Note: Descriptions are shown in the official language in which they were submitted.
CA 02712809 2010-08-20
1
KCNQ2 and KCNQ3 - POTASSIUM CHANNEL GENES WHICH ARE MUTATED IN BENIGN
FAMILIAL NEONATAL CONVULSIONS (BFNC) AND OTHER EPILEPSIES
BACKGROUND OF THE INVENTION
Epileptic disorders affect about 20 to 40 million people worldwide.
Generalized idiopathic
epilepsies (IGE) cause 40% of all epileptic disorders and commonly have a
genetic basis (Plouin,
1994). Most of the IGEs that are inherited are complex, non-monogenic
diseases. One type of IGE
is Benign Familial Neonatal Convulsions (BFNC), a dominantly inherited
disorder of newborns
(Ronen et al., 1993; Hauser and Kurland, 1975). BFNC (OMIM 121200) is an
autosomal
dominantly inherited epilepsy of the newborn infant. This idiopathic,
generalized epilepsy typically
has an onset of seizures on day two to four of life. Spontaneous remission of
the seizures occurs
between two to fifteen weeks (Ronen et al., 1993; Plouin, 1994; Hauser and
Kurland, 1975).
Seizures typically start with a tonic posture, ocular symptoms and other
autonomic features which
then often progress to clonic movements and motor automatisms. These neonates
thrive normally
between the seizures, and their neurologic examinations and later development
indicate normal brain
functioning (Ronen et al., 1993; Plouin, 1994; Hauser and Kurland, 1975).
However, in spite of
normal neurologic development, seizures recur later in life in approximately
16% of BFNC cases
compared with a 2% cumulative lifetime risk of epilepsy in the general
population (Ronen et al.,
1993; Plouin, 1994; Hauser and Kurland, 1975).
Genetic heterogeneity of BFNC has been observed (Ryan etal., 1991). Two loci,
EBN1 and
EBN2, have been mapped by linkage analysis to chromosome 20q13 (Leppert etal.,
1989; Malafosse
et al., 1992) and chromosome 8q24 (Lewis et al., 1993; Steinlein et al.,
1995), respectively.
The nomenclature of the genes of this invention as well as related genes has
changed over
time. Two of the genes of this invention from humans are now referred to as
KCNQ2 and KCNQ3.
These had originally been named KVEBN1 and KVEBN2, respectively. The two sets
of names are
equivalent and can be used interchangeably, but the accepted nomenclature is
now KCNQ2 and
KCNQ3 and these names will be used herein. Also, the related gene KCNQ1 had
originally been
called KVLQT1 in the literature, but again the accepted name now is KCNQ1 and
this name will be
used herein.
Linkage analysis in a large kindred demonstrated that a gene, herein called
KCNQ2,
responsible for BFNC maps to chromosome 20q13.3 close to the markers D20S20
and D20S19
(Leppert et al., 1989). Following the initial report, two centers confirmed
linkage of BFNC to the
CA 02712809 2010-08-20
2
same two genetic markers on chromosome 20, termed the EBN1 (epilepsy benign
neonatal type 1)
locus (Ryan et al., 1991; Malafosse et al., 1992; Steinlein et al., 1992). A
more distal marker,
D20S24, shows complete co-segregation with the BFNC phenotype in chromosome 20
linked
families. Finding a distal flanking marker for the BFNC locus has not been
successful probably
because of its proximity to the telomere. This telomeric region is
characterized by a high
recombination rate between markers when compared to the physical distance
(Steinlein et al., 1992).
In fact, Steinlein et al. have demonstrated that the three markers D20S19,
D20S20 and D20S24 are
contained on the same 450 Mb Mlu I restriction fragment (Steinlein et al.,
1992). All of the families
in the present study used to find and study KCNQ2 show linkage to chromosome
20q markers with
LOD scores of greater than 3.0 or have probands with clinical manifestations
consistent with BFNC
(Leppert et al., 1993). Each subject and control signed a Consent for
Participation in these studies
approved by the Institutional Review Board for Human Subject Research at their
home institution.
To find a gene responsible for BFNC, we narrowed a BFNC region with a sub-
microscopic deletion
in a single family, identified candidate cDNAs in this deletion, and then
searched for mutations in
other BFNC families. The gene has been identified and sequenced. Several
distinct mutations have
been found in this gene. These include a large deletion, three missense
mutations, three frameshift
mutations, two nonsense mutations and one splice site mutation. One of these
mutations is
associated with rolandic epilepsy as described in the Examples below.
A second chromosomal locus, EBN2, has also been identified for BFNC. Lewis et
al. (1993)
demonstrated linkage to markers on chromosome 8q24 in a single Hispanic family
affected with
BFNC. Evidence for this second locus was also reported in a Caucasian pedigree
(Steinlein et al.,
1995). The gene, herein called KCNQ3, responsible for EBN2 was mapped to
chromosome 8,
between markers D8S256 and D8S284 on a radiation hybrid map (Lewis et al.,
1995). KCNQ3 has
been identified as set out in the examples of the instant disclosure. KCNQ3
was screened for
mutations in the large BFNC family previously linked to chromosome 8q24 in the
same marker
interval (Ryan et al., 1991; Lewis et al., 1993). A missense mutation was
found in the critical pore
region in perfect cosegregation with the BFNC phenotype. The same conserved
amino acid is also
mutated in KCNQ1 in an LQT patient (Wang et al., 1996). Furthermore, the
segment of mouse
chromosome 15 that harbors the stargazer (stg) locus (Noebels et al., 1990;
Letts et al., 1997) is
homologous to the human 8q24 region and the stg phenotype is close to a common
form of IGE, the
absence epilepsy. KCNQ2, KCNQ3 and other undiscovered genes of the same family
of IC channels
are strong candidates for other, more common IGEs. One individual with
juvenile myoclonic
CA 02712809 2010-08-20
,
3
epilepsy has been found who has a mutation in an alternative exon of KCNQ3 as
shown in the
Examples below.
IGEs include many different types of seizures. Common IGEs include generalized
tonic-
clonic seizure (GTCS), absence epilepsy of childhood (AEC), juvenile absence
epilepsy (JAE) and
juvenile myoclonic epilepsy (JME). Reutens and Berkovic (1995) have shown that
the boundaries
between the different IGE syndromes are indistinct and suggest that
neurobiological and possibly
genetic relationships exist between these syndromes. Interestingly, using non-
parametric linkage
methods, Zara et al. (1995) obtained evidence for involvement of an epilepsy
locus at chromosome
8q24 in a panel of families with multiple cases of IGEs. Furthermore, in a
population study,
Steinlein et al. (1997) recently described a weak allelic association at the
CHRNA4 locus, on
chromosome 20q13.3, physically close to KCNQ2, in a group of unrelated
patients with multiple
forms of IGEs. Finally, an epileptic mutant mouse stargazer (stg) (Noebels et
al., 1990) is a genetic
model of spike wave epilepsy. This is a recessive mutation and the phenotype
is related to a
common form of human IGE, the absence epilepsy. Stg has been mapped on mouse
chromosome 15
in a region homologous to the human 8q24 region. Screening the mouse homolog
of KCNQ3 for
mutations in an affected mouse will assess the hypothesis that the same gene
is responsible for both
BFNC and Stargazer phenotypes.
The present invention is directed to both KCNQ2 and KCNQ3 and their gene
products,
mutations in the genes, the mutated genes, probes for the wild-type and
mutated genes, and to a
process for the diagnosis and prevention of BFNC. Each of the genes encodes a
potassium channel
protein. The instant work shows that some families with BFNC have mutations in
either KCNQ2 or
KCNQ3. BFNC is diagnosed in accordance with the present invention by analyzing
the DNA
sequence of the KCNQ2 and/or KCNQ3 gene of an individual to be tested and
comparing the
respective DNA sequence to the known DNA sequence of a normal KCNQ2 and/or
KCNQ3 gene.
Alternatively, the KCNQ2 gene and/or KCNQ3 gene of an individual to be tested
can be screened for
mutations which cause BFNC. Prediction of BFNC will enable practitioners to
prevent this disorder
using existing medical therapy. Furthermore, a mutation in KCNQ2 has been
found which is
associated with rolandic epilepsy and a mutation in KCNQ3 has been found which
is associated with
JME. These two forms of epilepsy may also be diagnosed in accord with the
invention.
Mouse genes homologous to the human KCNQ2 and KCNQ3 have also been found and
sequenced and the sequences are disclosed. The mouse KCNQ2 gene has been only
partially
CA 02712809 2010-08-20
'
4
isolated and sequenced (shown as SEQ ID NO:88), the 3' end not yet having been
found. The
complete mouse KCNQ3 gene has been isolated and sequenced (shown as SEQ ID
NO:90).
The publications and other materials used herein to illuminate the background
of the
invention or provide additional details respecting the practice are
respectively grouped in the
appended List of References.
SUMMARY OF THE INVENTION
The present invention demonstrates a molecular basis of Benign Familial
Neonatal
Convulsions (BFNC) as well as for rolandic epilepsy and juvenile myoclonic
epilepsy. More
specifically, the present invention has determined that molecular variants of
either the KCNQ2 gene
or KCNQ3 gene cause or are involved in the pathogenesis of these three forms
of epilepsy.
Genotypic analyses show that KCNQ2 is linked to BFNC in ten unrelated families
and KCNQ3 is
linked to BFNC in one other family. Furthermore, one mutation in the KCNQ2
gene in two
individuals of one family has been associated with rolandic epilepsy and one
individual with a
mutation in KCNQ3 has been diagnosed with juvenile myoclonic epilepsy.
Analysis of the KCNQ2
and KCNQ3 genes will provide an early diagnosis of subjects with BFNC,
rolandic epilepsy or JME.
The diagnostic method comprises analyzing the DNA sequence of the KCNQ2 and/or
the KCNQ3
gene of an individual to be tested and comparing it with the DNA sequence of
the native, non-
variant gene. In a second embodiment, the KCNQ2 and/or KCNQ3 gene of an
individual to be
tested is screened for mutations which cause BFNC, rolandic epilepsy or JME.
The ability to predict
these epilepsies will enable physicians to prevent the disease with medical
therapy such as drugs
which directly or indirectly modulate K+ ion channels.
The invention shows that various genetic defects of a potassium channel are
responsible for
the human idiopathic epilepsy of BFNC, rolandic epilepsy and/or JME. This
finding adds to the
growing list of channelopathies in humans (Ptacek, 1997). Importantly, this
result suggests that
drugs which directly or indirectly modulate K+ ion channels will be helpful in
the treatment of
seizure disorders.
BRIEF DESCRIPTION OF THE FIGURES
The file of this patent contains at least one drawing executed in color.
Copies of this patent
with color drawing(s) will be provided by the Patent and Trademark Office upon
request and
payment of the necessary fee.
CA 02712809 2013-07-19
Figure 1. Southern blot of kindred 1547 (showing 4 generations listed as I,
II, III and IV)
genomic DNA cut with Taql and probed with the VNTR marker D20524 showing a
null allele in
affected individuals. Line A shows genotype misinheritances shown in boxes;
line B shows
corrected genotypes. The AN@ indicates non-penetrant individuals.
5 Figures 2A-C. Metaphase spreads of cell lines from affected individuals
of kindred 1547
probed with P1-K09-7 (Figure 2C) and P1 -K09-6b (Figure 2B) genomic P1 clones
and the 12 kb
D20S24 RFLP marker (Figure 2A) demonstrating a deletion of D20524.
Figures 3A and 3B. Amino acid alignment between human members (KCNQ2, KCNQ3
and
KCNQ1) and the C. elegans homologue (nKQT1) of the KQT-like family. The six
transmembrane
domains and the pore are indicated by a solid line located above the
corresponding sequence. The
conserved charged amino acids in the transmembrane domains are highlighted in
gray. The
sequence of KCNQ2 is SEQ ID NO:2, the sequence of KCNQ3 is SEQ ID NO:7, the
sequence of
nKQT1 is SEQ ID NO:3 and the sequence of KCNQ1 is SEQ ID NO:4.
Figure 4. Figure 4 shows a three generation pedigree with BFNC linked to
chromosome 20.
BFNC individuals are depicted by filled in black circles and squares. The data
is from kindred 1504
which shows variants in the KCNQ2 pores. The lower portion of the figure shows
the cosegregation
of the variant form which is present only in affected individuals. Sequence
analysis revealed the
existence of a two base pair insertion in affected individuals showing the
upper two (variant) bands.
Figure 5. Radiation Hybrid Mapping of the KCNQ3 locus. Interpair LOD scores
are given
above the center line and distance between marker pairs, in cR5000, is shown
below. The odds
against inversion for adjacent loci is also given for each marker pair.
Figure 6. Figure 6 shows a three generation pedigree with BFNC linked to
chromosome 8.
BFNC individuals are depicted by filled in black circles and squares. The non-
penetrant individual
111-8 is indicated by the symbol NP. The lower portion of the figure shows the
co-segregation of the
187 bp SSCP variant, present only in affected and non-penetrant individuals
(arrow).
Figures 7A-0. Intron/exon sequence is shown for KCNQ2. Exon sequence is shown
in bold
and primer sequence is in italics. The primer sequences are found in Table 4.
The sequences are
SEQ ID NOs:100-114.
Figures 8A-0. Intron/exon sequence is shown for KCNQ3. Exon sequence is shown
uppercase and intron is shown lowercase and primer sequences are underlined.
The primer
sequences are found in Table 5. The sequences are SEQ ID NOs:115-129. Figure
81 shows the
CA 02712809 2010-08-20
6
alternatively spliced exon found in a JME patient. Figure 8N shows an AN@ in
the 3' intron region.
This AN@ stands for Alu repeats which are found in this region.
BRIEF DESCRIPTION OF THE SEQUENCE LISTING
SEQ ID NO:1 is the cDNA sequence for KCNQ2.
SEQ ID NO:2 is the amino acid sequence for KCNQ2.
SEQ ID NO:3 is the amino acid sequence for nKQT1.
SEQ ID NO:4 is the amino acid sequence for KCNQ1
SEQ ID NO:5 is nucleotide sequence at the intron/exon junction of the 3' end
of the intron
interrupting the two exons which encode amino acid 544 of KCNQ2.
SEQ ID NO:6 is the cDNA sequence for KCNQ3.
SEQ ID NO:7 is the amino acid sequence for KCNQ3.
SEQ ID NOs:8-9 are primers used for somatic cell hybrid panel genotyping
(Example 7).
SEQ ID NOs:10-11 are primers used for genotyping a chromosome 8 radiation
hybrid panel
(Example 8).
SEQ ID NOs:12-17 are primers used to perform RACE to obtain full length cDNA
(Example 9).
SEQ ID NOs:18-19 are primers used to prepare a PCR fragment which identified
an SSCP variant
for KCNQ3.
SEQ ID NOs:20-21 are hypothetical nucleic acid sequences to demonstrate
calculation of percent
homology between two nucleic acids.
SEQ ID NOs:22-53 are primers for amplifying portions of KCNQ2.
SEQ ID NOs:54-87 are primers for amplifying portions of KCNQ3.
SEQ ID NO:88 is a partial mouse KCNQ2.
SEQ ID NO:89 is a partial mouse KCNQ2 encoded by SEQ ID NO:88.
SEQ ID NO:90 is a mouse KCNQ3.
SEQ ID NO:91 is the mouse KCNQ3 encoded by SEQ ID NO:90.
SEQ ID NO:92 is an alternative exon found in KCNQ3.
SEQ ID NOs:93-94 are primers based on mouse sequence to amplify 5' end of
human KCNQ3.
SEQ ID NO:95 is a mutated human KCNQ2 with a GGGCC insertion after nucleotide
2736.
SEQ ID NO:96 is a mutated human KCNQ2 encoded by SEQ ID NO:95.
SEQ ID NOs:97-99 are primers for amplifying portions of KCNQ2.
SEQ ID NOs:100-114 are intron/exon sequence for KCNQ2 (Figures 7A-0).
CA 02712809 2010-08-20
7
SEQ ID NOs:115-129 are intron/exon sequence for KCNQ3 (Figures 8A-0).
DETAILED DESCRIPTION OF THE INVENTION
The present invention is directed to the determination that BFNC maps to the
KCNQ2 gene
and to the KCNQ3 gene and that molecular variants of these genes cause or are
involved in the
pathogenesis of BFNC, rolandic epilepsy and/or JME. More specifically, the
present invention
relates to mutations in the KCNQ2 gene and in the KCNQ3 gene and their use in
the diagnosis of
BFNC, rolandic epilepsy and JME. The present invention is further directed to
methods of
screening humans for the presence of KCNQ2 and/or KCNQ3 gene variants which
cause BFNC,
rolandic epilepsy and/or JME. Since these forms of epilepsy can now be
detected earlier (i.e., before
symptoms appear) and more definitively, better treatment options will be
available in those
individuals identified as having BFNC, rolandic epilepsy or JME. The present
invention is also
directed to methods for screening for drugs useful in treating or preventing
BFNC, rolandic epilepsy
or JME.
The present invention provides methods of screening the KCNQ2 and/or KCNQ3
gene to
identify mutations. Such methods may further comprise the step of amplifying a
portion of the
KCNQ2 or KCNQ3 gene, and may further include a step of providing a set of
polynucleotides which
are primers for amplification of said portion of the KCNQ2 or KCNQ3 gene. The
method is useful
for identifying mutations for use in either diagnosis of or prognosis of BFNC,
rolandic epilepsy and
JME.
Benign Familial Neonatal Convulsion is an autosomal dominantly inherited
disorder that
causes epilepsy of the newborn infant. This idiopathic, generalized epilepsy
typically has an onset of
seizures on day two to four of life. Spontaneous remission of the seizures
occurs between two to
fifteen weeks (Ronen et al., 1993; Plouin, 1994; Hauser and Kurland, 1975).
Seizures typically start
with a tonic posture, ocular symptoms and other autonomic features which then
often progress to
clonic movements and motor automatisms. These neonates thrive normally between
the seizures,
and their neurologic examinations and later development indicate normal brain
functioning (Ronen
et al., 1993; Plouin, 1994; Hauser and Kurland, 1975). However, in spite of
normal neurologic
development, seizures recur later in life in approximately 16% of BFNC cases
compared with a 2%
cumulative lifetime risk of epilepsy in the general population (Ronen et al.,
1993; Plouin, 1994;
Hauser and Kurland, 1975).
CA 02712809 2010-08-20
=
8
Linkage analysis in a large kindred demonstrated that a gene responsible for
BFNC maps to
chromosome 20q13.3 close to the markers D20S20 and D20S19 (Leppert eta!,
1989). Following
the initial report, two centers confirmed linkage of BFNC to the same two
genetic markers on
chromosome 20, termed the EBN1 (epilepsy benign neonatal type 1) locus (Ryan
et al., 1991;
Malafosse et al., 1992). A more distal marker, D20S24, shows complete co-
segregation with the
BFNC phenotype in chromosome 20 linked families. Finding a distal flanking
marker for the BFNC
locus has not been successful probably because of its proximity to the
telomere. This telomeric
region is characterized by a high recombination rate between markers when
compared to the
physical distance (Steinlein et al., 1992). In fact, Steinlein et al. have
demonstrated that the three
markers D20S19, D20S20 and D20S24 are contained on the same 450 Mb Mlu I
restriction
fragment (Steinlein et al., 1992). All of the families in the present study
for KCNQ2 show linkage to
chromosome 20q markers with LOD scores of greater than 3.0 or have probands
with clinical
manifestations consistent with BFNC (Leppert et al., 1993). To find this gene
responsible for
BFNC, we narrowed the BFNC region with a sub-microscopic deletion in a single
family, identified
candidate cDNAs in this deletion, and then searched for mutations in other
BFNC families.
A second chromosomal locus, EBN2, has also been identified for BFNC. Lewis et
al. (1993)
demonstrated linkage to markers on chromosome 8q24 in a single Hispanic family
affected with
BFNC. Evidence for this second locus was also reported in a Caucasian pedigree
(Steinlein et al.,
1995). The gene for EBN2, KCNQ3, has now been found and characterized as
detailed in this
disclosure.
Finally, the present invention is directed to a method for screening drug
candidates to
identify drugs useful for treating or preventing BFNC, rolandic epilepsy or
JME. Drug screening is
performed by expressing mutant KCNQ2 or mutant KCNQ3 in cells, such as
oocytes, mammalian
cells or transgenic animals, and assaying the effect of a drug candidate on
the KCNQ2 or KCNQ3
potassium channel. The effect is compared to the KCNQ2 or KCNQ3 potassium
channel activity
obtained using the wild-type KCNQ2 or KCNQ3 gene.
Proof that the KCNQ2 and KCNQ3 genes are involved in causing BFNC, rolandic
epilepsy
and JME is obtained by finding sequences in DNA extracted from affected
kindred members which
create abnormal KCNQ2 or abnormal KCNQ3 gene products or abnormal levels of
the gene
products. Such susceptibility alleles will co-segregate with the disease in
large kindreds. They will
also be present at a much higher frequency in non-kindred individuals with
epilepsy than in
individuals in the general population. The key is to find mutations which are
serious enough to
CA 02712809 2010-08-20
9
cause obvious disruption to the normal function of the gene product. These
mutations can take a
number of forms. The most severe forms would be frame shift mutations or large
deletions which
would cause the gene to code for an abnormal protein or one which would
significantly alter protein
expression. Less severe disruptive mutations would include small in-frame
deletions and
nonconservative base pair substitutions which would have a significant effect
on the protein
produced, such as changes to or from a cysteine residue, from a basic to an
acidic amino acid or vice
versa, from a hydrophobic to hydrophilic amino acid or vice versa, or other
mutations which would
affect secondary or tertiary protein structure. Silent mutations or those
resulting in conservative
amino acid substitutions would not generally be expected to disrupt protein
function.
According to the diagnostic and prognostic method of the present invention,
alteration of the
wild-type KCNQ2 or KCNQ3 gene is detected. In addition, the method can be
performed by
detecting the wild-type KCNQ2 or KCNQ3 gene and confirming the lack of a cause
of epilepsy as a
result of this locus. AAlteration of a wild-type gene@ encompasses all forms
of mutations including
deletions, insertions and point mutations in the coding and noncoding regions.
Deletions may be of
the entire gene or of only a portion of the gene. Point mutations may result
in stop codons,
frameshift mutations or amino acid substitutions. Somatic mutations are those
which occur only in
certain tissues and are not inherited in the germline. Germline mutations can
be found in any of a
body's tissues and are inherited. Point mutational events may occur in
regulatory regions, such as in
the promoter of the gene, leading to loss or diminution of expression of the
mRNA. Point mutations
may also abolish proper RNA processing, leading to loss of expression of the
KCNQ2 or KCNQ3
gene product, or to a decrease in mRNA stability or translation efficiency.
Useful diagnostic techniques include, but are not limited to fluorescent in
situ hybridization
(FISH), direct DNA sequencing, PFGE analysis, Southern blot analysis, single
stranded
conformation analysis (SSCA), RNase protection assay, allele-specific
oligonucleotide (ASO), dot
blot analysis, hybridization using nucleic acid modified with gold
nanoparticles and PCR-SSCP, as
discussed in detail further below. Also useful is the recently developed
technique of DNA
microchip technology.
The presence of BFNC, rolandic epilepsy or JME may be ascertained by testing
any tissue of
a human for mutations of the KCNQ2 or KCNQ3 gene. For example, a person who
has inherited a
germline KCNQ2 mutation would be prone to develop BFNC. This can be determined
by testing
DNA from any tissue of the person's body. Most simply, blood can be drawn and
DNA extracted
from the cells of the blood. In addition, prenatal diagnosis can be
accomplished by testing fetal
CA 02712809 2010-08-20
cells, placental cells or amniotic cells for mutations of the KCNQ2 or KCNQ3
gene. Alteration of a
wild-type KCNQ2 or KCNQ3 allele, whether, for example, by point mutation or
deletion, can be
detected by any of the means discussed herein.
There are several methods that can be used to detect DNA sequence variation.
