Note: Descriptions are shown in the official language in which they were submitted.
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
New Lipid Binding Protein 2
Field of the Invention
This invention relates to newly identified polypeptides and
s polynucleotides encoding such polypeptides sometimes hereinafter
referred to as "New Lipid Binding Protein 2 (NLIBP2)", to their use in
diagnosis and in identifying compounds that may be agonists,
antagonists that are potentially useful in therapy, and to production of
such polypeptides and polynucleotides.
Background of the Invention
The drug discovery process is currently undergoing a fundamental
revolution as it embraces "functional genomics", that is, high throughput
genome- or gene-based biology. This approach as a means to identify
~s genes and gene products as therapeutic targets is rapidly superceding
earlier approaches based on "positional cloning". A phenotype, that is a
biological function or genetic disease, would be identified and this would
then be tracked back to the responsible gene, based on its genetic map
position.
2o Functional genomics relies heavily on high-throughput DNA sequencing
technologies and the various tools of bioinformatics to identify gene
sequences of potential interest from the many molecular biology databases
now available. There is a continuing need to identify and characterise
further genes and their related polypeptides/proteins, as targets for drug
2s discovery.
Summary of the Invention
The present invention relates to New Lipid Binding Protein 2, in particular
New Lipid Binding Protein 2 polypeptides and New Lipid Binding Protein 2
3o polynucleotides, recombinant materials and methods for their production.
Such polypeptides and polynucleotides are of interest in relation to methods
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 2 -
of treatment of certain diseases, including, but not limited to, cancer,
bacteremia, endotoximia, meningococcemia, hemorrhagic trauma, partial
hepatectomy, severe peritoneal infections, cystic fibrosis, coronary heart
disease, artheriosclerosis hereinafter referred to as " diseases of the
s invention". In a further aspect, the invention relates to methods for
identifying agonists and antagonists (e.g., inhibitors) using the materials
provided by the invention, and treating conditions associated with New
Lipid Binding Protein 2 imbalance with the identified compounds. In a still
further aspect, the invention relates to diagnostic assays for detecting
to diseases associated with inappropriate New Lipid Binding Protein 2 activity
or levels.
Description of the Invention
In a first aspect, the present invention relates to New Lipid Binding
is Protein 2 polypeptides. Such polypeptides include:
(a) a polypeptide encoded by a polynucleotide comprising the sequence
of SEQ ID N0:1;
(b) a polypeptide comprising a polypeptide sequence having at least
95%, 96%, 97%, 98%, or 99% identity to the polypeptide sequence of
SEQ ID N0:2;
(c) a polypeptide comprising the polypeptide sequence of SEQ ID N0:2;
(d) a polypeptide having at least 95%, 96%, 97%, 98%, or 99% identity
to the polypeptide sequence of SEQ ID N0:2;
(e) the polypeptide sequence of SEQ ID N0:2; and
~s (f) a polypeptide having or comprising a polypeptide sequence that has
an Identity Index of 0.95, 0.96, 0.97, 0.98, or 0.99 compared to the
polypeptide sequence of SEQ ID N0:2;
(g) fragments and variants of such polypeptides in (a) to (f).
Polypeptides of the present invention are believed to be members of the
;o Lipid Binding Proteins, such as lipopolysaccharide-binding protein (LBP) or
bactericidiallpermeability-increasing protein (BPI). They are therefore of
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 3 -
interest because lipid binding proteins show high-affinity binding to
lipopolysaccharide (LPS), a glycolipid found in the outer membrane of gram
negative bacteria. Accordingly, lipid binding proteins play a decisive role in
the host defense against bacterial infections.
s Further, all of the known members of the protein family of lipid binding
proteins are able to bind phospholipids. LBP, cholesteryl ester transfer
protein (CETP) and phospholipid-transfer protein (PLTP) can also bind
cholesterol and high-density lipoproteins (HDL). HDL plasma levels are
inversely correlated with coronary heart disease and artherosclerosis. Lipid
to binding and transfer proteins, such as CETP and PLTP, facilitate the
transfer of phospholipids and cholesterol from triglyceride-rich lipoproteins
(TRL) into HDL. Accordingly, members of the family of lipid binding proteins
are thought to play a role in the prevention of these disease.
Further, LBP is an acute phase serum protein secreted by the liver that
is catalyses the transfer of LPS monomers to CD14 thereby facilitating a
broad spectrum of cellular and tissue responses leading to antibacterial and
proinflammatory activities. BPI is a 456-residue cationic protein produced
by polymorphonuclear leukocytes (PMN) and is stored in the primary
granules of these cells. The biological effects of isolated BPI are linked to
2o complex formation with LPS. Binding of BPI to live bacteria via LPS
causes immediate growth arrest. Complex formation of BPI with cell-
associated or cell-free LPS inhibits all LPS-induced host cell responses.
BPI-blocking antibodies abolish the potent activity of whole PMN lysates
and inflammatory fluids against BPI-sensitive bacteria. The antibacterial
2s and the anti-endotoxin activities of BPI are fully expressed by the amino
terminal half of the molecule. These properties of BPI have prompted
preclinical and subsequent clinical testing of recombinant amino-terminal
fragments of BPI. In animals, human BPI protein products protect against
lethal injections of isolated LPS. Phase I trials in healthy human
~o volunteers and multiple Phase I/II clinical trials have been completed or
are in progress (severe pediatric meningococcemia, hemorrhagic trauma,
partial hepatectomy, severe peritoneal infections, and cystic fibrosis) and
phase III trials (meningococcemia and hemorrhagic trauma) have been
initiated. In none of >900 normal and severely ill individuals have issues
~s of safety or immunogenicity been encountered. Preliminary evidence
points to overall benefit in BPI-treated patients. These results suggest
that BPI, but also other lipid binding protein such as the present
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 4 -
invention, may have a place in the treatment of life-threatening infections
and conditions associated with bacteremia and endotoxemia.
The amino acid sequence of NLIBP2 shows significant homology to other
members of the protein family of lipid binding proteins such as LBP, BPI ,
CETP and NLiBP1. NLIBP2 contains several amino acids which are
conserved betwen the other members of the protein family of lipid binding
proteins such as Prolin-20, Cystein-138, Cystein-175, Prolin-212, Prolin-
322, Prolin-428 which corresponds e.g. to the amino acids Prolin-28.
Cystein-159, Cystein-198, Prolin-236, Prolin-347, Prolin-451 in LBP,
to respectively.. Further, NLIBP2 shows a similar exon/intron organisation to
LBP, BPI, NLIBP1 and CETP, suggesting that (i) NLIBP2 like other
members of the protein family of lipid binding proteins, has evolved from
a common primordial gene and (ii) that these proteins share similar
functional properties.
A further aspect relates to the finding that NLIBP1 is down regulated in
tumor tissues, e.g. in larynx carcinomas. This finding indicates a role of
lipid
binding proteins such as New Lipid Binding Protein 2 in mechanisms of
immune escape of the tumor and as such gives a rationale for therapeutic
interventions.
The biological properties of the New Lipid Binding Protein 2 are
hereinafter referred to as "biological activity of New Lipid Binding Protein
2" or "New Lipid Binding Protein 2 activity". Preferably, a polypeptide of
the present invention exhibits at least one biological activity of New Lipid
Binding Protein 2.
Polypeptides of the present invention also includes variants of the
aforementioned polypeptides, including all allelic forms and splice variants.
Such polypeptides vary from the reference polypeptide by insertions,
deletions, and substitutions that may be conservative or non-conservative,
or any combination thereof. Particularly preferred variants are those in
;o which several, for instance from 50 to 30, from 30 to 20, from 20 to 10,
from
to 5, from 5 to 3, from 3 to 2, from 2 to 1 or 1 amino acids are inserted,
substituted, or deleted, in any combination.
Preferred fragments of polypeptides of the present invention include a
polypeptide comprising an amino acid sequence having at least 30, 50 or
;; 100 contiguous amino acids from the amino acid sequence of SEQ ID
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 5 -
NO: 2, or a polypeptide comprising an amino acid sequence having at
least 30, 50 or 100 contiguous amino acids truncated or deleted from the
amino acid sequence of SEQ ID NO: 2. Preferred fragments are
biologically active fragments that mediate the biological activity of New
Lipid Binding Protein 2, including those with a similar activity or an
improved activity, or with a decreased undesirable activity. Also preferred
are those fragments that are antigenic or immunogenic in an animal,
especially in a human.
