such as a gene encoding a selectable marker which can be used to
monitor integration. Typically,
several ldlobases of unaltered flanking DNA (both at the 5' and 3' ends) are
included in the vector [see e.g.,
Thomas and Capecchi, -Ca, 51:503 (1987) for a description of homologous
recombination vectors]. The vector
is introduced into an embryonic stem cell line (e.g., by electroporation) and
cells in which the introduced DNA
has homologously recombined with the endogenous DNA are selected [see e.g., Li
et al., CeIl, 69:915 (1992)].
The selected cells are then injected into a blastocyst of an animal (e.g., a
mouse or rat) to form aggregation
chimeras [see e.g., Bradley, in Teratocarcinomas and E}nbryonic Stem Cells: A
Practical Approach, E. J.
Robertson, ed. (IRL, Oxford, 1987), pp. 113-152]. A chimeric embryo can then
be implanted into a suitable
pseudopregnant female foster animal and the embryo brought to term to create a
"knock out" animal. Progeny
harboring the homologously recombined DNA in their germ cells can be
identified by standard techniques and
used to breed animals in which all cells of the animat contain the
homologously recombined DNA. Knockout
animals can be characterized for instance, for their ability to defend against
certain pathological conditions and
for their development of pathological conditions due to absence of the PRO
polypeptide.
Nucleic acid encoding the PRO polypeptides may also be used in gene therapy.
In gene therapy
applications, genes are introduced into cells in order to achieve in vivo
synthesis of a therapeutically effective
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genetic product, for example for replacement of a defective gene. "Gene
therapy" includes both conventional
gene therapy where a lasting effect is achieved by a single treatment, and the
adaainistration of gene therapeutic
agents, which involves the one time or repeated administration of a
therapeutically effective DNA or mRNA.
Antisense RNAs and DNAs can be used as therapeutic agents for blocking the
expression of certain genes in vivo.
It has already been shown that short antisense oligonucleotides can be
imported into cells where they act as
inhibitors, despite their low intracellular concentrations caused by their
restricted uptake by the cell membrane.
(Zamecnik et al., Proc. Nat1. Acad. Sci. USA 83:4143-4146 [1986]). The
oligonucleotides can be modified to
enhance their uptake, e.g. by sabstitWing their negatively charged
phosphodiester groups by uncbarged groups.
There are a variety of tecbniques available for iniroducing nucleic acids into
viable cells. The techniques
vary depending upon whether the nucleic acid is transferred into eultured
cells in vitro, or in vivo in the cells of
the intended host. Techniques suitable for the transfer of nucleic acid into
mammalian cells in vitro include the
use of liposomes, electroporation, microinjection, cell fusion, DBAB-dextran,
the calcium phosphate precipitation
metbod, etc. The currently preferred in vivo gene tranafer tecbniques inelude
transfection with viral (typically
retroviral) vectors and viral coat protein-liposome mediated transfection
(Dzau et al., Trends in Biotechnology
11, 205-210 [1993]). In some situations it is desirable to provide the micleic
acid source with an agent that targets
the target cells, such as an antibody specific for a cell surface membrane
protein or the target cell, a li.gand for
a receptor on the target cell, etc. Where liposomes are employed, proteins
which bind to a cell surface membrane
protein associated with cndocytosis may be used for targeting and/or to
facilitate uptake, e.g. capsid proteins or
fragments thereof tropic for a particular cell type, antibodies for proteins
which undergo internalization in cycling,
proteins that target intracellular localization and enhance intracellular half-
life. The technique of receptor-
mediated endocytosis is described, for example, by Wu et al., J. Biol. Chem.
262, 4429-4432 (1987); and Wagner
et al., Pxoc. Natl. Acad. Sci. USA 87, 3410-3414 (1990). For review of gene
marldng and gene therapy
protocols see Anderson et al., Science 256, 808-813 (1992).
The PRO polypeptides described herein may also be employed as molecular weight
markers for protein
electrophoresis purposes and the isolated nucleic acid sequences may be used
for recombinantly expressing those
markers.
The nucleic acid molecules encoding the PRO polypeptides or fragments thereof
described herein are
useful for chromosome identification. In this regard, there exists an ongoing
need to identify new chromosome
markers, since relatively few chromosome marking reagents, based upon actual
sequence data are presently
available. Each PRO nucleic acid molecule of the present invention can be used
as a chromosome marker.
The PRO polypeptides and nueleic acid molecules of the present invention may
also be used
diagnostically for tissae typing, wherein the PRO polypeptides of the present
invention may be differentially
expressed in one tissue as compared to another, preferably in a diseased
tissue as compared to a normal tissue of
the same tissue type. PRO nucleic acid molecules will find use for generatiug
probes for PCR, Northern analysis,
Southern analysis and Western analysis.
The PRO polypeptides described herein may also be employed as therapeutic
agents. The PRO
polypeptides of the present invention can be formulated according to known
methods to prepare pharmaceutically
useful compositions, whereby the PRO product hereof is combined in admixture
with a pharmaceutically
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acceptable carrier vehicle. Therapeutic formulations are prepared for storage
by mixing the active ingredient
having the desired degree of purity with optional physiologically acceptable
carriers, excipients or stabilizers
(Reming,ton's Pharmaceutical Sciences 16th edition, Osol, A. Ed. (1980)), in
the form of lyophilized formulations
or aqueous solutions. Acceptable carriers, excipients or stabilizers are
nontoxic to recipients at the dosages and
concentrations employed, and include buffers such as phosphate, citrate and
other organic acids; antioxidants
including ascorbic acid; low molecular weight (less than about 10 residues)
polypeptides; proteins, such as serum
albumin, gelatin or immunoglobulins; hydrophilic polymers such as
polyvinylpyrrolidone, amino acids such as
glycine, glutamine, asparagine, arginine or lysine; monosaccharides,
disaccharides and other carbohydrates
including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar
alcohols such as mannitol or
sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants
such as TWEEN' , PLURONICS'
or PEG.
The formulations to be used for in vivo administration must be sterile. This
is readily accomplished by
filtration through sterile filtration membranes, prior to or following
lyophilization and reconstitution.
Therapeutic compositions herein generally are placed into a container having a
sterile access port, for
example, an intravenous solution bag or vial having a stopper pierceable by a
hypodermic injection needle.
The route of administration is in accord with known methods, e.g. injection or
infusion by intravenous,
intraperitoneal, intracerebral, intramuscular, intraocular, intraarterial or
intralesional routes, topical
administration, or by sustained release systems.
Dosages and desired drug concentrations of pharmaceutical compositions of the
present invention may
vary depending on the particular use envisioned. The determination of the
appropriate dosage or route of
administration is well within the skill of an ordinary physician. Animal
experiments provide reliable guidance
for the determination of effective doses for human therapy. Interspecies
scaling of effective doses can be
performed following the principles laid down by Mordenti, J. and Chappell, W.
"The use of interspecies scaling
in toxicokinetics" In Toxicokinetics and New Drug Development, Yacobi et al.,
Eds., Pergamon Press, New York
1989, pp. 42-96.
When in vivo administration of a PRO polypeptide or agonist or antagonist
thereof is employed, normal
dosage amounts may vary from about 10 ng/kg to up to 100 mg/kg of mammal body
weight or more per day,
preferably about 1 g/kg/day to 10 mg/kg/day, depending upon the route of
administration. Guidance as to
particular dosages and methods of delivery is provided in the literature; see,
for example, U.S. Pat. Nos.
4,657,760; 5,206,344; or 5,225,212. It is anticipated that different
formulations will be effective for different
treatment compounds and different disorders, that administration targeting one
organ or tissue, for example, may
necessitate delivery in a manner different from that to another organ or
tissue.
Where sustained-release administration of a PRO polypeptide is desired in a
formulation with release
characteristics suitable for the treatment of any disease or disorder
requiring administration of the PRO
polypeptide, microencapsulation of the PRO polypeptide is contemplated.
Microencapsulation of recombinant
proteins for sustained release has been successfully performed with human
growth hormone (rhGH), interferon-
(rhIFN- ), interleuldn-2, and MN rgpl2O. Johnson et al., Nat. Med., 2:795-799
(1996); Yasuda, Biomed. Ther.,
27:1221-1223 (1993); Hora et al., Bio/Technology. 8:755-758 (1990); Cleland,
"Design and Production of Single
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Immunization Vaccines Using Polylactide Polyglycolide Microsphere Systems," in
Vaccine DesiQn: The Subunit
and Adjuvant Approach, Powell and Newman, eds, (Plenum Press: New York, 1995),
pp. 439-462; WO
97/03692, WO 96/40072, WO 96/07399; and U.S. Pat. No. 5,654,010.
The sustained-release formulations of these proteins were developed using poly-
lactic-coglycolic acid
(PLGA) polymer due to its biocompatibility and wide range of biodegradable
properties. The degradation products
of PLGA, lactic and glycolic acids, can be cleared quickly within the human
body. Moreover, the degradability
of this polymer can be adjusted from months to years depending on its
molecular weight and composition. Lewis,
"Controlled release of bioactive agents from lactide/glycolide polymer," in:
M. Chasin and R. Langer (Eds.),
BiodeQSadable Polymers as Dra Delivery Systems (Marcel Dekker: New York,
1990), pp. 1-41.
This invention encompasses methods of screening compounds to identify those
that mimic the PRO
polypeptide (agonists) or prevent the effect of the PRO polypeptide
(antagonists). Screening assays for antagonist
drug candidates are designed to identify compounds that bind or complex with
the PRO polypeptides encoded by
the genes identified herein, or otherwise interfere with the interaction of
the encoded polypeptides with other
cellular proteins. Such screening assays will include assays amenable to high-
throughput screening of chemical
libraries, making them particularly suitable for identifying small molecule
drug candidates.
The assays can be performed in a variety of formats, including protein-protein
binding assays,
biochemical screening assays, immunoassays, and cell-based assays, which are
well characterized in the art.
All assays for antagonists are common in that they call for contacting the
drug candidate with a PRO
polypeptide encoded by a nucleic acid identified herein under conditions and
for a time sufficient to allow these
two components to interact.
In binding assays, the interaction is binding and the complex formed can be
isolated or detected in the
reaction mixture. In a particular embodiment, the PRO polypeptide encoded by
the gene identified herein or the
drug candidate is immobilized on a solid phase, e.g., on a microtiter plate,
by covalent or non-covalent
attachments. Non covalent attachment generally is accomplished by coating the
solid surface with a solution of
the PRO polypeptide and drying. Alternatively, an immobilized antibody, e.g.,
a monoclonal antibody, specific
for the PRO polypeptide to be immobilizxd can be used to anchor it to a solid
surface. The assay is performed
by adding the non-immobilized component, which may be labeled by a detectable
label, to the immobilized
component, e.g., the coated surface containing the anchored component. When
the reaction is complete, the non-
reacted components are removed, e.g., by washing, and complexes anchored on
the solid surface are detected.
When the originaIly non-immobilized component carries a detectable label, the
detection of label immobilized on
the surface indicates that complexing occurred. Where the originally non-
immobilized component does not carry
a label, complexing can be detected, for example, by using a labeled antibody
specifically binding the immobilized
complex.
If the candidate compound interacts with but does not bind to a particular PRO
polypeptide encoded by
a gene identified herein, its interaction with that polypeptide can be assayed
by methods weIl known for detecting
protein-protein interactions. Such assays include traditional approaches, such
as, e.g., cross-linldng, co-
immunoprecipitation, and co-purification through gradients or chromatographic
columns. In addition, protein-
protein interactions can be monitored by using a yeast-based genetic system
described by Fields and co-workers
CA 02591930 2007-03-30
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(Fields and Song, Nature (London), 340:245-246 (1989); Chien et al., Proc Natl
Acad. Sci USA 88:9578-9582
(1991)) as disclosed by Chevray and Nathans, Proc. Nati. Acad. Sci. USA. 89:
5789-5793 (1991). Many
transcriptional activators, such as yeast GAL4, consist of two physically
discrete modular domains, one acting
as the DNA-binding domain, the other one functioning as the transcription-
activation domain. The yeast
expression system described in the foregoing publications (generally referred
to as the "two-hybrid system") talces
advantage of this property, and employs two hybrid proteins, one in which the
target protein is fused to the DNA-
binding domain of GAL4, and another, in which candidate activating proteins
are fused to the activation domain.
The expression of a GAL1-lacZ reporter gene under control of a GAL4-activated
promoter depends on
reconstitution of GAL4 activity via protein-protein interaction. Colonies
containing interacting polypeptides are
detected with a chromogenic substrate for p-galactosidase. A complete ldt
(MATCHMAxRR''"t) for identifying
protein-protein interactions between two specific proteins usmg the two-hybrid
technique is commercially available
from Clontech. This system can also be extended to map protein domains
involved in specific protein interactions
as well as to pinpoint amino acid residues that are crucial for these
interaotions.
Compounds that interfere with the interaction of a gene encoding a PRO
polypeptide identified herein
and other intra- or extracellular components can be tested as follows: usually
a reaction mixture is prepared
containing the product of the gene and the intra- or extracellular component
under conditions and for a time
allowing for the interaction and binding of the two products. To test the
ability of a candidate compound to inhibit
binding, the reaction is run in the absence and in the presence of the test
compound. In addition, a placebo may
be added to a tbird reaction mixtnre, to serve as positive control. The
binding (complex formation) between the
test compound and the intra- or extracellular component present in the mixture
is monitored as described
hereinabove. The formation of a complex in the control reaction(s) but not in
the reaction mixture containing the
test compoimd indicates that the test compound interferes with the imeraction
of the test compound and its reaction
partner.
To assay for antagonists, the PRO polypeptide may be added to a cell along
with the compound to be
screened for a particular activity and the ability of the compound to inhibit
the activity of interest in the presence
of the PRO polypeptide indicates that the compound is an antagonist to the PRO
polypeptide. Alternatively,
antagonists may be detected by combining the PRO polypeptide and a potential
antagonist with membrane-bound
PRO polypeptide receptors or recombinant receptors under appropriate
conditions for a competitive inhibition
assay. The PRO polypeptide can be labeled, such as by radioactivity, such that
the number of PRO polypeptide
molecules bound to the receptor can be used to determine the effectiveness of
the potential antagonist. The gene
encoding the receptor can be identified by numerous methods known to those of
skill in the art, for example,
ligand panning and FACS sorting. Coligan et al., Current Protocols in Immun..
1(2): Chapter 5 (1991).
Preferably, expression cloning is employed wherein polyadenylated RNA is
prepared from a cell responsive to
the PRO polypeptide and a cDNA library created from this RNA is divided into
pools and used to transfect COS
cells or other cells that are not responsive to the PRO polypeptide.
