U.S. patent application number 10/481613 was filed with the patent office on 2005-04-21 for atopy.
Invention is credited to Cookson, William, Moffatt, Miriam, Tinsley, Jon, Zhang, Youming.
Application Number | 20050085627 10/481613 |
Document ID | / |
Family ID | 27256198 |
Filed Date | 2005-04-21 |
United States Patent
Application |
20050085627 |
Kind Code |
A1 |
Zhang, Youming ; et
al. |
April 21, 2005 |
Atopy
Abstract
The present invention relates to isolated nucleic acid sequences
of ANGE, CLLD8 and CLLD7 or sequences complementary or
substantially homologous thereto or fragments thereof. Also
provided are sequences comprising hybrid nucleic add sequences from
two or more of the genes. Also provided are nucleic acid expression
vectors, polypeptides, antibodies to the polypeptides, host cells,
non-human transgenic animals and pharmaceutical compositions and
agents. Also provided is the use of the nucleic acid sequence
and/or protein in medicine and research, methods for diagnosing or
determining predisposition to disease or severity of disease,
methods for preventing or treating disease, and kits for use in the
methods and the use of the nucleic acid sequence and protein in
treating or preventing IgE mediated diseases and non-atopic asthma,
and in screens for identifying new agents for use in the
methods.
Inventors: |
Zhang, Youming; (Oxford,
GB) ; Moffatt, Miriam; (Bicester, GB) ;
Cookson, William; (Oxford, GB) ; Tinsley, Jon;
(Didcot, GB) |
Correspondence
Address: |
FISH & RICHARDSON P.C.
3300 DAIN RAUSCHER PLAZA
60 SOUTH SIXTH STREET
MINNEAPOLIS
MN
55402
US
|
Family ID: |
27256198 |
Appl. No.: |
10/481613 |
Filed: |
September 14, 2004 |
PCT Filed: |
June 21, 2002 |
PCT NO: |
PCT/GB02/02859 |
Current U.S.
Class: |
530/387.1 |
Current CPC
Class: |
A61P 43/00 20180101;
C07K 14/47 20130101; A61P 37/02 20180101; A61P 11/06 20180101; A01K
2217/075 20130101; A61K 48/00 20130101; A61P 11/02 20180101; A01K
2217/05 20130101; Y10T 436/143333 20150115; A61P 17/00 20180101;
A61P 17/02 20180101; A61P 37/08 20180101 |
Class at
Publication: |
530/387.1 |
International
Class: |
C07K 016/18 |
Foreign Application Data
Date |
Code |
Application Number |
Jun 21, 2001 |
GB |
0115211.5 |
Jun 21, 2001 |
GB |
0115212.3 |
Jun 21, 2001 |
GB |
0115213.1 |
Claims
1. An isolated or recombinant nucleic acid sequence comprising an
ANGE mRNA sequence or a sequence complementary or substantially
homologous thereto, or a fragment thereof.
2. An isolated or recombinant nucleic acid sequence comprising a
CLLD8 mRNA sequence or a sequence complementary or substantially
homologous thereto, or a fragment thereof.
3. An isolated or recombinant nucleic acid sequence comprising a
CLLD7 mRNA sequence or a sequence complementary or substantially
homologous thereto, or a fragment thereof.
4. An isolated or recombinant nucleic acid sequence comprising an
ANGE CLLD8 hybrid mRNA sequence or a sequence complementary or
substantially homologous thereto, or a fragment thereof.
5. An isolated or recombinant nucleic acid sequence comprising an
ANGE CLLD7 hybrid mRNA sequence or a sequence complementary or
substantially homologous thereto, or a fragment thereof.
6. An isolated or recombinant nucleic acid sequence comprising a
CLLD7-CLLD8 hybrid mRNA sequence or a sequence complementary or
substantially homologous thereto, or a fragment thereof.
7. An isolated or recombinant nucleic acid sequence comprising an
ANGE-CLLD8-CLLD7 hybrid mRNA sequence or a sequence complementary
or substantially homologous thereto, or a fragment thereof.
8-86. (canceled)
Description
[0001] The present invention relates to isolated nucleic acid
sequences of ANGE, CLLD8 and CLLD7 or sequences complementary or
substantially homologous thereto or fragments thereof. Also
provided are sequences comprising hybrid nucleic acid sequences
from two or more of the genes. Also provided are nucleic acid
expression vectors, polypeptides, antibodies to the polypeptides,
host cells, non-human transgenic animals and pharmaceutical
compositions and agents. Also provided is the use of the nucleic
acid sequence and/or protein in medicine and research, methods for
diagnosing or determining predisposition to disease or severity of
disease, methods for preventing or treating disease, and kits for
use in the methods and the use of the nucleic acid sequence and
protein in treating or preventing IgE mediated diseases and
non-atopic asthma, and in screens for identifying new agents for
use in the methods.
[0002] Atopic or Immunoglobulin E (IgE) mediated diseases include,
but are not limited to, asthma, hayfever, eczema, atopic dermatitis
and allergic rhinitis. These disorders are a major cause of disease
in children and young adults (Jarvis, D. & Burney, P. British
Medical Journal 316, 607-10 (1998) [published erratum appears in
BMJ 1998 Apr. 4;316(7137):1078]; and Cookson, W. Nature 402, B5-11
(1999).
[0003] Atopy and asthma are due to the interaction between strong
environmental and genetic factors (Cookson, W. Nature 402, B5-11
(1999). Asthma is usually recognised epidemiologically by standard
symptom questionnaires or by physician diagnosis (O'Connor, G. T.
& Weiss, S. T. Am J Respir Crit Care Med 149, S21-8; discussion
S29-30 (1994)). Atopy is detected by skin prick tests, or by
measurement of specific serum IgE titres against allergens with
RAST or ELISA techniques, or by quantifying the total serum IgE.
The examination of quantitative traits offers significant
advantages for both linkage and association analyses in general
(Risch, N. J. & Zhang, H. Am J Hum Genet 58, 836-43 (1996)) and
in the case of asthma (Cookson, W. & Palmer, L. Clin Exp
Allergy 28 Suppl 1, 88-9; discussion 108-10 (1998)). A number of
quantitative traits underlie asthma and atopy, including the total
serum IgE concentration, the Skin Test Index (STI), the RAST index
and the Dose-Response Slope (DRS) of bronchial responsiveness to
methacholine (Daniels, S. E. et al. Nature 383, 247-50 (1996)). The
total serum IgE is log-normally distributed, and has a high
heritability (Gerrard, J., Rao, D. & Morton, N. Am J Hum Genet
30, p46-58 (1978)) and Palmer, L. J. et al. Am J Respir Crit Care
Med 161, 183643 (2000)). It is influenced by genetic effects, which
incompletely overlap DRS and the STI.