Fragments of the polypeptides of the invention may be employed for
producing the corresponding full-length polypeptide by peptide synthesis;
therefore, these variants may be employed as intermediates for
producing the full-length polypeptides of the invention.The polypeptides of
the present invention may be in the form of the "mature" protein or may
be a part of a larger protein such as a precursor or a fusion protein. It is
15 often advantageous to include an additional amino acid sequence that
contains secretory or leader sequences, pro-sequences, sequences that
aid in purification, for instance multiple histidine residues, or an
additional
sequence for stability during recombinant production.
Polypeptides of the present invention can be prepared in any suitable
o manner, for instance by isolation form naturally occuring sources, from
genetically engineered host cells comprising expression systems (vide
infra) or by chemical synthesis, using for instance automated peptide
synthesisers, or a combination of such methods. Means for preparing such
polypeptides are well understood in the art.
2~
In a further aspect, the present invention relates to New Lipid Binding
Protein 2 polynucleotides. Such polynucleotides include:
(a) a polynucleotide comprising a polynucleotide sequence having at
least 95%, 96%, 97%, 98%, or 99% identity to the polynucleotide
3o squence of SEQ ID N0:1;
(b) a polynucleotide comprising the polynucleotide of SEQ ID N0:1;
(c) a polynucleotide having at least 95%, 96%, 97%, 98%, or 99% identity
to the polynucleotide of SEQ ID N0:1;
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 6 -
(d) the polynucleotide of SEQ ID N0:1;
(e) a polynucleotide comprising a polynucleotide sequence encoding a
polypeptide sequence having at least 95%, 96%, 97%, 98%, or 99%
identity to the polypeptide sequence of SEQ ID N0:2;
s (f) a polynucleotide comprising a polynucleotide sequence encoding the
polypeptide of SEQ ID N0:2;
(g) a polynucleotide having a polynucleotide sequence encoding a
polypeptide sequence having at least 95%, 96%, 97%, 98%, or 99%
identity to the polypeptide sequence of SEQ ID N0:2;
to (h) a polynucleotide encoding the polypeptide of SEQ ID N0:2;
(i) a polynucleotide having or comprising a polynucleotide sequence that
has an Identity Index of 0.95, 0.96, 0.97, 0.98, or 0.99 compared to the
polynucleotide sequence of SEQ ID N0:1;
(j) a polynucleotide having or comprising a polynucleotide sequence
is encoding a polypeptide sequence that has an Identity Index of 0.95, 0.96,
0.97, 0.98, or 0.99 compared to the polypeptide sequence of SEQ ID
N0:2; and
polynucleotides that are fragments and variants of the above mentioned
polynucleotides or that are complementary to above mentioned
o polynucleotides, over the entire length thereof.
Preferred fragments of polynucleotides of the present invention include a
polynucleotide comprising an nucleotide sequence having at least 15, 30,
50 or 100 contiguous nucleotides from the sequence of SEQ ID NO: 1, or
a pofynucleotide comprising an sequence having at least 30, 50 or 100
25 contiguous nucleotides truncated or deleted from the sequence of SEQ
ID NO: 1.
Preferred variants of polynucleotides of the present invention include
splice variants, allelic variants, and polymorphisms, including
polynucleotides having one or more single nucleotide polymorphisms
;o (SNPs).
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
Polynucleotides of the present invention also include polynucleotides
encoding polypeptide variants that comprise the amino acid sequence of
SEQ ID N0:2 and in which several, for instance from 50 to 30, from 30 to
20, from 20 to 10, from 10 to 5, from 5 to 3, from 3 to 2, from 2 to 1 or 1
s amino acid residues are substituted, deleted or added, in any combination.
In a further aspect, the present invention provides polynucleotides that
are RNA transcripts of the DNA sequences of the present invention.
Accordingly, there is provided an RNA polynucleotide that:
(a) comprises an RNA transcript of the DNA sequence encoding
to the polypeptide of SEQ ID N0:2;
(b) is the RNA transcript of the DNA sequence encoding the
polypeptide of SEQ ID N0:2;
(c) comprises an RNA transcript of the DNA sequence of SEQ ID
N0:1; or
is (d) is the RNA transcript of the DNA sequence of SEQ ID N0:1;
and RNA polynucleotides that are complementary thereto.
The polynucleotide sequence of SEQ ID N0:1 shows homology with
bactericidal/permeability-increasing protein (Acc.: NM 001725);
lipopolysaccharide-binding protein (Acc.: AF105067); cholesteryl ester
transfer protein (Acc.:NM 000078); phospholipid transfer protein (Acc.:
NM_006227) . The polynucleotide sequence of SEQ ID N0:1 is a cDNA
sequence that encodes the polypeptide of SEQ ID N0:2. The
polynucleotide sequence encoding the polypeptide of SEQ ID N0:2 may
2s be identical to the polypeptide encoding sequence of SEQ ID N0:1 or it
may be a sequence other than SEQ ID N0:1, which, as a result of the
redundancy (degeneracy) of the genetic code, also encodes the
polypeptide of SEQ ID N0:2. The polypeptide of the SEQ ID N0:2 is
related to other proteins of the Lipid Binding Proteins family, having
;o homology and/or structural similarity with bactericidal/permeability-
increasing protein (Acc.: NP 001716); lipopolysaccharide-binding protein
(Acc.: -P18428); cholesteryl ester transfer protein (Acc.: NP 000069);
phospholipid _transfer protein (Acc.: NP 006218).
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
_ g _
Preferred polypeptides and polynucleotides of the present invention are
expected to have, inter alia, similar biological functions/properties to their
homologous polypeptides and polynucleotides. Furthermore, preferred
polypeptides and polynucleotides of the present invention have at least one
New Lipid Binding Protein 2 activity.
Polynucleotides of the present invention may be obtained using standard
cloning and screening techniques from a cDNA library derived from mRNA
in cells of human trachea, larynx, larynx carcinoma, palate, pharynx,
endometrium, olfactory epithelium, (see for instance, Sambrook et al.,
Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, N.Y. (1989)). Polynucleotides of
the invention can also be obtained from natural sources such as genomic
DNA libraries or can be synthesized using well known and commercially
available techniques.
When polynucleotides of the present invention are used for the
recombinant production of polypeptides of the present invention, the
polynucleotide may include the coding sequence for the mature
polypeptide, by itself, or the coding sequence for the mature polypeptide in
?o reading frame with other coding sequences, such as those encoding a
leader or secretory sequence, a pre-, or pro- or prepro- protein sequence,
or other fusion peptide portions. For example, a marker sequence that
facilitates purification of the fused polypeptide can be encoded. In certain
preferred embodiments of this aspect of the invention, the marker sequence
is a hexa-histidine peptide, as provided in the pQE vector (Qiagen, Inc.)
and described in Gentz et al., Proc Natl Acad Sci USA (1989) 86:821-824,
or is an HA tag. The polynucleotide may also contain non-coding 5' and 3'
sequences, such as transcribed, non-translated sequences, splicing and
polyadenylation signals, ribosome binding sites and sequences that
;o stabilize mRNA.
Polynucleotides that are identical, or have sufficient identity to a
polynucleotide sequence of SEQ ID N0:1, may be used as hybridization
probes for cDNA and genomic DNA or as primers for a nucleic acid
amplification reaction (for instance, PCR). Such probes and primers may
be used to isolate full-length cDNAs and genomic clones encoding
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 9 -
polypeptides of the present invention and to isolate cDNA and genomic
clones of other genes (including genes encoding paralogs from human
sources and orthologs and paralogs from species other than human) that
have a high sequence similarity to SEQ ID N0:1, typically at least 95%
identity. Preferred probes and primers will generally comprise at least 15
nucleotides, preferably, at least 30 nucleotides and may have at least 50, if
not at least 100 nucleotides. Particularly preferred probes will have
between 30 and 50 nucleotides. Particularly preferred primers will have
between 20 and 25 nucleotides.
to A polynucleotide encoding a polypeptide of the present invention, including
homologs from species other than human, may be obtained by a process
comprising the steps of screening a library under stringent hybridization
conditions with a labeled probe having the sequence of SEQ ID NO: 1 or a
fragment thereof, preferably of at least 15 nucleotides; and isolating full-
Is length cDNA and genomic clones containing said polynucleotide sequence.