Transfected cells that are grown on glass
slides are exposed to labeled PRO polypeptide. The PRO polypeptide can be
labeled by a variety of means
including iodination or inclusion of a recognition site for a site-specific
protein ldnase. Following fixation and
incubation, the slides are subjected to autoradiographic analysis. Positive
pools are identified and sub-pools are
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prepared and re-transfected using an interactive sub-pooling and re-screening
process, eventually yielding a single
clone that encodes the putative receptor.
As an alternative approach for receptor identification, labeled PRO
polypeptide can be photoaffnity-
linked with cell membrane or extract preparations that express the receptor
molecule. Cross-linked material is
resolved by PAGE and exposed to X-ray film. The labeled complex containing the
receptor can be excised,
resolved into peptide fragments, and subjected to protein micro-sequencing.
The amino acid sequence obtained
from micro- sequencing would be used to design a set of degenerate
oligonucleotide probes to screen a cDNA
library to identify the gene encoding the putative receptor.
In another assay for antagonists, mammalian cells or a membrane preparation
expressing the receptor
would be incubated with labeled PRO polypeptide in the presence of the
candidate compound. The ability of the
compound to enhance or block this interaction could then be measured.
More specific examples of potential antagonists include an oligonucleotide
that binds to the fusions of
immunoglobulin with PRO polypeptide, and, in particular, antibodies including,
without limitation, poly- and
monoclonai antibodies and antibody fragments, single-chain antibodies, anti-
idiotypic antibodies, and chimeric
or humanized versions of such antibodies or fragments, as well as human
antibodies and antibody fragments.
Alternatively, a potential antagonist may be a closely related protein, for
example, a mutated form of the PRO
polypeptide that recognizes the receptor but imparts no effect, thereby
competitively inhibiting the action of the
PRO polypeptide.
Another potential PRO polypeptide antagonist is an antisense RNA or DNA
construct prepared using
antisense technology, where, e.g., an antisense RNA or DNA molecule acts to
block directly the translation of
mRNA by hybridizing to targeted mRNA and preventing protein translation.
Antisense technology can be used
to control gene expression through triple-helix formation or antisense DNA or
RNA, both of which methods are
based on binding of a polynucleotide to DNA or RNA. For example, the 5' coding
portion of the polynucleotide
sequence, which encodes the mature PRO polypeptides herein, is used to design
an antisense RNA oligonucleotide
of from about 10 to 40 base pairs in length. A DNA oligonucleotide is designed
to be complementary to a region
of the gene involved in transcription (triple helix - see Lee et al., Nucl.
Acids Res., 6:3073 (1979); Cooney et
al., Science, 241: 456 (1988); Dervan et at., Science, 251:1360 (1991)),
thereby preventing transcription and the
production of the PRO polypeptide. The antisense RNA, oligonucleotide
hybridizes to the mRNA in vivo and
block.s translation of the mRNA molecule into the PRO polypeptide (antisense -
Okano, Neurochem., 56:560
(1991); Oli~odeoxymxcleotides as Antisense Inhibitors of Gene Expression (CRC
Press: Boca Raton, FL, 1988).
The oligonucleotides described above can also be delivered to cells such that
the antisense RNA or DNA may be
expressed in vivo to inhibit production of the PRO polypeptide. When antisense
DNA is used,
oligodeoxyribonucleotides derived from the translation-initiation site, e.g.,
between about -10 and + 10 positions
of the target gene nucleotide sequence, are preferred.
Potential antagonists include small molecules that bind to the active site,
the receptor binding site, or
growth factor or other relevant binding site of the PRO polypeptide, thereby
blocking the normal biological
activity of the PRO polypeptide. Examples of small molecules include, but are
not limited to, small peptides or
peptide-like molecules, preferabiy soluble peptides, and synthetic non-
peptidyl organic or inorganic compounds.
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Ribozymes are enzymatic RNA molecules capable of catalyzing the specific
cleavage of RNA.
Ribozymes act by sequence-specific hybridization to the complementary target
RNA, followed by endonucleolytic
cleavage. Specific ribozyme cleavage sites within a potential RNA target can
be identified by known techniques.
For further details see, e.g., Rossi, Current Bioloe~v, 4:469-471(1994), and
PCT publication No. WO 97/33551
(published September 18, 1997).
Nucleic acid molecules in triple-helix formation used to inhibit transcription
should be single-stranded
and composed of deoxynucleotides. The base composition of these
oligonucleotides is designed such that it
promotes triple-helix formation via Hoogsteen base-pairing rules, which
generally require sizeable stretches of
purines or pyrimidines on one strand of a duplex. For further details see,
e.g., PCT publication No. WO
97/33551, supra.
These small molecules can be identified by any one or more of the screening
assays discussed
hereinabove and/or by any other screening techniques well known for those
sldlled in the art.
Diagnostic and therapeutic uses of the herein disclosed molecules may also be
based upon the positive
functional assay hits disclosed and described below.
F. Anti-PRO Antibodies
The present iavention fiuther provides anti-PRO antibodies. Bxemplary
antibodies include polyclonal,
monoclonal, humanized, bispecific, and heteroconjugate antibodies.
1. Polymlonal Antibodies
The anti-PRO antibodies may comprise polyclonal antibodies. Methods of
preparing polyclonal
antibodies are known to the skilled artisan. Polyclonal antibodies can be
raised in a mammal, for example, by
one or more injections of an immunizing agent and, if desired, an adjuvant.
Typically, the immunizing agent
and/or adjuvant will be injectod in the mammal by multiple subcutaneous or
intraperitoneal injections. The
immunizing agent may include the PRO polypeptide or a fasion protein thereof.
It may be useful to conjugate
the immunizing agent to a protein known to be immunogenic in the mammal being
immunized. Examples of such
immunogenic proteins include but are not limited to keyhole limpet hemocyanin,
serum albumin, bovine
thyroglobulin, and soybean trypsin inhibitor. Examples of adjuvants which may
be employed include Freund's
complete adjuvant and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic
trehalose dicorynomycolate).
The immunization protocol may be seleoted by one sldlled in the art without
undue experimentation.
2. Monoclonal Antibodies
The anti-PRO antibodies may, alternatively, be monoclonal aatibodies.
Monoclonal antibodies may be
prepared using hybridoma methods, such as those described by Kohler and
Milstein, Nature, 256:495 (1975).
In a hybridoma method, a mouse, hamster, or other appropriate host animal, is
typically immunized with an
immunizing agent to elicit lymphocytes that produce or are capable of
producing antiibodies that wi11 specifically
bind to the immunizing agent. Altesnatively, the lympbocytes may be immunized
in vitm.
The immunizing agent will typically include the PRO polypeptide or a fusion
protein thereof. Generally,
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either peripheral blood lymphocytes ("PBLs") are used if cells of human origin
are desired, or spleen cells or
lymph node cells are used if non-human mammalian sources are desired. The
lymphocytes are then fused with
an immortalized ceIl line using a suitable fusing agent, such as polyethylene
glycol, to form a hybridoma cell
[Goding, Monoclonal Antibodies: Princi~les and Practice, Academic Press,
(1986) pp. 59-103]. Immortalized
cell lines are usually transformed mammalian cells, particularly myeloma cells
of rodent, bovine and human
origin. Usually, rat or mouse myeloma cell lines are employed. The hybridoma
cells may be cultured in a
suitable culture medium that preferably contains one or more substances that
inhibit the growth or survival of the
unfused, immortalized cells. For example, if the parental cells lack the
enzyme hypoxanthine guanine
phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the
hybridomas typically will include
hypoxanthine, aminopterin, and thymidine ("HAT medium"), which substances
prevent the growth of HGPRT-
deficient cells.
Preferred immortalized cell lines are those that fuse efficiently, support
stable high level expression of
-antibody by the selected antibody-producing cells, and are sensitive to a
medium such as HAT medium. More
preferred immortalized cell lines are murine myeloma lines, which can be
obtained, for instance, from the Salk
Institute Cell Distribution Center, San Diego, California and the American
Type Culture Collection, Manassas,
Virginia. Human myeloma and mouse-human heteromyeloma cell lines also have
been described for the
produotionofhnmanmonoclonalantibodies [Kozbor, J. Immunol., 133:3001(1984);
Brodeur et al., Monoclonal
Antibody Production Techniaues and Applications, Marcel Deldter, Inc., New
York, (1987) pp. 51-63].
The culture medium in which the hybridoma cells are cultured can then be
assayed for the presence of
monoclonal antibodies directed against PRO. Preferably, the binding
specificity of monoclonal antibodies
produced by the hybridoma cells is determined by immunoprecipitation or by an
in vitto binding assay, such as
radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA). Such
techniques and assays are
known in the art. The binding affinity of the monoclonal antibody can, for
example, be determined by the
Scatchard analysis of Munson and Pollard, Anal. Biochem.. 107:220 (1980).
After the desired hybridoma cells are identified, the clones may be subcloned
by limiting dilution
procedures and grown by standard methods [Goding, su ra . Suitable culture
media for this purpose include, for
example, Dulbecco's Modified Eagle's Medium and RPMI-1640 medium.
Alternatively, the hybridoma cells may
be grown in vivo as ascites in a mammal.
The monoclonal antibodies secreted by the subclones may be isolated or
purified from the culture medium
or ascites fluid by conventional immunoglobulin purification procedures such
as, for example, protein A-
Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or
affinity chromatography.
The monoclonal antibodies may also be made by recombinant DNA methods, such as
those described
in U.S. Patent No. 4,816,567. DNA encoding the monoclonal antibodies of the
invention can be readily isolated
and sequenced using conventional procedures (e.g., by using oligonucleotide
probes tlfat are capable of binding
specificaIly to genes encoding the heavy and light chains of murine
antibodies). The hybridoma cells of the
invention serve as a preferred source of such DNA. Once isolated, the DNA may
be placed into expression
vectors, which are then transfected into host cells such as simian COS cells,
Chinese hamster ovary (CHO) cells,
or myeloma cells that do not otherwise produce immunoglobulin protein, to
obtain the synthesis of monoclonal
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antibodies in the recombinant host cells. The DNA also may be modified, for
example, by substituting the coding
sequence for human heavy and light chain constant domains in place of the
homologous murine sequences [U.S.
Patent No. 4,816,567; Morrison et al., su ra or by covalently joining to the
immunoglobulin coding sequence
all or part of the coding sequence for a non-immunoglobulin polypeptide. Such
a non-immunoglobulin polypeptide
can be substitnted for the constant domains of an antibody of the invention,
or can be substituted for the variable
domains of one antigen-combining site of an antibody of the invention to
create a chimeric bivalent antibody.
The antibodies may be monovalent antibodies. Methods for preparing monovalent
antibodies are well
known in the art. For example, one method involves recombinant expression of
immunoglobulin light chain and
modified heavy chain. The heavy chain is truncated generally at any point in
the Fc region so as to prevent heavy
chain crosslinldng. Alternatively, the relevant cysteine residues are
substituted with another amino acid residue
or are deleted so as to prevent crosslinking.
In vitro methods are also suitable for preparing monovalent antibodies.
Digestion of antibodies to
produce fragments thereof, particularly, Fab fragments, can be accomplished
using routine techniques known in
the art.
3. Human and Humanized Antibodies
The anti-PRO antibodies of the invention may further comprise humanized
antibodies or human
antibodies. Humanized forms of non-human (e.g., murine) antibodies are
chimeric immunoglobulins,
immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab')2 or
other antigen-binding
subsequences of antibodies) which contain minimal sequence derived from non-
human immunoglobulin.
H manized antibodies include human immunoglobulins (recipient antibody) in
which residues from a
complementary determining region (CDR) of the recipient are replaced by
residues from a CDR of a non-human
species (donor antibody) such as mouse, rat or rabbit having the desired
specificity, aftinity and capacity. In some
instances, Fv framework residues of the human. immunoglobulin are replaced by
corresponding non-human
residues. Humanized antibodies may also comprise residues which are found
neither in the recipient antibody nor
in the imported CDR or framework sequences. In general, the humanized antibody
will comprise substantially
all of at least one, and typically two, variable domains, in which all or
substantially all of the CDR regions
correspond to those of a non-human immunoglobulin and all or substantially all
of the FR regions are those of a
human immunoglobulin consensus sequence. The humanized antibody optimally also
will comprise at least a
portion of an immunoglobulin constant region (Fc), typically that of a human
immunoglobulin [Jones et al.,
Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-329 (1988); and
Presta, Curr. O. Strnct. Biol.,
2:593-596 (1992)].
Methods for humanizing non-human antibodies are well known in the art.
Generally, a humanized
antibody has one or more amino acid residues introduced into it from a source
which is non-human. These non-
human amino acid residues are often referred to as "import" residues, which
are typically taken from an "import"
variable domain. H manization can be essentially performed following the
method of Winter and co-workers
[Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-
327 (1988); Verhoeyen et al.,
Science, 239:1534-1536 (1988)], by substituting rodent CDRs or CDR sequences
for the corresponding sequences
CA 02591930 2007-03-30
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of a human antibody. Accordingly, such "humanized" antibodies are chimeric
antibodies (U.S. Patent No.
4,816,567), wherein substantially less than an intact human variable domain
has been substituted by the
corresponding sequence from a non-human species. In practice, humanized
antibodies are typically human
antibodies in which some CDR residues and possibly some FR residues are
substituted by residues from analogous
sites in rodent antibodies.
Human antibodies can also be produced using various techniques known in the
art, including phage
display libraries [Hoogenboom and Winter, J. Mol. Biol., 227:381(1991); Marks
et al., J. Mol. Biol., 222:581
(1991)]. The techniques of Cole et al. and Boerner et al. are also available
for the preparation of human
monoclonal antibodies (Cole et al., Monoclonal Antibodies and Cancer Therapy,
Alan R. Liss, p. 77 (1985) and
Boerner et al., J. Immunol., 147(11:86-95 (1991)]. Similarly, human antibodies
can be made by introducing of
human immunoglobulin loci into transgenic animals, e.g., mice in which the
endogenous immunoglobulin genes
have been partially or completely inactivated. Upon challenge, human antibody
production is observed, which
closely resembles that seen in humans in all respects, including gene
rearrangement, assembly, and antibody
repertoire. This approach is described, for example, in U.S. Patent Nos.
5,545,807; 5,545,806; 5,569,825;
5,625,126; 5,633,425; 5,661,016, and in the following scientific publications:
Marks et al., Bio/Technolosv 10,
779-783 (1992); Lonberg et al., Nature 368 856-859 (1994); Morrison, Nature
368, 812-13 (1994); Fishwild et
al., Nature Biotechnoloev 14, 845-51 (1996); Neuberger, Nature Biotechnoloav
14, 826 (1996); Lonberg and
Huszar, Intern. Rev. Immunol. 13 65-93 (1995).
The antibodies may also be affinity matured using known selection and/or
mutagenesis methods as
described above. Preferred affinity matured antibodies have an affinity which
is five times, more preferably 10
times, even more preferably 20 or 30 times greater than the starting antibody
(generally murine, humanized or
human) from which the matured antibody is prepared.