[0004] The heritability of physician-diagnosed asthma is
60-70%.sup.7 and that of the (log normal) total serum IgE
concentration is 40-50%.sup.8,9. The heritability of the STI is
lower and is approximately 30%9. The examination of quantitative
rather than categorical traits offers significant advantages of
power for both linkage and association analyses in general.sup.10
and in the case of asthma.sup.11. The total serum IgE is
log-normally distributed with standardised measurement protocols,
and the effects of age and sex are well defined .sup.12.
Consequently, we have used the total serum IgE as quantitative
trait to map susceptibility genes for atopy and asthma.
[0005] Differing indices of atopy may be elevated in the same
family (Cookson, W. O. C. M. & Hopkin, J. M. Lancet 1, 86-88
(1988) and Young, R. P., Lynch, J., Sharp, P. A. & et al.
Journal of Medical Genetics 29, 236-238 (1992)). RAST and skin test
responses reach a peak later in childhood than the total serum IgE,
and decline at a slower rate thereafter (Cline, M. G. &
Burrows, B. B. Thorax 44, 425431 (1989)). To account for this
heterogeneity of phenotype (pleiotropy), the categorical trait of
"atopy" is based on a combination of the STI, RAST index, and the
total serum IgE (Daniels, S. E. et al. Nature 383, 247-50 (1996)
and Cookson, W. O. C. M. & Hopkin, J. M. Lancet 1, 86-88
(1988)).
[0006] Atopy is due to the interaction between genetic and
environmental factors. The genetic factors are thought to be
variants of DNA structure ("polymorphisms") that alter the level of
expression or the function of genes to predispose to asthma.
Variants of DNA sequence at a particular site ("locus") are known
as "alleles". Genome-wide scans for linkage to atopy and
asthma-associated phenotypes have been conducted (Daniels, S. E. et
al. Nature 383, 247-50 (1996)). Strong linkage of the atopy
phenotype to chromosome 13q14 was observed, and confirmed in a
second panel of families at the time of our initial genome screen.
An earlier study had found linkage of the total serum IgE to the
esterase D (ESD) protein polymorphism on chromosome 13q14 (Eiberg,
H., et al. Cytogenetics. And Cell Genetics 40, 622 (1985)).
[0007] Linkage to the region has also been confirmed by a single
locus study of Japanese families (Kimura, K. et al. Hum Mol Genet
8, 1487-90 (1999)). A two-stage screen in Hutterite families from
the US found linkage of asthma to 13q21.3 (Ober, C. et al. The
Collaborative Study on the Genetics of Asthma. Hum Mol Genet 7,
1393-8 (1998)) in the first stage families but not in the second.
Linkage to 13q14 has also been observed to house dust mite allergy
in children with asthma (Hizawa, N. et al. Collaborative Study on
the Genetics of Asthma (CSGA). J Allergy Clin Immunol 102, p43642
(1998)), and to children with atopic dermatitis (Beyer K, W. U et
al J Allergy Clin Immunol 101, 152 (1998)). These results suggest
that chromosome 13 contains an important atopy locus. A locus for
atopic dermatitis has recently been mapped to the same region of
chromosome 13-13q14. Susceptibility loci for atopic dermatitis on
chromosomes 3, 13, 15, 17 and 18 in a Swedish population: Bradley
M, Soderhall C, Luthman H, Wahlgren C F, Kockum I, Nordenskjold M
Hum Mol Genet 2002 Jun. 15;11(13):1539-48.
[0008] Close localisation of disease causing genes may be
accomplished by the detection of associations between particular
alleles and the disease phenotype. Over short segments of DNA,
distinctive alleles of the individual polymorphisms will show
non-random association with alleles of neighbouring polymorphisms.
This phenomenon, known as "linkage disequilibrium" typically occurs
over 50-500 Kilobases (Kb) of DNA (Jorde, L. B. et al. Am J Hum
Genet 54, 884-98 (1994); Collins, A., Lonjou, C. & Morton, N.
E. Proc Natl Acad Sci U S A 96, 15173-7 (1999) and Abecasis, G. R.
et al. Am J Hum Genet 68, 191-197 (2001)), and associations between
polymorphism and disease are in general unlikely to extend beyond
500 Kb. Linkage disequilibrium may be detected by the study of
individuals and by the study of families.
[0009] Disease causing alleles will be in linkage disequilibrium
with non-functional polymorphisms from the same chromosomal
segment. It is therefore possible to detect allelic association
with disease from particular chromosomal segments, without
identifying the exact polymorphism and gene underlying the disease
state.
[0010] The detection of allelic association may therefore give
information as to disease susceptibility in a particular
individual. Furthermore, allelic association is indicative of a
disease-causing gene being present within a limited distance of DNA
in either direction from the allele.
[0011] Identification of the disease causing gene will allow the
identification of children at risk of atopy before the disease has
developed (for example immediately after birth), with the potential
for prevention of disease. Knowledge of the gene and its activity
will enable predictions to be made regarding the type of disease
(i.e. asthma, dermatitis or allergies) and the clinical course of
disease (e.g. severe as opposed to mild) or the response to
particular treatments. This diagnostic information will be of use
to the health care, pharmaceutical and insurance industries.
[0012] According to a first aspect of the invention there is
provided an isolated or recombinant nucleic acid sequence
comprising a sequence as shown in FIG. 5, or a sequence which
excludes one or more of the exons as set out in FIG. 3a or a
sequence complementary or substantially homologous thereto, or a
fragment thereof. The sequence of FIG. 5 comprises the human ANGE,
CLLD7 and CLLD8 nucleotide sequences. FIG. 5a (i) shows the Exon
sequences of the ANGE gene including the 2 alternative first exons;
FIG. 5a (ii) shows the ANGE mRNA sequence and 5a (iii) the
translated protein sequence. The NY-REN-34 mRNA sequence is shown
in FIG. 5b (i) and the protein sequence of NY-REN-34 in FIG. 5b
(ii) an alternative NY-REN-34 protein sequence is shown in FIG. 5b
(iii).
[0013] For the purposes of the present invention, the ANGE gene is
the gene known in the prior art as NY-REN-34, and shown as
nucleotides 313649-346509 of BAC bA103J18.03548 (FIG. 5).