Direct DNA
5
sequencing, either manual sequencing or automated fluorescent sequencing can
detect sequence
variation. Another approach is the single-stranded conformation polymorphism
assay (SSCP) (Orita
et al., 1989). This method does not detect all sequence changes, especially if
the DNA fragment size
is greater than 200 bp, but can be optimized to detect most DNA sequence
variation. The reduced
detection sensitivity is a disadvantage, but the increased throughput possible
with SSCP makes it an
10
attractive, viable alternative to direct sequencing for mutation detection on
a research basis. The
fragments which have shifted mobility on SSCP gels are then sequenced to
determine the exact
nature of the DNA sequence variation. Other approaches based on the detection
of mismatches
between the two complementary DNA strands include clamped denaturing gel
electrophoresis
(CDGE) (Sheffield et at., 1991), heteroduplex analysis (HA) (White et al.,
1992) and chemical
mismatch cleavage (CMC) (Grompe et al., 1989). None of the methods described
above will detect
large deletions, duplications or insertions, nor will they detect a regulatory
mutation which affects
transcription or translation of the protein. Other methods which might detect
these classes of
mutations such as a protein truncation assay or the asymmetric assay, detect
only specific types of
mutations and would not detect missense mutations. A review of currently
available methods of
detecting DNA sequence variation can be found in a recent review by Grompe
(1993). Once a
mutation is known, an allele specific detection approach such as allele
specific oligonucleotide
(ASO) hybridization can be utilized to rapidly screen large numbers of other
samples for that same
mutation. Such a technique can utilize probes which are labeled with gold
nanoparticles to yield a
visual color result (Elghanian et al., 1997).
A rapid preliminary analysis to detect polymorphisms in DNA sequences can be
performed
by looking at a series of Southern blots of DNA cut with one or more
restriction enzymes, preferably
with a large number of restriction enzymes. Each blot contains a series of
normal individuals and a
series of BFNC, rolandic epilepsy or JME cases. Southern blots displaying
hybridizing fragments
differing in length from control DNA when probed with sequences near or
including the KCNQ2
locus indicate a possible mutation. If restriction enzymes which produce very
large restriction
fragments are used, then pulsed field gel electrophoresis (PFGE) is employed.
CA 02712809 2010-08-20
11
Detection of point mutations may be accomplished by molecular cloning of the
KCNQ2 or
KCNQ3 allele and sequencing the allele using techniques well known in the art.
Also, the gene or
portions of the gene may be amplified, e.g., by PCR or other amplification
technique, and the
amplified gene or amplified portions of the gene may be sequenced.
There are six well known methods for a more complete, yet still indirect, test
for confirming
the presence of a susceptibility allele: 1) single stranded conformation
analysis (SSCP) (Orita et al.,
1989); 2) denaturing gradient gel electrophoresis (DGGE) (Wartell et al.,
1990; Sheffield et al.,
1989); 3) RNase protection assays (Finkelstein et al., 1990; Kinszler et al.,
1991); 4) allele-specific
oligonucleotides (AS0s) (Conner et al., 1983); 5) the use of proteins which
recognize nucleotide
mismatches, such as the E. coli mutS protein (Modrich, 1991); and 6) allele-
specific PCR (Ruano
and Kidd, 1989). For allele-specific PCR, primers are used which hybridize at
their 3' ends to a
particular KCNQ2 or KCNQ3 mutation. If the particular mutation is not present,
an amplification
product is not observed. Amplification Refractory Mutation System (ARMS) can
also be used, as
disclosed in European Patent Application Publication No. 0332435 and in Newton
et al., 1989.
Insertions and deletions of genes can also be detected by cloning, sequencing
and amplification. In
addition, restriction fragment length polymorphism (RFLP) probes for the gene
or surrounding
marker genes can be used to score alteration of an allele or an insertion in a
polymorphic fragment.
Such a method is particularly useful for screening relatives of an affected
individual for the presence
of the mutation found in that individual. Other techniques for detecting
insertions and deletions as
known in the art can be used.
In the first three methods (SSCP, DGGE and RNase protection assay), a new
electrophoretic
band appears. SSCP detects a band which migrates differentially because the
sequence change
causes a difference in single-strand, intramolecular base pairing. RNase
protection involves
cleavage of the mutant polynucleotide into two or more smaller fragments. DGGE
detects
differences in migration rates of mutant sequences compared to wild-type
sequences, using a
denaturing gradient gel. In an allele-specific oligonucleotide assay, an
oligonucleotide is designed
which detects a specific sequence, and the assay is performed by detecting the
presence or absence
of a hybridization signal. In the mutS assay, the protein binds only to
sequences that contain a
nucleotide mismatch in a heteroduplex between mutant and wild-type sequences.
Mismatches, according to the present invention, are hybridized nucleic acid
duplexes in
which the two strands are not 100% complementary. Lack of total homology may
be due to
deletions, insertions, inversions or substitutions. Mismatch detection can be
used to detect point
CA 02712809 2010-08-20
=
12
mutations in the gene or in its mRNA product. While these techniques are less
sensitive than
sequencing, they are simpler to perform on a large number of samples. An
example of a mismatch
cleavage technique is the RNase protection method. In the practice of the
present invention, the
method involves the use of a labeled riboprobe which is complementary to the
human wild-type
KCNQ2 or KCNQ3 gene coding sequence. The riboprobe and either mRNA or DNA
isolated from
the person are annealed (hybridized) together and subsequently digested with
the enzyme RNase A
which is able to detect some mismatches in a duplex RNA structure. If a
mismatch is detected by
RNase A, it cleaves at the site of the mismatch. Thus, when the annealed RNA
preparation is
separated on an electrophoretic gel matrix, if a mismatch has been detected
and cleaved by RNase A,
an RNA product will be seen which is smaller than the full length duplex RNA
for the riboprobe and
the mRNA or DNA. The riboprobe need not be the full length of the mRNA or gene
but can be a
segment of either. If the riboprobe comprises only a segment of the mRNA or
gene, it will be
desirable to use a number of these probes to screen the whole mRNA sequence
for mismatches.
In similar fashion, DNA probes can be used to detect mismatches, through
enzymatic or
chemical cleavage. See, e.g., Cotton et al., 1988; Shenk et al., 1975; Novack
et al., 1986.
Alternatively, mismatches can be detected by shifts in the electrophoretic
mobility of mismatched
duplexes relative to matched duplexes. See, e.g., Cariello, 1988. With either
riboprobes or DNA
probes, the cellular mRNA or DNA which might contain a mutation can be
amplified using PCR
(see below) before hybridization. Changes in DNA of the KCNQ2 or KCNQ3 gene
can also be
detected using Southern hybridization, especially if the changes are gross
rearrangements, such as
deletions and insertions.
DNA sequences of the KCNQ2 or KCNQ3 gene which have been amplified by use of
PCR
may also be screened using allele-specific probes. These probes are nucleic
acid oligomers, each of
which contains a region of the gene sequence harboring a known mutation. For
example, one
oligomer may be about 30 nucleotides in length, corresponding to a portion of
the gene sequence.
By use of a battery of such allele-specific probes, PCR amplification products
can be screened to
identify the presence of a previously identified mutation in the gene.
Hybridization of allele-specific
probes with amplified KCNQ2 or KCNQ3 sequences can be performed, for example,
on a nylon
filter. Hybridization to a particular probe under high stringency
hybridization conditions indicates
the presence of the same mutation in the tissue as in the allele-specific
probe. High stringency
hybridization conditions are defined as those conditions which allow an 8
basepair stretch of a first
nucleic acid (a probe) to bind to a 100% perfectly complementary 8 basepair
stretch of nucleic acid
CA 02712809 2010-08-20
13
while simultaneously preventing binding of said first nucleic acid to a
nucleic acid which is not
100% complementary, i.e., binding will not occur if there is a mismatch.
The newly developed technique of nucleic acid analysis via microchip
technology is also
applicable to the present invention. In this technique, literally thousands of
distinct oligonucleotide
probes are built up in an array on a silicon chip. Nucleic acid to be analyzed
is fluorescently labeled
and hybridized to the probes on the chip. It is also possible to study nucleic
acid-protein interactions
using these nucleic acid microchips. Using this technique one can determine
the presence of
mutations or even sequence the nucleic acid being analyzed or one can measure
expression levels of
a gene of interest. The method is one of parallel processing of many, even
thousands, of probes at
once and can tremendously increase the rate of analysis. Several papers have
been published which
use this technique. Some of these are Hacia et al., 1996; Shoemaker et al.,
1996; Chee et al., 1996;
Lockhart et al., 1996; DeRisi et al., 1996; Lipshutz et al., 1995. This method
has already been used
to screen people for mutations in the breast cancer gene BRCA1 (Hacia et al.,
1996). This new
technology has been reviewed in a news article in Chemical and Engineering
News (Borman, 1996)
and been the subject of an editorial (Nature Genetics, 1996). Also see Fodor
(1997).
The most definitive test for mutations in a candidate locus is to directly
compare genomic
KCNQ2 or KCNQ3 sequences from patients with those from a control population.
Alternatively,
one could sequence messenger RNA after amplification, e.g., by PCR, thereby
eliminating the
necessity of determining the exon structure of the candidate gene.
Mutations from patients falling outside the coding region of KCNQ2 or KCNQ3
can be
detected by examining the non-coding regions, such as introns and regulatory
sequences near or
within the genes. An early indication that mutations in noncoding regions are
important may come
from Northern blot experiments that reveal messenger RNA molecules of abnormal
size or
abundance in patients as compared to control individuals.
Alteration of KCNQ2 or KCNQ3 mRNA expression can be detected by any techniques
known in the art. These include Northern blot analysis, PCR amplification and
RNase protection.
Diminished mRNA expression indicates an alteration of the wild-type gene.
Alteration of wild-type
genes can also be detected by screening for alteration of wild-type KCNQ2 or
KCNQ3 protein. For
example, monoclonal antibodies immunoreactive with KCNQ2 or KCNQ3 can be used
to screen a
tissue. Lack of cognate antigen would indicate a mutation. Antibodies specific
for products of
mutant alleles could also be used to detect mutant gene product. Such
immunological assays can be
done in any convenient formats known in the art.
These include Western blots,
CA 02712809 2010-08-20
14
immunohistochemical assays and ELISA assays. Any means for detecting an
altered KCNQ2 or
KCNQ3 protein can be used to detect alteration of the wild-type KCNQ2 or KCNQ3
gene.
Functional assays, such as protein binding determinations, can be used. In
addition, assays can be
used which detect KCNQ2 or KCNQ3 biochemical function. Finding a mutant KCNQ2
or KCNQ3
gene product indicates alteration of a wild-type KCNQ2 or KCNQ3 gene.
A mutant KCNQ2 or KCNQ3 gene or gene product can also be detected in other
human body
samples, such as serum, stool, urine and sputum. The same techniques discussed
above for
detection of mutant genes or gene products in tissues can be applied to other
body samples. By
screening such body samples, a simple early diagnosis can be achieved for
BFNC, rolandic epilepsy
.. or JME.
The primer pairs of the present invention are useful for determination of the
nucleotide
sequence of a particular KCNQ2 or KCNQ3 allele using PCR. The pairs of single-
stranded DNA
primers for KCNQ2 or KCNQ3 can be annealed to sequences within or surrounding
the KCNQ2
gene on chromosome 20 or KCNQ3 gene on chromosome 8 in order to prime
amplifying DNA
synthesis of the gene itself. A complete set of these primers allows synthesis
of all of the
nucleotides of the gene coding sequences, i.e., the exons. The set of primers
preferably allows
synthesis of both intron and exon sequences. Allele-specific primers can also
be used. Such primers
anneal only to particular KCNQ2 or KCNQ3 mutant alleles, and thus will only
amplify a product in
the presence of the mutant allele as a template.
In order to facilitate subsequent cloning of amplified sequences, primers may
have restriction
enzyme site sequences appended to their 5' ends. Thus, all nucleotides of the
primers are derived
from KCNQ2 or KCNQ3 sequence or sequences adjacent to KCNQ2 or KCNQ3, except
for the few
nucleotides necessary to form a restriction enzyme site. Such enzymes and
sites are well known in
the art. The primers themselves can be synthesized using techniques which are
well known in the
art. Generally, the primers can be made using oligonucleotide synthesizing
machines which are
commercially available. Given the sequence of KCNQ2 and KCNQ3, design of
particular primers is
well within the skill of the art.
The nucleic acid probes provided by the present invention are useful for a
number of
purposes. They can be used in Southern hybridization to genomic DNA and in the
RNase protection
method for detecting point mutations already discussed above. The probes can
be used to detect
PCR amplification products. They may also be used to detect mismatches with
the KCNQ2 or
KCNQ3 gene or mRNA using other techniques.
CA 02712809 2010-08-20
It has been discovered that most individuals with the wild-type KCNQ2 and
KCNQ3 genes
do not have BFNC. However, mutations which interfere with the function of the
KCNQ2 or KCNQ3
gene product are involved in the pathogenesis of BFNC. Thus, the presence of
an altered (or a
mutant) KCNQ2 or KCNQ3 gene which produces a protein having a loss of
function, or altered
5 function, directly causes BFNC which increases the risk of seizures. In
order to detect a KCNQ2 or
KCNQ3 gene mutation, a biological sample is prepared and analyzed for a
difference between the
sequence of the allele being analyzed and the sequence of the wild-type
allele. Mutant KCNQ2 or
KCNQ3 alleles can be initially identified by any of the techniques described
above. The mutant
alleles are then sequenced to identify the specific mutation of the particular
mutant allele.
10 Alternatively, mutant alleles can be initially identified by identifying
mutant (altered) proteins, using
conventional techniques. The mutant alleles are then sequenced to identify the
specific mutation for
each allele. The mutations, especially those which lead to an altered function
of the protein, are then
used for the diagnostic and prognostic methods of the present invention.
This is the first human idiopathic generalized epilepsy for which a K+ channel
has been
15 implicated. BFNC is considered to be a true idiopathic epilepsy without
the degenerative
characteristics associated with other syndromes such as progressive myoclonus
epilepsy of the
Unverricht-Lundborg type. It is not surprising, therefore, that an alteration
in a gene which directly
regulates neuronal excitability causes this epileptic disorder. Voltage-gated
potassium channels
repolarize neuronal membranes that have been depolarized by Na+ and Ca++
voltage-gated ion
channels. K+ channels are also thought to repolarize neuronal membranes
following activation of
excitatory neurotransmitter ion channels, including glutamate and
acetylcholine. In the presence of
mutant KCNQ2 or KCNQ3 channels with reduced function, excitatory ligand and
voltage-gated
channels that are activated would remain open for a longer duration (Keating
and Sanguinetti, 1996;
Meldrum, 1995; McNamara, 1994). Such unchecked activity of excitatory systems
could lead to an
epileptic phenotype. Electrophysiologic analysis of the mutant KCNQ2 and KCNQ3
channels will
shed light on how the mutations identified in the current study produce an
epileptic phenotype. It is
likely that KCNQ2 and KCNQ3 will have biophysical properties similar to the
delayed rectifier
KCNQ1 channel. KCNQ1 alpha subunits coassemble with minK beta subunits to form
heteromultimeric 'Ks channels in the heart (Sanguinetti et al., 1996). It is
possible that KCNQ2 and
KCNQ3 subunits coassemble with minK-like beta subunits in the brain. This
interaction may also
alter the gating properties of the resulting heteromultimeric channel as is
the case for KCNQ1.
CA 02712809 2010-08-20
16
Mutations in K+ channels have been associated with epilepsy in only one other
case, the
weaver mouse, where a single missense mutation in the GIRK2 gene produces
spontaneous seizures
(Patil et al., 1995; Signorini et al., 1997). Mutations in K+ channels have
been implicated in other
human disorders such as the Long QT syndrome on chromosome 11 and
ataxia/myokymia on
chromosome 12 (Wang et al., 1996; Neyroud et al., 1997; Russell et al., 1996;
Chandy and Gutman,
1995; Browne et al., 1994). Long QT is associated with four loci, two of which
are the K+ channel
genes HERG and KCNQ 1. In KCNQ1, mutational hot spots have been identified in
the pore and S6
domains where missense mutations in these regions account for a majority of
the disease causing
mutations in LQT (Russell et al., 1996; Wang et al., 1996).
Since the first publications of the finding of the KCNQ2 and KCNQ3 genes,
there have been
several more publications. Iannotti et al. (1998) found that there are two
splice variants of KCNQ2
These are a long and a short form which differ in their C-termini. The long
form is expressed
exclusively in human brain (adult and fetal), where it is restricted to
neuronal rather than glial cells.
The short form is expressed weakly in adult brain but is prominent in fetal
brain and testes (Iannotti
et al., 1998). Gribkoff et al. (1998) cloned and expressed a mouse homologue
of KCNQ2 in
Xenopus oocytes and performed two-elecrode voltage clamp studies. Dworetzky et
al. (1998) cloned
a mouse homologue of KCNQ2 and also noted alternative splice variants in the
3' region of the gene.
They also performed Northern blots and measured polarization in Xenopus
oocytes expressing the
mouse gene. Yang et al. (1998) have also cloned and expressed the human KCNQ2
and KCNQ3.
They note that the encoded proteins act like KCNQ1 in eliciting voltage-gated,
rapidly activating K+
-selective currents, but in contrast to KCNQ1, the KCNQ2 and KCNQ3 protein
induced currents are
not augmented by coexpression of KCNE1. However, coexpression of KCNQ2 and
KCNQ3 results
in a substantial synergistic increase in current amplitude (Yang et al.,
1998). Finally, Biervert et al.
(1998) cloned human KCNQ2 and expressed it in Xenopus oocytes.
Definitions
The present invention employs the following definitions.
"Amplification of Polynucleotides" utilizes methods such as the polymerase
chain reaction
(PCR), ligation amplification (or ligase chain reaction, LCR) and
amplification methods based on
the use of Q-beta replicase. Also useful are strand displacement amplification
(SDA), thermophilic
SDA, and nucleic acid sequence based amplification (3SR or NASBA). These
methods are well
known and widely practiced in the art. See, e.g., U.S. Patents 4,683,195 and
4,683,202 and Innis et
CA 02712809 2010-08-20
17
al., 1990 (for PCR); Wu and Wallace, 1989 (for LCR); U.S. Patents 5,270,184
and 5,455,166 and
Walker et al., 1992 (for SDA); Spargo et al., 1996 (for thermophilic SDA) and
U.S. Patent
5,409,818, Fahy et al., 1991 and Compton, 1991 for 3SR and NASBA. Reagents and
hardware for
conducting PCR are commercially available. Primers useful to amplify sequences
from the KCNQ2
or KCNQ3 region are preferably complementary to, and hybridize specifically to
sequences in the
KCNQ2 or KCNQ3 region or in regions that flank a target region therein. KCNQ2
or KCNQ3
sequences generated by amplification may be sequenced directly. Alternatively,
but less desirably,
the amplified sequence(s) may be cloned prior to sequence analysis. A method
for the direct cloning
and sequence analysis of enzymatically amplified genomic segments has been
described by Scharf et
al., 1986.
"Analyte polynucleotide" and "analyte strand" refer to a single- or double-
stranded
polynucleotide which is suspected of containing a target sequence, and which
may be present in a
variety of types of samples, including biological samples.
"Antibodies." The present invention also provides polyclonal and/or monoclonal
antibodies
and fragments thereof, and immunologic binding equivalents thereof, which are
capable of
specifically binding to the KCNQ2 or KCNQ3 polypeptide and fragments thereof
or to
polynucleotide sequences from the KCNQ2 KCNQ3 region. The term "antibody" is
used both to
refer to a homogeneous molecular entity, or a mixture such as a serum product
made up of a
plurality of different molecular entities. Polypeptides may be prepared
synthetically in a peptide
synthesizer and coupled to a carrier molecule (e.g., keyhole limpet
hemocyanin) and injected over
several months into rabbits. Rabbit sera is tested for immunoreactivity to the
KCNQ2 or KCNQ3
polypeptide or fragment. Monoclonal antibodies may be made by injecting mice
with the protein
polypeptides, fusion proteins or fragments thereof. Monoclonal antibodies will
be screened by
ELISA and tested for specific immunoreactivity with KCNQ2 or KCNQ3 polypeptide
or fragments
thereof. See, Harlow and Lane, 1988. These antibodies will be useful in assays
as well as
pharmaceuticals.
Once a sufficient quantity of desired polypeptide has been obtained, it may be
used for
various purposes. A typical use is the production of antibodies specific for
binding. These
antibodies may be either polyclonal or monoclonal, and may be produced by in
vitro or in vivo
techniques well known in the art. For production of polyclonal antibodies, an
appropriate target
immune system, typically mouse or rabbit, is selected. Substantially purified
antigen is presented to
the immune system in a fashion determined by methods appropriate for the
animal and by other
CA 02712809 2010-08-20
18
parameters well known to immunologists. Typical sites for injection are in
footpads,
intramuscularly, intraperitoneally, or intradermally. Of course, other species
may be substituted for
mouse or rabbit. Polyclonal antibodies are then purified using techniques
known in the art, adjusted
for the desired specificity.
An immunological response is usually assayed with an immunoassay. Normally,
such
immunoassays involve some purification of a source of antigen, for example,
that produced by the
same cells and in the same fashion as the antigen. A variety of immunoassay
methods are well
known in the art. See, e.g., Harlow and Lane, 1988, or Goding, 1986.
Monoclonal antibodies with affinities of 10-8 M-I or preferably le to 10-10 M-
I or stronger
will typically be made by standard procedures as described, e.g., in Harlow
and Lane, 1988 or
Goding, 1986. Briefly, appropriate animals will be selected and the desired
immunization protocol
followed. After the appropriate period of time, the spleens of such animals
are excised and
individual spleen cells fused, typically, to immortalized myeloma cells under
appropriate selection
conditions. Thereafter, the cells are clonally separated and the supernatants
of each clone tested for
their production of an appropriate antibody specific for the desired region of
the antigen.
Other suitable techniques involve in vitro exposure of lymphocytes to the
antigenic
polypeptides, or alternatively, to selection of libraries of antibodies in
phage or similar vectors. See
Huse et al., 1989. The polypeptides and antibodies of the present invention
may be used with or
without modification. Frequently, polypeptides and antibodies will be labeled
by joining, either
covalently or non-covalently, a substance which provides for a detectable
signal. A wide variety of
labels and conjugation techniques are known and are reported extensively in
both the scientific and
patent literature. Suitable labels include radionuclides, enzymes, substrates,
cofactors, inhibitors,
fluorescent agents, chemiluminescent agents, magnetic particles and the like.
Patents teaching the
use of such labels include U.S. Patents 3,817,837; 3,850,752; 3,939,350;
3,996,345; 4,277,437;
4,275,149 and 4,366,241. Also, recombinant immunoglobulins may be produced
(see U.S. Patent
4,816,567).
"Binding partner" refers to a molecule capable of binding a ligand molecule
with high
specificity, as for example, an antigen and an antigen-specific antibody or an
enzyme and its
inhibitor. In general, the specific binding partners must bind with sufficient
affinity to immobilize
the analyte copy/complementary strand duplex (in the case of polynucleotide
hybridization) under
the isolation conditions. Specific binding partners are known in the art and
include, for example,
biotin and avidin or streptavidin, IgG and protein A, the numerous, known
receptor-ligand couples,
CA 02712809 2010-08-20
19
and complementary polynucleotide strands. In the case of complementary
polynucleotide binding
partners, the partners are normally at least about 15 bases in length, and may
be at least 40 bases in
length. It is well recognized by those of skill in the art that lengths
shorter than 15 (e.g., 8 bases),
between 15 and 40, and greater than 40 bases may also be used. The
polynucleotides may be
composed of DNA, RNA, or synthetic nucleotide analogs. Further binding
partners can be
identified using, e.g., the two-hybrid yeast screening assay as described
herein.
A "biological sample" refers to a sample of tissue or fluid suspected of
containing an
analyte polynucleotide or polypeptide from an individual including, but not
limited to, e.g., plasma,
serum, spinal fluid, lymph fluid, the external sections of the skin,
respiratory, intestinal, and
genitourinary tracts, tears, saliva, blood cells, tumors, organs, tissue and
samples of in vitro cell
culture constituents.
"Encode". A polynucleotide is said to "encode" a polypeptide if, in its native
state or when
manipulated by methods well known to those skilled in the art, it can be
transcribed and/or translated
to produce the mRNA for and/or the polypeptide or a fragment thereof. The anti-
sense strand is the
complement of such a nucleic acid, and the encoding sequence can be deduced
therefrom.
"Isolated" or "substantially pure". An "isolated" or "substantially pure"
nucleic acid (e.g.,
an RNA, DNA or a mixed polymer) is one which is substantially separated from
other cellular
components which naturally accompany a native human sequence or protein, e.g.,
ribosomes,
polymerases, many other human genome sequences and proteins. The term embraces
a nucleic acid
.. sequence or protein which has been removed from its naturally occurring
environment, and includes
recombinant or cloned DNA isolates and chemically synthesized analogs or
analogs biologically
synthesized by heterologous systems.
"KCNQ2 Allele" refers to normal alleles of the KCNQ2 locus as well as alleles
of KCNQ2
carrying variations that cause BFNC and/or rolandic epilepsy.
"KCNQ3 Allele" refers to normal alleles of the KCNQ3 locus as well as alleles
of KCNQ3
carrying variations that cause BFNC and/or JME.