4. Bispecific Antibodies
Bispecific antibodies are monoclonal, preferably human or humanized,
antibodies that have binding
specificities for at least two different antigens. In the present case, one of
the binding specificities is for the PRO,
the other one is for any other antigen, and preferably for a cell-surface
protein or receptor or receptor subunit.
Methods for making bispecific antibodies are lmown in the art. Traditionally,
the recombinant production
of bispecific antibodies is based on the co-expression of two immunoglobulin
heavy-chain/light-chain pairs, where
the two heavy chains have different specibcities [Milstein and Cuello, Nature,
305:537-539 (1983)]. Because of
the random assortment of immunoglobulin heavy and light chains, these
hybridomas (quadromas) produce a
potential mixture of ten different antibody molecules, of which only one has
the correct bispecific structure. The
purification of the correct molecule is usually accomplished by affinity
chromatography steps. Similar procedures
are disclosed in WO 93/08829, published 13 May 1993, and in Traunecker et al.,
EMBO J., 10:3655-3659
(1991).
Antibody variable domains with the desired binding specificities (antibody-
antigen combining sites) can
be fused to immunoglobulin constant domain sequences. The fusion preferably is
with an immunoglobulin heavy-
chain constant doniain, comprising at least part of the hinge, CH2, and CH3
regions. It is preferred to have the
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first heavy-chain constant region (CH1) containing the site necessary for
light-chain binding present in at least
one of the fusions. DNAs encoding the immunoglobulin heavy-chain fusions and,
if desired, the immunoglobulin
light chain, are inserted into separate expression vectors, and are co-
transfected into a suitable host organism.
For further details of generating bispecific antibodies see, for example,
Suresh et al., Methods in Enzvmoloav,
121:210 (1986).
According to another approach described in WO 96/27011, the interface between
a pair of antibody
molecules can be engineered to maxim;~e the percentage of heterodimers which
are recovered from recombinant
cell culture. The preferred interface comprises at least a part of the CH3
region of an antibody constant domain.
In this method, one or more small amino acid side chains from the interface of
the first antibody molecule are
replaced with larger side chains (e.g. tyrosine or tryptophan). Compensatory
"cavities" of identical or similar
size to the large side chain(s) are created on the interface of the second
antibody molecule by replacing large
amino acid side chains with smaller ones (e.g. alanine or threonine). This
provides a mechanism for increasing
the yield of the heterodimer over other unwanted end-products such as
homodimers.
Bispecific antibodies can be prepared as full length antibodies or antibody
fragments (e.g. F(ab')2
bispecific antibodies). Tecbniques for generating bispecific antibodies from
antibody fragments have been
described in the literature. For example, bispecific antibodies can be
prepared can be prepared using chemical
linkage. Brennan et al., Science 229: 81(1985) descn'be a procedure wherein
intact antibodies are proteolytically
cleaved to generate F(ab')2 fragments. These fragments are reduced in the
presence of the dithiol complexing
agent sodium arsenite to stabilize vicinal dithiols and prevent intermolecular
disulfide formation. The Fab'
fragments generated are then converted to thionitrobenzoate (TNB) derivatives.
One of the Fab'-TNB derivatives
is then reconverted to the Fab'-thiol by reduction with mercaptoethylamine and
is mixed with an equimolar
amount of the other Fab'-TNB derivative to form the bispecific antibody. The
bispecific antibodies produced can
be used as agents for the selective immobilization of enzymes.
Fab' fragments may be directly recovered from E. coli and chemically coupled
to form bispecific
antibodies. Shalaby et al., J.cE p. Med. 175:217-225 (1992) describe the
production of a fully humanized
bispecific antibody F(ab')Z molecule. Each Fab' fragment was separately
secreted from E. codi and subjected to
directed chemical coupling in vitro to form the bispecific antibody. The
bispecific antibody thus formed was able
to bind to cells overexpressing the ErbB2 receptor and normal human T cells,
as well as trigger the lytic activity
of human cytotoxic lymphocytes against human breast tumor targets.
Various technique for making and isolating bispecific antibody fragments
directly from recombinant cell
culture have also been described. For example, bispecific antibodies have been
produced using leucine zippers.
Kostelny et al. , J. Immunol. 148(5):1547-1553 (1992). The leucine zipper
peptides from the Fos and Jun proteins
were linked to the Fab' portions of two different antibodies by gene fusion.
The antibody homodimers were
reduced at the hinge region to form monomers and then re-oxidized to form the
antibody heterodimers. This
method can also be utilized for the production of antibody homodimers. The
"diabody" technology described by
Hollinger et a1., Proc. Natl. Acad. Sci. USA 90:6444-6448 (1993) has provided
an alternative mechanism for
maldng bispecific antibody fragments. The fragments comprise a heavy-chain
variable domain (VH) connected
to a light-chain variable domain (V,,) by a linker which is too short to allow
pairing between the two domains on
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the same chain. Accordingly, the V. and VL domains of one fragment are forced
to pair with the complementary
VL and VH domains of another fragment, thereby forming two antigen-binding
sites. Another strategy for making
bispecific antibody fragments by the use of single-chain Fv (sFv) dimers has
also been reported. See, Gruber et
al., J. Immunol. 152:5368 (1994).
Antibodies with more than two valencies are contemplated. For example,
trispecific antibodies can be prepared.
'Iutt et ad., J. Immunol. 147:60 (1991).
Exemplary bispecific antibodies may bind to two different epitopes on a given
PRO polypeptide herein.
Alternatively, an anti-PRO polypeptide arm may be combined with an arm which
binds to a triggering molecule
on a leukocyte such as a T-cell receptor molecule (e.g. CD2, CD3, CD28, or
B7), or Fe receptors for IgG
(FcyR), such as FcyRI (CD64), FcyRII (CD32) and FcyRIII (CD16) so as to focus
cellular defense mechanisms
to the cell expressing the particular PRO polypeptide. Bispecific antibodies
may also be used to localize cytotoxic
agents to cells which express a particular PRO polypeptide. These antibodies
possess a PRO-binding arm and
an arm which binds a cytotoxic agent or a radionuclide chelator, such as
EOTUBE, DPTA, DOTA, or TETA.
Another bispecific antibody of interest binds the PRO polypeptide and further
binds tissue factor (TF).
5. Heteroconjug,ate Antibodies
Heteroconjugate antibodies are also within the scope of the present invention.
Heteroconjugate antibodies
are composed of two covalently joined antibodies. Such antibodies have, for
example, been proposed to target
immune system cells to unwanted cells [U.S. Patent No. 4,676,980], and for
treatment of HIV infection [WO
91/00360; WO 92/200373; EP 030891. It is contemplated that the antibodies may
be prepared in vitro using
known methods in synthetic protein chemistry, including those involving
crosslinking agents. For example,
immunotoxins may be constructed using a disulfide exchange reaction or by
forming a thioether bond. Examples
of suitable reagents for this purpose include iminothiolate and methyl-4-
mercaptobutyrimidate and those disclosed,
for example, in U.S. Patent No. 4,676,980.
6. Effector Function En~ineerirlg
It may be desirable to modify the antibody of the invention with respect to
effector function, so as to
enhance, e.g., the effectiveness of the antibody in treating cancer. For
example, cysteine residue(s) may be
introduced into the Fc region, thereby allowing interchain disulfide bond
formation in this region. The
homodimeric antibody thus generated may have improved internalization
capability and/or increased complement-
mediated cell killing and antibody-dependent cellular cytotoxicity (ADCC). See
Caron et al., J. Exp 1Vled., 176:
1191-1195 (1992) and Shopes, J. Immunol., 148: 2918-2922 (1992). Homodimeric
antibodies with enhanced anti-
tumor activity may also be prepared using heterobifanctional cross-linkers as
described in Wolff et al. Cancer
Research, 53: 2560-2565 (1993). Alternatively, an antibody can be engineered
that has dual Fc regions and may
thereby have enhanced complement lysis and ADCC capabilities. See Stevenson et
al., Anti-Cancer Dru~ Design,
3: 219-230 (1989).
7. lmnJ nunoconu.gates
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The invention also pertains to immunoconjugates comprising an antibody
conjugated to a cytotoxic agent
such as a chemotherapeutic agent, toxin (e. g. , an enzymatically active toxin
of bacterial, fungal, plant, or animal
origin, or fragments thereof), or a radioactive isotope (i.e., a
radioconjugate).
Chemotherapeutic agents useful in the generation of such immunoconjugates have
been described above.
Enzymatically active toxins and fragments thereof that can be used include
diphtheria A chain, nonbinding active
fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa),
ricin A chain, abrin A chain,
modeccin A chain, alpha-sarcin, Aleuritesfordii proteins, dianthin proteins,
Phytolaca americana proteins (PAPI,
PAPII, and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria
officinalis inhibitor, gelonin,
mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes. A
variety of radionuclides are available
for the production of radioconjugated antibodies. Examples include 212Bi,
13iI, 131In, 90Y, and 186Re
Conjugates of the antibody and cytotoxic agent are made using a variety of
bifunctional protein-coupling agents
such as N-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP), iminothiolane
(IT), bifunctional derivatives of
imidoesters (such as dimethyl adipimidate HCL), active esters (such as
disuccinimidyl suberate), aldehydes (such
as glutareldehyde), bis-azido compounds (such as bis (p-azidobenzoyl)
hexanediamine), bis-diazonium derivatives
(such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as
tolyene 2,6-diisocyanate), and bis-
active fluorine compounds (such as 1,5-difluoro-2,4-dinitrobenzene). For
example, a ricin immunotoxin can be
prepared as described in Vitetta et al., Science, 238: 1098 (1987). Carbon-14-
labeled 1-isothiocyanatobenzyl-3-
methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating
agent for conjugation of
radionucleotide to the antibody. See W094/11026.
In another embodiment, the antibody may be conjugated to a "receptor" (such
streptavidin) for utilization
in tumor pretargeting wherein the antibody-receptor conjugate is administered
to the patient, followed by removal
of unbound conjugate from the circulation using a clearing agent and then
administration of a "ligand" (e.g.,
avidin) that is conjugated to a cytotoxic agent (e.g., a radionucleotide).
8. Immunolinosomes
The antibodies disclosed herein may also be formulated as immunoliposomes.
Liposomes containing
the antibody are prepared by methods known in the art, such as described in
Epstein et al., Proc. Natl. Acad. Sci.
USA, 82: 3688 (1985); Hwang et al., Proc. Natl Acad. Sci. USA, 77: 4030
(1980); and U.S. Pat. Nos.
4,485,045 and 4,544,545. Liposomes with enhanced circulationtime are disclosed
in U.S. Patent No. 5,013,556.
Particularly useful liposomes can be generated by the reverse-phase
evaporation method with a lipid
composition comprising phosphatidylcholine, cholesterol, and PEG-derivatized
phosphatidylethanolamine (PEG-
PE). Liposomes are extruded through fllters of defined pore size to yield
liposomes with the desired diameter.
Fab' fragments of the antibody of the present invention can be conjugated to
the liposomes as described in Martin
et al., J. Biol. Chem., 257: 286-288 (1982) via a disulfide-interchange
reaction. A chemotherapeutic agent (such
as Doxorubicin) is optionally contained within the liposome. See Gabizon et
al. , J. National Cancer Inst., 81(19):
1484 (1989).
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9. Pharmaceutical Compositions of Antibodies
Antibodies specifically binding a PRO polypeptide identified herein, as well
as other molecules identified
by the screening assays disclosed hereinbefore, can be administered for the
treatment of various disorders in the
form of pharmaceutical compositions.
If the PRO polypeptide is intracellular and whole antibodies are used as
inbibitors, internalizing
antibodies are preferred. However, lipofections or liposomes can also be used
to deliver the antibody, or an
antibody fragment, into cells. Where antibody fragments are used, the smallest
inhibitory fragment that
specifically binds to the binding domain of the target protein is preferred.
For example, based upon the variable-
region sequences of an antibody, peptide molecules can be designed that retain
the ability to bind the target protein
sequence. Such peptides can be synthesized chemically and/or produced by
recombinant DNA technology. See,
e.g., Marasco et al., Proc. Natl. Acad. Sci. USA, 90: 7889-7893 (1993). The
formulation herein may also
contain'more than one active compound as necessary for the particular
indication being treated, preferably those
with complementary activities that do not adversely affect each other.
Alternatively, or in addition, the
composition may comprise an agent that enhances its function, such as, for
example, a cytotoxic agent, cytokine,
chemotherapeutic agent, or growth-inhibitory agent. Such molecules are
suitably present in combination in
amounts that are effective for the purpose intended.
The active ingredients may also be entrapped in microcapsules prepared, for
example, by coacervation
techniques or by interfacial polymerization, for example,
hydroxymethylcellulose or gelatin-microcapsules and
poly-(methylmethacylate) microcapsules, respectively, in colloidal drug
delivery systems (for example, liposomes,
albuminmicrospheres, microemulsions, nano-particles,
andnanocapsules)orinmacroemuisions. Suchtechniques
are disclosed in Remington's Pharmaceutical Sciences, supra.
The formulations to be used for in vivo administration must be sterile. This
is readily accomplished by
filtration through sterile filtration membranes.
Sustained-release preparations may be prepared. Suitable examples of sustained-
release preparations
include semipermeable matrices of solid hydrophobic polymers containing the
antibody, which matrices are in
the form of shaped articles, e.g., films, or microcapsules. Examples of
sustained-release matrices include
polyesters, hydrogels (for example, poly(2-hydroxyethyl-methacrylate), or
poly(vinylalcohol)), polylactides (U.S.
Pat. No. 3,773,919), copolymers of L-glutamic acid and y ethyl-L-glutamate,
non-degradable ethylene-vinyl
acetate, degradable lactic acid-glycolic acid copolymers such as the LUPRON
DEPOT T"' (injectable microspheres
composed of lactic acid-glycolic acid copolymer and leuprolide acetate), and
poly-D-(-)-3-hydroxybutyric acid.
While polymers such as ethylene-vinyl acetate and lactic acid-glycolic acid
enable release of molecules for over
100 days, certain hydrogels release proteins for shorter time periods. When
encapsulated antibodies remain in
the body for a long time, they may denature or aggregate as a result of
exposure to moisture at 370C, resulting
in a loss of biological activity and possible changes in immunogenicity.
Rational strategies can be devised for
stabilization depending on the mechanism involved. For example, if the
aggregation mechanism is discovered
to be intermolecular S-S bond formation through thio-disulfide interchange,
stabilization may be achieved by
modifying sulfhydryl residues, lyophilizing from acidic solutions, controlling
moisture content, using appropriate
additives, and developing specific polymer matrix compositions.