References to the ANGE gene in the present application include
variant sequences showing 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%,
88%, 89%, 90%, 915, 92%, 93%, 95%, 96%, 97%, 98%, 99% or 100%
homology with the ANGE gene of FIG. 5, and preferably sharing one
or more functional characteristics with the ANGE gene.
[0014] The ANGE nucleic acid sequence can comprise any combination
of one or more exons from FIGS. 3a, 5a (i) and Table 5 or a
sequence substantially homologous thereto, or a fragment thereof.
These combinations are for all ANGE sequences including human and
mouse.
[0015] All the sequences of the present invention are isolated, or
alternatively may be recombinant. By isolated is meant a nucleic
acid or polypeptide sequence which has been purified, and is
substantially free of other protein and nucleic acid. Such
sequences may be obtained by PCR amplification, cloning techniques,
or synthesis on a synthesiser. By recombinant is meant nucleic acid
sequences which have been recombined by the hand of man.
[0016] The polynucleotide sequences of the invention may be genomic
or cDNA, or RNA, preferably mRNA, or PNA or other nucleic acid
analogue known to the person skilled in the art. In the present
invention, gene products include polynucleotide sequences and
protein. References to polypeptide sequences include proteins and
peptides.
[0017] The public domain REFSEQ entries for the mRNA sequences of
CLLD7, CLLD8 and NY-REN-34 are NM.sub.--018191.2, NM.sub.--031915.1
and NM.sub.--016119.1 respectively. These show minor differences at
the nucleotide level to the sequences shown above. However for
NY-REN-34 these alterations result in a truncated putative protein
compared to our sequence which is shown below.
[0018] In the present application, sequences which are
complementary or substantially homologous are those sequences which
hybridise under stringent conditions to the defined sequence or its
gene products. Thus, for example, a nucleic acid sequence
substantially homologous to a reference nucleic acid will be
capable of hybridising to a gene product (i.e. mRNA) of the
reference nucleic acid, under stringent conditions. A complementary
sequence is one which is capable of hybridising to the nucleic acid
sequence itself, under stringent conditions. Also provided in the
present invention are complements of the substantially homologous
sequences. A substantially homologous sequence preferably has at
least 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89,
90, 91, 92, 93, 94, 95, 96, 97, 98 or 100% sequence identity with
the defined sequence. This definition of substantially homologous
applies to both nucleic acid and polypeptide sequences. Thus,
polypeptide sequences having conservative amino acid substitutions
that do not affect structure or function are also included. For any
given DNA sequence, references to a complementary sequence include
the corresponding mRNA sequence and any cDNA sequence derived on
such an RNA sequence. "% identity" is a measure of the relationship
between two nucleic acid or polypeptide sequences, as determined by
comparing their sequences. In general, the two sequences to be
compared are aligned to give a maximum correlation between the
sequences. The alignment of the two sequences is examined and the
number of positions giving an exact amino acid or nucleotide
correspondence is determined, and divided by the total length of
the alignment, and the result is multiplied by 100 to give a %
identity. The % identity may be determined over the whole length of
the sequence to be compared, which is particularly suitable for
sequences of the same or similar lengths or for sequences which are
highly homologous, or over shorter defined lengths which is more
suitable for sequences of unequal lengths and with a lower
homology.
[0019] Methods for comparing the identity of two or more sequences
are known in the art. For example, programs available in the
Wisconsin Sequence Analysis Package version 9.1 (Devereux J et al.,
Nucl Acid Res 12 387-395 (1984), available from Genetics Computer
Group, Madison, Wis., USA), such as BESTFIT and GAP may be
used.
[0020] BESTFIT uses the "local homology" algorithm of Smith and
Waterman (Advances in Applied Mathematics, 2:482489, 1981) and
finds the best single region of similarity between two sequences.
BESTFIT is more suited to comparing two polynucleotide or two
polypeptide sequences which are dissimilar in length, the program
assuming that the shorter sequence represents a portion of the
longer. In comparison, GAP aligns two sequences finding a "maximum
similarity" according to the algorithm of Neddleman and Wunsch (J.
Mol. Biol. 48:443-354, 1970). GAP is more suited to comparing
sequences which are approximately the same length and an alignment
is expected over the entire length. Preferably, the parameters "Gap
Weight" and "Length Weight" used in each program are 50 and 3 for
polynucleotide sequences and 12 and 4 for polypeptide sequences,
respectively. Preferably, % identities and similarities are
determined when the two sequences being compared are optimally
aligned.
[0021] Other programs for determining identity and/or similarity
between sequences are also known in the art, for instance the BLAST
family of programs (Altschul et al, J. Mol. Biol., 215:403-410,
(1990) and Altschul et al, Nuc Acids Res., 25:289-3402 (1997),
available from the National Center for Biotechnology Information
(NCB), Bethesda, Md., USA and accessible through the home page of
the NCBI at www.ncbi.nlm.nih.gov) and FASTA (Pearson W. R. and
Lipman D. J., Proc. Nat. Acac. Sci., USA, 85:2444-2448 (1988),
available as part of the Wisconsin Sequence Analysis Package).
Preferably, the BLOSUM62 amino acid substitution matrix (Henikoff
S. and Henikoff J. G., Proc. Nat. Acad. Sci., USA, 89:10915-10919,
(1992)) is used in polypeptide sequence comparisons including where
nucleotide sequences are first translated into amino acid sequences
before comparison.
[0022] Preferably, the program BESTFIT is used to determine the %
identity of a query polynucleotide or a polypeptide sequence with
respect to a polynucleotide or a polypeptide sequence of the
present invention, the query and the reference sequence being
optimally aligned and the parameters of the program set at the
default value.
[0023] In relation to the present invention, "stringent conditions"
refers to the washing conditions used in a hybridisation protocol.
In general, the washing conditions should be a combination of
temperature and salt concentration so that the denaturation
temperature is approximately 5 to 20.degree. C. below the
calculated T.sub.m of the nucleic acid under study. The T.sub.m of
a nucleic acid probe of 20 bases or less is calculated under
standard conditions (1M NaCl) as [4.degree.
C..times.(G+C)+2.degree. C..times.(A+T)], according to Wallace
rules for short oligonucleotides. For longer DNA fragments, the
nearest neighbour method, which combines solid thermodynamics and
experimental data may be used, according to the principles set out
in Breslauer et al., PNAS 83: 3746-3750 (1986). The optimum salt
and temperature conditions for hybridisation may be readily
determined in preliminary experiments in which DNA samples
immobilised on filters are hybridised to the probe of interest and
then washed under conditions of different stringencies. While the
conditions for PCR may differ from the standard conditions, the
T.sub.m may be used as a guide for the expected relative stability
of the primers. For short primers of approximately 14 nucleotides,
low annealing temperatures of around 44.degree. C. to 50.degree. C.
are used.