Such hybridization techniques are well known to the skilled artisan.
Preferred stringent hybridization conditions include overnight incubation at
42oC in a solution comprising: 50% formamide, 5xSSC (150mM NaCI,
15mM trisodium citrate), 50 mM sodium phosphate (pH7.6), 5x Denhardt's
2o solution, 10 % dextran sulfate, and 20 microgram/ml denatured, sheared
salmon sperm DNA; followed by washing the filters in 0.1 x SSC at about
65oC. Thus the present invention also includes isolated polynucleotides,
preferably with a nucleotide sequence of at least 100, obtained by
screening a library under stringent hybridization conditions with a labeled
2s probe having the sequence of SEQ ID N0:1 or a fragment thereof,
preferably of at least 15 nucleotides.
The skilled artisan will appreciate that, in many cases, an isolated cDNA
sequence will be incomplete, in that the region coding for the polypeptide
does not extend all the way through to the 5' terminus. This is a
3o consequence of reverse transcriptase, an enzyme with inherently low
"processivity" (a measure of the ability of the enzyme to remain attached
to the template during the polymerisation reaction), failing to complete a
DNA copy of the mRNA template during first strand cDNA synthesis.
There are several methods available and well known to those skilled in
;s the art to obtain full-length cDNAs, or extend short cDNAs, for example
those based on the method of Rapid Amplification of cDNA ends (RACE)
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 10 -
(see, for example, Frohman et al., Proc Nat Acad Sci USA 85, 8998-
9002, 1988). Recent modifications of the technique, exemplified by the
Marathon (trade mark) technology (Clontech Laboratories Inc.) for
example, have significantly simplified the search for longer cDNAs. In the
Marathon (trade mark) technology, cDNAs have been prepared from
rnRNA extracted from a chosen tissue and an 'adaptor' sequence ligated
onto each end. Nucleic acid amplification (PCR) is then carried out to
amplify the "missing" 5' end of the cDNA using a combination of gene
specific and adaptor specific oligonucleotide primers. The PCR reaction
to is then repeated using 'nested' primers, that is, primers designed to
anneal within the amplified product (typically an adaptor specific primer
that anneals further 3' in the adaptor sequence and a gene specific
primer that anneals further 5' in the known gene sequence). The
products of this reaction can then be analysed by DNA sequencing and a
Is full-length cDNA constructed either by joining the product directly to the
existing cDNA to give a complete sequence, or carrying out a separate
full-length PCR using the new sequence information for the design of the
5' primer.
2o Recombinant polypeptides of the present invention may be prepared by
processes well known in the art from genetically engineered host cells
comprising expression systems. Accordingly, in a further aspect, the
present invention relates to expression systems comprising a
polynucleotide or polynucleotides of the present invention, to host cells
?5 which are genetically engineered with such expression sytems and to the
production of polypeptides of the invention by recombinant techniques.
Cell-free translation systems can also be employed to produce such
proteins using RNAs derived from the DNA constructs of the present
invention.
;o For recombinant production, host cells can be genetically engineered to
incorporate expression systems or portions thereof for polynucleotides of
the present invention. Polynucleotides may be introduced into host cells by
methods described in many standard laboratory manuals, such as Davis et
al., Basic Methods in Molecular Biology (1986) and Sambrook et al.(ibicn.
;5 Preferred methods of introducing polynucleotides into host cells include,
for
instance, calcium phosphate transfection, DEAE-dextran mediated
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
transfection, transvection, microinjection, cationic lipid-mediated
transfection, electroporation, transduction, scrape loading, ballistic
introduction or infection.
Representative examples of appropriate hosts include bacterial cells, such
s as Streptococci, Staphylococci, E. coli, Streptomyces and Bacillus subtilis
cells; fungal cells, such as yeast cells and Aspergillus cells; insect cells
such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as
CHO, COS, HeLa, C127, 3T3, BHK, HEK 293 and Bowes melanoma cells;
and plant cells.
to A great variety of expression systems can be used, for instance,
chromosomal, episomal and virus-derived systems, e.g., vectors derived
from bacterial plasmids, from bacteriophage, from transposons, from yeast
episomes, from insertion elements, from yeast chromosomal elements,
from viruses such as baculoviruses, papova viruses, such as SV40,
is vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabies viruses and
retroviruses, and vectors derived from combinations thereof, such as those
derived from plasmid and bacteriophage genetic elements, such as
cosmids and phagemids. The expression systems may contain control
regions that regulate as well as engender expression. Generally, any
?o system or vector that is able to maintain, propagate or express a
polynucleotide to produce a polypeptide in a host may be used. The
appropriate polynucleotide sequence may be inserted into an expression
system by any of a variety of well-known and routine techniques, such as,
for example, those set forth in Sambrook et al., (ibid). Appropriate secretion
2s signals may be incorporated into the desired polypeptide to allow secretion
of the translated protein into the lumen of the endoplasmic reticulum, the
periplasmic space or the extracellular environment. These signals may be
endogenous to the polypeptide or they may be heterologous signals.
If a polypeptide of the present invention is to be expressed for use in
;o screening assays, it is generally preferred that the polypeptide be
produced at the surface of the cell. In this event, the cells may be
harvested prior to use in the screening assay. If the polypeptide is
secreted into the medium, the medium can be recovered in order to
recover and purify the polypeptide. If produced intracellularly, the cells
;s must first be lysed before the polypeptide is recovered.
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 12 -
Polypeptides of the present invention can be recovered and purified from
recombinant cell cultures by well-known methods including ammonium
sulfate or ethanol precipitation, acid extraction, anion or cation exchange
chromatography, phosphocellulose chromatography, hydrophobic
interaction chromatography, affinity chromatography, hydroxylapatite
chromatography and lectin chromatography. Most preferably, high
performance liquid chromatography is employed for purification. Well
known techniques for refolding proteins may be employed to regenerate
active conformation when the polypeptide is denatured during intracellular
to synthesis, isolation and/or purification.
Polynucleotides of the present invention may be used as diagnostic
reagents, through detecting mutations in the associated gene. Detection of
a mutated form of the gene characterised by the polynucleotide of SEQ ID
N0:1 in the cDNA or genomic sequence and which is associated with a
dysfunction will provide a diagnostic tool that can add to, or define, a
diagnosis of a disease, or susceptibility to a disease, which results from
under-expression, over-expression or altered spatial or temporal expression
of the gene. Individuals carrying mutations in the gene may be detected at
the DNA level by a variety of techniques well known in the art.
?o Nucleic acids for diagnosis may be obtained from a subject's cells, such as
from blood, urine, saliva, tissue biopsy or autopsy material. The genomic
DNA may be used directly for detection or it may be amplified enzymatically
by using PCR, preferably RT-PCR, or other amplification techniques prior to
analysis. RNA or cDNA may also be used in similar fashion. Deletions and
2s insertions can be detected by a change in size of the amplified product in
comparison to the normal genotype. Point mutations can be identified by
hybridizing amplified DNA to labeled New Lipid Binding Protein 2
nucleotide sequences. Perfectly matched sequences can be distinguished
from mismatched duplexes by RNase digestion or by differences in melting
~o temperatures. DNA sequence difference may also be detected by
alterations in the electrophoretic mobility of DNA fragments in gels, with or
without denaturing agents, or by direct DNA sequencing (see, for instance,
Myers et al., Science (1985) 230:1242). Sequence changes at specific
locations may also be revealed by nuclease protection assays, such as
;s RNase and S1 protection or the chemical cleavage method (see Cotton et
al., Proc Natl Acad Sci USA (1985) 85: 4397-4401).
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 13 -
An array of oligonucleotides probes comprising New Lipid Binding Protein
2 polynucleotide sequence or fragments thereof can be constructed to
conduct efficient screening of e.g., genetic mutations. Such arrays are
preferably high density arrays or grids. Array technology methods are well
s known and have general applicability and can be used to address a variety
of questions in molecular genetics including gene expression, genetic
linkage, and genetic variability, see, for example, M.Chee et al., Science,
274, 610-613 (1996) and other references cited therein.