"KCNQ2 Locus", "KCNQ2 Gene", "KCNQ2 Nucleic Acids" or "KCNQ2
Polynucleotide" each refer to polynucleotides, all of which are in the KCNQ2
region, that are likely
to be expressed in normal tissue, certain alleles of which result in BFNC
and/or rolandic epilepsy.
The KCNQ2 locus is intended to include coding sequences, intervening sequences
and regulatory
elements controlling transcription and/or translation. The KCNQ2 locus is
intended to include all
allelic variations of the DNA sequence.
CA 02712809 2010-08-20
"KCNQ3 Locus", "KCNQ3 Gene", "KCNQ3 Nucleic Acids" or "KCNQ3
Polynucleotide" each refer to polynucleotides, all of which are in the KCNQ3
region, that are likely
to be expressed in normal tissue, certain alleles of which result in BFNC
and/or JME. The KCNQ3
locus is intended to include coding sequences, intervening sequences and
regulatory elements
5 controlling transcription and/or translation. The KCNQ3 locus is intended
to include all allelic
variations of the DNA sequence.
These terms, when applied to a nucleic acid, refer to a nucleic acid which
encodes a human
KCNQ2 or KCNQ3 polypeptide, fragment, homolog or variant, including, e.g.,
protein fusions or
deletions. The nucleic acids of the present invention will possess a sequence
which is either derived
10 from, or substantially similar to a natural KCNQ2- or KCNQ3-encoding gene
or one having
substantial homology with a natural KCNQ2- or KCNQ3-encoding gene or a portion
thereof.
The KCNQ2 or KCNQ3 gene or nucleic acid includes normal alleles of the KCNQ2
or
KCNQ3 gene, respectively, including silent alleles having no effect on the
amino acid sequence of
the KCNQ2 or KCNQ3 polypeptide as well as alleles leading to amino acid
sequence variants of the
15 KCNQ2 or KCNQ3 polypeptide that do not substantially affect its
function. These terms also
include alleles having one or more mutations which adversely affect the
function of the KCNQ2 or
KCNQ3 polypeptide. A mutation may be a change in the KCNQ2 or KCNQ3 nucleic
acid sequence
which produces a deleterious change in the amino acid sequence of the KCNQ2 or
KCNQ3
polypeptide, resulting in partial or complete loss of KCNQ2 or KCNQ3 function,
respectively, or
20 may be a change in the nucleic acid sequence which results in the loss
of effective KCNQ2 or
KCNQ3 expression or the production of aberrant forms of the KCNQ2 or KCNQ3
polypeptide.
The KCNQ2 or KCNQ3 nucleic acid may be that shown in SEQ ID NO:1 (KCNQ2) or
SEQ
ID NO:6 (KCNQ3) or it may be an allele as described above or a variant or
derivative differing from
that shown by a change which is one or more of addition, insertion, deletion
and substitution of one
or more nucleotides of the sequence shown. Changes to the nucleotide sequence
may result in an
amino acid change at the protein level, or not, as determined by the genetic
code.
Thus, nucleic acid according to the present invention may include a sequence
different from
the sequence shown in SEQ ID NOs:1 and 6 yet encode a polypeptide with the
same amino acid
sequence as shown in SEQ ID NOs:2 (KCNQ2) and 7 (KCNQ3). That is, nucleic
acids of the
present invention include sequences which are degenerate as a result of the
genetic code. On the
other hand, the encoded polypeptide may comprise an amino acid sequence which
differs by one or
more amino acid residues from the amino acid sequence shown in SEQ ID NOs:2
and 7. Nucleic
CA 02712809 2010-08-20
21
acid encoding a polypeptide which is an amino acid sequence variant,
derivative or allele of the
amino acid sequence shown in SEQ ID NOs:2 and 7 is also provided by the
present invention.
The KCNQ2 or KCNQ3 gene, respectively, also refers to (a) any DNA sequence
that (i)
hybridizes to the complement of the DNA sequences that encode the amino acid
sequence set forth
in SEQ ID NO:1 or SEQ ID NO:6 under highly stringent conditions (Ausubel
etal., 1992) and (ii)
encodes a gene product functionally equivalent to KCNQ2 or KCNQ3, or (b) any
DNA sequence
that (i) hybridizes to the complement of the DNA sequences that encode the
amino acid sequence set
forth in SEQ ID NO:2 or SEQ ID NO:7 under less stringent conditions, such as
moderately stringent
conditions (Ausubel et al., 1992) and (ii) encodes a gene product functionally
equivalent to KCNQ2
or KCNQ3. The invention also includes nucleic acid molecules that are the
complements of the
sequences described herein.
The polynucleotide compositions of this invention include RNA, cDNA, genomic
DNA,
synthetic forms, and mixed polymers, both sense and antisense strands, and may
be chemically or
biochemically modified or may contain non-natural or derivatized nucleotide
bases, as will be
readily appreciated by those skilled in the art. Such modifications include,
for example, labels,
methylation, substitution of one or more of the naturally occurring
nucleotides with an analog,
internucleotide modifications such as uncharged linkages (e.g., methyl
phosphonates,
phosphotriesters, phosphoramidates, carbamates, etc.), charged linkages (e.g.,
phosphorothioates,
phosphorodithioates, etc.), pendent moieties (e.g., polypeptides),
intercalators (e.g., acridine,
psoralen, etc.), chelators, alkylators, and modified linkages (e.g., alpha
anomeric nucleic acids, etc.).
Also included are synthetic molecules that mimic polynucleotides in their
ability to bind to a
designated sequence via hydrogen bonding and other chemical interactions. Such
molecules are
known in the art and include, for example, those in which peptide linkages
substitute for phosphate
linkages in the backbone of the molecule.
The present invention provides recombinant nucleic acids comprising all or
part of the
KCNQ2 or KCNQ3 region. The recombinant construct may be capable of replicating
autonomously
in a host cell. Alternatively, the recombinant construct may become integrated
into the chromosomal
DNA of the host cell. Such a recombinant polynucleotide comprises a
polynucleotide of genomic,
cDNA, semi-synthetic, or synthetic origin which, by virtue of its origin or
manipulation, 1) is not
associated with all or a portion of a polynucleotide with which it is
associated in nature; 2) is linked
to a polynucleotide other than that to which it is linked in nature; or 3)
does not occur in nature.
CA 02712809 2010-08-20
22
Where nucleic acid according to the invention includes RNA, reference to the
sequence shown
should be construed as reference to the RNA equivalent, with U substituted for
T.
Therefore, recombinant nucleic acids comprising sequences otherwise not
naturally
occurring are provided by this invention. Although the wild-type sequence may
be employed, it will
often be altered, e.g., by deletion, substitution or insertion. cDNA or
genomic libraries of various
types may be screened as natural sources of the nucleic acids of the present
invention, or such
nucleic acids may be provided by amplification of sequences resident in
genomic DNA or other
natural sources, e.g., by PCR. The choice of cDNA libraries normally
corresponds to a tissue source
which is abundant in mRNA for the desired proteins. Phage libraries are
normally preferred, but
other types of libraries may be used. Clones of a library are spread onto
plates, transferred to a
substrate for screening, denatured and probed for the presence of desired
sequences.
The DNA sequences used in this invention will usually comprise at least about
five codons
(15 nucleotides), more usually at least about 7-15 codons, and most
preferably, at least about 35
codons. One or more introns may also be present. This number of nucleotides is
usually about the
minimal length required for a successful probe that would hybridize
specifically with a KCNQ2- or
KCNQ3-encoding sequence. In this context, oligomers of as low as 8
nucleotides, more generally 8-
17 nucleotides, can be used for probes, especially in connection with chip
technology.
Techniques for nucleic acid manipulation are described generally, for example,
in Sambrook
et al., 1989 or Ausubel et al., 1992. Reagents useful in applying such
techniques, such as restriction
enzymes and the like, are widely known in the art and commercially available
from such vendors as
New England BioLabs, Boehringer Mannheim, Amersham, Promega, U. S.
Biochemicals, New
England Nuclear, and a number of other sources. The recombinant nucleic acid
sequences used to
produce fusion proteins of the present invention may be derived from natural
or synthetic sequences.
Many natural gene sequences are obtainable from various cDNA or from genomic
libraries using
appropriate probes. See, GenBank, National Institutes of Health.
As used herein, a "portion" of the KCNQ2 or KCNQ3 locus or region or allele is
defined as
having a minimal size of at least about eight nucleotides, or preferably about
15 nucleotides, or more
preferably at least about 25 nucleotides, and may have a minimal size of at
least about 40
nucleotides. This definition includes all sizes in the range of 8-40
nucleotides as well as greater than
40 nucleotides. Thus, this definition includes nucleic acids of 8, 12, 15, 20,
25, 40, 60, 80, 100, 200,
300, 400, 500 nucleotides, or nucleic acids having any number of nucleotides
within these ranges of
values (e.g., 9, 10, 11, 16, 23, 30, 38, 50, 72, 121, etc., nucleotides), or
nucleic acids having more
CA 02712809 2010-08-20
23
than 500 nucleotides. The present invention includes all novel nucleic acids
having at least 8
nucleotides derived from SEQ ID NO:1 or SEQ ID NO:6, its complement or
functionally equivalent
nucleic acid sequences. The present invention does not include nucleic acids
which exist in the prior
art. That is, the present invention includes all nucleic acids having at least
8 nucleotides derived
from SEQ ID NO:1 or SEQ ID NO:6 with the proviso that it does not include
nucleic acids existing
in the prior art.
"KCNQ2 protein" or "KCNQ2 polypeptide" refers to a protein or polypeptide
encoded by
the KCNQ2 locus, variants or fragments thereof The term "polypeptide" refers
to a polymer of
amino acids and its equivalent and does not refer to a specific length of the
product; thus, peptides,
oligopeptides and proteins are included within the definition of a
polypeptide. This term also does
not refer to, or exclude modifications of the polypeptide, for example,
glycosylations, acetylations,
phosphorylations, and the like. Included within the definition are, for
example, polypeptides
containing one or more analogs of an amino acid (including, for example,
unnatural amino acids,
etc.), polypeptides with substituted linkages as well as other modifications
known in the art, both
naturally and non-naturally occurring. Ordinarily, such polypeptides will be
at least about 50%
homologous to the native KCNQ2 sequence, preferably in excess of about 90%,
and more preferably
at least about 95% homologous. Also included are proteins encoded by DNA which
hybridize under
high or low stringency conditions, to KCNQ2-encoding nucleic acids and closely
related
polypeptides or proteins retrieved by antisera to the KCNQ2 protein(s).
"KCNQ3 protein" or "KCNQ3 polypeptide" refers to a protein or polypeptide
encoded by
the KCNQ3 locus, variants or fragments thereof The term "polypeptide" refers
to a polymer of
amino acids and its equivalent and does not refer to a specific length of the
product; thus, peptides,
oligopeptides and proteins are included within the definition of a
polypeptide. This term also does
not refer to, or exclude modifications of the polypeptide, for example,
glycosylations, acetylations,
phosphorylations, and the like. Included within the definition are, for
example, polypeptides
containing one or more analogs of an amino acid (including, for example,
unnatural amino acids,
etc.), polypeptides with substituted linkages as well as other modifications
known in the art, both
naturally and non-naturally occurring. Ordinarily, such polypeptides will be
at least about 50%
homologous to the native KCNQ3 sequence, preferably in excess of about 90%,
and more preferably
at least about 95% homologous. Also included are proteins encoded by DNA which
hybridize under
high or low stringency conditions, to KCNQ3-encoding nucleic acids and closely
related
polypeptides or proteins retrieved by antisera to the KCNQ3 protein(s).
CA 02712809 2010-08-20
24
The KCNQ2 or KCNQ3 polypeptide may be that shown in SEQ ID NO:2 or SEQ ID NO:7
which may be in isolated and/or purified form, free or substantially free of
material with which it is
naturally associated. The polypeptide may, if produced by expression in a
prokaryotic cell or
produced synthetically, lack native post-translational processing, such as
glycosylation.
Alternatively, the present invention is also directed to polypeptides which
are sequence variants,
alleles or derivatives of the KCNQ2 or KCNQ3 polypeptide. Such polypeptides
may have an amino
acid sequence which differs from that set forth in SEQ ID NO:2 or SEQ ID NO:7
by one or more of
addition, substitution, deletion or insertion of one or more amino acids.
Preferred such polypeptides
have KCNQ2 or KCNQ3 function.
Substitutional variants typically contain the exchange of one amino acid for
another at one or
more sites within the protein, and may be designed to modulate one or more
properties of the
polypeptide, such as stability against proteolytic cleavage, without the loss
of other functions or
properties. Amino acid substitutions may be made on the basis of similarity in
polarity, charge,
solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of
the residues involved.
Preferred substitutions are ones which are conservative, that is, one amino
acid is replaced with one
of similar shape and charge. Conservative substitutions are well known in the
art and typically
include substitutions within the following groups: glycine, alanine; valine,
isoleucine, leucine;
aspartic acid, glutamic acid; asparagine, glutamine; serine, threonine;
lysine, arginine; and tyrosine,
phenylalanine.
Certain amino acids may be substituted for other amino acids in a protein
structure without
appreciable loss of interactive binding capacity with structures such as, for
example, antigen-binding
regions of antibodies or binding sites on substrate molecules or binding sites
on proteins interacting
with the KCNQ2 or KCNQ3 polypeptide. Since it is the interactive capacity and
nature of a protein
which defines that protein=s biological functional activity, certain amino
acid substitutions can be
made in a protein sequence, and its underlying DNA coding sequence, and
nevertheless obtain a
protein with like properties. In making such changes, the hydropathic index of
amino acids may be
considered. The importance of the hydrophobic amino acid index in conferring
interactive
biological function on a protein is generally understood in the art (Kyte and
Doolittle, 1982).
Alternatively, the substitution of like amino acids can be made effectively on
the basis of
hydrophilicity. The importance of hydrophilicity in conferring interactive
biological function of a
protein is generally understood in the art (U.S. Patent 4,554,101). The use of
the hydrophobic index
or hydrophilicity in designing polypeptides is further discussed in U.S.
Patent 5,691,198.
CA 02712809 2010-08-20
The length of polypeptide sequences compared for homology will generally be at
least about
16 amino acids, usually at least about 20 residues, more usually at least
about 24 residues, typically
at least about 28 residues, and preferably more than about 35 residues.
"Operably linked" refers to a juxtaposition wherein the components so
described are in a
5 relationship permitting them to function in their intended manner. For
instance, a promoter is
operably linked to a coding sequence if the promoter affects its transcription
or expression.
The term peptide mimetic or mimetic is intended to refer to a substance which
has the
essential biological activity of the KCNQ2 or KCNQ3 polypeptide. A peptide
mimetic may be a
peptide-containing molecule that mimics elements of protein secondary
structure (Johnson et al.,
10 1993). The underlying rationale behind the use of peptide mimetics is
that the peptide backbone of
proteins exists chiefly to orient amino acid side chains in such a way as to
facilitate molecular
interactions, such as those of antibody and antigen, enzyme and substrate or
scaffolding proteins. A
peptide mimetic is designed to permit molecular interactions similar to the
natural molecule. A
mimetic may not be a peptide at all, but it will retain the essential
biological activity of natural
15 KCNQ2 or KCNQ3 polypeptide.
"Probes". Polynucleotide polymorphisms associated with KCNQ2 or KCNQ3 alleles
which
predispose to BFNC, rolandic epilepsy or JME are detected by hybridization
with a polynucleotide
probe which forms a stable hybrid with that of the target sequence, under
highly stringent to
moderately stringent hybridization and wash conditions. If it is expected that
the probes will be
20 perfectly complementary to the target sequence, high stringency
conditions will be used.
Hybridization stringency may be lessened if some mismatching is expected, for
example, if variants
are expected with the result that the probe will not be completely
complementary. Conditions are
chosen which rule out nonspecific/adventitious bindings, that is, which
minimize noise. (It should
be noted that throughout this disclosure, if it is simply stated that
Astringent@ conditions are used
25 that is meant to be read as Ahigh stringency@ conditions are used.)
Since such indications identify
neutral DNA polymorphisms as well as mutations, these indications need further
analysis to
demonstrate detection of a KCNQ2 or KCNQ3 susceptibility allele.
Probes for KCNQ2 alleles may be derived from the sequences of the KCNQ2
region, its
cDNA, functionally equivalent sequences, or the complements thereof. Probes
for KCNQ3 alleles
may be derived from the sequences of the KCNQ3 region, its cDNA, functionally
equivalent
sequences, or the complements thereof. The probes may be of any suitable
length, which span all or
a portion of the KCNQ2 or KCNQ3 region, and which allow specific hybridization
to the region. If
CA 02712809 2010-08-20
26
the target sequence contains a sequence identical to that of the probe, the
probes may be short, e.g.,
in the range of about 8-30 base pairs, since the hybrid will be relatively
stable under even highly
stringent conditions. If some degree of mismatch is expected with the probe,
i.e., if it is suspected
that the probe will hybridize to a variant region, a longer probe may be
employed which hybridizes
to the target sequence with the requisite specificity.
The probes will include an isolated polynucleotide attached to a label or
reporter molecule
and may be used to isolate other polynucleotide sequences, having sequence
similarity by standard
methods. For techniques for preparing and labeling probes see, e.g., Sambrook
et al., 1989 or
Ausubel et al., 1992. Other similar polynucleotides may be selected by using
homologous
polynucleotides. Alternatively, polynucleotides encoding these or similar
polypeptides may be
synthesized or selected by use of the redundancy in the genetic code. Various
codon substitutions
may be introduced, e.g., by silent changes (thereby producing various
restriction sites) or to optimize
expression for a particular system. Mutations may be introduced to modify the
properties of the
polypeptide, perhaps to change the polypeptide degradation or turnover rate.
Probes comprising synthetic oligonucleotides or other polynucleotides of the
present
invention may be derived from naturally occurring or recombinant single- or
double-stranded
polynucleotides, or be chemically synthesized. Probes may also be labeled by
nick translation,
Klenow fill-in reaction, or other methods known in the art.
Portions of the polynucleotide sequence having at least about eight
nucleotides, usually at
least about 15 nucleotides, and fewer than about 9 kb, usually fewer than
about 1.0 kb, from a
polynucleotide sequence encoding KCNQ2 or KCNQ3 are preferred as probes. This
definition
therefore includes probes of sizes 8 nucleotides through 9000 nucleotides.
Thus, this definition
includes probes of 8, 12, 15, 20, 25, 40, 60, 80, 100, 200, 300, 400 or 500
nucleotides or probes
having any number of nucleotides within these ranges of values (e.g., 9, 10,
11, 16, 23, 30, 38, 50,
72, 121, etc., nucleotides), or probes having more than 500 nucleotides. The
probes may also be
used to determine whether mRNA encoding KCNQ2 or KCNQ3 is present in a cell or
tissue. The
present invention includes all novel probes having at least 8 nucleotides
derived from SEQ ID NO:1
or SEQ ID NO:6, its complement or functionally equivalent nucleic acid
sequences. The present
invention does not include probes which exist in the prior art. That is, the
present invention includes
all probes having at least 8 nucleotides derived from SEQ ID NO:1 or SEQ ID
NO:6 with the
proviso that they do not include probes existing in the prior art.
CA 02712809 2010-08-20
27
Similar considerations and nucleotide lengths are also applicable to primers
which may be
used for the amplification of all or part of the KCNQ2 or KCNQ3 gene. Thus, a
definition for
primers includes primers of 8, 12, 15, 20, 25, 40, 60, 80, 100, 200, 300, 400,
500 nucleotides, or
primers having any number of nucleotides within these ranges of values (e.g.,
9, 10, 11, 16, 23, 30,
38, 50, 72, 121, etc. nucleotides), or primers having more than 500
nucleotides, or any number of
nucleotides between 500 and 9000. The primers may also be used to determine
whether mRNA
encoding KCNQ2 or KCNQ3 is present in a cell or tissue. The present invention
includes all novel
primers having at least 8 nucleotides derived from the KCNQ2 or KCNQ3 locus
for amplifying the
KCNQ2 or KCNQ3 gene, its complement or functionally equivalent nucleic acid
sequences. The
present invention does not include primers which exist in the prior art. That
is, the present invention
includes all primers having at least 8 nucleotides with the proviso that it
does not include primers
existing in the prior art.
"Protein modifications or fragments" are provided by the present invention for
KCNQ2 or
KCNQ3 polypeptides or fragments thereof which are substantially homologous to
primary structural
sequence but which include, e.g., in vivo or in vitro chemical and biochemical
modifications or
which incorporate unusual amino acids. Such modifications include, for
example, acetylation,
carboxylation, phosphorylation, glycosylation, ubiquitination, labeling, e.g.,
with radionuclides, and
various enzymatic modifications, as will be readily appreciated by those well
skilled in the art. A
variety of methods for labeling polypeptides and of substituents or labels
useful for such purposes
are well known in the art, and include radioactive isotopes such as 32P,
ligands which bind to labeled
antiligands (e.g., antibodies), fluorophores, chemiluminescent agents,
enzymes, and antiligands
which can serve as specific binding pair members for a labeled ligand. The
choice of label depends
on the sensitivity required, ease of conjugation with the primer, stability
requirements, and available
instrumentation. Methods of labeling polypeptides are well known in the art.
See Sambrook et al.,
1989 or Ausubel et al., 1992.
Besides substantially full-length polypeptides, the present invention provides
for biologically
active fragments of the polypeptides. Significant biological activities
include ligand-binding,
immunological activity and other biological activities characteristic of KCNQ2
or KCNQ3
polypeptides. Immunological activities include both immunogenic function in a
target immune
system, as well as sharing of immunological epitopes for binding, serving as
either a competitor or
substitute antigen for an epitope of the KCNQ2 or KCNQ3 protein. As used
herein, "epitope" refers
to an antigenic determinant of a polypeptide. An epitope could comprise three
amino acids in a
CA 02712809 2010-08-20
28
spatial conformation which is unique to the epitope. Generally, an epitope
consists of at least five
such amino acids, and more usually consists of at least 8-10 such amino acids.
Methods of
determining the spatial conformation of such amino acids are known in the art.
For immunological purposes, tandem-repeat polypeptide segments may be used as
immunogens, thereby producing highly antigenic proteins. Alternatively, such
polypeptides will
serve as highly efficient competitors for specific binding. Production of
antibodies specific for
KCNQ2 or KCNQ3 polypeptides or fragments thereof is described below.
The present invention also provides for fusion polypeptides, comprising KCNQ2
or KCNQ3
polypeptides and fragments. Homologous polypeptides may be fusions between two
or more
KCNQ2 or KCNQ3 polypeptide sequences or between the sequences of KCNQ2 or
KCNQ3 and a
related protein. Likewise, heterologous fusions may be constructed which would
exhibit a
combination of properties or activities of the derivative proteins. For
example, ligand-binding or
other domains may be "swapped" between different new fusion polypeptides or
fragments. Such
homologous or heterologous fusion polypeptides may display, for example,
altered strength or
specificity of binding. Fusion partners include immunoglobulins, bacterial P-
galactosidase, trpE,
protein A, 13-lactamase, alpha amylase, alcohol dehydrogenase and yeast alpha
mating factor. See
Godowski et al., 1988.
Fusion proteins will typically be made by either recombinant nucleic acid
methods, as
described below, or may be chemically synthesized. Techniques for the
synthesis of polypeptides
are described, for example, in Merrifield, 1963.
"Protein purification" refers to various methods for the isolation of the
KCNQ2 or KCNQ3
polypeptides from other biological material, such as from cells transformed
with recombinant
nucleic acids encoding KCNQ2 or KCNQ3, and are well known in the art. For
example, such
polypeptides may be purified by immunoaffinity chromatography employing, e.g.,
the antibodies
provided by the present invention. Various methods of protein purification are
well known in the
art, and include those described in Deutscher, 1990 and Scopes, 1982.
The terms "isolated", "substantially pure", and "substantially homogeneous"
are used
interchangeably to describe a protein or polypeptide which has been separated
from components
which accompany it in its natural state. A monomeric protein is substantially
pure when at least
about 60 to 75% of a sample exhibits a single polypeptide sequence. A
substantially pure protein
will typically comprise about 60 to 90% W/W of a protein sample, more usually
about 95%, and
preferably will be over about 99% pure. Protein purity or homogeneity may be
indicated by a
CA 02712809 2010-08-20
29
number of means well known in the art, such as polyacrylamide gel
electrophoresis of a protein
sample, followed by visualizing a single polypeptide band upon staining the
gel. For certain
purposes, higher resolution may be provided by using HPLC or other means well
known in the art
which are utilized for purification.