[0024] The temperature may be higher depending upon the base
composition of the primer sequence used. Suitably stringent
conditions are those under which non-specific hybridisation (e.g.
to non-DPP10 encoding sequences) are avoided. Suitable stringent
conditions are 0.5.times.SSC/1% SDS/58.degree. C./30 mins for a
21mer oligonucleotide probe.
[0025] The complementary sequences of the invention (which may also
be referred to herein as "antisense") may be useful as probes or
primers, or in the regulation of ANGE expression. Preferably, the
primer sequences are capable of amplifying all or a portion of an
ANGE gene. Preferred primer sequences are disclosed in the Examples
and Table 4. Pairs of primers for amplification of all or part of
the gene, or alleles, or variants thereof, form another aspect of
the invention. Similarly, ANGE probes will be useful in detecting
the presence or expression levels of ANGE, or variant forms
thereof, in a sample from a subject. The probes may also be useful
in analysing the expression pattern of ANGE in a subject.
[0026] In the present application, fragments are any contiguous 10
residue sequence, or greater, such as 20, 30, 40, or 50 residue
sequence. Preferably, fragments of nucleic acid or polypeptide
sequences share one or more functional characteristics with ANGE or
its gene, or are capable of modulating (i.e. inhibiting or
enhancing) such a functional characteristic. The novelty of a
fragment according to the present embodiment may be easily
ascertained by comparing the nucleotide or polypeptide sequence of
the fragment with sequences catalogued in databases such as
Genebank at the priority date, or by using computer programs such
as DNASIS (Hitachi Engineering Inc) or Word Search or FASTA of the
Genetic Computer Group (Madison, USA).
[0027] The fragments may be used in a variety of diagnostic,
prognostic or therapeutic methods or may be useful as research
tools for example in screening. Fragments of the sequences of the
first aspect or their complements may be used as primer sequences
as described above.
[0028] In a second aspect of the invention there is provided an
isolated or recombinant nucleic acid sequence comprising a sequence
as shown in FIG. 5 or a sequence as shown in FIG. 5 which excludes
one or more of the exon sequences as set out in FIG. 5d (i) and
Table 5 or a sequence complementary or substantially homologous
thereto or a fragment thereof. The CLLD8 mRNA sequence is shown in
FIG. 5d (ii) and the CLLD8 protein sequence in FIG. 5d (iii). The
nucleotides 294727 to 309803 of FIG. 5 is the human CLLD8 nucleic
acid sequence.
[0029] In a third aspect of the invention there is provided an
isolated or recombinant nucleic acid sequence comprising a sequence
as shown in FIG. 5 or a sequence as shown in FIG. 5 which excludes
one or more of the exon sequences as set out in FIG. 5c (i) and
Table. The CLLD7 mRNA sequence is shown in FIG. 5c (ii) and the
CLLD7 protein sequence in FIG. 5c (iii). The nucleotides 349634 to
410846 of FIG. 5 is the human CLLD7 nucleic acid sequence.
[0030] In a fourth aspect of the invention there is provided an
isolated or recombinant nucleic acid sequence as claimed in claim 1
comprising a sequence as shown in FIG. 5 (nucleotides
313649-346509) (ANGE) contiguous with an isolated or recombinant
nucleic acid sequence as claimed in claim 2 comprising a sequence
as shown in FIG. 5 (nucleotides 294727-309803) (CLLD8) or a
sequence complementary or substantially homologous thereto or a
fragment thereof.
[0031] Alternatively, there is provided an isolated or recombinant
polynucleotide sequence comprising the CLLD8 gene and ANGE gene,
wherein both genes are under the control of a single regulatory
element. Preferably, the regulatory element is a promoter. More
preferably, the regulatory element is the CLLD8 promoter.
[0032] Alternatively, there is provided an isolated or recombinant
polynucleotide sequence encoding a protein having the domain
structure Pre-SET-SET-Post-SET-PHD-PHD. Preferably, the domain
structure is CpGBD-Pre-SET-SET-Post-SET-PHD-PHD. SET and PHD
domains will be known to persons skilled in the art.
[0033] Preferably, the polynucleotide sequences of the fourth
aspect encode a single gene product comprising both CLLD8 and ANGE.
This composite gene product is produced as a splice product of the
CLLD8 gene, under control of the CLLD8 promoter, and comprises the
ANGE gene product. This composite CLLD8-ANGE gene product results
from splicing together of the CLLD8 and ANGE genes and is shown to
be involved in atopy.
[0034] In a fifth aspect of the invention there is provided an
isolated or recombinant nucleic acid sequence as claimed in claim 1
comprising a sequence (nucleotides 313649-346509) as shown in FIG.
5 (ANGE) contiguous with an isolated or recombinant nucleic acid
sequence as claimed in claim 3 comprising a sequence (nucleotides
349634 to 410846) as shown in FIG. 5 (CLLD7) or a sequence
complementary or substantially homologous thereto or a fragment
thereof.
[0035] Alternatively, there is provided an isolated or recombinant
polynucleotide sequence comprising the ANGE gene and CLLD7 gene,
wherein both genes are under the control of a single regulatory
element. Preferably, the regulatory element is a promoter. More
preferably, the regulatory element is the ANGE promoter.
[0036] Preferably, the polynucleotide sequences of the fifth aspect
encode a single gene product comprising both ANGE and CLLD7. This
composite gene product is produced as a splice product of the ANGE
gene, under control of the ANGE promoter, and comprises the CLLD7
gene product. This composite CLLD7-ANGE gene product results from
splicing together of the CLLD7 and ANGE genes and is shown to be
involved in atopy.
[0037] In a sixth aspect of the invention there is provided an
isolated or recombinant nucleic acid sequence comprising a sequence
as claimed in claim 2 comprising a sequence (nucleotides
294727-309803) as shown in FIG. 5 (CLLD8) contiguous with an
isolated or recombinant nucleic acid sequence as claimed in claim 3
comprising a sequence (nucleotides 349634 to 410846) as shown in
FIG. 5 (CLLD7) or a sequence complementary or substantially
homologous thereto or a fragment thereof.
[0038] Alternatively, there is provided an isolated or recombinant
polynucleotide sequence comprising the CLLD8 gene and CLLD7 gene,
wherein both genes are under the control of a single regulatory
element. Preferably, the regulatory element is a promoter. More
preferably, the regulatory element is the CLLD7 promoter.