CA 02591930 2007-03-30
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0. Us4 f~or anti-PRO Antibodies
The snt4-PRO antibodies of the invention have various utilities. For example,
anti-PRO antibodies may
be used in diagaostic assays for PRO, e.g., detecting its expression (and in
some cases, differential expression)
in specific cells, tissues, or serum. Various diagnostic assay techniques
known in the art may be used, such as
competitive binding assays, direat or indirect sandwich assays and
immunoprecipitation assays conducted in either
heterogeneous or homogeneous phases [Zola, Monoclonal Antt'bodies: A Manual of
Techniaues, CRC Press, Inc.
(1987) pp. 147-158]. The antibodies used in the diagaostic assays can be
labeled with a detectable moiety. The
detectable moiety should be capable of producing, either directly or
indirectly, a detectable signal. For example,
the detectable moiety may be a radioisotope, such as 3H, 14C, -2P,'SS, or "I,
a fluorescent or chemiluminescent
compound, such as fluorescein isothiocyanate, rhodamine, or luciferin, or an
enzyme, such as allcaline
phosphatase, beta-galactosidase or horseradish peroxidase. Any method lmown in
the art for conjugating the
antibody to the detectable moiety may be employed, including those methods
described by Hunter et al., Nature,
jM:945 (1962); David et al., Biochemistrv,1J:1014 (1974); Pain et al., J.
Immunol. Meth., 4õQ:219 (1981); and
Nygren, J. Histochem. and Cvtochem., 3Q:407 (1982).
Anti-PRO antibodies also are useful for the affinity purification of PRO from
reaombinant cell culture
or natural sources. In this process, the antibodies against PRO are
immobilized on a suitable support, such a
Seplu<dex resin or filier paper, using methods weII known in the art. The
immobflized aatibody then is contacted
with a sample containing the PRO to be purified, and thereafter the support is
washed with a suitable solvent that
will remove substantially all the material in the sample except the PRO, which
is bound to the immobilized
antibody. Finally, the support is wasbed with another suitable solvent that
will release the PRO from the
antibody.
The following examples are offered for illustrative purposes only, and are not
intended to limit the scope
of the present invention in any way.
EJCAMPLBS
Commercially available reagents referred to in the examples were used
according to maanfacturer's
instrnctions unless otherwise indicated. The source of those cells identified
in the following examples, and
throughout the specification, by ATCC accession numbers is the American Type
Culture Collection, Manassas,
vA.
EXAMPLB 1: Exmcellniar Domain Homoloay Sereenine to Identify Novel
Polp,peptides and cDNA &icodinR
Tbmvfm
The extracellular domain (BCD) sequences (mcluding the secretion signal
sequence, if any) from about
950 known secreted proteins from the Swiss-Prot public database were used to
search EST databases. The EST
databases induded public databases (e.g., Dayhoff, GenBank), and proprietary
databases (e.g. LdFF.SEQ''"',
Incyte Phannaceutieals, Palo Alto, CA). The search was performed using the
computer program BLAST or
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BLAST-2 (Altsehal et a1., Metlods inRnzvmolo~v. 2&:460-480 (1996)) aa a
comparison of the ECD protein
sequences to a 6 frame iramladon of the EST seqaenoes. Thoso comparisons with
a BLAST score of 70 (or in
some cases 90) or greater that did not encode lmown proteins were clustered
and assembled into oonsensns DNA
sequences with the program 'phrap" (PW7 Green, University of Washington,
Seattle, WA).
Using tltis eaaraoeIIular domain homology screen, coosenaas DNA sequences were
assembled relative
to the other identilied EST sequences using phrap. In addition, the consensas
DNA seqneenlces obtained were often
(but'not always) extended using repeated cycles of BLAST or BLAST-2 and phrap
to extend the coasensus
sequence as far as possib1e usiag the sotuces of EST seqomoe3 discussed above.
Based upon the consensus seqnenees obtaiaed as described above,
oligmxcleotides were thon synthesized
and used to iden* by PCR a cDNA librarq that contained the sequence of
intei+est and for use as probes to
isolate a clone of the full-length coding seqaenae for a PRO polypeptide.
Forward and reverse PCR primers
generaily range from 20 to 30 nucleotldes and are often designed to give a PCR
product of about 100-1000 bp
in length. The ptobe sequenoes are typicaliy 40-55 bp in lengtR. In some cam,
additional oligonucleotides are
synahesized when the consensus sequence is greater than about 1-1.5kbp. Ip
order to screen several li'braries for
a ftill-lengfb cbne, DNA from ft libraries was screened by PCR amplificatim,
as per Ausnbel et at.,Cuffmt
Protocols in Molecular Bioloev, with the PCR primer pair. A positive library
was then used to iaolate elones
encoding the gene of interest using the probe oligonueleotide and one of the
primer pairs.
The cDNA libraries used to isolate the cDNA clones were oonsiructed by
standard methods using
camnmercially available reagerns such as those from Invitrogen, San Diego, CA.
The cDNA was primed with
oltgo dT csonWobg a Notl site, linked with bhmt to SaII hcmil3nased adaptors,
cleaved with NotI, sized
appropriately by gel electtophoresis, and cloned In a deSned orientation into
a suitable cloning vector (such as
pRKB or pRKD; pRKSB is a precnraor of pRKSD tbat does not contain the Sfil
site; see, Holmes et cl., Scknog,
M:1278-1280 (1991)) in 8ue unique JC1wI and Noti sioea.
MUMPLE 2: bolation of eD A clones by Amvlaae 3maft
.25 1. Pre,VffAtjM of Q]jgo QT nrimed cDDLA 1~'t~rv
mRNA was isolated from a human tissue of iaberest using reagents and protocols
from Invitrogen, San
Diego, CA (Fast Track 2). This RNA was used to generate an oligo dT prinred
cDNA 1'brary in the vector
pRKSD using reagents and protoools from Life Tocba Obgies, Claithersburg, MD
(Super ScriptPlasmid System).
In this procedure, ft double stranded cDNA was sized to greater than 1000 bp
and the Sail/Noti linkered cDNA
was clamed inm JOiolMotl cleaved vecw. pItK3D is a cloning vector that hAs an
sp6 transcription initiation site
foilowed by an SSI resaiction enzyme site precxding the Xhol/Notl cDNA cloning
sites.
2. prauaration of random vrimed cDNA libraty
A secondary cDNA library was generaoed in order to prefer~entiat2y
representthe 5' ends of the primary
cDNA clones. Sp6 RNA was genarated fram tbe primary flbrary (described above),
and alnis RNA was used t.o
generate a random primed cDNA library In tlie vector pSST-AMY.0 using reagents
and protocols from Life
Tecbanlogks (Saper Script Plasmid System, retierenced above). In this
procxdtire the double stranded cDNA was
77
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CA 02591930 2007-03-30
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sized to 500-1000 bp, linkered with blunt to NotI adaptors, cleaved with SfiI,
and cloned into SfiI/NotI cleaved
vector. pSST-AMY.0 is a cloning vector that has a yeast alcohol dehydrogenase
promoter preceding the cDNA
cloning sites and the mouse amylase sequence (the mature sequence without the
secretion signal) followed by the
yeast alcohol dehydrogenase terminator, after the cloning sites. Thus, cDNAs
cloned into this vector that are
fused in frame with amylase sequence will lead to the secretion of amylase
from appropriately transfected yeast
colonies.
3. Transformation and Detection
DNA from the library described in paragraph 2 above was chilled on ice to
which was added
electrocompetent DH10B bacteria (Life Technologies, 20 ml). The bacteria and
vector mixture was then
electroporated as recommended by the manufacturer. Subsequently, SOC media
(Life Technologies, 1 ml) was
added and the mixture was incubated at 37 C for 30 minutes. The transformants
were then plated onto 20
standard 150 mm LB plates containing ampicillin and incubated for 16 hours (37
C). Positive colonies were
scraped off the plates and the DNA was isolated from the bacterial pellet
using standard protocols, e.g. CsCl-
gradient. The purified DNA was then carried on to the yeast protocols below.
The yeast methods were divided into three categories: (1) Transformation of
yeast with the
plasmid/cDNA combined vector; (2) Detection and isolation of yeast clones
secreting amylase; and (3) PCR
amplification of the insert directly from the yeast colony and purification of
the DNA for sequencing and further
analysis.
The yeast strain used was HD56-5A (ATCC-90785). This strain has the following
genotype: MAT
alpha, ura3-52, leu2-3, leu2-112, his3-11, his3-15, MAL+, SUC+, GAL+.
Preferably, yeast mutants can be
employed that have deficient post-translational pathways. Such mutants may
have translocation deficient alleles
in sec7l, sec72, sec62, with truncated sec7l being most preferred.
Alternatively, antagonists (including antisense
nucleotides and/or ligands) which interfere with the normal operation of these
genes, other proteins implicated
in this post translation pathway (e.g., SEC61p, SEC72p, SEC62p, SEC63p, TDJ1p
or SSA1p-4p) or the complex
formation of these proteins may also be preferably employed in combination
with the amylase-expressing yeast.
Transformation was performed based on the protocol outlined by Gietz et al.,
Nucl. Acid. Res., 20:1425
(1992). Transformed cells were then inoculated from agar into YEPD complex
media broth (100 ml) and grown
overnight at 30 C. The YEPD broth was prepared as described in Kaiser et al.,
Methods in Yeast Genetics, Cold
Spring Harbor Press, Cold Spring Harbor, NY, p. 207 (1994). The overnight
culture was then diluted to about
2 x 106 cells/ml (approx. OD6,=0.1) into fresh YEPD broth (500 ml) and regrown
to 1 x 10' cells/ml (approx.
OD6w=0.4-0.5).
The cells were then harvested and prepared for transformation by transfer into
GS3 rotor bottles in a
Sorval GS3 rotor at 5,000 rpm for 5 minutes, the supernatant discarded, and
then resuspended into sterile water,
and centrifuged again in 50 ml falcon tubes at 3,500 rpm in a Beckman GS-6KR
centrifuge. The supernatant was
discarded and the cells were subsequently washed with LiAc/TE (10 ml, 10 mM
Tris-HCI, 1 mM EDTA pH 7.5,
100 mM LizOOCCH), and resuspended into LiAc/TE (2.5 ml).
Transformation took place by mixing the prepared cells (100 l) with freshly
denatured single stranded
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salmon testes DNA (Lofstrand Labs, Gaithersburg, MD) and transforming DNA (1
Ag, vol. < 10 1) in
microfuge tubes. The mixture was mixed briefly by vortexing, then 40% PEG/TE
(600 l, 40% polyethylene
glycol-4000, 10 mM Tris-HCI, 1 mM EDTA, 100 mM LizOOCCH3, pH 7.5) was added.
This mixture was
gently mixed and incubated at 30 C while agitating for 30 minutes. The cells
were then heat shocked at 42 C
for 15 minutes, and the reaction vessel cenirifuged in a microfuge at 12,000
rpm for 5-10 seconds, decanted and
resuspended into TE (500 E.cl, 10 mM Tris-HCI, 1 mM EDTA pH 7.5) followed by
recentrifugation. The cells
were then diluted into TE (1 ml) and aliquots (200 l) were spread onto the
selective media previously prepared
in 150 mm growth plates (VWR).
Alternatively, instead of multiple small reactions, the transformation was
performed using a single, large
scale reaction, wherein reagent amounts were scaled up accordingly.
The selective media used was a syntlietic complete dextrose agar lacking
uracil (SCD-Ura) prepared as
described in Kaiser et al., Methods in Yeast Genetics, Cold Spring Harbor
Press, Cold Spring Harbor, NY, p.
208-210 (1994). Transformants were grown at 30 C for 2-3 days.
The detection of colonies secreting amylase was performed by including red
starch in the selective growth
media. Starch was coupled to the red dye (Reactive Red-120, Sigma) as per the
procedure described by Biely
et al., Anal. Biochem., 172:176-179 (1988). The coupled starch was
incorporated into the SCD-Ura agar plates
at a final concentration of 0.15 % (w/v), and was buffered with potassium
phosphate to a pH of 7.0 (50-100 mM
final concentration).
The positive colonies were picked and streaked across fresh selective media
(onto 150 mm plates) in
order to obtain well isolated and identifiable single colonies. Well isolated
single colonies positive for amylase
secretion were detected by direct incorporation of red starch into buffered
SCD-Ura agar. Positive colonies were
determined by their ability to break down starch resulting in a clear halo
around the positive colony visualized
directly.
4. Isolation of DNA by PCR.A plification
When a positive colony was isolated, a portion of it was picked by a toothpick
and diluted into sterile
water (30 141) in a 96 well plate. At this time, the positive colonies were
either frozen and stored for subsequent
analysis or immediately amplified. An aliquot of cells (5 l) was used as a
template for the PCR reaction in a
25 l volume containing: 0.5 l Klentaq (Clontech, Palo Alto, CA); 4.0 110 mM
dNTP's (Perkin Elmer-Cetus);
2.5 l Kentaq buffer (Clontech); 0.25 l forward oligo 1; 0.25 l reverse
oligo 2; 12.5 l distilled water. The
sequence of the forward oligonucleotide 1 was:
5'-TGTAAAACGACGGCCAGTTAAATAGACCTGCAATTATTAATCT-3' (SEQ ID NO:245)
The sequence of reverse oligonucleotide 2 was:
5'-CAGGAAACAGCTATGACCACCTGCACACCTGCAAATCCATT-3' (SEQ ID NO:246)
PCR was then performed as follows:
a. Denature 92 C, 5 minutes
b. 3 cycles of: Denature 92 C, 30 seconds
Anneal 59 C, 30 seconds
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Extend 72 C, 60 seconds
c. 3 cycles of: Denature 92 C, 30 seconds
Anneal 57 C, 30 seconds
Eztend 72 C, 60 seconds
d. 25 cycles of: Denature 92 C, 30 seconds
Anneal 55 C, 30 seconds
Extend 72 C, 60 saconds
e. Hold 4 C
The underlined regions of the oligonucleotides annealed to the ADH promoter
region and the amylase
region, respectively, and amplified a 307 bp region from vector pSST-AMY.0
when no insert was present.
Typically, the first 18 nucleotides of the 5' end of these oligonucleotides
contained annealing sites for the
sequencing primers. Thus, the total product of the PCR reaetion from an empty
vector was 343 bp. However,
signal sequence-fused cDNA resulted in considerably longer nucleotide
sequences.
Following the PCR, an aliquot of the reaction (5 Fcl) was examined by agarose
gel electrophoresis in a
1% agarose gel using a Tris-Borate-EDTA (TBE) buffering system as described by
Sambrook et al., supra.
Clones resulting in a single strong PCR product larger than 400 bp were
further analyzed by DNA sequencing
after purification with a 96 Qiaquick PCR clean-up column (Qiagen Inc.,
Chatsworth, CA).