Detection of abnormally decreased or increased levels of polypeptide or
to mRNA expression may also be used for diagnosing or determining
susceptibility of a subject to a disease of the invention. Decreased or
increased expression can be measured at the RNA level using any of the
methods well known in the art for the quantitation of polynucleotides,
such as, for example, nucleic acid amplification, for instance PCR, RT-
ts PCR, RNase protection, Northern blotting and other hybridization
methods. Assay techniques that can be used to determine levels of a
protein, such as a polypeptide of the present invention, in a sample derived
from a host are well-known to those of skill in the art. Such assay methods
include radioimmunoassays, competitive-binding assays, Western Blot
?o analysis and ELISA assays.
Thus in another aspect, the present invention relates to a diagonostic kit
comprising:
(a) a polynucleotide of the present invention, preferably the nucleotide
sequence of SEQ ID NO: 1, or a fragment or an RNA transcript thereof;
2s (b) a nucleotide sequence complementary to that of (a);
(c) a polypeptide of the present invention, preferably the polypeptide of
SEQ ID N0:2 or a fragment thereof; or
(d) an antibody to a polypeptide of the present invention, preferably to the
polypeptide of SEQ ID N0:2.
3o It will be appreciated that in any such kit, (a), (b), (c) or (d) may
comprise
a substantial component. Such a kit will be of use in diagnosing a
disease or susceptibility to a disease, particularly diseases of the
invention, amongst others.
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 14 -
The polynucleotide sequences of the present invention are valuable for
chromosome localisation studies. The sequence is specifically targeted to,
and can hybridize with, a particular location on an individual human
s chromosome. The mapping of relevant sequences to chromosomes
according to the present invention is an important first step in correlating
those sequences with gene associated disease. Once a sequence has
been mapped to a precise chromosomal location, the physical position of
the sequence on the chromosome can be correlated with genetic map data.
to Such data are found in, for example, V. McKusick, Mendelian Inheritance in
Man (available on-line through Johns Hopkins University Welch Medical
Library). The relationship between genes and diseases that have been
mapped to the same chromosomal region are then identified through
linkage analysis (co-inheritance of physically adjacent genes). Precise
Is human chromosomal localisations for a genomic sequence (gene
fragment etc.) can be determined using Radiation Hybrid (RH) Mapping
(Walter, M. Spillett, D., Thomas, P., Weissenbach, J., and Goodfellow, P.,
(1994) A method for constructing radiation hybrid maps of whole
genomes, Nature Genetics 7, 22-28). A number of RH panels are
2o available from Research Genetics (Huntsville, AL, USA) e.g. the
GeneBridge4 RH panel (Hum Mol Genet 1996 Mar;S(3):339-46 A
radiation hybrid map of the human genome. Gyapay G, Schmitt K,
Fizames C, Jones H, Vega-Czarny N, Spillett D, Muselet D, Prud'Homme
JF, Dib C, Auffray C, Morissette J, Weissenbach J, Goodfellow PN). To
2s determine the chromosomal location of a gene using this panel, 93 PCRs
are performed using primers designed from the gene of interest on RH
DNAs. Each of these DNAs contains random human genomic fragments
maintained in a hamster background (human / hamster hybrid cell lines).
These PCRs result in 93 scores indicating the presence or absence of
;o the PCR product of the gene of interest. These scores are compared
with scores created using PCR products from genomic sequences of
known location. This comparison is conducted at
http://www.genome.wi.mit.edu/. The gene of the present invention maps
to human chromosome 20.
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 15 -
The polynucleotide sequences of the present invention are also valuable
tools for tissue expression studies. Such studies allow the determination of
expression patterns of polynucleotides of the present invention which may
give an indication as to the expression patterns of the encoded
s polypeptides in tissues, by detecting the mRNAs that encode them. The
techniques used are well known in the art and include in situ hydridisation
techniques to clones arrayed on a grid, such as cDNA microarray
hybridisation (Schena et al, Science, 270, 467-470, 1995 and Shalon et al,
Genome Res, 6, 639-645, 1996) and nucleotide amplification techniques
to such as PCR. A preferred method uses the TAQMAN (Trade mark)
technology available from Perkin Elmer. Results from these studies can
provide an indication of the normal function of the polypeptide in the
organism. In addition, comparative studies of the normal expression
pattern of mRNAs with that of mRNAs encoded by an alternative form of
is the same gene (for example, one having an alteration in polypeptide coding
potential or a regulatory mutation) can provide valuable insights into the
role
of the polypeptides of the present invention, or that of inappropriate
expression thereof in disease. Such inappropriate expression may be of a
temporal, spatial or simply quantitative nature.
2o The polypeptides of the present invention are expressed in trachea, larynx,
larynx carcinoma, palate, pharynx, endometrium, olfactory epithelium.
A further aspect of the present invention relates to antibodies. The
polypeptides of the invention or their fragments, or cells expressing them,
2s can be used as immunogens to produce antibodies that are immunospecific
for polypeptides of the present invention. The term "immunospecific"
means that the antibodies have substantially greater affinity for the
polypeptides of the invention than their affinity for other related
polypeptides
in the prior art.
;o Antibodies generated against polypeptides of the present invention may be
obtained by administering the polypeptides or epitope-bearing fragments, or
cells to an animal, preferably a non-human animal, using routine protocols.
For preparation of monoclonal antibodies, any technique which provides
antibodies produced by continuous cell line cultures can be used.
;s Examples include the hybridoma technique (Kohler, G. and Milstein, C.,
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 16 -
Nature (1975) 256:495-497), the trioma technique, the human B-cell
hybridoma technique (Kozbor et al., Immunology Today (1983) 4:72) and
the EBV-hybridoma technique (Cole et al., Monoclonal Antibodies and
Cancer Therapy, 77-96, Alan R. Liss, Inc., 1985).
s Techniques for the production of single chain antibodies, such as those
described in U.S. Patent No. 4,946,778, can also be adapted to produce
single chain antibodies to polypeptides of this invention. Also, transgenic
mice, or other organisms, including other mammals, may be used to
express humanized antibodies.
to The above-described antibodies may be employed to isolate or to identify
clones expressing the polypeptide or to purify the polypeptides by affinity
chromatography. Antibodies against polypeptides of the present invention
may also be employed to treat diseases of the invention, amongst others.
Is Polypeptides and polynucleotides of the present invention may also be
used as vaccines. Accordingly, in a further aspect, the present invention
relates to a method for inducing an immunological response in a mammal
that comprises inoculating the mammal with a polypeptide of the present
invention, adequate to produce antibody and/or T cell immune response,
2o including, for example, cytokine-producing T cells or cytotoxic T cells, to
protect said animal from disease, whether that disease is already
established within the individual or not. An immunological response in a
mammal may also be induced by a method comprises delivering a
polypeptide of the present invention via a vector directing expression of
2s the polynucleotide and coding for the polypeptide in vivo in order to
induce such an immunological response to produce antibody to protect
said animal from diseases of the invention. One way of administering the
vector is by accelerating it into the desired cells as a coating on particles
or otherwise. Such nucleic acid vector may comprise DNA, RNA, a
;o modified nucleic acid, or a DNA/RNA hybrid. For use a vaccine, a
polypeptide or a nucleic acid vector will be normally provided as a
vaccine formulation (composition). The formulation may further comprise
a suitable carrier. Since a polypeptide may be broken down in the
stomach, it is preferably administered parenterally (for instance,
;~ subcutaneous, intramuscular, intravenous, or intradermal injection).
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 17 -
Formulations suitable for parenteral administration include aqueous and
non-aqueous sterile injection solutions that may contain anti-oxidants,
buffers, bacteriostats and solutes that render the formulation instonic with
the blood of the recipient; and aqueous and non-aqueous sterile
s suspensions that may include suspending agents or thickening agents.
The formulations may be presented in unit-dose or multi-dose containers,
for example, sealed ampoules and vials and may be stored in a freeze-
dried condition requiring only the addition of the sterile liquid carrier
immediately prior to use. The vaccine formulation may also include
to adjuvant systems for enhancing the immunogenicity of the formulation,
such as oil-in water systems and other systems known in the art. The
dosage will depend on the specific activity of the vaccine and can be
readily determined by routine experimentation.
is Polypeptides of the present invention have one or more biological functions
that are of relevance in one or more disease states, in particular the
diseases of the invention hereinbefore mentioned. It is therefore useful to
to identify compounds that stimulate or inhibit the function or level of the
polypeptide. Accordingly, in a further aspect, the present invention
?o provides for a method of screening compounds to identify those that
stimulate or inhibit the function or level of the polypeptide. Such methods
identify agonists or antagonists that may be employed for therapeutic and
prophylactic purposes for such diseases of the invention as hereinbefore
mentioned. Compounds may be identified from a variety of sources, for
2s example, cells, cell-free preparations, chemical libraries, collections of
chemical compounds, and natural product mixtures. Such agonists or
antagonists so-identified may be natural or modified substrates, ligands,
receptors, enzymes, etc., as the case may be, of the polypeptide; a
structural or functional mimetic thereof (see Coligan et al., Current
~o Protocols in Immunology 1 (2):Chapter 5 (1991 )) or a small molecule.