[0039] Preferably, the polynucleotide sequences of the sixth aspect
encode a single gene product comprising both CLLD8 and CLLD7. This
composite gene product is produced as a splice product of the CLLD8
gene, under control of the CLLD8 promoter, and comprises the CLLD7
gene product. This composite CLLD8-CLLD7 gene product results from
splicing together of the CLLD8 and CLLD7 genes and is shown to be
involved in atopy.
[0040] In a seventh aspect of the invention there is provided an
isolated or recombinant nucleic acid sequence comprising a sequence
as claimed in claim 1 comprising a sequence (nucleotides
313649-346509) as shown in FIG. 5 (ANGE) contiguous with an
isolated or recombinant nucleic acid sequence as claimed in claim 2
comprising a sequence (nucleotides 294727-309803) as shown in FIG.
5 (CLLD8) and contiguous with an isolated or recombinant nucleic
acid sequence as claimed in claim 3 comprising a sequence
(nucleotides 349634 to 410846) as shown in FIG. 5 (CLLD7) or a
sequence complementary or substantially homologous thereto or a
fragment thereof.
[0041] Alternatively, there is provided an isolated or recombinant
polynucleotide sequence comprising the ANGE gene, the CLLD8 gene
and the CLLD7 gene, wherein all the genes are under the control of
a single regulatory element. Preferably, the regulatory element is
a promoter. More preferably, the regulatory element is the CLLD8
promoter.
[0042] Preferably, the polynucleotide sequences of the seventh
aspect encode a single gene product comprising CLLD8, ANGE and
CLLD7. This composite gene product is produced as a splice product
of the CLLD8 gene, under control of the CLLD8 promoter, and
comprises the ANGE and CLLD7 gene products. This composite
CLLD8-ANGE-CLLD7 gene product results from splicing together of the
CLLD8, ANGE and CLLD7 genes and is shown to be involved in
atopy.
[0043] By the terms "ANGE" "CLLD7" and "CLLD8" are meant either the
complete gene product, or a part or parts thereof. Parts of the
gene products are preferably splice variants, and preferably
include at least one exon or a transcript produced from at least
one exon. Thus, the gene product of the fourth to seventh aspects
include at least one exon or part of an exon of CLLD7, CLLD8 and
ANGE.
[0044] In an eighth aspect of the invention there is provided an
isolated or recombinant nucleic acid sequence comprising at least a
part of the sequence of FIG. 5, and comprising one or more SNPs at
positions, which correspond to the positions of FIG. 5 listed in
Table 1.
[0045] Particular isolated nucleic acid molecules include
those:
[0046] as shown in Table 2c;
[0047] comprising a SNP at the position corresponding to position
185752b4.sub.--2 of FIG. 5;
[0048] comprising a SNP at the position corresponding to position
185752b5.sub.--3 of FIG. 5;
[0049] comprising a SNP at the position corresponding to position
4321017b38.sub.--1 of FIG. 5.
[0050] The isolated or recombinant nucleic acid molecules of the
eighth aspect of the present invention are different to the "wild
type" or "reference" sequence of FIG. 5.
[0051] This aspect of the invention also provides antisense
sequences. Such sequences are typically single stranded and are
capable of hybridising to the above mentioned nucleic acid
sequences of the invention, or to the sequence of FIG. 5, under
stringent conditions. Preferred antisense sequences are those which
are capable of hybridising to an allele of a polymorphism of the
invention, and most preferably is capable of distinguishing between
alleles of a polymorphism (of Table 1). Stringent conditions are
defined below. The antisense sequences may be prepared
synthetically or by nick translation, and are preferably isolated
or recombinant.
[0052] The antisense sequences include primers and probes, for
example, for use in the methods of the present invention. Primer
sequences are capable of acting as an initiation site for template
directed nucleic acid synthesis, under appropriate conditions,
which will be known to skilled persons. Probes are useful in the
detection, identification and isolation of particular nucleic acid
sequences. Probes and primers are preferably 15 to 30 nucleotides
in length.
[0053] For amplification purposes, pairs and primers are provided.
These include a 5' primer, which hybridises to the 5' end of the
nucleic acid sequence to be amplified, and a 3' primer, which
hybridises to the complementary strand of the 3' end of the nucleic
acid to be amplified. Preferred primers are those listed in Table
4.
[0054] Probes and primers may be labelled, for example to enable
their detection. Suitable labels include for example, a radiolabel,
enzyme label, fluoro-label, and biotin-avidin label for subsequent
visualisation in, for example, a southern blot procedure. A
labelled probe or primer may be reacted with a sample DNA or RNA,
and the areas of the DNA or RNA which carry complimentary sequences
will hybridise to the probe, and become labelled themselves. The
labelled areas may be visualised, for example by
autoradiography.
[0055] Preferably, the probes and/or primers hybridise under,
"stringent conditions", which refers to the washing conditions used
in a hybridisation protocol. The hybridisation conditions for
probes are preferably sufficiently stringent to allow distinction
between different alleles of a polymorphism upon binding of the
probes. In general, the washing conditions should be combination of
temperature and salt concentration so that the denaturation
temperature is approximately 5 to 20.degree. C. below the
calculated T.sub.m of the nucleic acid under study. The T.sub.m of
a nucleic acid probe of 20 bases or less is calculated under
standard conditions (1M NaCl) as [4.degree.
C..times.(G+C)+2.degree. C..times.(A+T)], according to Wallace
rules for short oligonucleotides. For longer DNA fragments, the
nearest neighbour method, which combines solid thermodynamics and
experimental data may be used, according to the principles set out
in Breslauer et al., PNAS 83: 3746-3750 (1986). The optimum salt
and temperature conditions for hybridisation may be readily
determined in preliminary experiments in which DNA samples
immobilised on filters are hybridised to the probe of interest and
then washed under conditions of different stringencies. While the
conditions for PCR may differ from the standard conditions, the
T.sub.m may be used as a guide for the expected relative stability
of the primers. For short primers of approximately 14 nucleotides,
low annealing temperatures of around 44.degree. C. to 50.degree. C.
are used. The temperature may be higher depending upon the base
composition of the primer sequence used. Typically, the salt
concentration is no more than 1M, and the temperature is at least
25.degree. C. Suitable conditions are 5.times.SSPE (750 mM NaCl, 50
mM NaPhosphate, 5 mM EDTA pH 7.4) and a temperature of
25-30.degree. C.