EXAMPLE 3: Isolation of cDNA Clones Usina Si~.nal AIaorithm Analvsis
Various polypeptide-encoding nucleic acid sequenoes were identified by
applying a proprietary signal
sequence finding algorithm developed by Genentech, Inc. (South San Francisco,
CA) upon ESTs as well as
clustered and assembled EST fragments from public (e.g.. GenBank) and/or
private (LIFFSEQ , Incyte
Pharmaceuticals, Inc., Palo Alto, CA) databases. The signal sequence algorithm
computes a secretion signal
score based on the character of the DNA nucleotides surrounding the first and
optionally the second methionine
codon(s) (ATG) at the 5'-end of the sequence or sequence fragment under
consideration. The nucleotides
following the first ATG must code for at least 35 unambiguous amino acids
without any stop codons. If the first
ATG has the required amiao acids, the second is not examined. If neither meets
the requirement, the candidate
sequence is not soored. In order to determine whether the EST sequence
contains an authentic signal sequence,
the DNA and corresponding amino acid sequences surrounding the ATG codon are
scored using a set of seven
sensors (evaluation parameters) known to be assoeiated with secretion signals.
Use of this algoritbm resulted in
the identification of numerous polypeptide-encoding nucleic acid sequences.
EXAMPLE 4: Isolation of cDNA clones F.ncodine Human PRO Polypentides
Using the techniques described in Examples 1 to 3 above, numerous full-length
cDNA clones were
identified as encoding PRO polypeptides as disclosed herein. These cDNAs were
then deposited under the terms
of the Budapest Treaty with the American Type Culture CoIlection, 10801
University Blvd., Manassas, VA
20110-2209, USA (ATCC) as shown in Table 7 below.
CA 02591930 2007-03-30
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Table 7
Material ATCC Dep. No. Deposit Date
DNA94849-2960 PTA-2306 July 25, 2000
DNA96883-2745 PTA-544 August 17, 1999
DNA96894-2675 PTA-260 June 22, 1999
DNA100272-2969 PTA-2299 July 25, 2000
DNA108696-2966 PTA-2315 August 1, 2000
DNA117935-2801 PTA-1088 December 22, 1999
DNA119474-2803 PTA-1097 December 22, 1999
DNA119498-2965 PTA-2298 July 25, 2000
DNA119502-2789 PTA-1082 December 22, 1999
DNA119516-2797 PTA-1083 December 22, 1999
DNA119530-2968 PTA-2396 August 8, 2000
DNA121772-2741 PTA-1030 December 7, 1999
DNA125148-2782 PTA-955 November 16, 1999
DNA125150-2793 PTA-1085 December 22, 1999
DNA125151-2784 PTA-1029 December 7, 1999
DNA125181-2804 PTA-1096 December 22, 1999
DNA125192-2794 PTA-1086 December 22, 1999
DNA125196-2792 PTA-1091 December 22, 1999
DNA125200-2810 PTA-1186 January 11, 2000
DNA125214-2814 PTA-1270 February 2, 2000
DNA125219-2799 PTA-1084 December 22, 1999
DNA128309-2825 PTA-1340 Februaiy 8, 2000
DNA129535-2796 PTA-1087 December 22, 1999
DNA129549-2798 PTA-1099 December 22, 1999
DNA129580-2863 PTA-1584 March 28, 2000
DNA 129794-2967 PTA-2305 July 25, 2000
DNA131590-2962 PTA-2297 July 25, 2000
DNA135173-2811 PTA-1184 January 11, 2000
DNA138039-2828 PTA-1343 February 8, 2000
DNA139540-2807 PTA-1187 January 11, 2000
DNA139602-2859 PTA-1588 March 28, 2000
DNA139632-2880 PTA-1629 Apri14, 2000
DNA139686-2823 PTA-1264 February 2, 2000
DNA142392-2800 PTA-1092 December 22, 1999
DNA143076-2787 PTA-1028 December 7, 1999
81
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Table 7 (~t
Materi ATCC Dep. No. Denosit Date
DNA143294-2818 PTA-1182 January 11, 2000
DNA143514-2817 PTA-1266 February 2, 2000
DNA144841-2816 PTA-1188 January 11, 2000
DNA148380-2827 PTA-1181 January 11, 2000
DNA149995-2871 PTA-1971 May 31, 2000
DNA167678-2963 PTA-2302 July 25, 2000
DNA168028-2956 PTA 2304 July 25, 2000
DNA173894-2947 PTA-2108 June 20, 2000
DNA176775-2957 PTA-2303 July 25, 2000
DNA177313-2982 PTA 2251 July 19, 2000
DNA57700-1408 203583 Jannary 12, 1999
DNA62872-1509 203100 August 4, 1998
DNA62876-1517 203095 August 4, 1998
DNA66660-1585 203279 September 22, 1998
DNA34434-1139 209252 September 16, 1997
DNA44804-1248 209527 December 10, 1997
DNA52758-1399 209773 April 14, 1998
DNA59849-1504 209986 June 16, 1998
DNA65410-1569 203231 September 15, 1998
DNA71290-1630 203275 September 22, 1998
DNA33100-1159 209377 October 16, 1997
DNA64896-1539 203238 September 9, 1998
DNA84920-2614 203966 Apri127, 1999
DNA23330-1390 209775 Apri114, 1998
DNA32286-1191 209385 October 16, 1997
DNA35673-1201 209418 October 28, 1997
DNA43316-1237 209487 November 21, 1997
DNA441841319 209704 March 26, 1998
DNA45419-1252 209616 Febraary 5, 1998
DNA48314-1320 209702 March 26, 1998
DNA50921-1458 209859 May 12, 1998
DNA53987 209858 May 12, 1998
DNA56047-1456 209948 June 9, 1998
DNA56405-1357 209849 May 6, 1998
DNA56531-1648 203286 September 29, 1998
DNA56865-1491 203022 June 23, 1998
82
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Table 7 (cont')
DNA57694-1341 203017 June 23, 1998
DNA57708-1411 203021 June 23, 1998
DNA57836-1338 203025 June 23, 1998
DNA57841-1522 203458 November 3, 1998
DNA58847-1383 209879 May 20, 1998
DNA59212-1627 203245 September 9, 1998
DNA59588-1571 203106 August 11, 1998
DNA59622-1334 209984 June 16, 1998
DNA59847-2510 203576 January 12, 1999
DNA60615-1483 209980 June 16, 1998
DNA60621-1516 203091 Augnst 4, 1998
DNA62814-1521 203093 August 4, 1998
DNA64883-1526 203253 September 9, 1998
DNA64889-1541 203250 September 9, 1998
DNA64897-1628 203216 September 15, 1998
DNA64903-1553 203223 September 15, 1998
DNA64907-1163-1 203242 September 9, 1998
DNA64950-1590 203224 September 15, 1998
DNA64952-1568 203222 September 15, 1998
DNA65402-1540 203252 September 9, 1998
DNA65405-1547 203476 November 17, 1998
DNA66663-1598 203268 September 22, 1998
DNA66667 203267 September 22, 1998
DNA66675-1587 203282 September 22, 1998
DNA67300-1605 203163 August 25, 1998
DNA68872-1620 203160 Augast 25, 1998
DNA71269-1621 203284 September 22, 1998
DNA73736-1657 203466 November 17, 1998
DNA73739-1645 203270 September 22, 1998
DNA76400-2528 203573 January 12, 1999
DNA76532-1702 203473 November 17, 1998
DNA76541-1675 203409 October 27, 1998
DNA79862-2522 203550 December 22, 1998
DNA81754-2532 203542 December 15, 1998
DNA81761-2583 203862 March 23, 1999
DNA83500-2506 203391 October 29, 1998
DNA84210-2576 203818 March 2, 1999
83
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Table 7 (cont')
DNA86571-2551 203660 February 9, 1999
DNA92218-2554 203834 March 9, 1999
DNA92223-2567 203851 March 16, 1999
DNA92265-2669 PTA-256 June 22, 1999
DNA92274-2617 203971 Apri127, 1999
DNA108760-2740 PTA-548 August 17, 1999
DNA108792-2753 PTA-617 August 31, 1999
DNA111750-2706 PTA-489 August 3, 1999
DNA119514-2772 PTA-946 November 9, 1999
DNA125185-2806 PTA-1031 December 7, 1999
These deposits were made under the provisions of the Budapest Treaty on the
International Recognition
of the Deposit of Microorganisms for the Pmrpose of Patent Procedure and the
Regulations thereunder (Budapest
Treaty). This assures maintenance of a viable culture of the deposit for 30
years from the date of deposit. The
deposits will be made available by ATCC under the terms of the Budapest
Treaty, and subject to an agreement
between Genentech, Inc. and ATCC, which assures permanent and unt+estricted
availability of the progeny of the
culture of the deposit to the public upon issuance of the pertinent U.S.
patent or upon laying open to the public
of any U.S. or foreign patent application, whichever comes first, and assures
availability of the progeny to one
determined by the U.S. Commissioner of Patents and Trademarks to be entitled
thereto according to 35 USC
122 and the Commissioner's rules pursuant thereto (including 37 CFR 1.14
with particular reference to 886 OG
638).
The assignee of the present application has agreed that if a cultare of the
materials on deposit should die
or be lost or destroyed when cultivated under suitable conditions, the
materials will be promptly replaced on
notification with another of the same. Availability of the deposited material
is not to be constraed as a license
to practice the invention in contravention of the rights granted under the
authority of any government in
aecordance with its patent laws.
EXAMPLE 5: Isolation of eDNA clones Encodin,gHuman PR06004. PR05723. PR03444.
and PR09940
DNA molecules encoding the PR0840, PR01338, PR06004, PR05723, PR03444, and
PR09940
polypeptides shown in the accompanying figures were obtained through GenBank.
fiXAMPI.E 6: Use of PRO as a hybri ';sn probe
The follownng method describes use of a nucleotide sequence encoding PRO as a
hybridization probe.
DNA comprising the coding sequence of fuII-length or mature PRO as disclosed
herein is employed as
a probe to screen for homologous DNAs (such as those encoding naturally-
occuaring variants of PRO)= in human
tissue cDNA h'braries or human tissue genomic libraries.
Hybridization and washing of filters containing either library DNAs is
performed under the following
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CA 02591930 2007-03-30
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high stringency conditions. Hybridization of radiolabeled PRO-derived probe to
the filters is performed in a
solution of 50% formamide, 5x SSC, 0.19b SDS, 0.196 sodium pyrophosphate, 50
mM sodium phosphate, pH
6.8, 2x Denhardt's solution, and 10% dextran sulfate at 42 C for 20 hours.
Washing of the filters is performed
in an aqueous solution of 0. lx SSC and 0.1 % SDS at 42 C.
DNAs having a desired sequence identity with the DNA encoding full-Iength
native sequence PRO can
then be identified using standard techniques lmown in the art.
EXAMPLE 7: Exoression of PRO in E. coli
This example illustrates preparation of an unglycosylated form of PRO by
recombinant expression in E.
coli.
The DNA sequence encodiag PRO is initially amplified using selected PCR
primers. The primers should
contain restriction enzyme sites which correspond to the restriction enzyme
sites on the selected expression vector.
A variety of expression vectors may be employed. An example of a suitable
vector is pBR322 (derived from E.
coli; see Bolivar et al., _(2M, 2:95 (1977)) which contains genes for
ampicillin and Detracycline resistance. The
vector is digested with restriction enzyme and dephosphorylated. The PCR
amplified sequences are then ligated
into the vector. The vector will preferably include sequences which encode for
an antibiotic resistance gene, a
trp promoter, a polyhis leader (including the first six STII codons, polyhis
sequence, and enteroldnase cleavage
site), the PRO coding region, lambda transcriptional teriminator, and an argU
gene.
The ligation mixture is then used to transform a selected E. coli strain using
the methods described in
Sambrook et a1., sunra. Transformants are identified by their ability to grow
on LB plates and antibiotic resistant
colonies are then selected. Plasmid DNA can be isolated and confumed by
restriction analysis and DNA
sequencing.
Selected clones can be grown overnight in liquid culture medium such as LB
broth supplemented with
antibiotics. The overnight culture may subsequently be used to inoculate a
larger scale culture. The cells are then
grown to a desired optical density, during which the expression promoter is
turned on.
After culturing the cells for several more hours, the cells can be harvested
by centrifugation. The cell
pellet obtained by the centrifugation can be solubilized using various agents
known in the art, and the solubilized
PRO protein can then be purified using a metal chelating column under
conditions that allow tight binding of the
protein.
PRO may be expressed in E. coli in a poly-His tagged form, usit4g the
following procedure. The DNA
encoding PRO is initially amplified using selected PCR primers. The primers
will contain restriction enzyme sites
which correspond to the restriction enzyme sites on the selected expression
vector, and other useful sequences
providing for efficient and reli.able translation inidation, rapid
purification on a metal chelation column, and
proteolytic removal with enterokinase. The PCR-amplified, poly-His tagged
sequences are then li,gated into an
expression vector, which is used to transform an E. codi host based on strain
52 (W31 10 fuhA(tonA) lon galE
rpoHts(htpRts) clpP(lacIq). 17ansformants are first grown in LB containing 50
mg/ml carbenicillin at 30 C wit,h
shaking until an O.D.600 of 3-5 is reached. Cnltures are then diluted 50-100
fold into CRAP media (prepared
by mixing 3.57 g(NH4)aSO4, 0.71 g sodium citrate=2H2O, 1.07 g KCI, 5.36 g
Difco yeast extract, 5.36 g
CA 02591930 2007-03-30
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Sheffield hycase SF in 500 mL water, as well as 110 mM MPOS, pH 7.3, 0.55%
(w/v) glucose and 7 mM
MgSO4) and grown for approximately 20-30 hours at 30 C with shaking. Samples
are removed to verify
expression by SDS-PAGB analysis, and the bulk culture is centrifuged to pellet
the cells. Cell pellets are frozen
until purification and refolding.
E. coli paste from 0.5 to I L fermentations (6-10 g pellets) is resuspended in
10 volumes (w/v) in 7 M
guanidine,# 20 mM Tris, pH 8 buffer. Solid sodium sulfite and sodium
tetrathionate is added to make final
concentrations of 0. 1M and 0.02 M, respectively, and the solution is stirred
overnight at 4 C. This step results
in a denatured protein with all cysteine residues blocked by sulfitolization.
The solution is centrifuged at 40,000
rpm in a Beckman Ultracentifuge for 30 min. The supernatant is diluted with 3-
5 volumes of metal chelate
column buffer (6 M guanidine, 20 mM Tris, pH 7.4) and filtered through 0.22
micron filters to clarify. The
clarified extract is loaded onto a 5 ml Qiagen Ni-NTA metal chelate column
equilibrated in the metal chelate
column buffer. The column is washed with additional buffer containing 50 mM
imidazole (Calbiochem, Utrol
grade), pH 7.4. The protein is eluted with buffer containing 250 mM imidazole.
Fractions containing the desired
protein are pooled and stored at 4 C. Protein concentration is estimated by
its absorbance at 280 nm using the
calculated extinction coefficient based on its amino acid sequence.