A KCNQ2 or KCNQ3 protein is substantially free of naturally associated
components when
it is separated from the native contaminants which accompany it in its natural
state. Thus, a
polypeptide which is chemically synthesized or synthesized in a cellular
system different from the
cell from which it naturally originates will be substantially free from its
naturally associated
components. A protein may also be rendered substantially free of naturally
associated components
by isolation, using protein purification techniques well known in the art.
A polypeptide produced as an expression product of an isolated and manipulated
genetic
sequence is an "isolated polypeptide," as used herein, even if expressed in a
homologous cell type.
Synthetically made forms or molecules expressed by heterologous cells are
inherently isolated
molecules.
"Recombinant nucleic acid" is a nucleic acid which is not naturally occurring,
or which is
made by the artificial combination of two otherwise separated segments of
sequence. This artificial
combination is often accomplished by either chemical synthesis means, or by
the artificial
manipulation of isolated segments of nucleic acids, e.g., by genetic
engineering techniques. Such is
usually done to replace a codon with a redundant codon encoding the same or a
conservative amino
acid, while typically introducing or removing a sequence recognition site.
Alternatively, it is
performed to join together nucleic acid segments of desired functions to
generate a desired
combination of functions.
"Regulatory sequences" refers to those sequences normally within 100 kb of the
coding
region of a locus, but they may also be more distant from the coding region,
which affect the
expression of the gene (including transcription of the gene, and translation,
splicing, stability or the
like of the messenger RNA).
"Substantial homology or similarity". A nucleic acid or fragment thereof is
"substantially
homologous" ("or substantially similar") to another if, when optimally aligned
(with appropriate
nucleotide insertions or deletions) with the other nucleic acid (or its
complementary strand), there is
nucleotide sequence identity in at least about 60% of the nucleotide bases,
usually at least about
70%, more usually at least about 80%, preferably at least about 90%, and more
preferably at least
about 95-98% of the nucleotide bases.
CA 02712809 2010-08-20
To determine homology between two different nucleic acids, the percent
homology is to be
determined using the BLASTN program ABLAST 2 sequences@. This program is
available for
public use from the National Center for Biotechnology Information (NCBI) over
the Internet
(http://www.ncbi.nlm.nih.gov/gorf/b12.html) (Altschul et al., 1997). The
parameters to be used are
5 whatever combination of the following yields the highest calculated
percent homology (as calculated
below) with the default parameters shown in parentheses:
Program - blastn
Matrix -0 BLOSUM62
Reward for a match - 0 or 1 (1)
10 Penalty for a mismatch - 0, -1, -2 or -3 (-2)
Open gap penalty - 0, 1, 2, 3, 4 or 5(5)
Extension gap penalty - 0 or 1 (1)
Gap x_dropoff - 0 or 50 (50)
Expect - 10
15 Along with a variety of other results, this program shows a percent
identity across the
complete strands or across regions of the two nucleic acids being matched. The
program shows as
part of the results an alignment and identity of the two strands being
compared. If the strands are of
equal length then the identity will be calculated across the complete length
of the nucleic acids. If
the strands are of unequal lengths, then the length of the shorter nucleic
acid is to be used. If the
20 nucleic acids are quite similar across a portion of their sequences but
different across the rest of their
sequences, the blastn program ABLAST 2 Sequences@ will show an identity across
only the similar
portions, and these portions are reported individually. For purposes of
determining homology
herein, the percent homology refers to the shorter of the two sequences being
compared. If any one
region is shown in different alignments with differing percent identities, the
alignments which yield
25 the greatest homology are to be used. The averaging is to be performed
as in this example of SEQ
ID NOs:20 and 21.
5'-AC C GTAGC TAC GTAC GTATATAGAAAGGGC GC GATCGTC GTC GC GTATGAC GAC
TTAGCATGC-3' (SEQ ID NO:20)
5'-ACCGGTAGCTACGTACGTTATTTAGAAAGGGGTGTGTGTGTGTGTGTAAACCGGG
30 GTTTTC GGGATC GTC C GTC GC GTATGAC GAC TTAGC CATGCAC GGTATATC GTATTAGG
ACTAGCGATTGACTAG-3' (SEQ ID NO:21)
CA 02712809 2010-08-20
31
The program ABLAST 2 Sequences@ shows differing alignments of these two
nucleic acids
depending upon the parameters which are selected. As examples, four sets of
parameters were
selected for comparing SEQ ID NOs:20 and 21 (gap x_dropoff was 50 for all
cases), with the results
shown in Table 1. It is to be noted that none of the sets of parameters
selected as shown in Table 1
is necessarily the best set of parameters for comparing these sequences. The
percent homology is
calculated by multiplying for each region showing identity the fraction of
bases of the shorter strand
within a region times the percent identity for that region and adding all of
these together. For
example, using the first set of parameters shown in Table 1, SEQ ID NO:20 is
the short sequence
(63 bases), and two regions of identity are shown, the first encompassing
bases 4-29 (26 bases) of
.. SEQ ID NO:20 with 92% identity to SEQ ID NO:21 and the second encompassing
bases 39-59 (21
bases) of SEQ ID NO:20 with 100% identity to SEQ ID NO:21. Bases 1-3, 30-38
and 60-63 (16
bases) are not shown as having any identity with SEQ ID NO:21. Percent
homology is calculated as:
(26/63)(92) + (21/63)(100) + (16/63)(0) = 71.3% homology. The percents of
homology calculated
using each of the four sets of parameters shown are listed in Table 1. Several
other combinations of
.. parameters are possible, but they are not listed for the sake of brevity.
It is seen that each set of
parameters resulted in a different calculated percent homology. Because the
result yielding the
highest percent homology is to be used, based solely on these four sets of
parameters one would
state that SEQ ID NOs:20 and 21 have 87.1% homology. Again it is to be noted
that use of other
parameters may show an even higher homology for SEQ ID NOs:20 and 21, but for
brevity not all
the possible results are shown.
Alternatively, substantial homology or (similarity) exists when a nucleic acid
or fragment
thereof will hybridize to another nucleic acid (or a complementary strand
thereof) under selective
hybridization conditions, to a strand, or to its complement. Selectivity of
hybridization exists when
CA 02712809 2010-08-20
32
TABLE 1
Parameter Values
Match Mismatch Open Extension
Regions of identity (%)
Homology
Gap Gap
1 -2 5 1 4-29 of 20 and 39-59 of 20 and 71.3
5-31 of 21 71-91 of 21
(92%) (100%)
1 -2 2 1 4-29 of 20 and 33-63 of 20 and 83.7
5-31 of 21 64-96 of 21
(92%) (93%)
1 -1 5 1 30-59 of 20 and 44.3
61-91 of 21
(93%)
1 -1 2 1 4-29 of 20 and 30-63 of 20 and 87.1
5-31 of 21 61-96 of 21
(92%) (91%)
CA 02712809 2010-08-20
33
hybridization which is substantially more selective than total lack of
specificity occurs. Typically,
selective hybridization will occur when there is at least about 55% homology
over a stretch of at
least about 14 nucleotides, preferably at least about 65%, more preferably at
least about 75%, and
most preferably at least about 90%. See, Kanehisa, 1984. The length of
homology comparison, as
described, may be over longer stretches, and in certain embodiments will often
be over a stretch of at
least about nine nucleotides, usually at least about 20 nucleotides, more
usually at least about 24
nucleotides, typically at least about 28 nucleotides, more typically at least
about 32 nucleotides, and
preferably at least about 36 or more nucleotides.
Nucleic acid hybridization will be affected by such conditions as salt
concentration,
temperature, or organic solvents, in addition to the base composition, length
of the complementary
strands, and the number of nucleotide base mismatches between the hybridizing
nucleic acids, as
will be readily appreciated by those skilled in the art. Stringent temperature
conditions will
generally include temperatures in excess of 30EC, typically in excess of 37EC,
and preferably in
excess of 45EC. Stringent salt conditions will ordinarily be less than 1000
mM, typically less than
500 mM, and preferably less than 200 mM. However, the combination of
parameters is much more
important than the measure of any single parameter. The stringency conditions
are dependent on the
length of the nucleic acid and the base composition of the nucleic acid and
can be determined by
techniques well known in the art. See, e.g., Wetmur and Davidson, 1968.
Probe sequences may also hybridize specifically to duplex DNA under certain
conditions to
form triplex or other higher order DNA complexes. The preparation of such
probes and suitable
hybridization conditions are well known in the art.
The terms "substantial homology" or "substantial identity", when referring to
polypeptides, indicate that the polypeptide or protein in question exhibits at
least about 30% identity
with an entire naturally-occurring protein or a portion thereof, usually at
least about 70% identity,
more usually at least about 80% identity, preferably at least about 90%
identity, and more preferably
at least about 95% identity.
Homology, for polypeptides, is typically measured using sequence analysis
software. See,
e.g., the Sequence Analysis Software Package of the Genetics Computer Group,
University of
Wisconsin Biotechnology Center, 910 University Avenue, Madison, Wisconsin
53705. Protein
analysis software matches similar sequences using measures of homology
assigned to various
substitutions, deletions and other modifications. Conservative substitutions
typically include
CA 02712809 2010-08-20
34
substitutions within the following groups: glycine, alanine; valine,
isoleucine, leucine; aspartic acid,
glutamic acid; asparagine, glutamine; serine, threonine; lysine, arginine; and
phenylalanine, tyrosine.
"Substantially similar function" refers to the function of a modified nucleic
acid or a
modified protein, with reference to the wild-type KCNQ2 or KCNQ3 nucleic acid
or wild-type
KCNQ2 or KCNQ3 polypeptide. The modified polypeptide will be substantially
homologous to the
wild-type KCNQ2 or KCNQ3 polypeptide and will have substantially the same
function. The
modified polypeptide may have an altered amino acid sequence and/or may
contain modified amino
acids. In addition to the similarity of function, the modified polypeptide may
have other useful
properties, such as a longer half-life. The similarity of function (activity)
of the modified
polypeptide may be substantially the same as the activity of the wild-type
KCNQ2 or KCNQ3
polypeptide. Alternatively, the similarity of function (activity) of the
modified polypeptide may be
higher than the activity of the wild-type KCNQ2 or KCNQ3 polypeptide. The
modified polypeptide
is synthesized using conventional techniques, or is encoded by a modified
nucleic acid and produced
using conventional techniques. The modified nucleic acid is prepared by
conventional techniques.
A nucleic acid with a function substantially similar to the wild-type KCNQ2 or
KCNQ3 gene
function produces the modified protein described above.
A polypeptide "fragment," "portion" or "segment" is a stretch of amino acid
residues of at
least about five to seven contiguous amino acids, often at least about seven
to nine contiguous amino
acids, typically at least about nine to 13 contiguous amino acids and, most
preferably, at least about
20 to 30 or more contiguous amino acids.
The polypeptides of the present invention, if soluble, may be coupled to a
solid-phase
support, e.g., nitrocellulose, nylon, column packing materials (e.g.,
Sepharose beads), magnetic
beads, glass wool, plastic, metal, polymer gels, cells, or other substrates.
Such supports may take the
form, for example, of beads, wells, dipsticks, or membranes.
"Target region" refers to a region of the nucleic acid which is amplified
and/or detected.
The term "target sequence" refers to a sequence with which a probe or primer
will form a stable
hybrid under desired conditions.
The practice of the present invention employs, unless otherwise indicated,
conventional
techniques of chemistry, molecular biology, microbiology, recombinant DNA,
genetics, and
immunology. See, e.g., Maniatis et al., 1982; Sambrook et al., 1989; Ausubel
et al., 1992; Glover,
1985; Anand, 1992; Guthrie and Fink, 1991. A general discussion of techniques
and materials for
CA 02712809 2010-08-20
human gene mapping, including mapping of human chromosome 1, is provided,
e.g., in White and
Lalouel, 1988.
Preparation of recombinant or chemically synthesized
5 nucleic acids; vectors, transformation, host cells
Large amounts of the polynucleotides of the present invention may be produced
by
replication in a suitable host cell. Natural or synthetic polynucleotide
fragments coding for a desired
fragment will be incorporated into recombinant polynucleotide constructs,
usually DNA constructs,
capable of introduction into and replication in a prokaryotic or eukaryotic
cell. Usually the
10 polynucleotide constructs will be suitable for replication in a
unicellular host, such as yeast or
bacteria, but may also be intended for introduction to (with and without
integration within the
genome) cultured mammalian or plant or other eukaryotic cell lines. The
purification of nucleic
acids produced by the methods of the present invention are described, e.g., in
Sambrook et al., 1989
or Ausubel et al., 1992.
15 The polynucleotides of the present invention may also be produced by
chemical synthesis,
e.g., by the phosphoramidite method described by Beaucage and Carruthers
(1981) or the triester
method according to Matteucci and Caruthers (1981), and may be performed on
commercial,
automated oligonucleotide synthesizers. A double-stranded fragment may be
obtained from the
single-stranded product of chemical synthesis either by synthesizing the
complementary strand and
20 annealing the strands together under appropriate conditions or by adding
the complementary strand
using DNA polymerase with an appropriate primer sequence.
Polynucleotide constructs prepared for introduction into a prokaryotic or
eukaryotic host may
comprise a replication system recognized by the host, including the intended
polynucleotide
fragment encoding the desired polypeptide, and will preferably also include
transcription and
25 translational initiation regulatory sequences operably linked to the
polypeptide encoding segment.
Expression vectors may include, for example, an origin of replication or
autonomously replicating
sequence (ARS) and expression control sequences, a promoter, an enhancer and
necessary
processing information sites, such as ribosome-binding sites, RNA splice
sites, polyadenylation
sites, transcriptional terminator sequences, and mRNA stabilizing sequences.
Such vectors may be
30 .. prepared by means of standard recombinant techniques well known in the
art and discussed, for
example, in Sambrook et al., 1989 or Ausubel et al., 1992.
An appropriate promoter and other necessary vector sequences will be selected
so as to be
functional in the host, and may include, when appropriate, those naturally
associated with the
CA 02712809 2010-08-20
36
KCNQ2 or KCNQ3 gene. Examples of workable combinations of cell lines and
expression vectors
are described in Sambrook et al., 1989 or Ausubel et al., 1992; see also,
e.g., Metzger et al., 1988.
Many useful vectors are known in the art and may be obtained from such vendors
as Stratagene,
New England Biolabs, Promega Biotech, and others. Promoters such as the trp,
lac and phage
promoters, tRNA promoters and glycolytic enzyme promoters may be used in
prokaryotic hosts.
Useful yeast promoters include promoter regions for metallothionein, 3-
phosphoglycerate kinase or
other glycolytic enzymes such as enolase or glyceraldehyde-3-phosphate
dehydrogenase, enzymes
responsible for maltose and galactose utilization, and others. Vectors and
promoters suitable for use
in yeast expression are further described in Hitzeman et al., EP 73,675A.
Appropriate non-native
mammalian promoters might include the early and late promoters from SV40
(Fiers et al., 1978) or
promoters derived from murine Molony leukemia virus, mouse tumor virus, avian
sarcoma viruses,
adenovirus II, bovine papilloma virus or polyoma. Insect promoters may be
derived from
baculovirus. In addition, the construct may be joined to an amplifiable gene
(e.g., DHFR) so that
multiple copies of the gene may be made. For appropriate enhancer and other
expression control
sequences, see also Enhancers and Eukaryotic Gene Expression, Cold Spring
Harbor Press, Cold
Spring Harbor, New York (1983). See also, e.g., U.S. Patent Nos. 5,691,198;
5,735,500; 5,747,469
and 5,436,146.
While such expression vectors may replicate autonomously, they may also
replicate by being
inserted into the genome of the host cell, by methods well known in the art.
Expression and cloning vectors will likely contain a selectable marker, a gene
encoding a
protein necessary for survival or growth of a host cell transformed with the
vector. The presence of
this gene ensures growth of only those host cells which express the inserts.
Typical selection genes
encode proteins that a) confer resistance to antibiotics or other toxic
substances, e.g. ampicillin,
neomycin, methotrexate, etc., b) complement auxotrophic deficiencies, or c)
supply critical nutrients
not available from complex media, e.g., the gene encoding D-alanine racemase
for Bacilli. The
choice of the proper selectable marker will depend on the host cell, and
appropriate markers for
different hosts are well known in the art.
The vectors containing the nucleic acids of interest can be transcribed in
vitro, and the
resulting RNA introduced into the host cell by well-known methods, e.g., by
injection (see, Kubo et
al., 1988), or the vectors can be introduced directly into host cells by
methods well known in the art,
which vary depending on the type of cellular host, including electroporation;
transfection employing
calcium chloride, rubidium chloride, calcium phosphate, DEAE-dextran, or other
substances;
CA 02712809 2010-08-20
37
microprojectile bombardment; lipofection; infection (where the vector is an
infectious agent, such as
a retroviral genome); and other methods. See generally, Sambrook et al., 1989
and Ausubel et al.,
1992. The introduction of the polynucleotides into the host cell by any method
known in the art,
including, inter alia, those described above, will be referred to herein as
"transformation." The cells
into which have been introduced nucleic acids described above are meant to
also include the progeny
of such cells.
Large quantities of the nucleic acids and polypeptides of the present
invention may be
prepared by expressing the KCNQ2 or KCNQ3 nucleic acid or portions thereof in
vectors or other
expression vehicles in compatible prokaryotic or eukaryotic host cells. The
most commonly used
prokaryotic hosts are strains of Escherichia coli, although other prokaryotes,
such as Bacillus
subtilis or Pseudomonas may also be used.
Mammalian or other eukaryotic host cells, such as those of yeast, filamentous
fungi, plant,
insect, or amphibian or avian species, may also be useful for production of
the proteins of the
present invention. Propagation of mammalian cells in culture is per se well
known. See, Jakoby
and Pastan (eds.) (1979). Examples of commonly used mammalian host cell lines
are VERO and
HeLa cells, Chinese hamster ovary (CHO) cells, and W138, BHK, and COS cell
lines, although it
will be appreciated by the skilled practitioner that other cell lines may be
appropriate, e.g., to
provide higher expression, desirable glycosylation patterns, or other
features. An example of a
commonly used insect cell line is SF9.
Clones are selected by using markers depending on the mode of the vector
construction. The
marker may be on the same or a different DNA molecule, preferably the same DNA
molecule. In
prokaryotic hosts, the transformant may be selected, e.g., by resistance to
ampicillin, tetracycline or
other antibiotics. Production of a particular product based on temperature
sensitivity may also serve
as an appropriate marker.
Prokaryotic or eukaryotic cells transformed with the polynucleotides of the
present invention
will be useful not only for the production of the nucleic acids and
polypeptides of the present
invention, but also, for example, in studying the characteristics of KCNQ2 or
KCNQ3 polypeptide.
The probes and primers based on the KCNQ2 or KCNQ3 gene sequence disclosed
herein are
used to identify homologous KCNQ2 or KCNQ3 gene sequences and proteins in
other species. These
gene sequences and proteins are used in the diagnostic/prognostic, therapeutic
and drug screening
methods described herein for the species from which they have been isolated.
CA 02712809 2010-08-20
38
Methods of Use: Drug Screening
This invention is particularly useful for screening compounds by using the
KCNQ2 or
KCNQ3 polypeptide or binding fragment thereof in any of a variety of drug
screening techniques.
The KCNQ2 or KCNQ3 polypeptide or fragment employed in such a test may either
be free
in solution, affixed to a solid support, or borne on a cell surface. One
method of drug screening
utilizes eucaryotic or procaryotic host cells which are stably transformed
with recombinant
polynucleotides expressing the polypeptide or fragment, preferably in
competitive binding assays.
Such cells, either in viable or fixed form, can be used for standard binding
assays. One may
measure, for example, for the formation of complexes between a KCNQ2 or KCNQ3
polypeptide or
fragment and the agent being tested, or examine the degree to which the
formation of a complex
between a KCNQ2 or KCNQ3 polypeptide or fragment and a known ligand is
interfered with by the
agent being tested.
Thus, the present invention provides methods of screening for drugs comprising
contacting
such an agent with a KCNQ2 or KCNQ3 polypeptide or fragment thereof and
assaying (i) for the
presence of a complex between the agent and the KCNQ2 or KCNQ3 polypeptide or
fragment, or
(ii) for the presence of a complex between the KCNQ2 or KCNQ3 polypeptide or
fragment and a
ligand, by methods well known in the art. In such competitive binding assays
the KCNQ2 or
KCNQ3 polypeptide or fragment is typically labeled. Free KCNQ2 or KCNQ3
polypeptide or
fragment is separated from that present in a protein:protein complex, and the
amount of free (i.e.,
uncomplexed) label is a measure of the binding of the agent being tested to
KCNQ2 or KCNQ3 or
its interference with KCNQ2(or KCNQ3):ligand binding, respectively. One may
also measure the
amount of bound, rather than free, KCNQ2 or KCNQ3. It is also possible to
label the ligand rather
than the KCNQ2 or KCNQ3 and to measure the amount of ligand binding to KCNQ2
or KCNQ3 in
the presence and in the absence of the drug being tested.
Another technique for drug screening provides high throughput screening for
compounds
having suitable binding affinity to the KCNQ2 or KCNQ3 polypeptides and is
described in detail in
Geysen (published PCT published application WO 84/03564). Briefly stated,
large numbers of
different small peptide test compounds are synthesized on a solid substrate,
such as plastic pins or
some other surface. The peptide test compounds are reacted with KCNQ2 or KCNQ3
polypeptide
and washed. Bound KCNQ2 or KCNQ3 polypeptide is then detected by methods well
known in the
art.
CA 02712809 2010-08-20
39
Purified KCNQ2 or KCNQ3 can be coated directly onto plates for use in the
aforementioned
drug screening techniques. However, non-neutralizing antibodies to the
polypeptide can be used to
capture antibodies to immobilize the KCNQ2 or KCNQ3 polypeptide on the solid
phase.
This invention also contemplates the use of competitive drug screening assays
in which
neutralizing antibodies capable of specifically binding the KCNQ2 or KCNQ3
polypeptide compete
with a test compound for binding to the KCNQ2 or KCNQ3 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 determinants of the KCNQ2 or KCNQ3 polypeptide.
The invention is particularly useful for screening compounds by using KCNQ2 or
KCNQ3
protein in transformed cells, transfected oocytes or transgenic animals. The
drug is added to the
cells in culture or administered to a transgenic animal containing mutant
KCNQ2 or KCNQ3 and the
effect on the current of the potassium channel is compared to the current of a
cell or animal
containing the wild-type KCNQ2 or KCNQ3. Drug candidates which alter the
current to a more
normal level are useful for treating or preventing BFNC, rolandic epilepsy and
JME.
The above screening methods are not limited to assays employing only KCNQ2 or
KCNQ3
but are also applicable to studying KCNQ2- or KCNQ3-protein complexes. The
effect of drugs on
the activity of this complex is analyzed.
In accordance with these methods, the following assays are examples of assays
which can be
used for screening for drug candidates.
A mutant KCNQ2 or KCNQ3 (per se or as part of a fusion protein) is mixed with
a wild-type
protein (per se or as part of a fusion protein) to which wild-type KCNQ2 or
KCNQ3 binds. This
mixing is performed in both the presence of a drug and the absence of the
drug, and the amount of
binding of the mutant KCNQ2 or KCNQ3 with the wild-type protein is measured.
If the amount of
the binding is more in the presence of said drug than in the absence of said
drug, the drug is a drug
candidate for treating BFNC, rolandic epilepsy or JME resulting from a
mutation in KCNQ2 or
KCNQ3.
A wild-type KCNQ2 or KCNQ3 (per se or as part of a fusion protein) is mixed
with a wild-
type protein (per se or as part of a fusion protein) to which wild-type KCNQ2
or KCNQ3 binds.
This mixing is performed in both the presence of a drug and the absence of the
drug, and the amount
of binding of the wild-type KCNQ2 or KCNQ3 with the wild-type protein is
measured. If the
amount of the binding is more in the presence of said drug than in the absence
of said drug, the drug
CA 02712809 2010-08-20
is a drug candidate for treating BFNC, rolandic epilepsy or JME resulting from
a mutation in
KCNQ2 or KCNQ3.
A mutant protein, which as a wild-type protein binds to KCNQ2 or KCNQ3 (per se
or as part
of a fusion protein) is mixed with a wild-type KCNQ2 or KCNQ3 (per se or as
part of a fusion
5
protein). This mixing is performed in both the presence of a drug and the
absence of the drug, and
the amount of binding of the mutant protein with the wild-type KCNQ2 or KCNQ3
is measured. If
the amount of the binding is more in the presence of said drug than in the
absence of said drug, the
drug is a drug candidate for treating BFNC, rolandic epilepsy or JME resulting
from a mutation in
the gene encoding the protein.