[0056] The use of one or more of the SNP markers of Table 1 in the
identification of a gene or genetic element which influences IgE
mediated disease or non-atopic asthma is also included.
[0057] As is the use of one or more of the SNP markers in medicine
or in the identification of an agent for use in the diagnosis,
prevention or treatment of an IgE mediated disease or non-atopic
asthma.
[0058] In a preferred embodiment the SNP marker is as shown in
Table 2c, or 185752%.sub.--2, 185752b5.sub.--3, 432103b43.sub.--1
or 4321017b38.sub.--1 or any SNP in linkage disequilibrium with the
SNP markers selected in Table 1. The polynucleotides of the first
to eight aspects are used in the diagnosis of individuals having an
IgE mediated disease or non-atopic asthma, or in the treatment of
individuals having such disease. The polynucleotides may also be
used in the manufacture of a diagnostic for diagnosing individuals
having an IgE mediated disease or non-atopic asthma or in the
treatment of individuals having such diseases.
[0059] In a ninth aspect of the invention, the isolated nucleic
acid sequences of the invention may be provided in the form of a
vector to enable the in vitro or in vivo expression of the isolated
nucleic acid sequences of any of the first to eighth aspects.
Vectors include plasmids, chromosomes, artificial chromosomes and
viruses and may be expression vectors, which are capable of
expressing nucleic acid sequences in vitro or in vivo, or
transformation vectors which are capable of transferring the
nucleic acid sequence from one environment to another. The nucleic
acid molecules of the invention may be operably linked to one or
more regulatory elements including a promoter.
[0060] The term regulatory elements includes response elements,
consensus sites, methylation sites, locus control regions,
post-transcriptional modifications, splice variants, homeoboxes,
inducible factors, DNA binding domains, enhancer sequences,
initiation codons, secretion signals and, polyA sequences. Regions
upstream or downstream of a promoter such as enhancers, which
regulate the activity of the promoter, are also regulatory
elements.
[0061] The vector may also comprise an origin of replication;
appropriate restriction sites to enable cloning of inserts adjacent
to the polynucleotide molecule; markers, for example antibiotic
resistance genes; ribosome binding sites: RNA splice sites and
transcription termination regions; polymerisation sites; or any
other element, such a secretion signals, which may facilitate the
cloning and/or expression of the polynucleotide molecule.
[0062] Within a vector the gene may be expressed upstream or
downstream of an expressed protein tag such as a histidine tag, V5
epitope tag, green fluorescent protein tag, MHC tag or other such
tag known to those skilled in the art. Use of such a tag allows
easy localisation, affinity purification and detection of the
fusion protein with an antibody to the tag moiety.
[0063] Where two or more nucleic acid molecules of the invention
are introduced into the same vector, each may be controlled by its
own regulatory sequences, or all molecules may be controlled by the
same regulatory sequence. In the same manner, each molecule may
comprise a 3' polyadenylation site. Examples of suitable vectors
will be known to persons skilled in the art and include pBluescript
II, lambdaZap, and pCMV-Script (Stratagene Cloning Systems, La
Jolla, USA).
[0064] Appropriate regulatory elements, in particular promoters,
will usually depend upon the host cell into which the expression
vector is to be inserted. Where microbial host cells are used,
promoters such as lactose promoter system, tryptophan (Trp)
promoter system, .beta.-lactamase promoter system or phage lambda
promoter systems are suitable. Where yeast cells are used,
preferred promoters include alcohol dehydrogenase I or glycolytic
promoters. In mammalian host cells, preferred promoters are those
derived from immunoglobulin genes, SV40, Adenovirus, Bovine
Papilloma virus etc. Suitable promoters for use in various host
cells would be readily apparent to a person skilled in the art
(See, for example, Current Protocols in Molecular Biology Edited by
Ausubel et al, published by Wiley). In addition, the regulatory
elements may be modified, for example by the addition of further
regulatory elements, to achieve a desired expression pattern.
[0065] By operably linked is meant that the components of the
vector or sequence are in a relationship which allows them to
function as intended.
[0066] These vectors may be used to transform host cells, for
example, prokaryotic or eukaryotic cells. These cells may be used
in the production of recombinant gene products produced from the
isolated nucleic acid sequences of the first to eighth aspects, or
in the regulation or analysis of the nucleic acid sequences of the
first to eighth aspects. The transformed host cells form part of
the invention. Preferred cells include E. coli, yeast, filamentous
fungi, insect cells, mammalian cells, preferably immortalised, such
as mouse, CHO, HeLa, Myeloma or Jurkat cell lines, human and monkey
cell lines and derivatives thereof.
[0067] According to a tenth aspect of the invention, there is
provided a polypeptide sequence comprising a polypeptide sequence
encoded by a nucleic acid sequence of the first to eighth aspects
of the invention. Preferably the polypeptide sequences are encoded
by a nucleic acid sequence of FIG. 5.
[0068] The tenth aspect of the invention includes a polypeptide
sequence comprising a polypeptide sequence as shown in any one of
FIGS. 5a (iii), 5a (v), 5b (ii), 5b (iii), 5c (iii), 5d (iii) or a
sequence homologous thereto, or a fragment thereof. The sequences
of FIGS. 5a (iii), 5a (v), 5b (ii), 5b (iii), 5c (iii), 5d (iii)
are the predicted human ANGE, CLLD7 and CLLD8 polypeptide sequences
respectively.
[0069] The ANGE, CLLD7 and CLLD8 polypeptides or sequences
substantially homologous thereto or a fragments thereof may be
subject to post-translational modification. Post-translational
modification (PTM) is defined herein as including modification of a
protein following translation by proteolytic cleavage e.g. cleavage
of a preprotein, a proprotein or a preproprotein by removal of a
signal sequence or activation of a zymogen. PIM also includes the
attachment of a carbohydrate to a protein, the predominant sugars
attached include glucose, galactose, mannose, fucose, GalNAC,
GlcNAC and NANA. The carbohydrates may be linked to the protein
either by O-glycosidic or N-glycosidic bonds e.g. glycosylation.
Also included are acylation; methylation; phosphorylation;
sulfation and prenylation. Vitamin C-dependent modifications such
as proline and lysine hydroxylation and carboxy terminal amidation
and vitamin K-dependent modifications such as carboxylation of
glutamine residues are also included as is the addition of selenium
as selenocysteine in a protein.