The proteins are refolded by diluting the sample slowly into freshly prepared
refolding buffer consisting
of: 20 mM Tris, pH 8.6, 0.3 M NaCI, 2.5 M urea, 5 mM cysteine, 20 mM glycine
and 1 mM EDTA. Refolding
volumes are chosen so that the final protein concentration is between 50 to
100 micrograms/mi. The refolding
solution is stirred gently at 4 C for 12-36 hours. The refolding reaction is
quenched by the addition of TFA to
a final concentration of 0.4% (pH of approximately 3). Before further
purification of the protein, the solution
is filtered through a 0.22 micron filter and acetonitrile is added to 2-10%
fmal concentration. The refolded
protein is chromatographed on a Poros Rl/H reversed phase column using a
mobile buffer of 0.1 % TFA with
elution with a gradient of acetonitrile from 10 to 80%. Aliquots of fractions
with A280 absorbance are analyzed
on SDS polyacrylamide gels and fractions containing homogeneous refolded
protein are pooled. Generally, the
properly refolded species of most proteins are eluted at the lowest
concentrations of acetonitrile since those species
are the most compact with their hydrophobic interiors sbielded from
interaction with the reversed phase resin.
Aggregated species are usually eluted at higher acetonitrile concentrations.
In addition to resolving misfolded
forms of proteins from the desired form, the reversed phase step also removes
endotoxin from the samples.
Fractions containing the desired folded PRO polypeptide are pooled and the
acetonitrile removed using
a gentle stream of nitrogen directed at the solution. Proteins are formulated
into 20 mM Hepes, pH 6.8 with 0.14
M sodium chloride and 4% mannitol by dialysis or by gel filtration using 025
Superfine (Pharmacia) resins
equilibrated in the formulation buffer and sterile filtered.
Many of the PRO polypeptides disclosed herein were successfully expressed as
described above.
EXAMPLE g: F.preasion of PRO in mammalian cells
This example illustrates preparation of apotentially glycosylated form of PRO
by recombinant expression
in mammalian cells.
The vector, pRK5 (see EP 307,247, published March 15, 1989), is employed as
the expression vector.
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Optionally, the PRO DNA is ligated into pRK5 with selected restriction enzymes
to allow insertion of the PRO
DNA using ligation methods such as deson-bed in Sambrook et al., ugõ~a. The
resulting vector is called pRK5-
PRO.
In one embodiment, the selected host cells may be 293 cells. Human 293 cells
(ATCC CCL 1573) are
grown to confluence in tissue culture plates in medium such as DMEM
supplemented with fetal calf serum and
optionally, nutrient components and/or antibiotics. About 10 g pRK5-PRO DNA
is mixed with about 1 g DNA
encoding the VA RNA gene [Thimmappaya et al., CCU, 31:543 (1982)] and
dissolved in 500 l of 1 mM Tris-
HC1, 0.1 mM EDTA, 0.227 M CaCLz. To this mixture is added, dropwise, 500 l of
50 mM HEP}3S (pH 7.35),
280 mM NaCI, 1.5 mM NaPO4, and a precipitate is allowed to form for 10 minutes
at 25 C. The precipitate is
suspended and added to the 293 cells and allowed to settle for about four
hours at 37 C. The culture medium is
aspirated off and 2 ml of 20% glycerol in PBS is added for 30 seconds. The 293
cells are then washed with serum
free medium, fresh medium is added and the cells are incubated for about 5
days.
Approximately 24 hours after the transfections, the culture medium is removed
and replaced with culture
medium (alone) or culture medium containing 200 Ci/mI 'S-cysteine and 200
p,Ci/m135S-methionine. After a
12 hour incubation, the conditioned medium is collected, concentrated on a
spin filter, and loaded onto a 159b
SDS gel. The processed gel may be dried and exposed to film for a selected
period of tinte to reveal the presence
of PRO polypeptide. The cultures containing transfected cells may undergo
further incubation (in sernm free
medium) and the medium is tesbed in selected bioassays.
In an alternative technique, PRO may be introduced into 293 cells transiently
using the dextran sulfate
method described by Somparyrac et al., Proc. Natl. Acad. Sci., 12:7575 (1981).
293 cells are grown to maximal
density in a spinner flask and 700 g pRK5-PRO DNA is added. The cells are
first concentrated from the spinner
flaskby centrifugation and wasbsd with PBS. The DNA-deatran precipitate is
incubated on the cell pellet for four
hours. The cells are treated with 20% glycerol for 90 seconds, washed with
tissue culture medium, and re-
introduced into the spinner flask containing tissue culture medium, 5 g/ml
bovine insulin and 0.1 glml bovine
transfenrin. After about four days, the conditioned media is centrifuged and
5ltered to remove cells and debris.
The sample containing expressed PRO can then be concentrated and purified by
any selected method, such as
dialysis and/or column chromatography.
In another embodiment, PRO can be expressed in CHO cells. The pRK5-PRO can be
transfected into
CHO cells using known reagents such as CaPO4 or DEAE-dextran. As described
above, the cell cultures can be
incubated, and the medium replaced with culture medium (alone) or medium
conttaiining a radiolabel such as 35S-
methionine. After determining the presence of PRO polypeptide, the culture
medium may be replaced with serum
free medium. Preferably, the cultures are incubated for about 6 days, and then
the conditioned medium is
harvested. The medium containing the expressed PRO can then be concentrated
and purified by any selected
method.
Bpitope-tagged PRO may also be expressed ia host CHO cells. The PRO may be
subcloned out of the
pRK5 vector. The subolone insert can undergo PCR to fuse in frame with a
selected epitope tag such as a poly-his
tag into a Baculovirus expression vector. The poly-his tagged PRO insert can
then be subcloned into a SV40
driven veotor containing a selection marker such as DHFR for selection of
stable elones. Finally, the CHO cells
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can be transfected (as described above) with the SV40 driven vector. Labeling
may be performed, as described
above, to verify expression. The culture medium containing the expressed poly-
His tagged PRO can then be
concentrated and purified by any selected method, such as by N?}-chelate
affinity chromatography.
PRO may also be expressed in CHO and/or COS ceIls by a transient expression
procedure or in CHO
cells by another stable expression procedure.
Stable expression in CHO cells is performed using the following procedure. The
proteins are expressed
as an IgG construct (immunoadhesin), in which the coding sequences for the
soluble forms (e.g. extracellular
domains) of the respective proteins are fused to an IgGi constant region
sequence containing the hinge, CH2 and
CH2 domains and/or is a poly-His tagged form.
Following PCR amplification, the respective DNAs are subcloned in a CHO
expression vector using
standard techniques as described in Ausubel et al., Current Protocols of
Molecular Biology, Unit 3.16, John Wiley
and Sons (1997). CHO expression vectors are constructed to have compatible
restriction sites 5' and 3' of the
DNA of interest to allow the convenient shuttling of cDNA's. The vector used
expression in CHO cells is as
described in Lucas et al., Nucl. Acids Res. 24:9 (1774-1779 (1996), and uses
the SV40 early promoter/enhancer
to drive expression of the cDNA of interest and dihydrofolate reductase
(DHFR). DHFR expression permits
selection for stable maintenance of the plasmid following transfection.
Twelve micrograms of the desired plasmid DNA is introduced into approximately
10 million CHO cells
using commercially available transfection reagents Superfec? (Qiagen), Dosper
or Fugene' (Boehringer
Mannheim). '1'he cells are grown as described in Lucas et al., Mm.
Approximately 3 x 10' cells are frozen in
an ampule for further growth and production as described below.
The ampules cantaining the plasmid DNA are thawed by placement into water bath
and mixed by
vortexing. The contents are pipetted into a centrifuge tube containing 10 mLs
of media and centrifuged at 1000
rpm for 5 minutes. The supernatant is aspirated and the cells are resuspended
in 10 mL of selective media (0.2
,um filtered PS20 with 5% 0.2 m diafiltered fetal bovine serum). The cells
are then aliquoted into a 100 mL
spinner containing 90 mL of selective media. After 1-2 days, the cells are
transferred into a 250 mL spinner filled
with 150 mL selective growth medium and incubated at 37 C. After another 2-3
days, 250 mL, 500 mL and 2000
mL spinners are seeded with 3 x lOs cells/mL. The cell media is exchanged with
fresh media by centrifugation
and resuspension in production medium. Although any suitable CHO media may be
employed, a production
medium descnbed in U.S. Patent No. 5,122,469, issued June 16, 1992 may
actually be used. A 3L production
spinner is seeded at 1.2 x 106 cells/mL. On day 0, the cell number pH ie
determined. On day 1, the spinner is
sampied and sparging with filtered air is commenced. On day 2, the spimw is
sampled, the temperature shifted
to 33 C, and 30 mL of 500 g/L glucose and 0.6 mL of 10% antifoam (e.g., 35%
polydimethylsiloxane emulsion,
Dow Corn'ung 365 Medical Grade Emulsion) iaken. Throughout the production, the
pH is adjusted as necessary
to keep it at around 7.2. After 10 days, or until the viability dropped below
70%, the cell culture is harvested
by centrifiigation and 5ltering through a 0.22 /,cm filter. The fltrate was
either stored at 4 C or immediately
loaded onto cohunns for purification.
For the poly-His tagged constructs, the proteins are pwrified using a Ni-NTA
column (Qiagen). Before
purification, imidazole is added to the conditioned media to a concentration
of 5 mM. The conditioned media is
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pumped onto a 6 ml Ni-NTA column equilibrated in 20 mM Hepes, pH 7.4, buffer
containing 0.3 M NaC1 and
mM imidazole at a flow rate of 4-5 ml/min. at 4 C. After loading, the column
is washed with additional
equilibration baffer and the protein eluted with equilibration buffer
containing 0.25 M imidazole. The highly
purified protein is subsequently desalted into a storage buffer containing 10
mM Hepes, 0.14 M NaCI and 4%
mannitol, pH 6.8, with a 25 ml G25 Superfine (Pharmacia) column and stored at -
80 C.
5 Immunoadhesin (Fc-containing) constivcts are purifiled from the conditioned
media as follows. The
conditioned medium is pumped onto a 5 ml Protein A column (Pharmacia) which
had been equilibrated in 20 mM
Na phosphate buffer, pH 6.8. After loading, the column is washed extensively
with equilibration buffer before
elution with 100 mM citric acid, pH 3.5. The eluted protein is immediately
neutralized by collecting 1 ml
fractions into tubes containing 275 gL of 1 M Tris buffer, pH 9. The higbly
purified protein is subsequently
desalted into storage buffer as descrmed above for the poly-His tagged
proteins. The homogeneity is assessed by
SDS polyacrylamide gels and by N-terminal amino acid sequencing by Edman
degradation.
Many of the PRO polypeptides disclosed herein were successfully expressed as
described above.
EXAMPLE 9: Ezaression of PRO in Yeast
The following method descrnbes recombinant eapression of PRO in yeast.
First, yeast expression vectors are constructed for intracellular production
or secretion of PRO from the
ADH2/GAPDH promoter. DNA encoding PRO and the promoter is inserted into
suitable restriction enzyme sites
in the seleoted plasmid tD direct intracellular expression of PRO. For
secretion, DNA encoding PRO can be
cloned into the selected plasmid, together with DNA encoding the ADH2/GAPDH
promoter, a native PRO signal
peptide or other mammalian signal peptide, or, for exatnple, a yeast alpha-
factor or invertase secretory
signal/leader sequence, and linker sequences (if needed) for expression of
PRO.
Yeast cells, such as yeast strain AB110, can then be transfornied with the
expression plasmids described
above and cultured in selected fermentation media. The transformed yeast
supernatants can be analyzed by
precipitation with 10% trichloroacetic acid and separation by SDS-PAGE,
followed by staining of the gels with
Coomassie Blue stain.
Recombinant PRO can subsequently be isolated and purified by removing the
yeast cells from the
fermentation medium by centrifugation and then concentrating the medium using
selected cartridge filters. The
concentrate containing PRO may further be purified using selected column
chromatography resins.
Many of the PRO polypeptides disclosed herein were successfully expressed as
described above.
EXAMPLE 10: EMression of PRO in Baculovirus-Infecbed Insect Cells
The following method describes recombinant expression of PRO in Baculovirus-
infected insect cells.
The sequence coding for PRO is fused upstream of an epitope tag contained
within a baculovirus
expression vector. Such epitope tags include poly-his tags and immunoglobulin
tags (like Fc regions of IgG).
A variety of plasmids may be employed, incIuding plasmids derived from
commercially available plasmids such
as pVL1393 (Novagen): Briefly, the sequence encoding PRO or the desired
portion of the coding sequence of
PRO such as the sequence encoding the extracellular domain of a transmembrane
protein or the sequence encoding
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the mature protein if the protein is extracellular is amplified by PCR with
primers complementary to the 5' and
3' regions. The 5' primer may incarporate tlanking (selected) restriction
enzyme sites. The product is then
digested with those selected restriction enzymes and subcloned into the
expression vector.
Recombinant baculovirns is generated by co-transfecting the above plasmid and
BaculoGold" virus DNA
(Pharmingen) into 4,odoPtera frugtperda ("Sf9") celIs (ATCC CRL 1711) usiAg
lipofectin (commercially
available from GIBCO-BRL). After 4- 5 days of incubation at 28 C, the released
viruses are harvested and used
for further amplifications. Viral infection and protein expression are
performed as described by O'Reilley et al.,
Baculovirns exnression vecGors: A Iaboratorv Manual, Oxford: Oxford University
Press (1994).
Expressed poly-his tagged PRO can then be purified, for example, by Ni2+-
chelate affmity
chromatography as follows. Extracts are prepared from recombinant virus-
infected Sf9 cells as described by
Rupert et al., Nature, 362:175-179 (1993). Briefly, Sfrl cells are washed,
resuspended in sonication buffer (25
mL Hepes, pH 7.9; 12.5 mM MgC4; 0.1 mM EDTA; 10% glycerol; 0.1 % NP-40; 0.4 M
KCI), and sonicated
twice for 20 seconds on ice. The sonicates are cleared by centrifugarion, and
the supernatant is diluted 50-fold
in loading buffer (50 mM phosphate, 300 mM NaCl, 10 % glycerol, pH 7.8) and
filtered through a 0.45,um filter.
A Ni2+-NTA agarose column (commercially available from Qiagen) is prepared
with a bed volume of 5 mL,
washed with 25 mL of water and equilibrated with 25 mL of loading buffer. The
filtered celi extract is loaded
onto the column at 0.5 mL per minute. The column is washed to baseline Ano
with loading buffer, at which point
fraction collection is started. Next, the column is washed with a seoondary
wash buffer (50 mM phosphate; 300
mM NaCl, 10% glycerol, pH 6.0), which elutes nonspecifically bound protein.