10
The polypeptide of the invention may also be used for screening compounds
developed as a
result of combinatorial library technology. Combinatorial library technology
provides an efficient
way of testing a potential vast number of different substances for ability to
modulate activity of a
polypeptide. Such libraries and their use are known in the art. The use of
peptide libraries is
preferred. See, for example, WO 97/02048.
15
Briefly, a method of screening for a substance which modulates activity of a
polypeptide may
include contacting one or more test substances with the polypeptide in a
suitable reaction medium,
testing the activity of the treated polypeptide and comparing that activity
with the activity of the
polypeptide in comparable reaction medium untreated with the test substance or
substances. A
difference in activity between the treated and untreated polypeptides is
indicative of a modulating
20 effect of the relevant test substance or substances.
Prior to or as well as being screened for modulation of activity, test
substances may be
screened for ability to interact with the polypeptide, e.g., in a yeast two-
hybrid system (e.g., Bartel et
al., 1993; Fields and Song, 1989; Chevray and Nathans, 1992; Lee et al.,
1995). This system may be
used as a coarse screen prior to testing a substance for actual ability to
modulate activity of the
25
polypeptide. Alternatively, the screen could be used to screen test substances
for binding to a
KCNQ2 or KCNQ3 specific binding partner, or to find mimetics of the KCNQ2 or
KCNQ3
polypeptide.
Following identification of a substance which modulates or affects polypeptide
activity, the
substance may be investigated further. Furthermore, it may be manufactured
and/or used in
30 preparation, i.e., manufacture or formulation, or a composition such as a
medicament,
pharmaceutical composition or drug. These may be administered to individuals.
CA 02712809 2010-08-20
41
Thus, the present invention extends in various aspects not only to a substance
identified
using a nucleic acid molecule as a modulator of polypeptide activity, in
accordance with what is
disclosed herein, but also a pharmaceutical composition, medicament, drug or
other composition
comprising such a substance, a method comprising administration of such a
composition comprising
such a substance, a method comprising administration of such a composition to
a patient, e.g., for
treatment (which may include preventative treatment) of BFNC, rolandic
epilepsy or JME, use of
such a substance in the manufacture of a composition for administration, e.g.,
for treatment of
BFNC, rolandic epilepsy or JME, and a method of making a pharmaceutical
composition comprising
admixing such a substance with a pharmaceutically acceptable excipient,
vehicle or carrier, and
optionally other ingredients.
A substance identified as a modulator of polypeptide function may be peptide
or non-peptide
in nature. Non-peptide Asmall molecules@ are often preferred for many in vivo
pharmaceutical uses.
Accordingly, a mimetic or mimic of the substance (particularly if a peptide)
may be designed for
pharmaceutical use.
The designing of mimetics to a known pharmaceutically active compound is a
known
approach to the development of pharmaceuticals based on a Alead@ compound.
This might be
desirable where the active compound is difficult or expensive to synthesize or
where it is unsuitable
for a particular method of administration, e.g., pure peptides are unsuitable
active agents for oral
compositions as they tend to be quickly degraded by proteases in the
alimentary canal. Mimetic
design, synthesis and testing is generally used to avoid randomly screening
large numbers of
molecules for a target property.
There are several steps commonly taken in the design of a mimetic from a
compound having
a given target property. First, the particular parts of the compound that are
critical and/or important
in determining the target property are determined. In the case of a peptide,
this can be done by
systematically varying the amino acid residues in the peptide, e.g., by
substituting each residue in
turn. Alanine scans of peptide are commonly used to refine such peptide
motifs. These parts or
residues constituting the active region of the compound are known as its
Apharmacophore@.
Once the pharmacophore has been found, its structure is modeled according to
its physical
properties, e.g., stereochemistry, bonding, size and/or charge, using data
from a range of sources,
e.g., spectroscopic techniques, x-ray diffraction data and NMR. Computational
analysis, similarity
mapping (which models the charge and/or volume of a pharmacophore, rather than
the bonding
between atoms) and other techniques can be used in this modeling process.
CA 02712809 2010-08-20
42
In a variant of this approach, the three-dimensional structure of the ligand
and its binding
partner are modeled. This can be especially useful where the ligand and/or
binding partner change
conformation on binding, allowing the model to take account of this in the
design of the mimetic.
A template molecule is then selected onto which chemical groups which mimic
the
pharmacophore can be grafted. The template molecule and the chemical groups
grafted onto it can
conveniently be selected so that the mimetic is easy to synthesize, is likely
to be pharmacologically
acceptable, and does not degrade in vivo, while retaining the biological
activity of the lead
compound. Alternatively, where the mimetic is peptide-based, further stability
can be achieved by
cyclizing the peptide, increasing its rigidity. The mimetic or mimetics found
by this approach can
then be screened to see whether they have the target property, or to what
extent they exhibit it.
Further optimization or modification can then be carried out to arrive at one
or more final mimetics
for in vivo or clinical testing.
Methods of Use: Nucleic Acid Diagnosis and Diagnostic Kits
In order to detect the presence of a KCNQ2 or KCNQ3 allele predisposing an
individual to
BFNC, rolandic epilepsy or JME, a biological sample such as blood is prepared
and analyzed for the
presence or absence of susceptibility alleles of KCNQ2 or KCNQ3. In order to
detect the presence
of BFNC, rolandic epilepsy or JME, or as a prognostic indicator, a biological
sample is prepared and
analyzed for the presence or absence of mutant alleles of KCNQ2 or KCNQ3.
Results of these tests
and interpretive information are returned to the health care provider for
communication to the tested
individual. Such diagnoses may be performed by diagnostic laboratories, or,
alternatively,
diagnostic kits are manufactured and sold to health care providers or to
private individuals for self-
diagnosis.
Initially, the screening method involves amplification of the relevant KCNQ2
or KCNQ3
sequences. In another preferred embodiment of the invention, the screening
method involves a non-
PCR based strategy. Such screening methods include two-step label
amplification methodologies
that are well known in the art. Both PCR and non-PCR based screening
strategies can detect target
sequences with a high level of sensitivity.
The most popular method used today is target amplification. Here, the target
nucleic acid
sequence is amplified with polymerases. One particularly preferred method
using polymerase-
driven amplification is the polymerase chain reaction (PCR). The polymerase
chain reaction and
other polymerase-driven amplification assays can achieve over a million-fold
increase in copy
CA 02712809 2010-08-20
43
number through the use of polymerase-driven amplification cycles. Once
amplified, the resulting
nucleic acid can be sequenced or used as a substrate for DNA probes.
When the probes are used to detect the presence of the target sequences the
biological sample
to be analyzed, such as blood or serum, may be treated, if desired, to extract
the nucleic acids. The
sample nucleic acid may be prepared in various ways to facilitate detection of
the target sequence,
e.g. denaturation, restriction digestion, electrophoresis or dot blotting. The
targeted region of the
analyte nucleic acid usually must be at least partially single-stranded to
form hybrids with the
targeting sequence of the probe. If the sequence is naturally single-stranded,
denaturation will not be
required. However, if the sequence is double-stranded, the sequence will
probably need to be
denatured. Denaturation can be carried out by various techniques known in the
art.
Analyte nucleic acid and probe are incubated under conditions which promote
stable hybrid
formation of the target sequence in the probe with the putative targeted
sequence in the analyte. The
region of the probes which is used to bind to the analyte can be made
completely complementary to
the targeted region of human chromosome 20 for KCNQ2 or to the targeted region
of human
chromosome 8 for KCNQ3. Therefore, high stringency conditions are desirable in
order to prevent
false positives. However, conditions of high stringency are used only if the
probes are
complementary to regions of the chromosome which are unique in the genome. The
stringency of
hybridization is determined by a number of factors during hybridization and
during the washing
procedure, including temperature, ionic strength, base composition, probe
length, and concentration
of formamide. These factors are outlined in, for example, Maniatis et al.,
1982 and Sambrook et al.,
1989. Under certain circumstances, the formation of higher order hybrids, such
as triplexes,
quadraplexes, etc., may be desired to provide the means of detecting target
sequences.
Detection, if any, of the resulting hybrid is usually accomplished by the use
of labeled
probes. Alternatively, the probe may be unlabeled, but may be detectable by
specific binding with a
ligand which is labeled, either directly or indirectly. Suitable labels, and
methods for labeling
probes and ligands are known in the art, and include, for example, radioactive
labels which may be
incorporated by known methods (e.g., nick translation, random priming or
kinasing), biotin,
fluorescent groups, chemiluminescent groups (e.g., dioxetanes, particularly
triggered dioxetanes),
enzymes, antibodies, gold nanoparticles and the like. Variations of this basic
scheme are known in
the art, and include those variations that facilitate separation of the
hybrids to be detected from
extraneous materials and/or that amplify the signal from the labeled moiety. A
number of these
CA 02712809 2010-08-20
44
variations are reviewed in, e.g., Matthews and Kricka, 1988; Landegren etal.,
1988; Mifflin, 1989;
U.S. Patent 4,868,105; and in EPO Publication No. 225,807.
As noted above, non-PCR based screening assays are also contemplated in this
invention.
This procedure hybridizes a nucleic acid probe (or an analog such as a methyl
phosphonate
backbone replacing the normal phosphodiester), to the low level DNA target.
This probe may have
an enzyme covalently linked to the probe, such that the covalent linkage does
not interfere with the
specificity of the hybridization. This enzyme-probe-conjugate-target nucleic
acid complex can then
be isolated away from the free probe enzyme conjugate and a substrate is added
for enzyme
detection. Enzymatic activity is observed as a change in color development or
luminescent output
resulting in a 103-106 increase in sensitivity. For an example relating to the
preparation of
oligodeoxynucleotide-alkaline phosphatase conjugates and their use as
hybridization probes, see
Jablonski et al., 1986.
Two-step label amplification methodologies are known in the art. These assays
work on the
principle that a small ligand (such as digoxigenin, biotin, or the like) is
attached to a nucleic acid
probe capable of specifically binding KCNQ2 or KCNQ3. Allele specific probes
are also
contemplated within the scope of this example and exemplary allele specific
probes include probes
encompassing the predisposing mutations of this disclosure.
In one example, the small ligand attached to the nucleic acid probe is
specifically recognized
by an antibody-enzyme conjugate. In one embodiment of this example,
digoxigenin is attached to
the nucleic acid probe. Hybridization is detected by an antibody-alkaline
phosphatase conjugate
which turns over a chemiluminescent substrate. For methods for labeling
nucleic acid probes
according to this embodiment see Martin et al., 1990. In a second example, the
small ligand is
recognized by a second ligand-enzyme conjugate that is capable of specifically
complexing to the
first ligand. A well known embodiment of this example is the biotin-avidin
type of interactions. For
.. methods for labeling nucleic acid probes and their use in biotin-avidin
based assays see Rigby et al.,
1977 and Nguyen et al., 1992.
It is also contemplated within the scope of this invention that the nucleic
acid probe assays of
this invention will employ a cocktail of nucleic acid probes capable of
detecting KCNQ2 or KCNQ3.
Thus, in one example to detect the presence of KCNQ2 or KCNQ3 in a cell
sample, more than one
probe complementary to the gene is employed and in particular the number of
different probes is
alternatively two, three, or five different nucleic acid probe sequences. In
another example, to detect
the presence of mutations in the KCNQ2 or KCNQ3 gene sequence in a patient,
more than one probe
CA 02712809 2010-08-20
complementary to these genes is employed where the cocktail includes probes
capable of binding to
the allele-specific mutations identified in populations of patients with
alterations in KCNQ2 or
KCNQ3. In this embodiment, any number of probes can be used, and will
preferably include probes
corresponding to the major gene mutations identified as predisposing an
individual to BFNC,
5 rolandic epilepsy or JME.
Methods of Use: Peptide Diagnosis and Diagnostic Kits
The presence of BFNC, rolandic epilepsy or JME can also be detected on the
basis of the
alteration of wild-type KCNQ2 or KCNQ3 polypeptide. Such alterations can be
determined by
10 sequence analysis in accordance with conventional techniques. More
preferably, antibodies
(polyclonal or monoclonal) are used to detect differences in, or the absence
of KCNQ2 or KCNQ3
peptides. Techniques for raising and purifying antibodies are well known in
the art and any such
techniques may be chosen to achieve the preparations claimed in this
invention. In a preferred
embodiment of the invention, antibodies will immunoprecipitate KCNQ2 or KCNQ3
proteins from
15 solution as well as react with these proteins on Western or immunoblots
of polyacrylamide gels. In
another preferred embodiment, antibodies will detect KCNQ2 or KCNQ3 proteins
in paraffin or
frozen tissue sections, using immunocytochemical techniques.
Preferred embodiments relating to methods for detecting KCNQ2 or KCNQ3 or
their
mutations include enzyme linked immunosorbent assays (ELISA),
radioimmunoassays (RIA),
20 immunoradiometric assays (IRMA) and immunoenzymatic assays (IEMA),
including sandwich
assays using monoclonal and/or polyclonal antibodies. Exemplary sandwich
assays are described by
David et al., in U.S. Patent Nos. 4,376,110 and 4,486,530.
Methods of Use: Rational Drug Design
25 The goal of rational drug design is to produce structural analogs of
biologically active
polypeptides of interest or of small molecules with which they interact (e.g.,
agonists, antagonists,
inhibitors) in order to fashion drugs which are, for example, more active or
stable forms of the
polypeptide, or which, e.g., enhance or interfere with the function of a
polypeptide in vivo. See, e.g.,
Hodgson, 1991. In one approach, one first determines the three-dimensional
structure of a protein of
30 interest (e.g., KCNQ2 or KCNQ3 polypeptide) by x-ray crystallography, by
computer modeling or
most typically, by a combination of approaches. Less often, useful information
regarding the
structure of a polypeptide may be gained by modeling based on the structure of
homologous
CA 02712809 2010-08-20
46
proteins. An example of rational drug design is the development of HIV
protease inhibitors
(Erickson et al., 1990). In addition, peptides (e.g., KCNQ2 or KCNQ3
polypeptide) are analyzed by
an alanine scan (Wells, 1991). In this technique, an amino acid residue is
replaced by Ala, and its
effect on the peptide=s activity is determined. Each of the amino acid
residues of the peptide is
analyzed in this manner to determine the important regions of the peptide.
It is also possible to isolate a target-specific antibody, selected by a
functional assay, and
then to solve its crystal structure. In principle, this approach yields a
pharmacore upon which
subsequent drug design can be based. It is possible to bypass protein
crystallography 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 banks of peptides. Selected peptides
would then act as the
pharmacore.
Thus, one may design drugs which have, e.g., improved KCNQ2 or KCNQ3
polypeptide
activity or stability or which act as inhibitors, agonists, antagonists, etc.
of KCNQ2 or KCNQ3
polypeptide activity. By virtue of the availability of cloned KCNQ2 and KCNQ3
sequences,
sufficient amounts of the KCNQ2 and KCNQ3 polypeptides may be made available
to perform such
analytical studies as x-ray crystallography. In addition, the knowledge of the
KCNQ2 and KCNQ3
protein sequences provided herein will guide those employing computer modeling
techniques in
place of, or in addition to x-ray crystallography.
Methods of Use: Gene Therapy
According to the present invention, a method is also provided of supplying
wild-type
KCNQ2 or KCNQ3 function to a cell which carries a mutant KCNQ2 or KCNQ3
allele, respectively.
Supplying such a function should allow normal functioning of the recipient
cells. The wild-type
gene or a part of the gene may be introduced into the cell in a vector such
that the gene remains
extrachromosomal. In such a situation, the gene will be expressed by the cell
from the
extrachromosomal location. More preferred is the situation where the wild-type
gene or a part
thereof is introduced into the mutant cell in such a way that it recombines
with the endogenous
mutant gene present in the cell. Such recombination requires a double
recombination event which
results in the correction of the gene mutation. Vectors for introduction of
genes both for
recombination and for extrachromosomal maintenance are known in the art, and
any suitable vector
CA 02712809 2010-08-20
47
may be used. Methods for introducing DNA into cells such as electroporation,
calcium phosphate
co-precipitation and viral transduction are known in the art, and the choice
of method is within the
competence of the practitioner.
As generally discussed above, the KCNQ2 or KCNQ3 gene or fragment, where
applicable,
may be employed in gene therapy methods in order to increase the amount of the
expression
products of such gene in cells. It may also be useful to increase the level of
expression of the
KCNQ2 or KCNQ3 gene even in those persons in which the mutant gene is
expressed at a Anormal@
level, but the gene product is not fully functional.
Gene therapy would be carried out according to generally accepted methods, for
example, as
described by Friedman (1991) or Culver (1996). Cells from a patient would be
first analyzed by the
diagnostic methods described above, to ascertain the production of KCNQ2
and/or KCNQ3
polypeptide in the cells. A virus or plasmid vector (see further details
below), containing a copy of
the KCNQ2 or KCNQ3 gene linked to expression control elements and capable of
replicating inside
the cells, is prepared. The vector may be capable of replicating inside the
cells. Alternatively, the
vector may be replication deficient and is replicated in helper cells for use
in gene therapy. Suitable
vectors are known, such as disclosed in U.S. Patent 5,252,479 and PCT
published application WO
93/07282 and U.S. Patent Nos. 5,691,198; 5,747,469; 5,436,146 and 5,753,500.
The vector is then
injected into the patient. If the transfected gene is not permanently
incorporated into the genome of
each of the targeted cells, the treatment may have to be repeated
periodically.
Gene transfer systems known in the art may be useful in the practice of the
gene therapy
methods of the present invention. These include viral and nonviral transfer
methods. A number of
viruses have been used as gene transfer vectors or as the basis for repairing
gene transfer vectors,
including papovaviruses (e.g., SV40, Madzak et al., 1992), adenovirus
(Berkner, 1992; Berkner et
al., 1988; Gorziglia and Kapikian, 1992; Quantin et al., 1992; Rosenfeld et
al., 1992; Wilkinson and
Akrigg, 1992; Stratford-Perricaudet et al., 1990; Schneider et al., 1998),
vaccinia virus (Moss, 1992;
Moss, 1996), adeno-associated virus (Muzyczka, 1992; Ohi et al., 1990; Russell
and Hirata, 1998),
herpesviruses including HSV and EBV (Margolskee, 1992; Johnson et al., 1992;
Fink et al., 1992;
Breakefield and Geller, 1987; Freese et al., 1990; Fink et al., 1996),
lentiviruses (Naldini et al.,
1996), Sindbis and Semliki Forest virus (Berglund et al., 1993), and
retroviruses of avian
(Bandyopadhyay and Temin, 1984; Petropoulos et al., 1992), murine (Miller,
1992; Miller et al.,
1985; Sorge et al., 1984; Mann and Baltimore, 1985; Miller et al., 1988), and
human origin
(Shimada et al., 1991; Helseth et al., 1990; Page et al., 1990; Buchschacher
and Panganiban, 1992).
CA 02712809 2010-08-20
48
Most human gene therapy protocols have been based on disabled murine
retroviruses, although
adenovirus and adeno-associated virus are also being used.
Nonviral gene transfer methods known in the art include chemical techniques
such as
calcium phosphate coprecipitation (Graham and van der Eb, 1973; Pellicer et
al., 1980); mechanical
.. techniques, for example microinjection (Anderson et al., 1980; Gordon
etal., 1980; Brinster et al.,
1981; Costantini and Lacy, 1981); membrane fusion-mediated transfer via
liposomes (Feigner etal.,
1987; Wang and Huang, 1989; Kaneda et al., 1989; Stewart et al., 1992; Nabel
etal., 1990; Lim et
al., 1991); and direct DNA uptake and receptor-mediated DNA transfer (Wolff et
al., 1990; Wu et
al., 1991; Zenke etal., 1990; Wu et al., 1989; Wolff et al., 1991; Wagner
etal., 1990; Wagner etal.,
1991; Cotten et al., 1990; Curiel etal., 1992; Curiel etal., 1991). Viral-
mediated gene transfer can
be combined with direct in vitro gene transfer using liposome delivery,
allowing one to direct the
viral vectors to the tumor cells and not into the surrounding nondividing
cells. Alternatively, the
retroviral vector producer cell line can be injected into tumors (Culver et
al., 1992). Injection of
producer cells would then provide a continuous source of vector particles.
This technique has been
approved for use in humans with inoperable brain tumors.
In an approach which combines biological and physical gene transfer methods,
plasmid DNA
of any size is combined with a polylysine-conjugated antibody specific to the
adenovirus hexon
protein, and the resulting complex is bound to an adenovirus vector. The
trimolecular complex is
then used to infect cells. The adenovirus vector permits efficient binding,
internalization, and
degradation of the endosome before the coupled DNA is damaged. For other
techniques for the
delivery of adenovirus based vectors see Schneider et al. (1998) and U.S.
Patent Nos. 5,691,198;
5,747,469; 5,436,146 and 5,753,500.
Liposome/DNA complexes have been shown to be capable of mediating direct in
vivo gene
transfer. While in standard liposome preparations the gene transfer process is
nonspecific, localized
in vivo uptake and expression have been reported in tumor deposits, for
example, following direct in
situ administration (Nabel, 1992).
Expression vectors in the context of gene therapy are meant to include those
constructs
containing sequences sufficient to express a polynucleotide that has been
cloned therein. In viral
expression vectors, the construct contains viral sequences sufficient to
support packaging of the
construct. If the polynucleotide encodes KCNQ2 or KCNQ3, expression will
produce KCNQ2 or
KCNQ3. If the polynucleotide encodes an antisense polynucleotide or a
ribozyme, expression will
produce the antisense polynucleotide or ribozyme. Thus in this context,
expression does not require
CA 02712809 2010-08-20
49
that a protein product be synthesized. In addition to the polynucleotide
cloned into the expression
vector, the vector also contains a promoter functional in eukaryotic cells.
The cloned polynucleotide
sequence is under control of this promoter. Suitable eukaryotic promoters
include those described
above. The expression vector may also include sequences, such as selectable
markers and other
sequences described herein.
Gene transfer techniques which target DNA directly to brain tissue is
preferred. Receptor-
mediated gene transfer, for example, is accomplished by the conjugation of DNA
(usually in the
form of covalently closed supercoiled plasmid) to a protein ligand via
polylysine. Ligands are
chosen on the basis of the presence of the corresponding ligand receptors on
the cell surface of the
target cell/tissue type. These ligand-DNA conjugates can be injected directly
into the blood if
desired and are directed to the target tissue where receptor binding and
internalization of the DNA-
protein complex occurs. To overcome the problem of intracellular destruction
of DNA, coinfection
with adenovirus can be included to disrupt endosome function.
The therapy is as follows: patients who carry a KCNQ2 or KCNQ3 susceptibility
allele are
treated with a gene delivery vehicle such that some or all of their brain
precursor cells receive at
least one additional copy of a functional normal KCNQ2 or KCNQ3 allele,
respectively. In this step,
the treated individuals have reduced risk of BFNC, rolandic epilepsy and/or
JME to the extent that
the effect of the susceptible allele has been countered by the presence of the
normal allele.
Methods of Use: Peptide Therapy
Peptides which have KCNQ2 or KCNQ3 activity can be supplied to cells which
carry mutant
or missing KCNQ2 or KCNQ3 alleles, respectively. Protein can be produced by
expression of the
cDNA sequence in bacteria, for example, using known expression vectors.
Alternatively, KCNQ2
or KCNQ3 polypeptide can be extracted from KCNQ2- or KCNQ3-producing mammalian
cells. In
addition, the techniques of synthetic chemistry can be employed to synthesize
KCNQ2 or KCNQ3
protein. Any of such techniques can provide the preparation of the present
invention which
comprises the KCNQ2 or KCNQ3 protein. The preparation is substantially free of
other human
proteins. This is most readily accomplished by synthesis in a microorganism or
in vitro.
Active KCNQ2 or KCNQ3 molecules can be introduced into cells by microinjection
or by
.. use of liposomes, for example. Alternatively, some active molecules may be
taken up by cells,
actively or by diffusion. Supply of molecules with KCNQ2 or KCNQ3 activity
should lead to
partial reversal of BFNC, rolandic epilepsy and/or JME. Other molecules with
KCNQ2 or KCNQ3
CA 02712809 2010-08-20
activity (for example, peptides, drugs or organic compounds) may also be used
to effect such a
reversal. Modified polypeptides having substantially similar function are also
used for peptide
therapy.