[0070] The ANGE, CLLD7 and CLLD8 polypeptides may be operably
linked to a secretion signal, to assist their secretion from the
golgi apparatus to another part of the cell. Suitable secretion
signals can be provided by recombinant vectors such as pSecTag2
(Invitrogen Corporation, Carlsbad, Calif.). Proteins expressed from
such vectors are fused at the N-terminus to the murine Ig kappa
chain leader sequence. The secretion signal may be linked to the
soluble ANGE, CLLD7 and CLLD8 polypeptide sequences using
techniques available in the art, including recombinant DNA
technology. The polypeptides may be linked to a tag such as a
histidine tag, V5 epitope tag, green fluorescent protein tag, MHC
tag or other tag known to those skilled in the art or to a carrier
molecule known to a person skilled in the art.
[0071] The polypeptide sequences of the tenth aspect are preferably
functional and may be useful in drug screening, diagnosis or
therapy. Functional fragments of ANGE, CLLD7 or CLLD8 are those
which share immunological or functional characteristics with the
full length, membrane bound or soluble form of ANGE, CLLD7 or
CLLD8. Fragments may be at least 10, preferably 15, 20, 25, 30, 35,
40 or 50 amino acids in length. Preferably, the polypeptide
sequences are isolated.
[0072] In an eleventh aspect of the present invention, there are
provided antibodies which are specific for an antigen of a
polypeptide sequence of the tenth aspect or an antigen of the
isolated nucleic acid of the first to eighth aspects, or fragments
of any of said aspects or which react with an antigen of a
polypeptide sequence of the tenth aspect or the isolated nucleic
acid of the first to eighth aspects, or fragments of any of said
aspects. Herein the term "react" has the meaning that the antibody
is able to interact with the polypeptide or isolated nucleic acid.
The term "specific for" has the meaning that the antibody
specifically reacts with the polypeptide or isolated nucleic
acid.
[0073] Antibodies can be made by the procedure set forth by
standard procedures (Harlow and Lane, "Antibodies; A Laboratory
manual" Cold Spring Harbour Laboratory, Cold Spring Harbour, New
York, 1998). Briefly, purified antigen can be injected into an
animal in an amount and in intervals sufficient to elicit an immune
response. Antibodies can either be purified directly, or spleen
cells can be obtained from the animal. The cells are then fused
with an immortal cell line and screened for antibody secretion. The
antibodies can be used to screen DNA clone libraries for cells
secreting the antigen. Those positive clones can then be sequenced
as described in, for example, Kelly et al., Bio/Technology
10:163-167 (1992) and Bebbington et al., Bio/Technology 10:169-175
(1992). Preferably, the antigen being detected and/or used to
generate a particular antibody will include polypeptide sequences
according to the tenth aspect or isolated nucleic acid sequences
according to the first to eighth aspects. The antibody may be a
polyclonal or monoclonal antibody, a chimeric antibody, a humanised
antibody or a bifunctional antibody or a fragment of any of the
above. A bifunctional antibody is an antibody that can bind to two
different antigens, these antigens may be different antigens
present in the ANGE, CLLD7 or CLLD8 polypeptides or isolated
nucleic acid or may be an antigen of ANGE, CLLD7 or CLLD8 combined
with e.g. a cellular antigen.
[0074] In a preferred embodiment polyclonal antibodies are raised
against peptide fragments as shown in Table 5.
[0075] In particular, the antibody may be raised against a
particular domain of ANGE, CLLD7 or CLLD8. Such antibodies will be
useful in diagnostic and therapeutic aspects of the invention. In
particular, the antibodies will be useful in the development of
assays for detecting or measuring ANGE, CLLD7 or CLLD8 individually
or as spliced hybrids in a sample.
[0076] According to a twelfth aspect of the invention, there is
provided a process for the preparation of a nucleic acid sequence
as defined above, the process comprising ligating together
successive nucleotide and/or oligonucleotide residues. Such a
process may be carried out using chemical synthesis methods or by
using enzymic catalysis. Alternatively, a suitable host cell may be
transfected with an appropriate DNA or RNA sequence so as to cause
production of the desired sequence in a host cell.
[0077] In a thirteenth aspect of the invention, there is provided a
process for the preparation of a polypeptide as defined above, the
process comprising ligating together successive amino acids and/or
oligopeptides. Such a process may be carried out using chemical
synthesis methods or by using enzymic catalysis. Alternatively, a
suitable host cell may be transfected with an appropriate DNA or
RNA sequence so as to cause production of the desired polypeptide
in a host cell. The polypeptide may be produced in a cell free
system.
[0078] In a fourteenth aspect, there is provided a host cell
comprising a vector or isolated or recombinant nucleic acid
molecule according to the aforementioned aspects. The host cell may
comprise an expression vector, or naked DNA encoding the nucleic
acid molecules of the invention. A wide variety of suitable host
cells are available, both eukaryotic and prokaryotic. Examples
include bacteria such as E. coli, yeast, filamentous fungi, insect
cells, mammalian cells, preferably immortalised, such as mouse,
CHO, HeLa, myeloma or Jurkat cell lines, human and monkey cell
lines and derivatives thereof. The host cells are preferably
capable of expression of the nucleic acid sequence to produce a
gene product (i.e. RNA or protein). Such host cells are useful in
drug screening systems to regulate or analyse the polypeptides of
the tenth aspect or to identify agents for use in diagnosis or
treatment of individuals having, or being susceptible to
disease.
[0079] The method by which said nucleic acid molecules are
introduced into a host cell will usually depend upon the nature of
both the vector/DNA and the target cell, and will include those
known to a person skilled in the art. Suitable known methods
include but are not limited to fusion, conjugation, liposomes,
immunoliposomes, lipofectin, transfection, transduction,
eletroporation or injection, as described in Sambrook et al.
[0080] In a fifteenth aspect of the present invention, there is
provided a transgenic non-human animal comprising a nucleic acid
sequence according to an aforementioned aspect of the invention.
Such transgenic non-human animals are useful for the analysis of
single nucleotide polymorphisms and their phenotypic effect and so
for the analysis of the ANGE, CLLD7 and CLLD8 gene cluster and its
phenotypic effect. Expression of a polynucleotide sequence of the
invention in a transgenic non-human animal is usually achieved by
operably linking the polynucleotide to a promoter and/or enhancer
sequence, preferably to produce a vector of the above aspect, and
introducing this into an embryonic stem cell of a host animal by
microinjection techniques (Hogan et al., A Laboratory Manual, Cold
Spring harbour and Capecchi Science (1989) 244: 1288-1292). The
transgene construct should then undergo homologous recombination
with the endogenous gene of the host. Those embryonic stem cells
comprising the desired nucleic acid sequence may be selected,
usually by monitoring expression of a marker gene, and used to
generate a non-human transgenic animal. Preferred host animals
include mice, rabbits and other rodents.