The screening method may simply measure the binding of a candidate
compound to the polypeptide, or to cells or membranes bearing the
polypeptide, or a fusion protein thereof, by means of a label directly or
indirectly associated with the candidate compound. Alternatively, the
~s screening method may involve measuring or detecting (qualitatively or
quantitatively) the competitive binding of a candidate compound to the
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 18 -
polypeptide against a labeled competitor (e.g. agonist or antagonist).
Further, these screening methods may test whether the candidate
compound results in a signal generated by activation or inhibition of the
polypeptide, using detection systems appropriate to the cells bearing the
s polypeptide. Inhibitors of activation are generally assayed in the
presence of a known agonist and the effect on activation by the agonist
by the presence of the candidate compound is observed. Further, the
screening methods may simply comprise the steps of mixing a candidate
compound with a solution containing a polypeptide of the present
to invention, to form a mixture, measuring a New Lipid Binding Protein 2
activity in the mixture, and comparing the New Lipid Binding Protein 2
activity of the mixture to a control mixture which contains no candidate
compound.
Polypeptides of the present invention may be employed in conventional
is low capacity screening methods and also in high-throughput screening
(HTS) formats. Such HTS formats include not only the well-established
use of 96- and, more recently, 384-well micotiter plates but also emerging
methods such as the nanowell method described by Schullek et al, Anal
Biochem., 246, 20-29, (1997).
2o Fusion proteins, such as those made from Fc portion and New Lipid
Binding Protein 2 polypeptide, as hereinbefore described, can also be
used for high-throughput screening assays to identify antagonists for the
polypeptide of the present invention (see D. Bennett et al., J Mol
Recognition, 8:52-58 (1995); and K. Johanson et al., J Biol Chem,
2s 270(16):9459-9471 (1995)).
Screening techniques
The polynucleotides, polypeptides and antibodies to the polypeptide of the
~o present invention may also be used to configure screening methods for
detecting the effect of added compounds on the production of mRNA and
polypeptide in cells. For example, an ELISA assay may be constructed
for measuring secreted or cell associated levels of polypeptide using
monoclonal and polyclonal antibodies by standard methods known in the
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 19 -
art. This can be used to discover agents that may inhibit or enhance the
production of polypeptide (also called antagonist or agonist, respectively)
from suitably manipulated cells or tissues.
A polypeptide of the present invention may be used to identify membrane
s bound or soluble receptors, if any, through standard receptor binding
techniques known in the art. These include, but are not limited to, ligand
binding and crosslinking assays in which the polypeptide is labeled with a
radioactive isotope (for instance, X251), chemically modified (for instance,
biotinylated), or fused to a peptide sequence suitable for detection or
to purification, and incubated with a source of the receptor (cells, cell
membranes, cell supernatants, tissue extracts, bodily fluids). Other
methods include biophysical techniques such as surface plasmon
resonance and spectroscopy. These screening methods may also be
used to identify agonists and antagonists of the polypeptide that compete
is with the binding of the polypeptide to its receptors, if any. Standard
methods for conducting such assays are well understood in the art.
Examples of antagonists of polypeptides of the present invention include
antibodies or, in some cases, oligonucleotides or proteins that are closely
related to the ligands, substrates, receptors, enzymes, etc., as the case
?o may be, of the polypeptide, e.g., a fragment of the ligands, substrates,
receptors, enzymes, etc.; or a small molecule that bind to the polypeptide of
the present invention but do not elicit a response, so that the activity of
the
polypeptide is prevented.
Screening methods may also involve the use of transgenic technology
2s and New Lipid Binding Protein 2 gene. The art of constructing transgenic
animals is well established. For example, the New Lipid Binding Protein
2 gene may be introduced through microinjection into the male
pronucleus of fertilized oocytes, retroviral transfer into pre- or post-
implantation embryos, or injection of genetically modified, such as by
~o electroporation, embryonic stem cells into host blastocysts. Particularly
useful transgenic animals are so-called "knock-in" animals in which an
animal gene is replaced by the human equivalent within the genome of
that animal. Knock-in transgenic animals are useful in the drug discovery
process, for target validation, where the compound is specific for the
;5 human target. Other useful transgenic animals are so-called "knock-out"
animals in which the expression of the animal ortholog of a polypeptide of
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 20 -
the present invention and encoded by an endogenous DNA sequence in
a cell is partially or completely annulled. The gene knock-out may be
targeted to specific cells or tissues, may occur only in certain cells or
tissues as a consequence of the limitations of the technology, or may
s occur in all, or substantially all, cells in the animal. Transgenic animal
technology also offers a whole animal expression-cloning system in
which introduced genes are expressed to give large amounts of
polypeptides of the present invention
Screening kits for use in the above described methods form a further
to aspect of the present invention. Such screening kits comprise:
(a) a polypeptide of the present invention;
(b) a recombinant cell expressing a polypeptide of the present invention;
(c) a cell membrane expressing a polypeptide of the present invention; or
(d) an antibody to a polypeptide of the present invention;
Is which polypeptide is preferably that of SEQ ID N0:2.
It will be appreciated that in any such kit, (a), (b), (c) or (d) may comprise
a substantial component.
Glossary
2o The following definitions are provided to facilitate understanding of
certain
terms used frequently hereinbefore.
"Antibodies" as used herein includes polyclonal and monoclonal
antibodies, chimeric, single chain, and humanized antibodies, as well as
Fab fragments, including the products of an
2s Fab or other immunoglobulin expression library.
"Isolated" means altered "by the hand of man" from its natural state, i.e.,
if it occurs in nature, it has been changed or removed from its original
environment, or both. For example, a polynucleotide or a polypeptide
naturally present in a living organism is not "isolated," but the same
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 21 -
polynucleotide or polypeptide separated from the coexisting materials of
its natural state is "isolated", as the term is employed herein. Moreover,
a polynucleotide or polypeptide that is introduced into an organism by
transformation, genetic manipulation or by any other recombinant method
s is "isolated" even if it is still present in said organism, which organism
may be living or non-living.
"Polynucleotide" generally refers to any polyribonucleotide (RNA) or
polydeoxribonucleotide (DNA), which may be unmodified or modified
RNA or DNA. "Polynucleotides" include, without limitation, single- and
to double-stranded DNA, DNA that is a mixture of single- and double-
stranded regions, single- and double-stranded RNA, and RNA that is
mixture of single- and double-stranded regions, hybrid molecules
comprising DNA and RNA that may be single-stranded or, more typically,
double-stranded or a mixture of single- and double-stranded regions. In
Is addition, "polynucleotide" refers to triple-stranded regions comprising
RNA or DNA or both RNA and DNA. The term "polynucleotide" also
includes DNAs or RNAs containing one or more modified bases and
DNAs or RNAs with backbones modified for stability or for other reasons.
"Modified" bases include, for example, tritylated bases and unusual bases
2o such as inosine. A variety of modifications may be made to DNA and
RNA; thus, "polynucleotide" embraces chemically, enzymatically or
metabolically modified forms of polynucleotides as typically found in
nature, as well as the chemical forms of DNA and RNA characteristic of
viruses and cells. "Polynucleotide" also embraces relatively short
?s polynucleotides, often referred to as oligonucleotides.
"Polypeptide" refers to any polypeptide comprising two or more amino
acids joined to each other by peptide bonds or modified peptide bonds,
i.e., peptide isosteres. "Polypeptide" refers to both short chains,
commonly referred to as peptides, oligopeptides or oligomers, and to
~o longer chains, generally referred to as proteins. Polypeptides may
contain amino acids other than the 20 gene-encoded amino acids.
"Polypeptides" include amino acid sequences modified either by natural
processes, such as post-translational processing, or by chemical
modification techniques that are well known in the art. Such
~s modifications are well described in basic texts and in more detailed
monographs, as well as in a voluminous research literature.