5 Methods of Use: Transformed Hosts
Animals for testing therapeutic agents can be selected after mutagenesis of
whole animals or
after treatment of germline cells or zygotes. Such treatments include
insertion of mutant KCNQ2
and/or KCNQ3 alleles, usually from a second animal species, as well as
insertion of disrupted
homologous genes. Alternatively, the endogenous KCNQ2 or KCNQ3 gene of the
animals may be
10 disrupted by insertion or deletion mutation or other genetic alterations
using conventional techniques
(Capecchi, 1989; Valancius and Smithies, 1991; Hasty et al., 1991; Shinkai et
al., 1992; Mombaerts
et al., 1992; Philpott et al., 1992; Snouwaert et al., 1992; Donehower et al.,
1992). After test
substances have been administered to the animals, the presence of BFNC,
rolandic epilepsy or JME
must be assessed. If the test substance prevents or suppresses the appearance
of BFNC, rolandic
15 epilepsy or JME, then the test substance is a candidate therapeutic
agent for treatment of BFNC,
rolandic epilepsy or JME. These animal models provide an extremely important
testing vehicle for
potential therapeutic products.
The identification of the association between the KCNQ2 and KCNQ3 gene
mutations and
BFNC, rolandic epilepsy and JME permits the early presymptomatic screening of
individuals to
20 identify those at risk for developing BFNC, rolandic epilepsy or JME. To
identify such individuals,
KCNQ2 and/or KCNQ3 alleles are screened for mutations either directly or after
cloning the alleles.
The alleles are tested for the presence of nucleic acid sequence differences
from the normal allele
using any suitable technique, including but not limited to, one of the
following methods: fluorescent
in situ hybridization (FISH), direct DNA sequencing, PFGE analysis, Southern
blot analysis, single
25 stranded conformation analysis (SSCP), linkage analysis, RNase
protection assay, allele specific
oligonucleotide (ASO), dot blot analysis and PCR-SSCP analysis. Also useful is
the recently
developed technique of DNA microchip technology. For example, either (1) the
nucleotide
sequence of both the cloned alleles and normal KCNQ2 or KCNQ3 gene or
appropriate fragment
(coding sequence or genomic sequence) are determined and then compared, or (2)
the RNA
30 .. transcripts of the KCNQ2 or KCNQ3 gene or gene fragment are hybridized
to single stranded whole
genomic DNA from an individual to be tested, and the resulting heteroduplex is
treated with
CA 02712809 2010-08-20
51
Ribonuclease A (RNase A) and run on a denaturing gel to detect the location of
any mismatches.
Two of these methods can be carried out according to the following procedures.
The alleles of the KCNQ2 or KCNQ3 gene in an individual to be tested are
cloned using
conventional techniques. For example, a blood sample is obtained from the
individual. The
genomic DNA isolated from the cells in this sample is partially digested to an
average fragment size
of approximately 20 kb. Fragments in the range from 18-21 kb are isolated. The
resulting fragments
are ligated into an appropriate vector. The sequences of the clones are then
determined and
compared to the normal KCNQ2 or KCNQ3 gene.
Alternatively, polymerase chain reactions (PCRs) are performed with primer
pairs for the 5'
region or the exons of the KCNQ2 or KCNQ3 gene. PCRs can also be performed
with primer pairs
based on any sequence of the normal KCNQ2 or KCNQ3 gene. For example, primer
pairs for one of
the introns can be prepared and utilized. Finally, RT-PCR can also be
performed on the mRNA.
The amplified products are then analyzed by single stranded conformation
polymorphisms (SSCP)
using conventional techniques to identify any differences and these are then
sequenced and
compared to the normal gene sequence.
Individuals can be quickly screened for common KCNQ2 or KCNQ3 gene variants by
amplifying the individual's DNA using suitable primer pairs and analyzing the
amplified product,
e.g., by dot-blot hybridization using allele-specific oligonucleotide probes.
The second method employs RNase A to assist in the detection of differences
between the
normal KCNQ2 or KCNQ3 gene and defective genes. This comparison is performed
in steps using
small (-500 bp) restriction fragments of the KCNQ2 or KCNQ3 gene as the probe.
First, the
KCNQ2 or KCNQ3 gene is digested with a restriction enzyme(s) that cuts the
gene sequence into
fragments of approximately 500 bp. These fragments are separated on an
electrophoresis gel,
purified from the gel and cloned individually, in both orientations, into an
SP6 vector (e.g., pSP64 or
pSP65). The SP6-based plasmids containing inserts of the KCNQ2 or KCNQ3 gene
fragments are
transcribed in vitro using the SP6 transcription system, well known in the
art, in the presence of [a-
32MTP, generating radiolabeled RNA transcripts of both strands of the gene.
Individually, these RNA transcripts are used to form heteroduplexes with the
allelic DNA
using conventional techniques. Mismatches that occur in the RNA:DNA
heteroduplex, owing to
sequence differences between the KCNQ2 or KCNQ3 fragment and the KCNQ2 or
KCNQ3 allele
subclone from the individual, result in cleavage in the RNA strand when
treated with RNase A.
Such mismatches can be the result of point mutations or small deletions in the
individual's allele.
CA 02712809 2010-08-20
52
Cleavage of the RNA strand yields two or more small RNA fragments, which run
faster on the
denaturing gel than the RNA probe itself.
Any differences which are found, will identify an individual as having a
molecular variant of
the KCNQ2 or KCNQ3 gene and the consequent presence of BFNC, rolandic epilepsy
or JME.
These variants can take a number of forms. The most severe forms would be
frame shift mutations
or large deletions which would cause the gene to code for an abnormal protein
or one which would
significantly alter protein expression. Less severe disruptive mutations would
include small in-
frame deletions and nonconservative base pair substitutions which would have a
significant effect on
the protein produced, such as changes to or from a cysteine residue, from a
basic to an acidic amino
acid or vice versa, from a hydrophobic to hydrophilic amino acid or vice
versa, or other mutations
which would affect secondary or tertiary protein structure. Silent mutations
or those resulting in
conservative amino acid substitutions would not generally be expected to
disrupt protein function.
Genetic testing will enable practitioners to identify individuals at risk for
BFNC, rolandic
epilepsy or JME, at, or even before, birth. Presymptomatic diagnosis of these
epilepsies will enable
prevention of these disorders. Finally, this invention changes our
understanding of the cause and
treatment of BFNC, rolandic epilepsy and JME. It is possible, for example,
that potassium channel
opening agents will reduce the risk of seizures in patients with KCNQ2 or
KCNQ3 mutations.
Pharmaceutical Compositions and Routes of Administration
The KCNQ2 and KCNQ3 polypeptides, antibodies, peptides and nucleic acids of
the present
invention can be formulated in pharmaceutical compositions, which are prepared
according to
conventional pharmaceutical compounding techniques.
See, for example, Remington's
Pharmaceutical Sciences, 18th Ed. (1990, Mack Publishing Co., Easton, PA). The
composition may
contain the active agent or pharmaceutically acceptable salts of the active
agent. These
compositions may comprise, in addition to one of the active substances, a
pharmaceutically
acceptable excipient, carrier, buffer, stabilizer or other materials well
known in the art. Such
materials should be non-toxic and should not interfere with the efficacy of
the active ingredient. The
carrier may take a wide variety of forms depending on the form of preparation
desired for
administration, e.g., intravenous, oral, intrathecal, epineural or parenteral.
For oral administration, the compounds can be formulated into solid or liquid
preparations
such as capsules, pills, tablets, lozenges, melts, powders, suspensions or
emulsions. In preparing
the compositions in oral dosage form, any of the usual pharmaceutical media
may be employed, such
CA 02712809 2010-08-20
53
as, for example, water, glycols, oils, alcohols, flavoring agents,
preservatives, coloring agents,
suspending agents, and the like in the case of oral liquid preparations (such
as, for example,
suspensions, elixirs and solutions); or carriers such as starches, sugars,
diluents, granulating agents,
lubricants, binders, disintegrating agents and the like in the case of oral
solid preparations (such as,
for example, powders, capsules and tablets). Because of their ease in
administration, tablets and
capsules represent the most advantageous oral dosage unit form, in which case
solid pharmaceutical
carriers are obviously employed. If desired, tablets may be sugar-coated or
enteric-coated by
standard techniques. The active agent can be encapsulated to make it stable to
passage through the
gastrointestinal tract while at the same time allowing for passage across the
blood brain barrier. See
for example, WO 96/11698.
For parenteral administration, the compound may be dissolved in a
pharmaceutical carrier
and administered as either a solution or a suspension. Illustrative of
suitable carriers are water,
saline, dextrose solutions, fructose solutions, ethanol, or oils of animal,
vegetative or synthetic
origin. The carrier may also contain other ingredients, for example,
preservatives, suspending
agents, solubilizing agents, buffers and the like. When the compounds are
being administered
intrathecally, they may also be dissolved in cerebrospinal fluid.
The active agent is preferably administered in a therapeutically effective
amount. The actual
amount administered, and the rate and time-course of administration, will
depend on the nature and
severity of the condition being treated. Prescription of treatment, e.g.
decisions on dosage, timing,
etc., is within the responsibility of general practitioners or specialists,
and typically takes account of
the disorder to be treated, the condition of the individual patient, the site
of delivery, the method of
administration and other factors known to practitioners. Examples of
techniques and protocols can
be found in Remington=s Pharmaceutical Sciences.
Alternatively, targeting therapies may be used to deliver the active agent
more specifically to
certain types of cell, by the use of targeting systems such as antibodies or
cell specific ligands.
Targeting may be desirable for a variety of reasons, e.g. if the agent is
unacceptably toxic, or if it
would otherwise require too high a dosage, or if it would not otherwise be
able to enter the target
cells.
Instead of administering these agents directly, they could be produced in the
target cell, e.g.
in a viral vector such as described above or in a cell based delivery system
such as described in U.S.
Patent No. 5,550,050 and published PCT application Nos. WO 92/19195, WO
94/25503, WO
95/01203, WO 95/05452, WO 96/02286, WO 96/02646, WO 96/40871, WO 96/40959 and
WO
CA 02712809 2010-08-20
54
97/12635, designed for implantation in a patient. The vector could be targeted
to the specific cells to
be treated, or it could contain regulatory elements which are more tissue
specific to the target cells.
The cell based delivery system is designed to be implanted in a patient=s body
at the desired target
site and contains a coding sequence for the active agent. Alternatively, the
agent could be
administered in a precursor form for conversion to the active form by an
activating agent produced
in, or targeted to, the cells to be treated. See for example, EP 425,731A and
WO 90/07936.
The present invention is further detailed in the following Examples, which are
offered by
way of illustration and are not intended to limit the invention in any manner.
Standard techniques
well known in the art or the techniques specifically described below are
utilized.
EXAMPLE 1
Southern Blot Analysis
Five micrograms of genomic DNA were cut with Taql and transferred to a nylon
membrane.
Filters were hybridized overnight at 65EC in PEG hyb (7% PEG, 10% SDA, 50 mM
sodium
phosphate and 200 lig/m1 total human DNA) with the D20524 plasmid probe
labeled by random
priming (Stratagene). Filters were washed at 2 x SSC, 0.1% SDS twice at room
temperature
followed by one wash in 0.5 x SSC, 0.1% SDS at 65EC.
EXAMPLE 2
Fluorescence in situ Hybridization
Chromosomes from transformed lymphocytes were prepared using a 30 minute
ethidium
bromide treatment followed by 3 hours in colcemid. Cells were then pelleted
and resuspended in
hypotonic solution (0.75 M KC1) for 20 minutes followed by the addition of
four to five drops of
fresh fixative (3:1 methanol:acetic acid). Cells were again pelleted, vortexed
then carefully
resuspended in fixative. After three washes in fixative, metaphases were
stored at 4EC. Four
hundred ng probe was labeled with biotin and hybridized to slides of metaphase
spreads using
standard hybridization procedures. Probes were then fluorescently tagged with
avidin-FITC
(Vector) and the signal intensified using biotin-labeled anti-avidin followed
by avidin-FITC. The
chromosomes were then counterstained using DAPI and visualized using a Zeiss
Axioplan
Fluorescent microscope equipped with FITC, DAPI and triple band pass filter
sets. Images were
CA 02712809 2010-08-20
captured by computer using Applied Imaging (Pittsburgh, PA) software
Probevision and
photographs printed on a Kodak XL 7700 color image printer.
EXAMPLE 3
5 Localization of KCNQ2
Linkage analysis in a large kindred demonstrated that a gene responsible for
BFNC maps to
chromosome 20q13.3 close to the markers D20S20 and D20S19 (Leppert etal.,
1989). Following
the initial report, two centers confirmed linkage of BFNC to the same two
genetic markers on
chromosome 20, termed the EBN1 (epilepsy benign neonatal type 1) locus (Ryan
et al., 1991;
10
Malafosse et al., 1992). A more distal marker, D20S24, shows complete co-
segregation with the
BFNC phenotype in chromosome 20 linked families. Finding a distal flanking
marker for the BFNC
locus has not been successful probably because of its proximity to the
telomere. This telomeric
region is characterized by a high recombination rate between markers when
compared to the
physical distance (Steinlein et al., 1992). In fact, Steinlein et al. have
demonstrated that the three
15 markers D20S19, D20S20 and D20S24 are contained on the same 450 Mb Mlu I
restriction
fragment (Steinlein et al., 1992).
A second chromosomal locus, EBN2, has also been identified for BFNC. Lewis et
al. (1993)
demonstrated linkage to markers on chromosome 8q24 in a single Hispanic family
affected with
BFNC. Evidence for this second locus was also reported in a Caucasian pedigree
(Steinlein et al.,
20
1995). All of the families in the present study show linkage to chromosome 20q
markers with LOD
scores of greater than 3.0 or have probands with clinical manifestations
consistent with BFNC
(Leppert et al., 1993). To find the gene responsible for BFNC, we narrowed the
BFNC region with a
sub-microscopic deletion in a single family, identified candidate cDNAs in
this deletion, and then
searched for mutations in other BFNC families.
25
Evidence for a small deletion came first from a genotypic observation with a
three allele,
RFLP marker, D20S24. Analysis of one family, kindred 1547, revealed that a
null allele occurred
exclusively in those individuals with BFNC and in two individuals previously
shown to be non-
penetrant with the VNTR markers D20S20 and D20S19 (Figure 1). The existence of
a deletion co-
segregating with the BFNC phenotype in this family was confirmed by
fluorescence in situ
30
hybridization (FISH) in cell lines of kindred 1547 individuals using as
probes, the D20524 plasmid
and two genomic P1 clones containing this marker.
CA 02712809 2010-08-20
56
To confirm the presence of a deletion, two overlapping genomic P1 clones, P1 -
K09-6b and
P1-K09-7, each of approximately 80 kb in size and each of which contains the
D20S24 marker,
were obtained and these were hybridized to cell lines of kindred 1547 BFNC
affected individuals.
When metaphase spread chromosomes are hybridized with P1 -K09-7 and P 1 -K09-
6b, both
chromosome 20 homologs give signals on two sister chromatids. However when the
12 kb probe
D20S24 is hybridized only signal from the one chromosome homolog is observed
in 75% of
metaphase spreads examined. The remaining minority of cells showed no
hybridization for the 12
kb D20S24 probe (Figure 2). The plasmid containing the D20S24 marker was a
kind gift from J.
Weissenbach.
While the 12 kb D20S24 probe was deleted on one chromosome in affected
individuals, the
overlapping P1 clones of 80 kb in size, and which together span approximately
130 kb, showed a
positive FISH signal indicating that the deletion is smaller than 130 kb
(Figure 2).
EXAMPLE 4
Isolation and Characterization of KCNQ2 Clones
Using the same probes as in Example 3, cDNAs in the region of the deletion
were identified
by screening a fetal brain cDNA library. Three of the cDNAs isolated showed
significant homology
to KCNQ1, the chromosome 11 potassium channel gene responsible for the Long QT
syndrome and
the Jervell and Lange-Nielsen cardioauditory syndrome (Wang et al., 1996;
Altschul et al., 1990;
Neyroud et al., 1997).
A fetal brain cDNA library (Stratagene) (106 clones) was probed with inserts
from P1-K09-
6b and P1-K09-7 and the plasmid D20S24. Hybridizations were performed in 5 x
SSC, 10 x
Denhardt=s, 0.1 M sodium phosphate (pH 6.7), 100 g/mL salmon sperm DNA, 0.1%
SDS and 50%
formamide. Blots were washed in 2 x SSC, 0.1% SDS twice at room temperature
followed by one
wash in 0.5 x SSC, 0.1% SDS at 42EC.
A single cDNA isolated with D20S24, cIPK, showed 75% homology to amino acids
511-562
of KCNQl; a second probing of the fetal brain cDNA library using the probe P1-
K09-6b resulted in
the isolation of two additional cDNAs, c6b-6 and c6b-12, which showed
significant homology with
KCNQ1 amino acids 398-406 and 354-378, respectively (Altschul et al., 1990;
Wang et al., 1996;
Neyroud et al., 1997).
Additional sequence encoding this BFNC gene, named KVEBN1 (now KCNQ2) after
the
OMIM locus name, was obtained from RACE experiments using adaptor-ligated
double-stranded
CA 02712809 2013-07-19
57
cDNA from fetal and adult brain tissue and from other cDNA clones isolated
from a temporal cortex
cDNA library.
To identify the full length gene, 5' and 3' RACE were performed on adaptor-
ligated fetal and
adult brain cDNA (Clontech) using primers within c6b-6 and cIPK and screening
a temporal cortex
cDNA library (Stratagene) with sequence flanking cIPK. Unprocessed cDNAs were
repeatedly
isolated from cDNA libraries and RACE experiments. The longest transcript
isolated from brain
was 1455 nucleotides long and was obtained using 5' RACE and extended from the
Si domain
(amino acid 100) to the 3' conserved C-terminal domain (amino acid 585).
Composite clones encoding 872 amino acids of the KCNQ2 gene have been isolated
(Figures
3A and 3B). The cDNA sequence for KCNQ2 is shown as SEQ ID NO:1 and the amino
acid
sequence for KCNQ2 is shown as SEQ ID NO:2. The putative initiator methionine
lies within a
region similar to the Kozak consensus sequence (Kozak, 1987). KCNQ2 encodes a
highly
conserved six transmembrane motif as well as a pore region that are the
hallmarks of a K+ ion
channel gene. The S2, S3 and S4 transmembrane regions also contain charged
amino acids that are
found in all members of the K+ channel subfamilies, including Shaker, Shah,
Shaw and Shal. A
search of Genbank with KCNQ2 sequence shows identical nucleotide sequence to
HNSPC
(Accession # D82346), a 393 amino acid putative potassium channel cDNA
isolated from a human
neuroblastoma cell line (Yokoyama et al., 1996). However, the last 21 amino
acids of HNSPC
including a stop codon are encoded by a sequence that in KCNQ2 is intronic. A
search of the human
expressed sequence tag database (dbest) shows seven different clones encoding
portions of KCNQ2.
Wei et al. have identified a gene from C. elegans,nKQT1, that appears to be a
homolog of KCNQ2
(Wei et al., 1996). This group also described the human EST homolog of nKQT1,
hKQT2, which is
a partial clone of KCNQ2 (Wei et al., 1996). In addition to the six
transmembrane domains and the
pore, a small region 5' of transmembrane domain Si is also conserved between
KCNQ2, KCNQ3,
KCNQ1 and nKQT1. Unlike other K+ channel subfamilies, the C-terminal domain
appears to
contain highly conserved residues as shown in Figures 3A and 3B for KCNQ2,
KCNQ3, nKQT1
and KCNQl. The poly A tail for KCNQ2 has not been identified to date.
EXAMPLE 5
Northern Blot Analysis
The KCNQ2 cDNA hybridizes to transcripts approximately 1.5, 3.8 and 9.5 kb in
size on
Northern blots made from brain. Multiple Tissue Northerns (Clontech) of fetal
and adult brain were
CA 02712809 2010-08-20
58
probed with a RACE product containing transmembrane domains Si through S6 of
KCNQ2. The
1.5 and 9.5 kb transcripts appear to be expressed in both adult and fetal
brain. The 3.8 kb transcript
is expressed in select areas from adult brain, particularly in the temporal
lobe and the putamen.
EXAMPLE 6
Mutational Analysis of KCNQ2
Mutational analysis of KCNQ2 was performed on one affected individual from
each of our
12 BFNC families. Coding regions from Si to S6 and conserved regions in the 3'
end of KCNQ2
were amplified by PCR using primers within introns and analyzed by SSCP
(Novex) using 20%
TBE gels run at 4EC. The exon-intron boundaries were identified by sequencing
products obtained
by exon-exon PCR on genomic P1 clones or directly from RACE products which
contained
unprocessed transcripts. PCR products showing variants seen on SSCP were
either cloned and
sequenced or reamplified with M13 reverse and M13 universal-tailed primers and
sequenced directly
on an ABI 373 or 377 using dye-primer chemistry.
In addition to the substantial deletion in kindred 1547, mutations were
identified in five other
BFNC families. Mutational analysis was carried out by first screening probands
for SSCP variants
and then sequencing each individual=s DNA to determine the basis for the
molecular variation.
Mutations identified include two missense mutations, two frameshift mutations
and one splice site
mutation (Table 2). Later analyses resulted in the finding of four more BFNC
families with
mutations in KCNQ2. These include two nonsense mutations (families K1525 and
K4443), an
insertion resulting in a frameshift which results in readthrough beyond the
normal stop codon
(K3963), and a missense mutation (K4516). These latter 4 mutations are listed
in Table 2.
The splice site variant occurs in an intron which occurs between two exons
encoding amino
acid residue 544. The first exon includes the TG at the start of codon 544 and
the following exon
includes the final T of codon 544. The sequence at the 3' end of the intron
(shown in lower case
letters) and continuing into the exon region (shown in upper case letters)
encoding the end of codon
544 and codons 545-546 is: 5'-tgcagTGTCATG-3' (SEQ ID NO:5). The Ag@ at
position 5 of SEQ
ID NO:5 is mutated to an Aa@ in kindred K3933.
None of the mutations seen in the first six families identified was seen in
SSCP analysis of
our panel of 70 unrelated, unaffected individuals. Furthermore, mutations were
shown to segregate
completely with affection status in all of the BFNC families where mutations
were identified. In the
case of the splice site mutation in kindred 3933 only the proband was sampled.
An example
CA 02712809 2010-08-20
59
Table 2
Mutations in the KCNQ2 Gene in BFNC Families
Mutation at Region Kindred Controls Nucleotide Change
Amino Acid
large deletion not K1547 70 not available
available
frameshift at 283 pore K1504 70
insert GT between nucleotides
975 and 976 of SEQ ID NO:1
Y284C pore K3904 70 A6G at base 978 of SEQ ID
NO:1
A306T S6 K1705 70
G6A at base 1043 of SEQ ID
NO:1
Q323Stop C-terminal K4443 C6T at base 1094
of SEQ ID
NO:1
R333Q C-terminal
K4516 G6A at base 1125 of SEQ ID
NO:1
R448Stop C-terminal K1525 C6T at base 1469
of SEQ ID
NO:1
frameshift at 522 C-terminal K3369 70 delete bases 1691 through
1703 of SEQ ID NO:1
splice site variant C-terminal K3933 70 g6a at 3' end of intron which
occurs between bases 1758
and 1759 of SEQ ID NO:1
frameshift at 867 C-terminal K3963 70 insert GGGCC
after base 2736
of SEQ ID NO:1
CA 02712809 2010-08-20
of this segregation is shown in Figure 4 for the two base-pair insertion
identified in kindred 1504; all
11 affected members of the kindred have the SSCP variant and all seven
unaffected individuals have
wild type SSCP bands.
Of the four families (K1525, K3963, K4443 and K4516) which have been more
recently
5 found to have KCNQ2 mutations, three (K11525, K4443 and K4516) were found
through direct
sequencing and the mutation co-segregated in the family when other affected
members were
available for study. The mutation in K3963 was found via SSCP screening and
this mutation was
not detected in a panel of 70 normal, i.e., non BFNC, individuals. This
mutation was found to co-
segregate with affected individuals in family K3963. The wild-type gene
includes two sets of
10 GGGCC at bases 2727-2736 of SEQ ID NO:l. The sequence found in K3963 is
three sets of
GGGCC as a result of an insertion of GGGCC into this region. This results in
the gene encoding the
first 870 amino acids of the wild-type followed by an additional 60 amino
acids of new sequence
(amino acid residues 871 and 872 of the wild-type being replaced by the first
2 of the 60 additional
amino acid residues). The gene including the 5 base insertion is shown as SEQ
ID NO:95 and the
15 protein encoded by this mutated gene is shown as SEQ ID NO:96.