After reaahing Am baseline
again, the column is developed with a 0 to 500 mM Imidazole gradient in the
secondary wash buffer. One mL
fractions are collected and analyzed by SDS-PAGE and silver staining or
Westerablot with N?*-NTA-conjugated
to alkaliae phosphatase (Qiagen). Fractions c:omaining the eluted His,o tagged
PRO are pooled and dialyzed
against loading buffer.
Alternatively, purification of the IgG tagged (or Fc tagged) PRO can be
performed using known
chromatog.raphy techniques, including for instance, Protein A or protein G
cohnnn cbromatography.
Many of the PRO polypeptides disclosed herein were successfally expressed as
described above.
EXAMPLE 11: Preparation of Antibodies that Bind PRO
This example illustrates preparation of monoclonal antibodies which can
specifically bind PRO.
Techniques for producing the monoclonal andbodies are known in the art and are
described, for instance,
in Goding, su~r . Immunogens that may be employed include purified PRO, fusion
proteins containing PRO,
and cells expressing recombinant PRO on the cell surface. Selection of the
immunogen can be made by the skilled
artisan without undue experimentation.
Mice, such as Balb/c, are immunized with the PRO immunogen emulsified in
complete Freund's adjuvant
and injected subcutaneously or intraperitoneally in an amount from 1-100
micrograms. Alternatively, the
immunogen is emulsified in MPL-TDM adjuvant (Ribi Immunochemical Research,
Hamilton, MT) and injected
into the animal's hind foot pads. The immunized mice are then boosted 10 to 12
days later with additional
immunogen emulsified in the selected adjuvant. Thereafter, for several weeks,
the mice may also be boosted with
CA 02591930 2007-03-30
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additional immunization injections. Serum samples may be periodically obtained
from the mice by retro-orbital
bleeding for testing in ELISA assays to detect anti-PRO antibodies.
After a suitable antibody titer has been detected, the animals "positive" for
antibodies can be injected
with a final intravenous injection of PRO. Three to four days later, the mice
are sacrificed and the spleen cells
are harvested. The spleen cells are then fused (using 35 % polyethylene
glycol) to a selected murine myelonia cell
line such as P3X63AgU. 1, available from ATCC, No. CRL 1597. The fusions
generate hybridoma cells which
can then be plated in 96 well tissue culture plates containing HAT
(hypoxanthine, aminopterin, and thymidine)
medium to inhibit proliferation of non-fused cells, myeloma hybrids, and
spleen cell hybrids.
The hybridoma cells will be screened in an ELISA for reactivity against PRO.
Determination of
"positive" hybridoma cells secreting the desired monoclonal antibodies against
PRO is within the slcill in the art.
The positive hybridoma cells can be injected intraperitoneally into syngeneic
Balb/c mice to produce
ascites containing the anti-PRO monoclonal antibodies. Alternatively, the
hybridoma cells can be grown in tissue
culture flasks or roller bottles. Purification of the monoclonal antibodies
produced in the ascites can be
accomplished using ammonium sulfate precipitation, followed by gel exclusion
chromatography. Alternatively,
affinity chromatography based upon binding of antibody to protein A or protein
G can be employed.
EXAMPLE 12: Purification of PRO Polypeptides Usinc Specific Antibodies
Native or recombinant PRO polypeptides may be purified by a variety of
standard techniques in the art
of protein purification. For example, pro-PRO polypeptide, matare PRO
polypeptide, or pre-PRO polypeptide
is purified by immunoaffinity chromatography using antibodies specific for the
PRO polypeptide of interest. In
general, an immunoaffinity column is constructed by covalently coupling the
anti-PRO polypeptide antibody to
an activated chromatographic resin.
Polyclonal immunoglobulins are prepared from immune sera either by
precipitation with ammonium
sulfate or by purification on immobilized Protein A (PharmaciaLKB
Biotechnology, Piscataway, N.J.). Likewise,
monoclonal antibodies are prepared from mouse ascites fluid by ammonium
sulfate precipitation or
chromatography on immobilized Protein A. Partially purified immunoglobulin is
covalently attached to a
chromatographic resin such as CnBr-activated SEPHAROSETM (Pharmacia LKB
Biotechnology). The antibody
is coupled to the resin, the resin is blocked, and the derivative resin is
washed according to the manufacturer's
instructions.
Such an immunoaffinity column is utilized in the purification of PRO
polypeptide by preparing a fraction
from cells containing PRO polypeptide in a soluble form. This preparation is
derived by solubilization of the
whole cell or of a subcellular fraction obtained via differential
centrifugation by the addition of detergent or by
other methods well known in the art. Alternatively, soluble PRO polypeptide
containing a signal sequence may
be secreted in useful quantity into the medium in which the cells are grown.
A soluble PRO polypeptide-containing preparation is passed over the
immunoaffinity column, and the
column is washed under conditions that allow the preferential absorbance of
PRO polypeptide (e.g., high ionic
strength buffers in the presence of detergent). Then, the column is eluted
under conditions that disrupt
antibody/PRO polypeptide binding (e.g., a low pH buffer such as approximately
pH 2-3, or a high concentration
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of a chaotrope such as urea or thiocyanate ion), and PRO polypeptide is
collected.
BXAMPI,1313: Dru~ Soreenine
This invention is particularly useful for screening compounds by using PRO
polypeptides or binding
fragment thereof in any of a variety of drug screening techniques. The PRO
polypeptide or fragment employed
in such a test may either be free in solutlon, affixed to a solid support,
borne on a ceII surface, or located
intracellularly. One method of drug screening utilizes eukaryotic or
prokaryotic host cells which are stably
transformed with recombmant nucleic acids expressing the PRO polypeptide or
fragment. Drugs are screened
against such transformed cells in competitive binding assays. Such cells,
either in viable or fixed form, can be
used for standard binding assays. One may measure, for example, the formation
of complexes between PRO
polypeptide or a fragment and the agent being tested. Alternatively, one can
examine the diminution in complex
formation between the PRO polypeptide and its target cell or target receptors
caused by the agent being tested.
Thus, the present invention provides methods of screening for drugs or any
other agents which can affect
a PRO polypeptide-associated disease or disorder. These methods comprise
contacting such an agent with an PRO
polypeptide or fragment thereof and assaying (1) for the presence of a complex
between the agent and the PRO
polypeptide or fragment, or (ii) for the presence of a complex between the PRO
polypeptide or fragment and the
cell, by methods well known in the art. In such competitive binding assays,
the PRO polypeptide or fragment
is typically labeled. After suitable ineubation, free PRO polypeptide or
fragment is separated from that present
in bound form, and the amount of free or unoomplexed label is a measure of the
ability of the particular agent
to iiind to PRO polypeptide or to interfere with the PRO polypeptide%11
complex.
Another technique for drug screening provides high throughput screening for
compounds having suitable
binding affinity to a polypeptide and is described in detail in WO 84/03564,
published on September 13, 1984.
Briefly stated, large numbers of different small peptide test compounds are
synthesized on a solid substrate, such
as plastic pins or some other surface. As applied to a PRO polypeptide, the
peptide test compounds are reacted
with PRO polypeptide and washed. Bound PRO polypeptide is detected by methods
well known in the art.
Purified PRO polypeptide can also be coated directly onto plates for use in
the aforementioned drag screening
techniques. In addition, non-neutralizing antibodies can be used to capture
the peptide and immobilize it on the
solid support.
This invention also contemplates the use of competitive drug screening assays
in which neutralizing
antibodies capable of binding PRO polypeptide specifically compete with a test
compound for binding to PRO
polypeptide or fragments thereof. In this manner, the antibodies can be used
to detect the presence of any peptide
which shares one or more antigenic determinantc with PRO polypeptide.
EXAMPLE 14: Rational Drn Design
The goal of rational drug design is to produce stractural analogs of
biologically active polypeptide of
interest (i.e., a PRO polypeptide) or of small molecules with which they
interact, e.g., agonists, antagonists, or
inhibitors. Any of these examples can be used to fashion drugs which are more
active or stable forms of the PRO
polypeptide or which enhance or inLerfere with the function of the PRO
polypeptide in vivo (c.f., Hodgson,
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BiolTech~logy, Q: 19-21 (1991)).
In one approach, the three-dimensional stracture of the PRO polypeptide, or of
an PRO
polypeptide-inhibitor complex, is determined by x-ray cryatallography, by
computer modeling or, most typically,
by a combination of the two approaches. Both the shape and charges of the PRO
polypeptide must be ascertained
to elucidate the structure and to determine active site(s) of the molecule.
Less often, useful information regarding
the structure of the PRO polypeptide may be gained by modeling based on the
shvchire of homologous proteins.
In both cases, relevant struoAiral information is used to design analogous PRO
polypeptide-like molecules or to
identify efficient inhibitors. Useful examples of rational drug design may
include molecules which have improved
activity or stability as shown by Braxton and Wells, Biochemistrv. 31:7796-
7801(1992) or which act as inhibitors,
agonists, or antagonists of native peptides as shown by Athauda et ctl., J.
Biochem., 113:742-746 (1993).
It is also possible to isolate a target-specific antibody, selected by
functional assay, as described above,
and then to solve its crystal structure. This approach, in principle, yields a
pharmacore upon which subsequent
drug design can be based. It is possible to bypass protein crystaIlography
altogether by generating anti-idiotypic
antibodies (anti-ids) to a functional, pharmacologically active antibody. As a
mirror image of a mirror image, the
binding site of the anti-ids would be expected to be an analog of the original
receptor. The anti-id could then be
used to identify and isolate peptides from banks of chemically or biologically
produced peptides. The isolated
peptides would then act as the pharmacore.
By virtue of the present invention, sufficient amounts of the PRO polypeptide
may be made available to
perform such analytical studies as X-ray crystallography. In addition,
knowledge of the PRO polypeptide amino
acid sequence provided herein will provide guidance to those employing
computer modeling techniques in place
of or in addition to x-ray crystallography.
EXAMPLE 15: Pericvte c-Fos Induction (Assay 93)
This assay shows that certain polypeptides of the invention act to induce the
expression of c-fos in
pericyte cells and, therefore, are useful not only as diagnostic markers for
particular types of pericyte-associated
tumors but also for giving rise to antagonists which would be expected to be
useful for the therapeutic treatment
of pericyte-associated tumors. Induction of c-fos expression in pericytes is
also indicative of the induction of
angiogenesis and, as such, PRO polypeptides capable of inducing the expression
of c-fos would be expected to
be usefal for the treatment of conditions where induced angiogenesis would be
beneficial including, for example,
wound healing, and the like. Specifically, on day 1, pericytes are received
from VEC Technologies and all but
5 ml of media is removed from flask. On day 2, the pericytes are trypsinized,
washed, spun and then plated onto
96 well plates. On day 7, the media is removed and the pericytes are treated
with 100 Ecl of PRO polypeptide test
samples and controls (positive control = DME+5% seram. +/- PDGF at 500 ng/ml;
negative control = protein
32). Replicates are averaged and SD/CV are determined. Fold inarease over
Protein 32 (buffer control) value
indicated by chemiluminescence units (RLU) luminometer reading verses
frequency is plotted on a histogram.
Two-fold above Protein 32 value is considered positive for the assay. ASY
Matrix: Growth media =1ow glucose
DMEM = 20% FBS + 1X pen strep + 1X fungizone. Assay Media = low glucose DMEM
+5% FBS.
The following polypeptides tested positive in this assay: PR0982, PRO1160,
PRO1187, and PRO 1329.
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EXAMPLE 16: Chondrocvte Re-di~grentiation Assay (Assay~l0)
This assay shows that certain polypeptides of the invention act to induce
redifferentiation of chondrocytes,
therefore, are expected to be useful for the treatment of various bone and/or
cartilage disorders such as, for
example, sports injuries and arthritis. The assay is performed as follows.
Porcine chondrocytes are isolated by
overnight collagenase digestion of artioulary cartilage of
inetacarpophalangeal joints of 4-6 month old female pigs.
The isolated cells are then seeded at 25,000 cells/cmZ in Ham F-12 containing
10% FBS and 4 g/ml gentamycin.
The culture media is changed every third day and the cells are then seeded in
96 well plates at 5,000 cells/well
in 100 1 of the same media without serum and 100 p.l of the test PRO
polypeptide, 5 nM staurosporin (positive
control) or medium alone (negative control) is added to give a final volume of
200 pl/well. After 5 days of
incubation at 37 C, a picture of each well is taken and the differentiation
state of the chondrocytes is determined.
A positive result in the assay occurs when the redifferentiation of the
chondrocytes is determined to be more
similar to the positive control than the negative control.
The following polypept'ide tested positive in this assay: PR0357.
EXAMPLE 17: Idenfification of PRO Pblypentides That Stimulate TNF-a Release In
Human Blood (Assay 128)
This assay shows that certain PRO polypeptides of the present invention act to
stimulate the release of
TNF-a in human blood. PRO polypeptides testing positive in this assay are
useful for, among other things,
research purposes where stimulation of the release of TNF-a would be desired
and for the therapeutic treatment
of conditions wherein enhanced TNF-a release would be beneficial.
Specifically, 200 l of human blood
supplemented with 50mM Hepes buffer (pH 7.2) is aliquoted per well in a 96
well test plate. To each well is then
added 300k1 of either the t+est PRO polypeptide in 50 mM Hepes buffer (at
various concent<ations) or 50 mM
Hepes buffer alone (negative control) and the plates are incubated at 37 C for
6 hours. The samples are then
centrifuged and 50 1 of plasma is collected from each well and tested for the
presence of TNF-a by ELISA
assay. A positive in the assay is a higher amount of TNF-a in the PRO
polypeptide treated samples as compared
to the negative control samples.
The following PRO polypeptides tesDed positive in this assay: PR0231, PR0357,
PR0725, PRO1155,
PR01306, and PR01419.
EXAMPLE 18: Promotion of Chondrocvte Redifferentiation (Assay 129)
This assay is designed to determine whether PRO polypeptides of the present
invention show the abi7ity
to induce the proliferation and/or redifferentiation of chondrocytes in
culture. PRO polypeptides testing positive
in this assay would be expected to be useful for the therapeutic treatment of
various bone and/or cartilage
disorders such as, for example, sports injuries and arthritis.
Porcine chondrocytes are isolated by overnight collagenase digestion of
articular cartilage of the
metacarpophalangeal joint of 4-6 month old female pigs. The isolated cells are
then seeded at 25,000 cells/cm2
in Ham P-12 containing 10% PBS and 4 g/ml gentamycin. The culture media is
changed every third day. On
day 12, the cells are seeded in 96 weIl plates at 5,000 cells/well in 100 I of
the same media without serum and
100 N.1 of either sernm-free medium (negative control), staurosporin (final
concentration of 5 nM; positive control)
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or the test PRO polypeptide are added to give a final volume of 200 1/well.