Modifications may occur anywhere in a polypeptide, including the peptide
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 22 -
backbone, the amino acid side-chains and the amino or carboxyl termini.
It will be appreciated that the same type of modification may be present
to the same or varying degrees at several sites in a given polypeptide.
Also, a given polypeptide may contain many types of modifications.
s Polypeptides may be branched as a result of ubiquitination, and they may
be cyclic, with or without branching. Cyclic, branched and branched
cyclic polypeptides may result from post-translation natural processes or
may be made by synthetic methods. Modifications include acetylation,
acylation, ADP-ribosylation, amidation, biotinylation, covalent attachment
to of flavin, covalent attachment of a heme moiety, covalent attachment of a
nucleotide or nucleotide derivative. covalent attachment of a lipid or lipid
derivative, covalent attachment of phosphotidylinositol, cross-linking,
cyclization, disulfide bond formation, demethylation, formation of covalent
cross-links, formation of cystine, formation of pyroglutamate, formylation,
~s gamma-carboxylation, glycosylation, GPI anchor formation,
hydroxylation, iodination, methylation, myristoylation, oxidation,
proteolytic processing, phosphorylation, prenylation, racemization,
selenoylation, sulfation, transfer-RNA mediated addition of amino acids to
proteins such as arginylation, and ubiquitination (see, for instance,
2o Proteins - Structure and Molecular Properties, 2nd Ed., T. E. Creighton,
W. H. Freeman and Company, New York, 1993; Wold, F., Post-
translational Protein Modifications: Perspectives and Prospects, 1-12, in
Post-translational Covalent Modification of Proteins, B. C. Johnson, Ed.,
Academic Press, New York, 1983; Seifter et al., "Analysis for protein
2s modifications and nonprotein cofactors", Meth Enzymol, 182, 626-646,
1990, and Rattan et al., "Protein Synthesis: Post-translational
Modifications and Aging", Ann NY Acad Sci, 663, 48-62, 1992).
"Fragment" of a polypeptide sequence refers to a polypeptide sequence
that is shorter than the reference sequence but that retains essentially the
3o same biological function or activity as the reference polypeptide.
"Fragment" of a polynucleotide sequence refers to a polynucloetide
sequence that is shorter than the reference sequence of SEQ ID N0:1.
"Variant" refers to a polynucleotide or polypeptide that differs from a
reference polynucleotide or polypeptide, but retains the essential
3s properties thereof. A typical variant of a polynucleotide differs in
nucleotide sequence from the reference polynucleotide. Changes in the
nucleotide sequence of the variant may or may not alter the amino acid
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 23 -
sequence of a polypeptide encoded by the reference polynucleotide.
Nucleotide changes may result in amino acid substitutions, additions,
deletions, fusions and truncations in the polypeptide encoded by the
reference sequence, as discussed below. A typical variant of a
s polypeptide differs in amino acid sequence from the reference
polypeptide. Generally, alterations are limited so that the sequences of
the reference polypeptide and the variant are closely similar overall and,
in many regions, identical. A variant and reference polypeptide may differ
in amino acid sequence by one or more substitutions, insertions,
to deletions in any combination. A substituted or inserted amino acid
residue may or may not be one encoded by the genetic code. Typical
conservative substitutions include Gly, Ala; Val, Ile, Leu; Asp, Glu; Asn,
Gln;
Ser, Thr; Lys, Arg; and Phe and Tyr. A variant of a polynucleotide or
polypeptide may be naturally occurring such as an allele, or it may be a
is variant that is not known to occur naturally. Non-naturally occurring
variants of polynucleotides and polypeptides may be made by
mutagenesis techniques or by direct synthesis. Also included as variants
are polypeptides having one or more post-translational modifications, for
instance glycosylation, phosphorylation, methylation, ADP ribosylation
2o and the like. Embodiments include methylation of the N-terminal amino
acid, phosphorylations of serines and threonines and modification of C-
terminal glycines.
"Allele" refers to one of two or more alternative forms of a gene occuring
at a given locus in the genome.
2s "Polymorphism" refers to a variation in nucleotide sequence (and
encoded polypeptide sequence, if relevant) at a given position in the
genome within a population.
"Single Nucleotide Polymorphism" (SNP) refers to the occurence of
nucleotide variability at a single nucleotide position in the genome, within
~o a population. An SNP may occur within a gene or within intergenic
regions of the genome. SNPs can be assayed using Allele Specific
Amplification (ASA). For the process at least 3 primers are required. A
common primer is used in reverse complement to the polymorphism
being assayed. This common primer can be between 50 and 1500 bps
;s from the polymorphic base. The other two (or more) primers are identical
to each other except that the final 3' base wobbles to match one of the
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 24 -
two (or more) alleles that make up the polymorphism. Two (or more)
PCR reactions are then conducted on sample DNA, each using the
common primer and one of the Allele Specific Primers.
"Splice Variant" as used herein refers to cDNA molecules produced from
s RNA molecules initially transcribed from the same genomic DNA
sequence but which have undergone alternative RNA splicing.
Alternative RNA splicing occurs when a primary RNA transcript
undergoes splicing, generally for the removal of introns, which results in
the production of more than one mRNA molecule each of that may
to encode different amino acid sequences. The term splice variant also
refers to the proteins encoded by the above cDNA molecules.
"Identity" reflects a relationship between two or more polypeptide
sequences or two or more polynucleotide sequences, determined by
comparing the sequences. In general, identity refers to an exact
is nucleotide to nucleotide or amino acid to amino acid correspondence of
the two polynucleotide or two polypeptide sequences, respectively, over
the length of the sequences being compared.
"% Identity" - For sequences where there is not an exact
correspondence, a "% identity" may be determined. In general, the two
2o sequences to be compared are aligned to give a maximum correlation
between the sequences. This may include inserting "gaps" in either one
or both sequences, to enhance the degree of alignment. A % identity
may be determined over the whole length of each of the sequences being
compared (so-called global alignment), that is particularly suitable for
2s sequences of the same or very similar length, or over shorter, defined
lengths (so-called local alignment), that is more suitable for sequences of
unequal length.
"Similarity" is a further, more sophisticated measure of the relationship
between two polypeptide sequences. In general, "similarity" means a
~o comparison between the amino acids of two polypeptide chains, on a
residue by residue basis, taking into account not only exact
correspondences between a between pairs of residues, one from each of
the sequences being compared (as for identity) but also, where there is
not an exact correspondence, whether, on an evolutionary basis, one
;s residue is a likely substitute for the other. This likelihood has an
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 25 -
associated "score" from which the "% similarity" of the two sequences
can then be determined.
Methods for comparing the identity and similarity of two or more
sequences are well known in the art. Thus for instance, programs
s available in the Wisconsin Sequence Analysis Package, version 9.1
(Devereux J et al, Nucleic Acids Res, 12, 387-395, 1984, available from
Genetics Computer Group, Madison, Wisconsin, USA), for example the
programs BESTFIT and GAP, may be used to determine the % identity
between two polynucleotides and the % identity and the % similarity
io between two polypeptide sequences. BESTFIT uses the "local
homology" algorithm of Smith and Waterman (J Mol Biol, 147,195-197,
1981, Advances in Applied Mathematics, 2, 482-489, 1981 ) and finds the
best single region of similarity between two sequences. BESTFIT is
more suited to comparing two polynucleotide or two polypeptide
is sequences that are dissimilar in length, the program assuming that the
shorter sequence represents a portion of the longer. In comparison, GAP
aligns two sequences, finding a "maximum similarity", according to the
algorithm of Neddleman and Wunsch (J Mol Biol, 48, 443-453, 1970).
GAP is more suited to comparing sequences that are approximately the
2o same length and an alignment is expected over the entire length.
Preferably, the parameters "Gap Weight" and "Length Weight" used in
each program are 50 and 3, for polynucleotide sequences and 12 and 4
for polypeptide sequences, respectively. Preferably, % identities and
similarities are determined when the two sequences being compared are
2s optimally aligned.