Family K4443 has 6 BFNC affected individuals and two of these individuals have
in addition
seizures later in childhood that are classified as benign epilepsy with
centrotemporal spikes (BERS),
or rolandic epilepsy. The DNA of two affected individuals in this family was
examined. The
Q323 Stop mutation is found in one of the affected individuals that expresses
BFNC only and in one
20 individual which has both BFNC and BERS or rolandic epilepsy, which
developed later in
childhood after the newborn seizures. This finding directly implicates the
KCNQ2 gene on
chromosome 20 in causing rolandic epilepsy. Rolandic epilepsy, or BERS, is a
common childhood
epilepsy and may account for 25% of all school age epilepsy. This is a genetic
disorder that inherits
as an autosomal dominant with reduced penetrance. It is possible that several
genes may cause the
25 rolandic phenotype, but this finding strongly suggests that at least
some of the rolandic epilepsies
will be caused by defects in KCNQ2, a potentially important finding.
Two neutral polymorphisms were identified in the KCNQ2 gene. One polymorphism
is in
codon 304 (TTC to TTT) in the S6 transmembrane domain and was seen in 10 of 71
controls who
were each heterozygous (allelic frequency of 7.0%). The second polymorphism is
in codon 573
30 (GCC to GCT) in the 3' region and was observed in 1 of 87 controls
individuals as a heterozygote
(allelic frequency of 0.57%).
CA 02712809 2013-07-19
61
It is predicted that the splice site mutation in the conserved 3' region of
KCNQ2 and the two
frameshift mutations, one in the pore region and one before the highly
conserved 3' region, lead to
altered protein products. In the case of the 283insGT pore mutation a
predicted stop codon is found
36 amino acids downstream and in the case of the 522de1 13 3' mutation a
predicted stop codon is
found two amino acids downstream. Also, the two bp insertion mutation,
283insGT, would lead to a
completely altered S6 transmembrane domain. While the breakpoints of the
kindred 1547 deletion
have not been determined, it is known that the 12 kb plasmid which includes
the RFLP marker
locus, D20S24, contains 80 codons (residues 509 to 588 of KCNQ2) of sequence
from the highly
conserved 3' region of the KCNQ2 gene, indicating that at least this portion
of the gene is deleted in
kindred 1547 affected individuals. The two missense mutations in families
K3904 and K1705
change amino acid residues in key functional domains, the pore and S6 domain.
Ten unique mutations have been identified in KCNQ2 to date. The mutation
defined by a 13
base pair deletion at amino acid 522 in kindred 3369 is of interest in that
there is a greater variation
in the reported clinical ages of onset within this family when compared to
typical BFNC families. In
kindred 3369, three individuals had onset of seizures within the first 2 weeks
of life, while three
individuals had initial onset of seizures at 3, 4, and 5 months of age.
The mutation in the BFNC kindred 1705 is an alanine to threonine substitution
in the S6
transmembrane segment. This alanine residue is conserved in all members of the
Shaker, Shab,
Shaw and Shal subfamilies of potassium channels identified to date (Lopez et
al., 1994; Nakamura
et al., 1997; Tytgat, 1994). The KCNQ1 gene, which the KCNQ2 ion channel gene
is most closely
related to, also contains an alanine in this position. In six unrelated LQT1
families, the disease-
causing mutation occurs at this same position where the alanine is changed to
a valine (Wang et al.,
1996; Russell et al., 1996). This S6 transmembrane domain has been shown to be
involved in K+
ion permeation in the Shaker subtype (Lopez et al., 1994) and may serve a
similar function in
KCNQ2. The C-terminal region appears to be important for gene function because
a 13 bp deletion,
a splice site mutation, a missense mutation, a nonsense mutation, and an
insertion all produce an
epileptic phenotype in separate BFNC families (see Table 2 and Figures 3A and
3B). Interestingly,
this same region is known to have a deletion-insertion mutation in KCNQ1 in
individuals with the
Jervell and Lange-Nielsen recessive form of LQT and associated deafness
(Neyroud et al., 1997).
Disease-causing mutations in the C-terminal region further argue for a
functional protein encoded by
the KCNQ2 gene rather than the shorter HNSPC clone.
CA 02712809 2010-08-20
62
The pore region of K+ ion channels belonging to the same structural class have
been
characterized extensively by mutational analysis. The two base-pair insertion
observed in kindred
1504 occurs immediately after the universally conserved GYG motif. An
insertion here not only
alters the length of the pore that is believed to be crucial for function
(Nakamura et al., 1997; Tytgat,
1994) but also modifies the signature sequence of the pore and produces a
truncated protein.
In infants of families that have been linked to the chromosome 20 form of
BFNC, EEG
recordings show initial suppression of activity throughout the brain followed
by generalized
discharges of spikes and slow waves (Ronen et al., 1993; Plouin, 1994; Hauser
and Kurland, 1975).
It is therefore not surprising to find that the KCNQ2 gene is expressed in
multiple brain areas in
adults. Cortical regions as well as sub-cortical areas, such as the thalamus
and caudate nucleus,
contain multiple size transcripts of KCNQ2 (data not shown). It is possible
that this expression
pattern is also the same in the newborn infant.
The close homology (60% identity and 70% similarity of amino acids) of KCNQ2
to KCNQ1
and to the C. elegans nKQT1 gene and the reduced homology of these channels to
the Shaker, Shab,
Shaw and Shal subfamilies imply that they belong to a unique family of K+ ion
channels, called
KQT-like (Wei et al., 1996). A new K+ ion channel now known to be expressed in
the brain raises
the question of whether additional, undiscovered members of this gene family
may be responsible
for other forms of idiopathic, generalized epilepsies with tonic-clonic
convulsions. A similar
idiopathic seizure disorder seen early in development is Benign Familial
Infantile Convulsions
(BFIC). In BFIC the seizures begin at four to eight months of age and remit
after several years.
BFIC maps to chromosome 19q in five Italian families (Guipponi et al., 1997).
It is reasonable to
hypothesize that BFIC is also caused by mutations in as yet unidentified
members of the KQT-like
family of K+ ion channels or by minK-like proteins.
EXAMPLE 7
Somatic Cell Hybrid Panel Genotyping
Exploiting the putative conservation of intron-exon boundaries between KCNQ2
and
KCNQ3 in the highly homologous transmembrane domains, a primer pair was
designed from the
available EST sequences (primer A: 5'-TTCCTGATTGTCCTGGGGTGCT-3' (SEQ ID NO:8),
primer B: 5'-TTCATCTTTGGAGCCGAGTTTGC-3' (SEQ ID NO:9)) to cross an intron. The
amplified fragment contains an intron in human (1.8 kb) as well as in rodent
(800 bp) genomic
DNA. This primer was used to amplify the Cone!! panel. The reactions were
performed in a 25 ',IL
volume using 50 ng of template DNA and 1 unit of Taq DNA polymerase (Perkin
Elmer), 10 pmol
CA 02712809 2010-08-20
63
of each primer, 3 nmol of each deoxyribonucleotide in a 1.5 mM MgCl2 buffer.
Cycling conditions
were 94EC for 4 minutes, then 30 cycles of: denaturation at 94EC for 30
seconds, annealing at
58EC for 30 seconds and elongation at 72EC for 1.5 minutes, followed by a
final elongation at 72EC
for 10 minutes. The PCR products were electrophoresed in a 1.5% agarose gel.
EXAMPLE 8
Chromosome 8 Radiation Hybrids Panel
An HSA8 radiation hybrid panel (Lewis et al., 1995) was genotyped with
specific human
intronic primers (primer D: 5'-TCCATGTGGTACTCCATGTCTGAA-3' (SEQ ID NO:10),
primer
E: 5'-GCACGTCACATTGGGGATGTCAT-3' (SEQ ID NO:11)). The length of the PCR
product is
190 bp. The reactions were performed in a 25 [IL volume using 100 ng of
template DNA and 1 unit
of Taq polymerase (Perkin Elmer), 10 pmol of each primer, 3 nmol of each
deoxyribonucleotide in a
1.5 mM MgCl2 buffer. Cycling conditions were 94EC for 4 minutes, then 30
cycles of: denaturation
at 94EC for 30 seconds, annealing at 62EC for 30 seconds and elongation at
72EC for 30 seconds,
followed by a final elongation at 72EC for 10 minutes. The PCR products were
electrophoresed in a
2% agarose gel. The genotyping data was analyzed by the RHMAP V2.01 program
(BoehnIce et al.,
1991).
EXAMPLE 9
Full Length cDNA
To identify the full length KCNQ3 cDNA, 5' and 3' RACE were performed on
adaptor-
ligated fetal and adult brain cDNA (Clontech) using primers from the available
EST sequences. The
primers used for RACE experiments are given in Table 3. PCR products were
subcloned (T/A
cloning 7 Kit, Invitrogen) and both strands were sequenced on an ABI 377
instrument.
EXAMPLE 10
Genomic Organization/Intron-Exon Boundaries
A BAC genomic library was screened by PCR (as described for the Coriell panel)
and three
overlapping genomic clones were isolated. The intron/exon boundaries were
identified by cloning
(T/A cloning 7 Kit, Invitrogen) and sequencing (ABI 377) products obtained by
exon-exon PCR on
genomic human DNA and/or on BAC genomic clones containing the KCNQ3 gene.
CA 02712809 2010-08-20
64
Table 3
RACE Primers
5' RACE
KV1b: 5'-TGTGTTTTGGCGTGGAGGGAGGTC-3' (SEQ ID NO:12)
KV2b: 5'-CAGTAACAGAAGCCAGTCTCC-3' (SEQ ID
NO:13)
KV3b: 5'-GCAAACTCGGCTCCAAAGATGAA-3' (SEQ ID
NO:14)
KV4b: 5'-CACCAACGCGTGGTAAAGCAGC-3 (SEQ ID
NO:15)
3' RACE
KV1a: 5'-TTCCTGATTGTCCTGGGGTGCT-3' (SEQ ID
NO:16)
KV2a: 5'-AGTATCTGCCGGGCATCTCGACA-3' (SEQ ID
NO:17)
CA 02712809 2010-08-20
EXAMPLE 11
SSCP Analysis and Characterization of Mutant and Polymorphic Alleles
Sixty percent of the coding region of KCNQ3 was amplified by PCR using primers
within
introns when available and analyzed by SSCP (Novex) using 20% TBE gels run at
4EC as described
5 in Novex ThermoflowLT protocols (Novex, San Diego, CA). The PCR products
presenting an SSCP
polymorphism were cloned (T/A c10ning7 Kit, Invitrogen), nine clones were
sequenced on an ABI
373 or 377 using dye-primer chemistry and analyzed with the SequencherJ 3.0
program.
EXAMPLE 12
10 Characterization of the KCNQ3 Gene
The KQT-like family is a recently characterized family of voltage-gated
potassium channels
(Wei et al., 1996). Until now, only KCNQ2 (described in this disclosure) which
is the gene mutated
in the chromosome 20 BFNC disorder and KCNQ1, which is the chromosome 11 gene
responsible
for Long QT syndrome and the Jervell and Lange-Nielsen cardioauditory syndrome
(Neyroud et al.,
15 1997), were known to belong to this family. In order to identify new
members of that family,
possibly involved in other types of IGEs, a tBLASTx (Altschul et al., 1990)
search was started with
the KCNQ2 full length cDNA against the Expressed Sequence Tags (ESTs)
database. Five human
EST clones were identified that presented significant homologies with KCNQ2
(clone ID: 1-362079,
2-222324, 3-363215, 4-38822, 5-45636; Hillier et al., unpublished data).
Interestingly, these clones
20 come from two different cDNA libraries: retina (1-3) and infant brain (4-
5) (Soares et al., 1994) and
can be organized in two nonoverlapping contigs (1-3) and (4-5). It is
demonstrated here that the two
contigs belong to the same gene, KCNQ3.
The first step in the characterization of the new gene was genomic
localization of the ESTs.
Using a commercial somatic cell hybrid panel (Coriell panel (Drwinga et al.,
1993)), KCNQ3 was
25 mapped on HSA8. In order to refine that assignment, a panel of 97
radiation hybrids previously
constructed for determining the linear order and intermarker distance of
chromosome 8 loci (Lewis
et al., 1995) was genotyped. Specific human intronic primers were used and
each RH was scored by
PCR for the presence or absence of the locus. The data were analyzed using
RHMAP V2.01 against
results collected for other chromosome 8 markers. The retention frequency for
KCNQ3 in the RH
30 panel was 11.7%. Tight linkage of KCNQ3 locus was observed with markers
previously mapped to
chromosome band 8q24. The tightest linkage was seen with marker D85558 (LOD
13.87, 0 of
0.047 Rsoco). The resulting RH map is shown in Figure 5. The position of the
KCNQ3 locus is
localized to the interval defined by the markers previously linked to a
chromosome 8 BFNC family
CA 02712809 2013-07-19
66
(Lewis et at., 1993), making KCNQ3 a very strong positional candidate for the
chromosome 8 BFNC
locus. A second Caucasian family also demonstrates suggestive linkage to the
same markers
(Steinlein et al., 1995).
A partial cDNA sequence was obtained by a series of rapid amplification of
cDNA ends
(RACE) experiments. 5' and 3' RACE were performed by amplifying adult and
fetal brain
Marathon-Ready cDNAs (Clontech) using primers derived from the two EST contigs
previously
identified. The primer pairs are shown in Table 3. This was used to purify a
mouse genomic
homolog of KCNQ3. After determining the mouse sequence including intron/exon
junctions,
primers based upon the mouse sequence were used to clone the remainder of the
human cDNA for
KCNQ3.
The primers used to amplify the 5' end of the human gene were
CGCGGATCATGGCATTGGAGTTC (SEQ ID NO:93) and AAGCCCCAGAGACTTCTCAGCTC
(SEQ ID NO:94). The complete KCNQ3 cDNA sequence (SEQ ID NO:6) encodes an 872
amino
acid protein (SEQ ID NO:7) with six putative transmembrane domains, a pore
region, a stop codon,
and the 3' untranslated region containing the poly A+ tail. This protein
presents 58% similarity and
46% identity (calculated using BLAST) in the region from amino acid 101 to the
stop codon with
KCNQ2 and is also highly conserved with KCNQ1 (Yang et al., 1997) as well as
with the C. elegans
homologue nKQT1 (Wei et al., 1996). A comparison of sequences is shown in
Figures 3A and 3B.
The two EST contigs are identical to amino acids 86-265 and 477-575 of KCNQ3,
respectively (see
Figures 3A and 3B).
To test whether or not KCNQ3 is the gene responsible for the chromosome 8 BFNC
phenotype, mutations were looked for in one affected individual of a
phenotypically well
characterized three-generation Mexican-American BFNC family (Ryan et al.,
1991) (see Figure 6).
That family has been mapped by multipoint linkage analysis on chromosome 8q24
(Z=4.43) within
the interval spanned by markers D8S198 (proximal to D85284) and D85274 (distal
to D8S256) (see
Figure 5) (Lewis et al., 1993; Dib et al., 1996). It is here shown that this
chromosomal region
contains the KCNQ3 locus. So far, using intronic primers, 60% of the coding
region of KCNQ3,
containing the six transmembrane domains as well as the pore region, has been
screened by a cold
SSCP method. One SSCP variant was identified in a PCR fragment of 187 bp
containing the
transmembrane domain S5 and half of the pore. The primers used to prepare this
fragment are:
Ret.6a 5'-CATCACGGCCTGGTACATCGGTT-3' (SEQ ID NO:18) (corresponding to
nucleotides
801-823 of SEQ ID NO:6) and Hebn2.3b 5'-AATCTCACAGAATTGGCCTCCAAG-3' (SEQ ID
NO:19). The Ret.6a primer is from coding region and the Hebn2.3b primer is
from intronic region.
CA 02712809 2010-08-20
67
This SSCP variant is in perfect cosegregation with the BFNC phenotype and it
is also present in a
single non-penetrant individual carrying the disease-marker haplotype (Figure
6). Furthermore, this
SSCP variant is absent from a panel of 72 Caucasian and 60 Mexican-American
(264 chromosomes)
unrelated individuals used as the control group. To characterize the
nucleotide change of this
variant, the PCR product of one affected individual was cloned and nine clones
were sequenced on
both strands. Four clones contained the wild-type allele and five the mutated
allele. The mutation is
a single missense mutation Gly (GGC) to Val (GTC) in position 310 of the
highly conserved pore
region (the mutation occurring at base 947 of SEQ ID NO:6). In addition, a
silent polymorphism
(frequency of 0.4%) was found in one Mexican-American control in the
transmembrane region S5 at
L278 (CTT 6 CTC) (the polymorphism is at base 852 of SEQ ID NO:6). Four other
polymorphisms
in KCNQ3 have been seen. These are at N220 (AAC or AAT), Gly244 (GGT or GGC),
L357 (CTG
or CTC) and 1860 (ATT or ATC). These polymorphisms are at base numbers 678,
750, 1089 and
2598 of SEQ ID NO:6, respectively.
In addition, some individual probands with juvenile myoclonic epilepsy were
screened with
SSCP. JME is an inherited childhood seizure disorder. KCNQ3 was mutated in one
individual who
was tested. The mutation was found in an alternatively spliced exon that lies
in an intron which
splits codon 412. This alternatively spliced exon was found in adult brain
after RACE experiments.
This exon is SEQ ID NO:92. The exon was seen in an adult brain cDNA clone
obtained from
Clontech. This exon is 130 nucleotides long which is not a multiple of 3.
Therefore the presence of
this exon results not only in the addition of extra amino acid sequence but
causes a frameshift (1
extra base) which results in a stop codon within the normal coding region of
the gene. The mutation
found in the JME proband is a 1 base pair deletion in the alternatively
spliced exon (the loss of the G
at base 118 of SEQ ID NO:92) that results in the frameshift from the
alternative exon going back
into frame resulting in a KCNQ3 with an additional 43 amino acid residues
between amino acid
residues 412 and 413 of the wild-type, and thus alters the protein in the
brain cells of the JME
proband. The patient with this deletion has a mother who has epilepsy, however
this particular
mutation is from the father, not from the mother. JME is a common, inherited
childhood epilepsy
and most likely is caused by defects not only in KCNQ3 but also in other
genes.
This finding brings to three the number of human members of the KQT-like
family, two of
which are expressed in brain and one in heart. Defects in all three K+ channel
genes cause human
diseases associated with altered regulation of excitability. Taking all these
findings together, there is
strong evidence that KCNQ2 and KCNQ3, as well as undiscovered genes of the
same family or
CA 02712809 2010-08-20
68
genes belonging to the same pathway, are involved in IGEs. Screening these KQT-
like K+ channel
genes as well as other K+ channel genes belonging to different families (Wei
et al., 1996) for
mutations in individuals with common types of IGEs will be a powerful
alternative for identifying
disease-causing genes. This is especially true given the difficult and
controversial tentative linkages
.. described in IGE disease pedigrees (Leppert et al., 1993).
EXAMPLE 13
Generation of Polyclonal Antibody against KCNQ2 or KCNQ3
Segments of KCNQ2 or KCNQ3 coding sequence are expressed as fusion protein in
E. coll.
The overexpressed protein is purified by gel elution and used to immunize
rabbits and mice using a
procedure similar to the one described by Harlow and Lane, 1988. This
procedure has been shown
to generate Abs against various other proteins (for example, see Kraemer et
al., 1993).
Briefly, a stretch of KCNQ2 or KCNQ3 coding sequence is cloned as a fusion
protein in
plasmid PETS A (Novagen, Inc., Madison, WI). After induction with IPTG, the
overexpression of a
fusion protein with the expected molecular weight is verified by SDS/PAGE.
Fusion protein is
purified from the gel by electroelution. Identification of the protein as the
KCNQ2 or KCNQ3
fusion product is verified by protein sequencing at the N-terminus. Next, the
purified protein is used
as immunogen in rabbits. Rabbits are immunized with 100 cI)g of the protein in
complete Freund's
adjuvant and boosted twice in 3 week intervals, first with 100 (I)g of
immunogen in incomplete
Freund's adjuvant followed by 100 (I)g of immunogen in PBS. Antibody
containing serum is
collected two weeks thereafter.
This procedure is repeated to generate antibodies against the mutant forms of
the KCNQ2 or
KCNQ3 gene product. These antibodies, in conjunction with antibodies to wild
type KCNQ2 or
KCNQ3, are used to detect the presence and the relative level of the mutant
forms in various tissues
and biological fluids.
EXAMPLE 14
Generation of Monoclonal Antibodies Specific for KCNQ2 or KCNQ3
Monoclonal antibodies are generated according to the following protocol. Mice
are
immunized with immunogen comprising intact KCNQ2, intact KCNQ3, KCNQ2 peptides
or
KCNQ3 peptides (wild type or mutant) conjugated to keyhole limpet hemocyanin
using
glutaraldehyde or EDC as is well known.
CA 02712809 2010-08-20
69
The immunogen is mixed with an adjuvant. Each mouse receives four injections
of 10 to
100 (13g of immunogen and after the fourth injection blood samples are taken
from the mice to
determine if the serum contains antibody to the immunogen. Serum titer is
determined by ELISA or
RIA. Mice with sera indicating the presence of antibody to the immunogen are
selected for
hybridoma production.
Spleens are removed from immune mice and a single cell suspension is prepared
(see Harlow
and Lane, 1988). Cell fusions are performed essentially as described by Kohler
and Milstein, 1975.
Briefly, P3.65.3 myeloma cells (American Type Culture Collection, Rockville,
MD) are fused with
immune spleen cells using polyethylene glycol as described by Harlow and Lane,
1988. Cells are
plated at a density of 2x105 cells/well in 96 well tissue culture plates.
Individual wells are examined
for growth and the supernatants of wells with growth are tested for the
presence of KCNQ2 or
KCNQ3 specific antibodies by ELISA or RIA using wild type or mutant KCNQ2 or
KCNQ3 target
protein. Cells in positive wells are expanded and subcloned to establish and
confirm monoclonality.
Clones with the desired specificities are expanded and grown as ascites in
mice or in a
hollow fiber system to produce sufficient quantities of antibody for
characterization and assay
development.
EXAMPLE 15
Sandwich Assay for KCNQ2 or KCNQ3
Monoclonal antibody is attached to a solid surface such as a plate, tube, bead
or particle.
Preferably, the antibody is attached to the well surface of a 96-well ELISA
plate. 100 01, sample
(e.g., serum, urine, tissue cytosol) containing the KCNQ2 or KCNQ3
peptide/protein (wild-type or
mutants) is added to the solid phase antibody. The sample is incubated for 2
hrs at room
temperature. Next the sample fluid is decanted, and the solid phase is washed
with buffer to remove
unbound material. 100 (DC of a second monoclonal antibody (to a different
determinant on the
KCNQ2 or KCNQ3 peptide/protein) is added to the solid phase. This antibody is
labeled with a
detector molecule (e.g., 1251, enzyme, fluorophore, or a chromophore) and the
solid phase with the
second antibody is incubated for two hrs at room temperature. The second
antibody is decanted and
the solid phase is washed with buffer to remove unbound material.
The amount of bound label, which is proportional to the amount of KCNQ2 or
KCNQ3
peptide/protein present in the sample, is quantified. Separate assays are
performed using
CA 02712809 2010-08-20
monoclonal antibodies which are specific for the wild-type KCNQ2 or KCNQ3 as
well as
monoclonal antibodies specific for each of the mutations identified in KCNQ2
or KCNQ3.
EXAMPLE 16
5 Assay to Screen Drugs Affecting the KCNQ2 or KCNQ3 K+ Channel
With the knowledge that KCNQ2 and KCNQ3 each forms a potassium channel, it is
now
possible to devise an assay to screen for drugs which will have an effect on
one or both of these
channels. The gene is transfected into oocytes or mammalian cells and
expressed as described
above. When the gene used for transfection contains a mutation which causes
BFNC, rolandic
10 epilepsy or JME, a change in the induced current is seen as compared to
transfection with wild-type
gene only. A drug candidate is added to the bathing solution of the
transfected cells to test the
effects of the drug candidates upon the induced current. A drug candidate
which alters the induced
current such that it is closer to the current seen with cells cotransfected
with wild-type KCNQ2 or
wild-type KCNQ3 is useful for treating BFNC, rolandic epilepsy or JME.
EXAMPLE 17
PRIMER PAIRS FOR SCREENING EACH EXON OF KCNQ2 FOR MUTATION
The genomic KCNQ2 has been sequenced in the intron/exon borders and primer
pairs useful
for amplifying each exon have been developed. These primer pairs are shown in
Table 4. For exons
13 and 17 primers within the exons are also utilized. Some exon/intron
sequence is shown in
Figures 7A-0.