After 5 days at 37 C, 22 l of
media comtaining 1001ig/ml Hoechst 33342 and 50 g/m15-CFDA is added to each
well and incubated for an
additional 10 minutes at 37 C. A picture of the green fluorescence is taken
for each well and the differentiation
state of the chondrocytes is calculated by morphometric analysis. A positive
result in the assay is obtained when
the > 50 % of the PRO polypeptide treated cells are differentiated (compared
to the background obtained by the
negative control).
The following PRO polypeptides tested positive in this assay: PR0229, PRO
1272, and PR04405.
EXAMPLE 19: Normal Human Dermal Fibroblast Proliferation (Assay 141)
This assay is designed to determine whether PRO polypeptides of the present
invention show the ability
to induce proliferation of human dermal fibroblast cells in eultare and,
therefore, function as useful growth
factors.
On day 0, humian dermal ffbroblast cells (from cell lines, maximum of 12-14
passages) were plated in
96-well plates at 1000 cells/well per 100 microliter and incubated overnight
in complete media [fibroblast growth
media (FGM. Clonetics), plus supplements: itLSnl9n, human epithelial growth
factor (hBGF), gentamicin (GA-
1000), and fetal bovine sernm (FBS, Clonetics)]. On day 1, complete media was
replaced by basal media [FGM
plus 1% FBS] and addition of PRO polypeptides at 1%, 0.1% and 0.01%. On day 7,
an assessment of cell
proliferation was performed by Alamar Blue assay followed by Crystal Violet.
Results are expresses as % of the
cell growth observed with control buffer.
The following PRO polypeptides tested positive in this assay: PR0982, PR0357,
PR0725, PR01306,
PR01419, PR0229, PRO1272, PRO181, PR0214, PR0247, PR0337, PR0526, PR0363,
PR0531, PR01083,
PR0840, PRO1080, PR0788, PR01478, PRO1134, PR0826, PR01005, PR0809, PRO1194,
PR01071,
PRO1411, PR01309, PR01025, PRO1181, PR01126, PR01186, PR01192, PR01244,
PRO1274, PR01412,
PR01286, PR01330, PRO1347, PR01305, PR01273, PRO1279, PR01340, PR01338,
PR01343, PR01376,
PR01387, PR01409, PR01488, PR01474, PR01917, PR01760, PR01567, PR01887,
PR01928, PR04341,
PR05723, PRO1801, PR04333, PR03543, PR03444, PR04302, PR04322, PR05725,
PR04408, PR09940,
PR07154, PR07425, PR06079, PR09836 and PRO 10096.
EXAMPLE 20: Microarrav Analysis to Detect Overexvression of PRO Polvnentides
in Cancerous Tumors
Nucleic acid microarrays, often containiag thousands of gene sequences, are
usefnl for identifying
differentially expressed genes in diseased tissues as compared to their normal
counterparts. Using nucleic acid
mieroarrays, test and cantrol mRNA samples from test and control tissue
samples are reverse transcribed and
labeled to generate cDNA probes. The cDNA probes are then hybridized to an
array of nucleic acids immobilized
on a solid support. Tbe array is configured such that the sequence and
position of each member of the array is
known. For example, a selection of genes known to be expressed in certain
disease states may be arrayed on a
solid support. Hybridization of a labeled probe with a partieular array member
indicates that the sample from
which the probe was derived expresses that gene. If the hybridization signal
of a probe from a test (disease tissue)
sample is greater than hybridization signal of a probe from a control (normal
tissue) sample, the gene or genes
CA 02591930 2007-03-30
WO 011093983 PCT/US01/17800
overexpressed in the disease tissue are identified. The implication of this
result is that an overexpreased protein
in a diseased tissue is useful not only as a diagnostic tnariaer for the
presertce of the disease condition, but also
as a therapeutic target for treatment of the disease condition.
The methodology of hybridization of nucleic acida and microarray technology is
welI known in the art.
In the present example, the specifte preparation of nueleic aaids for
hybridizatiem and probes, slides, and
hybridization conditions are all detailed in U.S. Patent Application Serial
No. 20020081597 published
June 27, 2002.
In the present example, caneerous tumors derived from various human tissues
were studied for PRO
polypeptide-eaooding gene expression relative to non-cancerous human tissue iu
an attempt to identify those PRO
polypeptides which are overexpressed ia cancerous umoors. Cancerous human
tumor tissue from any of a variety
of different human tumors was obtained and compared to a"universal" epithelial
coatrol sample which was
prepared by pooling non-cattcerous human tissues of epithelial origin,
including liver, kidney, and lung. mRNA
isolated from the pooled t3ssues represents a.miature of expressed gene
products from these different tissues.
Microarray bybridizafion experimnenta using the pooled oontrol samples
generated a linear plot in a 2-color
analysis. The slope of the line generated in a 2-coior analysis was tben used
to naarmalize the ratios of (test:control
detection) within each experiment. The noraoalized ratios from varioua
experiments were then cempared and used
to identify clustering of gene expression. Thus, the pooled "universal
control" sample not only allowed effective
relative gene expression determinations in a simple 2-sample comparison, it
also allowed multi-sample
eompariaons across several experiments.
In the present experiments, mtcleic acid probes derived from the herein
described PRO polypeptido-
eneoding nuoleic acid sequences were used in the creation of the microarray
and RNA from a panel of nine
difterent tumor tissues (liated below) were used for the hybridization
thereto. A value based upon the normalized
ratio:experimental rat3o was designated as a=eutoff ratio". Only vahm that
were above this cutoff ratio were
detiermined to be significant. Table 8 below ahows the results of these
experiments, demorsirating that various
PRO polypeptides of the presetit invention are signif(cantly overexpressed in
various (nunan tumor tissttes, as
compared to a non-cancerous human tissue control or other human tumor tiasues.
As described above, these data
demonstrate tbat the PRO polypeptides of the proseat invention are useful not
only as diagnostic markers for the
preaence of one or more eancmons tumors, but also serve as therapeutic targats
for the treatment of those tumors.
TABLB 8
Molecule is overemressed in: as cQWRred tD normal c92tol=
PR06004 colon tumor universal normal control
PR04981 colon tumor universal normal control
PR04981 luag tumor uaiversal normal control
PZtO7174 colon tumor universd normal control
PR05778 luag tumor universal normal control
PR05778 breast tumpr universal nor'ma1 control
PR05778 liver tumor universal normal control
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TABLfi 8 (cont')
Molecule is overexnressed in: as conanared to normal controi:
PR04332 colon tumor universal normal control
PR09799 colon tumor universal normal control
PR09909 colon tumor universal normal control
PR09917 colon tumor universal normal control
PR09917 lung timnor universal normal control
PR09917 breast tumor universal normal control
PR09771 colon tumor universal normal control
PR09877 colon tumor universal normal control
PR09903 colon tumor universal normal control
PR09830 colon tumor universal normal control
PR07155 colon tumor universal normal control
PR07155 lung tumor universal normal control
PR07155 prostate tomor universal normal oontrol
PR09862 colon tumor universal normal control
PR09882 colon tumor universal normal control
PR09864 colon tumor universal normal control
PRO10013 colon tunior universal normal control
PR09885 colon tumor universal normal control
PR09879 colon tamor universal normal control
PRO10111 colon tumor universal normal control
PRO10111 rectal tumor universal normal control
PR09925 breast tnmor universal normal control
PR09925 rectal tumor universal normal control
PR09925 colon tumor universal normal control
PR09925 lung tamor universal normal control
PR09905 colon tumor universal normal control
PRO10276 colon tumor universal normal control
PR09898 colon tumor universal normal control
PR09904 oolon tumor umversal normal control
PRO19632 colon tumor universal normal control
PR019672 colon tumor universal normal control
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TABLE 8 (cont')
Molecule is oyereapr sed in: as c~mpared to normal control:
PR09783 colon tumoi universal normal control
PR09783 lung tumor universal normal control
PR09783 breast tumor universal normal control
PR09783 prostate tumor universal normal control
PR09783 rectal tumor universal normal control
PRO10112 colon iumor universal normal control
PR010284 colon tumor universal normal control
PRO10100 colon timnor universal normal control
PR019628 colon tumor universal normal control
PRO19684 colon tumor universal normal control
PR010274 colon tumor universal normal control
PR09907 colon tnmor universal normal control
PR09873 colon tumor universal normal control
PRO10201 colon tumor universal normal control
PRO10200 colon tumor universal normal control
PRO10196 colon tumor universal normal control
PR010282 lung tumor universal normal control
PRO10282 breast tumor universal normal control
PR010282 colon tumor universal normal control
PR010282 rectal tumor universal normal con.trol
PR019650 colon tumor universal normal control
PR021184 lung tumor universal normal control
PRO21184 breast tumor universal normal control
PR021184 coloa tumor universal normal control
PRO21201 breast tumor universal normal control
PR021201 colon tumor universal normal control
PRO21175 breast tumor universal normal control
PR021175 colon tumor universal normal control
PRO21175 lung tumor universal normal control
PRO21340 colon tumor universal normal control
PR021340 prostate tamor universal normal control
PR021384 colon tumor universal normal control
PR021384 lung timaor universal normal control
PR021384 breast tumor universal normal control
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EXAMPLE 21: Tissue Expression Distribution
Oligonucleotide probes were constructed from the PRO polypeptide-encoding
nucleotide sequence shown
in the accompanying figures for use in quantitative PCR amplification
reactions. The oligonucleotide probes were
chosen so as to give an approximately 200-600 base pair amplified fragment
from the 3' end of its associated
template in a standard PCR reaction. The oligonucleotide probes were employed
in standard quantitative PCR
amplification reactions with cDNA libraries isolated from different human
adult and/or fetal tissue sources and
analyzed by agarose gel electrophoresis so as to obtain a quantitative
determination of the level of expression of
the PRO polypeptide-encoding nucleic acid in the various tissues tested.
Knowledge of the expression pattern or
the differential expression of the PRO polypeptide-encoding nucleic acid in
various different human tissue types
provides a diagnostic marker useful for tissue typing, with or without other
tissue-specific markers, for
determining the primary tissue source of a metastatic tumor, and the like. The
results of these assays demonstrated
the following:
(1) the DNA94849-2960 molecule is significantly expressed in the following
tissues: car6lage, testis, colon
tumor, heart, placenta, bone marrow, adrenal gland, prostate, spleen aortic
endothelial cells and uterus, and not
significantly expressed in the following tissues: HUVEC.
(2) the DNA100272-2969 molecule is significantly expressed in cartilage,
testis, human umblilical vein
endothelial cells (HUVEC), colon tumor, heart, placenta, bone marrow, adrenal
gland, prostate, spleen and aortic
endothelial cells; and not significantly expressed in uterus. Among a panel of
normal and tumor cells examined,
the DNA100272-2969= was found to be expressed in normal esophagus, esophageal
tumor, normal stomach,
stomach tumor, normal kidney, Iddney tumor, normal lung, lung tumor, normal
rectum, rectal tumor, normal
liver and liver tumor.
(3) the DNA108696-2966 molecule is highly expressed in prostate and also
expressed in testis, bone marrow and
spleen. The DNA108696-2966 molecule is expressed in normal stomach, but not
expressed in stomach tumor.
The DNA108696-2966 molecule is not expressed in normal kidney, kidney tumor,
normal lung, or lung tumor.
The DNA108696-2966 molecule is highly expressed in normal rectum, lower
expression in rectal tumor. The
DNA 108696-2966 molecule is not expressed in normal liver or liver tumor. The
DNA108696-2966 molecule is
not expressed in normal esophagus, esophagial tumor, cartilage, HUVEC, colon
tumor, heart, placenta, adrenal
gland, aortic endothelial cells and uterus.
(4) the DNA119498-2965 molecule is significantly expressed in the following
tissues: highly expressed in aortic
endothelial cells, and also significantly expressed in cartilage, testis,
HUVEC, colon tumor, heart, placenta, bone
marrow, adrenal galnd, prostate and spleen. It is not significantly expressed
in uteras.
(5) the DNA119530-2968 molecule is expressed in the following tissues: normal
esophagus and not expressed
in the following tissues: esophageal tumors, stomach tumors, normal stomach,
normal kidney, kidney tumor,
normal lung, lung tumor, normal rectum, rectal tumors, normal liver or liver
tumors.
(6) the DNA129794-2967 molecule is significantly expressed in testis and
adrenal gland; and not significantly
expressed in cartilage, human umblilical vein endothelial cells (HUVEC), colon
tumor, heart, placenta, bone
marrow, prostate, spleen, aortic endothelial cells and uterus.
(7) the DNA131590-2962 molecule is significantly expressed in the following
tissues: bone marrow, adrenal
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gland, prostate, spleen, uterus, cartilage, testis, colon tumor, heart, and
placenta, and not significantly expressed
in the following tissues: HUVEC, and aortic endothelial cells.
(8) the DNA149995-2871 molecule is hitghly expressed in t.estis, and adrenal
gland; expressed in cartilage, human
umblilical vein endothelial cells (HUVEC), colon tumor, heart, prostate and
uterus; weakly expressed in bone
marrow, spleen and aortic endothelial cells; and not significantly expressed
in placenta.
(9) the DNA167678-2963 molecule is significantly expressed in the following
tissues: normal esophagus,
esophagial tumor, highly expressed in normal stomach, stomach tumor, highly
expressed in normal lddney, kidney
tamor, expressed in lung, lung tumor, normal reatum, rectal tumor, weakly
expressed in normal liver, and not
significantly expressed in liver tumor.
(10) the DNA168028-2956 molecule is highly expressed in bone marrow; expressed
in testis, human umblilical
vein endothelial cells (HUVEC), colon timnor, heart, placenta, adrenal gland,
prostate, spleen, aortic endothelial
cells and uterus; and is weakly expressed in cartilage. Among a panel of
normal and tumor samples examined,
the DNA168028-2956 was found to be expressed in stomach tumor, normal.IQdney,
kidney tumor, lung tumor,
normal rectum and rectal tumor; and not expressed in normal esophagas,
esophageal tumor, normal stomach,
normal lung, normal liver and liver tumor.
(11) the DNA176775-2957 molecule is highly expressed in testis; expressed in
cartilage and prostate; weakly
expressed in adrenal gland, spleen and uterus; and not significantly expressed
in human umblilical vein endothelial
cells (HUVEC), colon tumor, heart, placenta, bone marrow and aortic
endothelial cells.
(12) the DNA177313-2982 molecule is significantly expressed in prostate and
aortic endothelial cells; and not
significantly expressed in cartilage, testis, human umbilical vein endotheHal
cells (HUVEC), colon tumor, heart,
placenta, bone marrow, adrenal gland, spleen and uterus. Among a panel of
normal and tumor cells, the
DNA177313-2982 molecule was found to be expressed in esophageal tiunor but not
in normal esophagas, normal
stomach, stomach tumor, normal lddney, ladney tumor, normal lung, lung tumor,
normal rectum, rectal tumor,
normal liver and liver tumor.
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