Other programs for determining identity and/or similarity between
sequences are also known in the art, for instance the BLAST family of
programs (Altschul S F et al, J Mol Biol, 215, 403-410, 1990, Altschul S F
et al, Nucleic Acids Res., 25:389-3402, 1997, available from the National
~o Center for Biotechnology Information (NCBI), Bethesda, Maryland, USA
and accessible through the home page of the NCBI at
www.ncbi.nlm.nih.gov) and FASTA (Pearson W R, Methods in
Enzymology, 183, 63-99, 1990; Pearson W R and Lipman D J, Proc Nat
Acad Sci USA, 85, 2444-2448,1988, available as part of the Wisconsin
~s Sequence Analysis Package).
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 26 -
Preferably, the BLOSUM62 amino acid substitution matrix (Henikoff S
and Henikoff J G, Proc. Nat. Acad Sci. USA, 89, 10915-10919, 1992) is
used in polypeptide sequence comparisons including where nucleotide
sequences are first translated into amino acid sequences before
s comparison.
Preferably, the program BESTFIT is used to determine the % identity of a
query polynucleotide or a polypeptide sequence with respect to a
reference polynucleotide or a polypeptide sequence, the query and the
reference sequence being optimally aligned and the parameters of the
to program set at the default value, as hereinbefore described.
"Identity Index" is a measure of sequence relatedness which may be
used to compare a candidate sequence (polynucleotide or polypeptide)
and a reference sequence. Thus, for instance, a candidate
polynucleotide sequence having, for example, an Identity Index of 0.95
is compared to a reference polynucleotide sequence is identical to the
reference sequence except that the candidate polynucleotide sequence
may include on average up to five differences per each 100 nucleotides
of the reference sequence. Such differences are selected from the group
consisting of at least one nucleotide deletion, substitution, including
2o transition and transversion, or insertion. These differences may occur at
the 5' or 3' terminal positions of the reference polynucleotide sequence or
anywhere between these terminal positions, interspersed either
individually among the nucleotides in the reference sequence or in one or
more contiguous groups within the reference sequence. In other words,
?s to obtain a polynucleotide sequence having an Identity Index of 0.95
compared to a reference polynucleotide sequence, an average of up to 5
in every 100 of the nucleotides of the in the reference sequence may be
deleted, substituted or inserted, or any combination thereof, as
hereinbefore described. The same applies mutatis mutandis for other
~o values of the Identity Index, for instance 0.96, 0.97, 0.98 and 0.99.
Similarly, for a polypeptide, a candidate polypeptide sequence having, for
example, an Identity Index of 0.95 compared to a reference polypeptide
sequence is identical to the reference sequence except that the
polypeptide sequence may include an average of up to five differences
;s per each 100 amino acids of the reference sequence. Such differences
are selected from the group consisting of at least one amino acid
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 27 -
deletion, substitution, including conservative and non-conservative
substitution, or insertion. These differences may occur at the amino- or
carboxy-terminal positions of the reference polypeptide sequence or
anywhere between these terminal positions, interspersed either
s individually among the amino acids in the reference sequence or in one
or more contiguous groups within the reference sequence. In other
words, to obtain a polypeptide sequence having an Identity Index of 0.95
compared to a reference polypeptide sequence, an average of up to 5 in
every 100 of the amino acids in the reference sequence may be deleted,
to substituted or inserted, or any combination thereof, as hereinbefore
described. The same applies mutatis mutandis for other values of the
Identity Index, for instance 0.96, 0.97, 0.98 and 0.99.
The relationship between the number of nucleotide or amino acid
differences and the Identity Index may be expressed in the following
is equation:
na ~ xa - ~xa ' I),
in which:
na is the number of nucleotide or amino acid differences,
xa is the total number of nucleotides or amino acids in SEQ ID N0:1 or
2o SEQ ID N0:2, respectively,
I is the Identity Index ,
~ is the symbol for the multiplication operator, and
in which any non-integer product of xa and I is rounded down to the
nearest integer prior to subtracting it from xa.
2s "Homolog" is a generic term used in the art to indicate a polynucleotide or
polypeptide sequence possessing a high degree of sequence relatedness
to a reference sequence. Such relatedness may be auantified by
determining the degree of identity and/or similarity between the two
sequences as hereinbefore defined. Falling within this generic term are
3o the terms "ortholog", and "paralog". "Ortholog" refers to a polynucleotide
or polypeptide that is the functional equivalent of the polynucleotide or
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 28 -
polypeptide in another species. "Paralog" refers to a polynucleotideor
polypeptide that within the same species which is functionally similar.
"Fusion protein" refers to a protein encoded by two, unrelated, fused
genes or fragments thereof. Examples have been disclosed in US
s 5541087, 5726044. In the case of Fc-NLIBP2, employing an
immunoglobulin Fc region as a part of a fusion protein is advantageous
for performing the functional expression of Fc-NLIBP2 or fragments of
NLIBP2, to improve pharmacokinetic properties of such a fusion protein
when used for therapy and to generate a dimeric NLIBP2. The Fc-
to NLIBP2 DNA construct comprises in 5' to 3' direction, a secretion
cassette, i.e. a signal sequence that triggers export from a mammalian
cell, DNA encoding an immunoglobulin Fc region fragment, as a fusion
partner, and a DNA encoding NLIBP2 or fragments thereof. In some uses
it would be desirable to be able to alter the intrinsic functional properties
Is (complement binding, Fc-Receptor binding) by mutating the functional Fc
sides while leaving the rest of the fusion protein untouched or delete the
Fc part completely after expression.
All publications and references, including but not limited to patents and
patent applications, cited in this specification are herein incorporated by
2o reference in their entirety as if each individual publication or reference
were specifically and individually indicated to be incorporated by
reference herein as being fully set forth. Any patent application to which
this application claims priority is also incorporated by reference herein in
its entirety in the manner described above for publications and