EXAMPLE 18
INTRON SEQUENCE OF KCNQ3 AND
PRIMER PAIRS FOR AMPLIFYING THE EXONS OF KCNQ3
Although the complete cDNA for KCNQ3 has been obtained and sequenced, the
complete
genomic DNA has not yet been sequenced. However, much of the intron DNA has
been sequenced
and this sequence information has been utilized to develop primer pairs which
are useful for
amplifying each exon. The intron/exon sequence is shown in Figures 8A-0. Some
useful primer
pairs for amplifying each exon are shown in Table 5 although one of skill in
the art can easily
develop other primer pairs using the intron sequence shown in Figures 8A-0.
CA 02712809 2010-08-20
71
Table 4
Exon Domain , Primer Sequence (SEQ ID NO:)
1 met + SI
2 SI + SII TTCCTCCTGGTTTTCTCCTGCCT (SEQ ID NO:22)
- AAGACAGACGCCCAGGCAGCT (SEQ ID NO:23)
3 SII + SIII AGGCCTCAAGGTGGCCTCAGCTTT (SEQ ID NO:24)
CTGGCCCTGATTCTAGCAATAC (SEQ ID NO:25)
4 SIII + STY ACATCATGGTGCTCATCGCCTCC (SEQ ID NO:97)
TGTGGGCATAGACCACAGAGCC (SEQ ID NO:26)
SV + pore TGGTCACTGCCTGGTACATCGG (SEQ ID NO:27)
ATGGAGCAGGCTCAGCCAGTGAGA (SEQ ID NO:28)
6 pore + SVI GCAGGCCCTTCGTGTGACTAGA (SEQ ID NO::29)
ACCTAGGGAACTGTGCCCAGG (SEQ ID NO:30)
7 SVI ATGGTCTGACCCTGATGAATTGG (SEQ ID NO:31)
GCGGCCTCCACTCCTCAACAA (SEQ ID NO:32)
8 C-term
9 C-term
variable CCGCCGGGCACCTGCCACCAA (SEQ ID NO:33)
GCTTGCACAGCTCCATGGGCAG (SEQ ID NO:34)
11 C-term GCTGTGCAAGCAGAGGGAGGTG (SEQ ID NO:98)
CTGTCCTGGCGTGTCTTCTGTG (SEQ ID NO:99)
12 variable CCCAGGACTAACTGTGCTCTCC (SEQ ID NO:35)
cysteine CCGTGCAGCAGCCGTCAGTCC (SEQ ID NO:36)
insertion
13 C-term GCAGAGTGACTTCTCTCCCTGTT (SEQ ID NO:37)
GTCCCCGAAGCTCCAGCTCTT (SEQ ID NO:38)
AAGATCGTGTCTTCTCCAGCCC (SEQ ID NO:39)
GATGGACCAGGAGAGGATGCGG (SEQ ID NO:40)
14 C-term CCCTCACGGCATGTGTCCTTCC (SEQ ID NO:41)
AGCGGGAGGCCCCTCCTCACT (SEQ ID NO:42)
C-term GGTCTCTGGCCCAGGGCTCACA (SEQ ID NO:43)
CTTGTCCCCTGCTGGACAGGCA (SEQ ID NO:44)
16 C-term
TTGACGGCAGGCACCACAGCC (SEQ ID NO:45)
CA 02712809 2010-08-20
72
Exon Domain Primer Sequence (SEQ ID NO:)
17 C-term CCCAGCCCAGCAGCCCCTTTT (SEQ ID NO:46)
AGGTGGAGGGCGGACACTGGA (SEQ ID NO:47)
CTCCACGGGCCAGAAGAACTTC (SEQ ID NO:48)
GATGGAGATGGACGTGTCGCTGT (SEQ ID NO:49)
TGGAGTTCCTGCGGCAGGAGGACAC (SEQ ID NO:50)
GGTGTCTGACTCTCCCTCCGCAA (SEQ ID NO:51)
GTGGCGCCTTGTGCCAAAGTCA (SEQ ID NO:52)
ACCTCGGAGGCACCGTGCTGA (SEQ ID NO:53)
CA 02712809 2010-08-20
73
Table 5
Pair Sequence 51D' (SEQ ID NO:) Size Temp Part of the gene
1 GCGACGTGGAGCAAGTACCTTG (54) 245 62 before Si
CACCAACGCGTGGTAAAGCAGC (55)
2 ATGACTCAAAGGTTCCTTAGTCCA (56) 174 62 Si to beginning
GAAGCCCAACCAGAAGCATTTAC (57) of S2
3 TCAGTGCCTCTCCATATGCTCTT (58) 194 62 end of S2 to
ACTGAGGAGGCTGGGAGGCTC (59) beginning of S3
4 GATGACGCCATTGCTTTCGCATGA (60) 298 65 end of S3 to S4
GTGGGAAGCCCATGTGGTCCTG (61)
CATCCACTCAACGACTCCCCAG (62) 249 65 S5 to beginning
AATCTCACAGAATTGGCCTCCAAG (63) of the pore
6 TCCATGTGGTACTCCATGTCTGAA (64) 190 58 end of the pore to
GCACGTCACATTGGGGATGTCAT (65) beginning of S6
7 GGAATGCTGGGACAGTCTAGCTG (66) 203 58 end of S6 to start
TACATATGCATGGATCTTAATCCCAT(67) of C-terminal part
8 AAAGTTTCAGGTGGTGCCCACTCA (68) 230 65 C- terminal
GAGGCCACAGACACGAATACAGAC (69)
9 TGGGTAAACCCGCCTCCTTCATTG (70) 306 65 C- terminal
ACTCTATCTTGGGACCAGCATGAC (71)
TAAGAGCCTGCACTGAAGGAGGA (72) 302 65 C- terminal
GGGGAGGAAGAAGTGGAAGAGAC (73)
11 CAGGTCTGTGGCCTGCCGTTCAT (74) 233 65 C- terminal
CCTTCCTGTGGGAGTTGAGCTGG (75)
12 GTTTGCTAGCCTTCTGTTATAGCT (76) 239 62 C- terminal
GGGAGCGCAGTCCCTCCAGAT (77)
13 CTTATATATTCCAAACCCTTATCTCA (78) 277 62 C- terminal
GGTGGGGATCGTTGCTATTGGTT (79)
14 AACCAATAGCAACGATCCCCACC (80) 303 65 C- terminal after
CTGACTTTGTCAATGGTCACCTGG (81) last intron
CGGAACCACCCTACAGCTTCCA (82) 210 65 C- terminal after
GGGAGTGGCAGCTCACTCGGGA (83) last intron
16 AGGCCCACGGTCCTGCCTATCT (84) 236 65 C- terminal after
CCATTGGGGCCGAACACATAATC (85) last intron
17 CTTCAGCATCTCCCAGGACAGAG (86) 228 65 C- terminal after
AAGGAGGGGTCAGCCAGTGACCT (87) the STOP codon
CA 02712809 2013-07-19
74
While particular embodiments of the present invention have been illustrated
and described, it
would be obvious to those skilled in the art that various other changes and
modifications can be
made. The scope of the claims should not be limited by the preferred
embodiments set forth in the
examples, but should be given the broadest interpretation consistent with the
description as a whole.
CA 02712809 2010-08-20
LIST OF REFERENCES
Altschul SF, et al. (1990). J. Mol. Biol. 251:403-410.
Altschul SF, et al. (1997). NucL Acids Res. 25:3389-3402.
Anand, R (1992). Techniques for the Analysis of Complex Genomes, (Academic
Press).
Anderson WF, et al. (1980). Proc. NatL Acad. Sci. USA 77:5399-5403.
Ausubel FM, et al. (1992). Current Protocols in Molecular Biology, (John Wiley
and Sons, New
York, New York).
Bandyopadhyay PK and Temin HM (1984). MoL Cell. Biol. 4:749-754.
Bartel PL, et al. (1993). "Using the 2-hybrid system to detect protein-protein
interactions." In
Cellular Interactions in Development: A Practical Approach, Oxford University
Press, pp. 153-179.
Beaucage SL and Caruthers MH (1981). Tetra. Letts. 22:1859-1862.
Berglund P, et al. (1993). Biotechnology 11:916-920.
Berkner KL, et al. (1988). BioTechniques 6:616-629.
Berkner KL (1992). Curr. Top. Microbiol. ImmunoL 158:39-66.
Biervert C, et al. (1998). Science 279:403-406.
Boehnke M, et al. (1991). Am. J. Hum. Genet. 49:1174-1188.
Borman S (1996). Chemical & Engineering News, December 9 issue, pp. 42-43.
Breakefield X0 and Geller Al (1987). MoL Neurobiol. 1:337-371.
Brinster RL, et al. (1981). Cell 27:223-231.
Browne DL, et al. (1994). Nature Genetics 8:136-140.
Buchschacher GL and Panganiban AT (1992). J. Virol. 66:2731-2739.
Capecchi MR (1989). Science 244:1288-1292.
Cariello NF (1988). Am. J. Human Genetics 42:726-734.
Chandy KG and Gutman GA (1995). Handbook of Receptors and Channels: Ligand and
Voltage-
Gated Ion Channels (CRC Press, Ann Arbor, MI), pp. 1-71.
Chee M, et al. (1996). Science 274:610-614.
CA 02712809 2010-08-20
76
Chevray PM and Nathans DN (1992). Proc. Natl. Acad. Sci. USA 89:5789-5793.
Compton J (1991). Nature 350:91-92.
Conner BJ, et al. (1983). Proc. Natl. Acad. Sci. USA 80:278-282.
Costantini F and Lacy E (1981). Nature 294:92-94.
Cotten M, et al. (1990). Proc. Natl. Acad. Sci. USA 87:4033-4037.
Cotton RG, etal. (1988). Proc. Natl. Acad. Sci. USA 85:4397-4401.
Culver KW, et al. (1992). Science 256:1550-1552.
Culver K (1996). Gene Therapy: A Primer for Physicians, 2nd Ed., Mary Ann
Liebert.
Curie! DT, et al. (1991). Proc. Natl. Acad. Sci. USA 88:8850-8854.
Curie! DT, et al. (1992). Hum. Gene Ther. 3:147-154.
DeRisi J, et al. (1996). Nat. Genet. 14:457-460.
Deutscher M (1990). Meth. Enzymology 182:83-89 (Academic Press, San Diego,
Cal.).
Dib C, et al. (1996). Nature 380:152-154.
Donehower LA, etal. (1992). Nature 356:215-221.
Drwinga HL et al. (1993). Genomics 16:311-314.
Dworetzky SI, et al. (1998). Society for Neuroscience Abstracts 24(part
2):813.1 (28th Annual
Meeting, Los Angeles, Calif., November 7-12, 1998).
Editorial (1996). Nature Genetics 14:367-370.
Elghanian R, et al. (1997). Science 277:1078-1081.
Enhancers and Eukaryotic Gene Expression, Cold Spring Harbor Press, Cold
Spring Harbor, New
York (1983).
Erickson J, et al. (1990). Science 249:527-533.
Fahy E, et al. (1991). PCR Methods App!. 1:25-33.
Feigner PL, et al. (1987). Proc. Natl. Acad. Sci. USA M:7413-7417.
Fields S and Song 0-K (1989). Nature 340:245-246.
CA 02712809 2010-08-20
77
Fiers W, etal. (1978). Nature 273:113-120.
Fink DJ, et al. (1992). Hum. Gene Ther. 3:11-19.
Fink DJ, et al. (1996). Ann. Rev. Neurosci. 19:265-287.
Finkelstein J, et al. (1990). Genomics 7:167-172.
Fodor SPA (1997). Science 277:393-395.
Freese A, et al. (1990). Biochem. Pharmacol. 40:2189-2199.
Friedman T (1991). In Therapy for Genetic Diseases, T. Friedman, ed., Oxford
University Press, pp.
105-121.
Glover D (1985). DNA Cloning, I and II (Oxford Press).
Goding (1986). Monoclonal Antibodies: Principles and Practice, 2d ed.
(Academic Press, N.Y.).
Godowski PJ, et al. (1988). Science 241:812-816.
Gordon JW, et al. (1980). Proc. Natl. Acad. Sci. USA 77:7380-7384.
Gorziglia M and Kapikian AZ (1992). J. Virol. 66:4407-4412.
Graham FL and van der Eb AJ (1973). Virology 52:456-467.
Gribkoff VK, et al. (1998). Society for Neuroscience Abstracts 24(part
2):813.10 (28th Annual
Meeting, Los Angeles, Calif., November 7-12, 1998).
Grompe M (1993). Nature Genetics 5:111-117.
Grompe M, et al. (1989). Proc. Natl. Acad. Sci. USA 86:5855-5892.
Guipponi M, et al. (1997). Hum. Molec. Genet. 6:473-477.
Guthrie G and Fink GR (1991). Guide to Yeast Genetics and Molecular Biology
(Academic Press).
Hacia JG, et al. (1996). Nature Genetics 14:441-447.
Harlow E and Lane D (1988). Antibodies: A Laboratory Manual (Cold Spring
Harbor Laboratory,
Cold Spring Harbor, New York).
Hasty P, et al. (1991). Nature 350:243-246.
Hauser WA and Kurland LT (1975). Epilepsia 16:1-66.
Helseth E, et al. (1990). J. Virol. 64:2416-2420.
CA 02712809 2010-08-20
78
Hodgson J (1991). Bio/Technology 9:19-21.
Huse WD, et al. (1989). Science 246:1275-1281.
Iannotti C, et al. (1998). Society for Neuroscience Abstracts 24(part
1):330.14 (28th Annual
Meeting, Los Angeles, Calif., November 7-12, 1998).
Innis MA, et al. (1990). PCR Protocols: A Guide to Methods and Applications
(Academic Press,
San Diego).
Jablonski E, et al. (1986). Nucl. Acids Res. 14:6115-6128.
Jakoby WB and Pastan IH (eds.) (1979). Cell Culture. Methods in Enzymology
volume 58
(Academic Press, Inc., Harcourt Brace Jovanovich (New York)).
Johnson PA, et al. (1992). J. Virol. 66:2952-2965.
Johnson, et al. (1993). APeptide Turn Mimetics@ in Biotechnology and Pharmacy,
Pezzuto et al.,
eds., Chapman and Hall, New York.
Kaneda Y, et al. (1989). J. Biol. Chem. 264:12126-12129.
Kanehisa M (1984). Nucl. Acids Res. 12:203-213.
Keating MT and Sanguinetti MC (1996). Curr. Opinion Genet. Dev. 6:326-333.
Kinszler KW, et al. (1991). Science 251:1366-1370.
Kohler G and Milstein C (1975). Nature 256:495-497.
Kozak M (1987). J. MoL Biol. 196:947-950.
Kraemer FB, et al. (1993).1 Lipid Res. 34:663-672.
Kubo T, et al. (1988). FEBS Lett. 241:119-125.
Kyte J and Doolittle RF (1982). J. Mol. Biol. 157:105-132.
Landegren U, et al. (1988). Science 242:229-237.
Lee JE, et al. (1995). Science 268:836-844.
Leppert M, et al. (1989). Nature 337:647-648.
Leppert M, et al. (1993). Brain Pathology 3:357-369.
Letts VA, et al. (1997). Genomics 43:62-68.
CA 02712809 2010-08-20
79
Lewis TB, et al. (1993). Am. 1 Hum. Genet. 53:670-675.
Lewis TB, etal. (1995). Genome Res. 5:334-341.
Lim CS, etal. (1991). Circulation 83:2007-2011.
Lipshutz RJ, et al. (1995). BioTechniques 19:442-447.
Lockhart DJ, et al. (1996). Nature Biotechnology 14:1675-1680.
Lopez GA, et al. (1994). Nature 367:179-182.
Madzak C, et al. (1992). J. Gen. Virol. 73:1533-1536.
Malafosse A, et al. (1992). Hum. Genet. 89:54-58.
Maniatis T, et al. (1982). Molecular Cloning: A Laboratory Manual (Cold Spring
Harbor
Laboratory, Cold Spring Harbor, New York).
Mann R and Baltimore D (1985). 1 Virol. 54:401-407.
Margolskee RF (1992). Curr. Top. MicrobioL Immunol. 158:67-95.
Martin R, et al. (1990). BioTechniques 9:762-768.
Matteucci MD and Caruthers MH (1981). 1 Am. Chem. Soc. 103:3185.
Matthews JA and Kricka LJ (1988). Anal. Biochem. 169:1.
McNamara JO (1994). J. Neurosci. 14:3413-3425.
Meldrum BS (1995). Epilepsia 36:S30-S35.
Merrifield B (1963). 1 Am. Chem. Soc. 85:2149-2156.
Metzger D, et al. (1988). Nature 334:31-36.
Mifflin TE (1989). Clinical Chem. 35:1819-1825.
Miller AD (1992). Curr. Top. Microbiol. Immunol. 158:1-24.
Miller AD, etal. (1985). MoL Cell. Biol. 5:431-437.
Miller AD, et al. (1988). 1 Virol. 62:4337-4345.
Modrich P (1991). Ann. Rev. Genet. 25:229-253.
Mombaerts P, etal. (1992). Cell 68:869-877.
CA 02712809 2010-08-20
Moss B (1992). Curr. Top. Microbiol. Immunol. 158:25-38.
Moss B (1996). Proc. Natl. Acad. Sci. USA 93:11341-11348.
Muzyczka N (1992). Curr. Top. Microbiol. Immunol. 158:97-129.
Nabel EG, et al. (1990). Science 249:1285-1288.
Nabel (1992). Hum. Gene Ther. 3:399-410.
Nakamura RL, et al. (1997). J. Biol, Chem. 272:1011-1018.
Naldini L, et al. (1996). Science 272:263-267.
Newton CR, et al. (1989). NucL Acids Res. 17:2503-2516.
Neyroud N, et al. (1997). Nat. Genet. 15:186-189.
Nguyen Q, et al. (1992). BioTechniques 13:116-123.
Noebels JL, etal. (1990). Epilepsy Res. 7:129-135.
Novack DF, et al. (1986). Proc. Natl. Acad Sci. USA 83:586-590.
Ohi S. et al. (1990). Gene 89:279-282.
Orita M, et al. (1989). Proc. Natl. Acad. Sci. USA 86:2766-2770.
Page KA, et al. (1990). J. Virol. M:5270-5276.
Patil N, etal. (1995). Nature Genetics 11:126-129.
Pellicer A, et al. (1980). Science 209:1414-1422.
Petropoulos CJ, et al. (1992). J Virol. 66:3391-3397.
Philpott KL, et al. (1992). Science 256:1448-1452.
Plouin P (1994). Idiopathic Generalized Epilepsies: Clinical, Experimental and
Genetic Aspects
(John Libbey and Company Ltd., London), pp. 39-44.
Ptacek LJ (1997). Neuromuscular Disorders 7: 250-255.
Quantin B, et al. (1992). Proc. Natl. Acad Sci. USA 89:2581-2584.
Remington's Pharmaceutical Sciences, 18th Ed. (1990, Mack Publishing Co.,
Easton, PA).
Reutens DC and Berkovic SF (1995). Neurology 45:1469-1476.
CA 02712809 2010-08-20
81
Rigby PWJ, et al. (1977). J. Mol. Biol. 113:237-251.
Ronen GM, et al. (1993). Neurology 43:1355-1360.
Rosenfeld MA, et al. (1992). Cell 68:143-155.
Ruano G and Kidd KK (1989). Nucl. Acids Res. 17:8392.
Russell D and Hirata R (1998). Nature Genetics 18:323-328.
Russell MW, et al. (1996). Hum. Molec. Genet. 5:1319-1324.
Ryan SG, et al. (1991). Ann. Neurol. 29:469-473.
Sambrook J, et al. (1989). Molecular Cloning: A Laboratory Manual, 2nd Ed.
(Cold Spring Harbor
Laboratory, Cold Spring Harbor, New York).
Sanguinetti MC, et al. (1996). Nature 384:80-83.
Scharf SJ, et al. (1986). Science 233:1076-1078.
Schneider G, et al. (1998). Nature Genetics 18:180-183.
Scopes R (1982). Protein Purification: Principles and Practice, (Springer-
Verlag, N.Y.).
Sheffield VC, et al. (1989). Proc. Natl. Acad. Sci. USA 86:232-236.
Sheffield VC, et al. (1991). Am. J. Hum. Genet. 49:699-706.
Shenk TE, et al. (1975). Proc. Natl. Acad. Sci. USA 72:989-993.
Shimada T, et al. (1991). J. Clin. Invest. 88:1043-1047.
Shinkai Y, et al. (1992). Cell 68:855-867.
Shoemaker DD, et al. (1996). Nature Genetics 14:450-456.
Signorini S, et al. (1997). Proc. Natl. Acad. Sci. USA. 94:923-927.
Snouwaert JN, et al. (1992). Science 257:1083-1088.
Soares MB, et al. (1994). Proc. Natl. Acad. Sci. USA. 91, 9228-9232.
Sorge J, et al. (1984). Mol. Cell. Biol. 4:1730-1737.
Spargo CA, et al. (1996). Mol. Cell. Probes 10:247-256.
Steinlein 0, et al. (1992). Hum. Molec. Genet. 1:325-329.
CA 02712809 2010-08-20
82
Steinlein 0, et al. (1995). Hum. Genet. 95:411-415.
Steinlein 0, et al. (1997). Am. I Med. Genet. 74:445-449.
Sternberg N (1990). Proc. Natl. Acad. Sci. USA 87:103-107.
Stewart MJ, et al. (1992). Hum. Gene Ther. 3:267-275.
Stratford-Perricaudet LD, et al. (1990). Hum. Gene Ther. 1:241-256.
Tytgat J (1994). Biochem. Biophys. Res. Commun, 203:513-518.
Valancius V and Smithies 0 (1991). Mol. Cell Biol. 11:1402-1408.
Wagner E, et al. (1991). Proc. Natl. Acad. Sci. USA 88:4255-4259.
Wagner E, et al. (1990). Proc. Natl. Acad. Sci. USA 87:3410-3414.
Walker GT, et al., (1992). Nucl. Acids Res. 20:1691-1696.
Wang CY and Huang L (1989). Biochemistry 28:9508-9514.
Wang Q, et al. (1996). Nat. Genet. 12:17-23.
Wartell RM, et al. (1990). Nucl. Acids Res. 18:2699-2705.
Wei A, et al. (1996). Neuropharmacology 35:805-829.
Wells JA (1991). Methods Enzymol. 202:390-411.
Wetmur JG and Davidson N (1968). 1 MoL Biol. 31:349-370.
White MB, et al. (1992). Genomics 12:301-306.
White R and Lalouel JM (1988). Annu. Rev. Genet. 22:259-279.
Wilkinson GW and Akrigg A (1992). Nucleic Acids Res. 20:2233-2239.
Wolff JA, et al. (1990). Science 247:1465-1468.
Wolff JA, et al. (1991). BioTechniques 11:474-485.
Wu DY and Wallace RB (1989). Genomics 4:560-569.
Wu CH, etal. (1989). 1 Biol. Chem. 264:16985-16987.
Wu GY, et al. (1991). 1. Biol. Chem. 266:14338-14342.
CA 02712809 2010-08-20
83
Yang WP, et al. (1997). Proc. Natl. Acad. Sci. USA 94:4017-4021.
Yang WP, et al. (1998). .1. Biol. Chem. 273:19419-19423.
Yokoyama M, et al. (1996). DNA Res. 3:311-320.
Zara F, etal. (1995). Hum. Mol. Genet. 4:1201-1207.
Zenke M, et al. (1990). Proc. Natl. Acad. Sci. USA 87:3655-3659.
Patents and Patent Applications:
European Patent Application Publication No. 0332435.
EPO Publication No. 225,807.
Hitzeman et al., EP 73,675A.
EP 425,731A.
WO 84/03564.
WO 90/07936.
WO 92/19195.
WO 93/07282.
WO 94/25503.
WO 95/01203.
WO 95/05452.
WO 96/02286.
WO 96/02646.
WO 96/11698.
WO 96/40871.
WO 96/40959.
WO 97/02048.
WO 97/12635.
CA 02712809 2010-08-20
84
U.S. Patent 3,817,837.
U.S. Patent 3,850,752.
U.S. Patent 3,939,350.
U.S. Patent 3,996,345.
U.S. Patent 4,275,149.
U.S. Patent 4,277,437.
U.S. Patent 4,366,241.
U.S. Patent 4,376,110.
U.S. Patent 4,486,530.
U.S. Patent 4,554,101.
U.S. Patent 4,683,195.
U.S. Patent 4,683,202.
U.S. Patent 4,816,567.
U.S. Patent 4,868,105.
U.S. Patent 5,252,479.
U.S. Patent 5,270,184.
U.S. Patent 5,409,818.
U.S. Patent 5,436,146.
U.S. Patent 5,455,166.
U.S. Patent 5,550,050.
U.S. Patent 5,691,198.
U.S. Patent 5,735,500.
U.S. Patent 5,747,469.