2s references.
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 1 -
SEQUENCE LISTING
<110> Merck Patent GmbH
<120> New lipid binding protein 2
<130> NLI3P2MGWS
<140>
<141>
<160> 2
<170> Patentln Ver. 2.1
<210> 1
<211> 1365
<212> DNA
<213> Homo sa~_iens
<220>
<221> CDS
<222> (1)..;1365)
<400> 1
atg ctg cgg atc ctg tgc ctg gca ctc tgc agc ctg ctg act ggc acg 48
Met Leu Arg I1e Leu Cys Leu Ala Leu Cys Ser Leu Leu Thr Gly Thr
1 5 1C 15
cga get gac cct ggg gca ctg ctg cgg ttg ggc atg gac atc atg aac 96
Arg Ala Asp Pro Gly Ala Leu Leu Arg Leu Gly Met Asp Ile Met Asn
20 25 30
cgt gag gtc cag agc gcc atg gat gag agt cat atc ctg gag aag atg 144
Arg Giu Val Gln Ser Ala Met Asp Glu Ser His Ile Leu Glu Lys Met
35 40 45
gca gcc gag gca ggc aag aaa cag cca gig atg aaa cct atc aag ggc 192
Ala Aia Glu Ala Gly Lys Lys Gln Pro Gly Met Lys Pro Ile Lys Gly
50 55 60
atc acc aat ttg aag gtg aag gat gtc cag ctg ccc gtc atc aca ctg 240
Ile Thr Asn Leu Lys Val Lys Asp Val Gln Leu Pro Val Ile Thr Leu
65 70 75 80
aac ttt gta cct gga gtg ggc atc ttc caa tgt gtg tcc aca ggc atg 288
Asn Phe Val Pro Giy Vai Gly Ile Phe Gln Cys Val Ser Thr Giy Met
85 90 95
acc gtc act ggc aag agc ttc atg gga ggg aac atg gag atc atc gtg 336
Thr Val Thr Gly Lys Ser Phe Met Gly Gly Asn Met Glu Ile Ile Val
100 105 110
gcc ctg aac atc aca gcc acc aac cgg ctt ctg cgg gat gag gag aca 384
Ala Leu Asn Ile Thr Ala Thr Asn Arg Leu Leu Arg Asp Glu Glu Thr
115 120 125
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 2 -
ggc ctc cccgtgttc aagagtgag ggctg_gag gtcatcctg g~caat 432
Gly Leu ProValPhe LysSerGlu GlyCysGlu ValIleLeu VaiAsn
130 135 140
gtg aag actaacctg cctagcaac atgctcccc aagatggtc aacaag 480
Val Lys ThrAsnLeu ProSerAsr._~!etLeuPro LysMetVal AsnLys
145 150 155 160
ttc ctg gacagcacc ctgcacaaa gtcctccct gggctgatg tgtccc 528
Leu AspSerThr LeuHisLys ValLeuPro GlyLeuMet CysPro
Phe
165 170 175
gcc atc gatgcagtc ctggtgtat gtgaacagg aagtggacc aacctc 576
Ala Ile AspAlaVal LeuValTyr -iaiAsnArg LysTrpThr AsnLeu
180 '~85 190
agt gac cccatgcct gtgggccag atgggcacc gncaaatat gttctg 624
Ser Asp ProMetPro ValGlyGln MetGlyThr ValLysTyr 'JaiLeu
195 20G 205
atg tcc gca cca gcc acc aca gcc agc tac atc caa ctg gac ttc agt '072
Met Ser Ala Pro Ala Thr Thr Ala Ser Tyr Ile Gln Leu Asp Phe Ser
210 215 220
eet gtg gtg cag cag caa aag ggc aaa ace atc aag ett get gat gcc 720
Pro Val Val Gln Gln G1n Lys Gly Lys Thr I1e Lys Leu Ala Asp Ala
225 230 235 240
ggg gag gcc ctc acg ttc cct gag ggt tat gcc aaa ggc tcg tcg cag 768
Gly Glu Ala Leu Thr Phe Pro Glu Gly Tyr Ala Lys Gly Ser Ser Gln
245 250 255
ctg ctg ctc cca gcc acc ttc ctc rct gca gag ctt gcc ctt ctg cag 816
Leu Leu Leu Pro Ala Thr Phe Leu Ser Ala Glu Leu Ala Leu Leu Gln
260 265 270
aag tcc ttt cat gtg aat atc cag gat aca atg att ggt gag ctg ccc 864
Lys Ser Phe His Val Asn Ile Gln Asp Thr Met Ile Gly Glu Leu Pro
275 280 285
cca caa acc acc aag acc ctg get cgc ttc att cct gaa gtg get gta 912
Pro Gln Thr Thr Lys Thr Leu Ala Arg Phe Ile Pro Glu Val Ala Val
290 295 300
get tat ccc aag tca aag ccc ttg acg acc cag atc aag ata aag aag 960
Ala Tyr Pro Lys Ser Lys Pro Leu Thr Thr Gln Ile Lys Ile Lys Lys
305 310 315 320
cct ccc aag gtc act atg aag aca ggc aag agc ctg ctg cac ctc cac 1008
Pro Pro Lys Val Thr Met Lys Thr Gly Lys Ser Leu Leu His Leu His
325 330 335
age ace etg gag atg ttc gca get cgg tgg egg age aag get cca atg 1056
Ser Thr Leu G1u Met Phe Ala Ala Arg Trp Arg Ser Lys Ala Pro Met
340 345 350
tcc ctc ttt ctc cta gaa gtg cac ttc aat ctg aag gtc cag tac tca 1104
Ser Leu Phe Leu Leu Glu Vai His Phe Asn Leu Lys Val Gln Tyr Ser
355 360 365
gtg cat gag aac cag ctg cag atg gcc act tct ttg gac aga tta ctg 1152
CA 02406087 2002-10-16
WO 01/79493 PCT/EPO1/04298
- 3 -
Val His Glu Asn G1n Leu Gln Met Ala Thr Ser Leu Asp Arg Lei Leu
370 375 380
agc ttg tcc cgg aag tcc tca tcg att ggc aac ttc aat gag agg gaa 1200
Ser Leu Ser Arg Lys Ser Ser Ser Ile Gly Asn Phe Asn Glu Arg Glu
385 390 395 400
tta act ggc ttc atc acc agc tat ctc gaa gaa gcc tac atc cca gtt 'x.248
Leu Thr Gly Phe Ile Thr Ser Tyr Leu Glu Glu Ala Tyr Iie ~_~ Val
405 410 4i5
gtc aat gat gtg ctt caa gtg ggg ctc cca ctc ccg gac ttt ctg gcc 1296
Val Asn Asp Val Leu Gln Val G1y Leu Pro Leu Pro Asp Phe Leu Aia
420 425 430
atg aat tac aac etg get gag ctg gac ata gta gag ett ggg ggc ate 1344
Met Asn Tyr Asn Leu Ala Glu Leu Asp I1e Val Giu Leu Giy G~~y Ile
435 440 445
atg gaa cct gcc gac ata tga 1365
Met Glu Pro Ala Asp_ Ile
450 455
<210> 2
<211> 454
<212> PRT
<213> Homo sapiens
<400> 2
Met Leu Arg I1e Leu Cys Leu Ala Leu Cys Ser Leu Leu Thr Gly Thr
1 5 10 15
Arg Ala Asp Pro Gly Ala Leu Leu Arg Leu G1y Met Asp Ile Met Asn
20 25 30
Arg Glu Val G1n Ser Ala Met Asp Glu Ser His Ile Leu Glu Lys Met
35 40 45
Ala Ala Glu Ala Gly Lys Lys Gln Pro Gly Met Lys Pro Ile L, Gly
50 55 60
Ile Thr Asn Leu Lys Val Lys Asp Val Gln Leu Pro Val Ile T::r Leu
65 70 75 80
Asn Phe Val Pro Gly Val Gly Ile Phe G1n Cys Val Ser Thr G~yr Met
85 90 95
Thr Val Thr Gly Lys Ser Phe Met Gly Gly Asn Met Glu Ile Ile Val
100 105 110
Ala Leu Asn Ile Thr Ala Thr Asn Arg Leu Leu Arg Asp Glu ~~'~u Thr
115 120 125
Gly Leu Pro Val Phe Lys Ser Glu Gly Cys Glu Val Ile Leu Vai Asn
130 135 140
Val Lys Thr Asn Leu Pro Ser Asn Met Leu Pro Lys Met Val Asn Ly
145 150 155 16~
Phe Leu Asp Ser Thr Leu His Lys Val Leu Pro Gly Leu Met Cys Pro
165 170 175
Ala Ile Asp Ala Va1 Leu Val Tyr Val Asn Arg Lys Trp Thr Asn Leu
180 185 190
Ser Asp Pro Met Pro Val Gly Gln Met Gly Thr Val Lys Tyr Val Leu
195 200 205
Met Ser Ala Pro Ala Thr Thr Ala Ser Tyr Ile Gln Leu Asp Phe Ser
210 215 220
Pro Val Val Gln Gln Gln Lys G1y Lys Thr I1e Lys Leu Ala Asp Ala
225 230 235 240
Gly Glu Ala Leu Thr Phe Pro G1u Gly Tyr Ala Lys Gly Ser Ser Gln
CA 02406087 2002-10-16
WO 01/79493 PCT/EPOi/04298
- 4 -
245 250 255
Leu Leu Leu Pro Ala ~_.~ Phe Leu Ser Ala Glu Leu Ala Leu Leu Gln
260 265 270
Lys Ser Phe His 'al Asn Ile Gln Asp Thr Met Ile Gly Glu Leu Pro
275 280 285
Pro Gln Thr Thr ~ys Thr Leu Ala Arg Phe Ile Pro Glu Val Ala Va1
290 295 300
Ala Tyr Pro Lys Ser Ls Pro Leu Thr Thr Gln Ile Lys Ile Lys Lys
305 .=0 315 320
Pro Pro Lys Va'~ '.'hr Met Lys Thr Gly Lys Ser Leu Leu His Leu His
325 330 335
Ser Thr Leu Glva _vet =:~:e Ala Ala Arg Trp Arg Ser Lys Ala Pro Met
34C 345 350
Ser Leu Phe Lea I:eu 3-a 'Jal His Phe Asn Leu Lys Val Gln Tyr Ser
1~ 355 360 365
Val His Glu Asn Gin Leu Gln Met Ala Thr Ser Leu Asp Arg Leu Leu
370 375 380
Ser Leu Ser Arg Lys S2r Ser Ser Ile Gly Asn Phe Asn G1u Arg Glu
385 390 395 400
?0 Leu Thr Gly Phe ~le '='~:r Ser Tyr Leu Glu Glu A1a Tyr Ile Pro Val
-'_05 410 415
Val Asn Asp Val Leu ,~_n Val Gly Leu Pro Leu Pro Asp Phe Leu Ala
42C 425 430
Met Asn Tyr Asn Leu A=a Glu Leu Asp Ile Val Glu Leu Gly Gly Ile
25 435 440 445
Met Glu Pro Ala Asp I-'~e
450