[0081] The nucleic acid sequence introduced may not be native to
the host animal, i.e. it may be foreign. Such transgenic animals
may be distinguished from native, non-transgenic animals using
methods known in the art, for example a nucleic acid sample from
the transgenic animal may be compared with that from a native
animal--the transgenic animal will have a nucleic acid sequence
such as a foreign promoter, marker genes etc. Alternatively, the
phenotypes of the animals can be compared.
[0082] Where it is desirable to use the transgenic non-human animal
of the fifteenth aspect to study disease, it may be desirable for
the nucleic acid introduced into the animal to encode a variant of
ANGE, CLLD7 or CLLD8 which results in asthma, atopy, hayfever,
eczema, atopic dermatitis or allergic rhinitis. A transgenic
non-human animal may be produced that no longer expresses a native
ANGE, CLLD7 or CLLD8 gene or any combination of these genes or any
particular splice variant of the genes. These animals may be
referred to as "knock-out" (Manipulating The Mouse Embryo--A
Laboratory Manual, Hogan et al 1986). In some cases, it may be
desirable to modulate the expression of the foreign nucleic acid
and/or the native gene in a temporal or spatial manner. This
approach removes viability problems if the expression of the native
gene is abolished in all tissues.
[0083] In a most preferred embodiment, there is provided a
transgenic mouse comprising a nucleic acid encoding a variant form
of ANGE, CLLD7 or CLLD8 or any combination of these genes or any
splice variant of the genes which causes asthma, atopy, hayfever,
eczema, atopic dermatitis or allergic rhinitis or non-atopic
asthma. Most preferably, the nucleic acid molecule comprises a SNP
at the position which corresponds one or more as shown in Table 2c,
or to Position 185752b4.sub.--2, Position 185752b5.sub.--3 and/or
Position 4321017b38.sub.--1 of FIG. 5.
[0084] Preferably, the mouse is modulated so that it no longer
expresses the ANGE, CLLD7 or the CLLD8 gene or any combination of
two or more of these genes or any splice variant of the genes in a
temporally and/or spatially appropriate manner using homologous
recombination techniques or alternatively to over express the ANGE,
CLLD7 or CLLD8 gene or any combination of two or more of these
genes or any splice variant of the genes to produce a protein as a
result of transgenic manipulation.
[0085] If a functional polymorphism as shown in Table 4c in the
ANGE e.g. ANGE1X3C148T, CLLD7 e.g. CL0703 or CLLD8 gene or any
combination of two or more of these genes or any splice variant of
the genes is identified (i.e. a "mutation") a construct containing
this polymorphism can be introduced into the mouse germ line (i.e.
a knock-in) to produce a pathological variant of a protein rather
than knocking it out. Alternatively a pathological variant of the
ANGE, CLLD7 or CLLD8 gene or any combination of these genes or any
splice variant of the genes may be overexpressed.
[0086] In the context of the present invention, atopic diseases
include those resulting from overexpression of the ANGE, CLLD7 or
CLLD8 gene or any combination of these genes or any splice variant
of the genes, or the presence of a variant form of the ANGE, CLLD7
or CLLD8 gene or any combination of these variant genes or any
splice variant of the variant genes. Specifically, such diseases
include asthma (atopic and non-atopic), atopy, hayfever, eczema,
atopic dermatitis or allergic rhinitis.
[0087] In a sixteenth aspect of the present invention, there is
provided a method of diagnosing, or determining predisposition or
susceptibility of a subject to atopy or predicting severity of
disease in an individual. The method may comprise determining the
presence of a variant form of the ANGE, CLLD7 or CLLD8 gene or any
combination of these genes or any splice variant of the genes which
is known to be associated with a disease state, or measuring the
levels of the ANGE, CLLD7 or CLLD8 gene or any combination of these
genes or any splice variant of the genes. A variant form of ANGE,
CLLD7 or CLLD8 or any combination of at least two of these genes or
any splice variant of the genes includes both nucleic acid and
amino acid variants. A variant includes any SNP producing an
alteration from the wild-type (e.g. for humans) (FIG. 5/Table 1) or
other mutation or alteration from the wild-type.
[0088] For example, probes or primers as described above may be
useful in detecting nucleic acid encoding ANGE, CLLD7 or CLLD8 or
any combination of these genes or any splice variant of the genes
or a variant thereof. Information regarding the expression pattern
or forms of ANGE, CLLD7 or CLLD8 or any combination of these genes
or any splice variant of the genes present will be useful in
determining whether the individual is susceptible to diseases,
resulting from altered expression of ANGE, CLLD7 or CLLD8 or any
combination of these genes or any splice variant of the genes.
[0089] In a preferred embodiment, the method may additionally, or
alternatively, comprise determining the presence or absence of a
risk allele which is associated with one or more of the SNP markers
of Table 1, where presence of a risk allele is indicative of
disease or predisposition to disease or severity of disease. The
method may also comprise genotyping one or more known
polymorphisms. Any combination of such polymorphisms may be
genotyped. Optionally any one or more SNPs in linkage
disequilibrium may be used in the method.
[0090] The SNPs of the invention are listed in Table 1 where the
nature of the polymorphism is described in the format wild type
allele/variant allele. The SNPs are positioned with respect to FIG.
5, where nucleotide position 1 is the 1.sup.st nucleotide in the
FIG. 5.
[0091] The alleles for the remaining SNPs identified in the present
invention are described in Table 1.
[0092] Any technique, including those known to persons skilled in
the art, may be used in the above method. These may include the use
of probes or primers as described above, or antibodies of the
eleventh aspect, for example in ELISA assays or in
immunolocalisation. Preferably, the method comprises first removing
a sample from a subject. More preferably, the method comprises
isolating from a sample a nucleic acid or a polypeptide
sequence.
[0093] In particular, methods for use in this aspect include those
known to persons skilled in the art for identifying differences
between nucleic acid sequences, for example direct probing, allele
specific hybridisation, PCR methodology including Pyrosequencing
(Ahmadian A, Gharizadeh B, Gustafsson A C, Sterky F, Nyren P, Uhlen
M, Lundeberg J. Single-nucleotide polymorphism analysis by
pyrosequencing, Anal Biochem. 2000 Apr. 10;280(1):103-10; Nordstrom
T, Ronaghi M, Forsberg L, de Faire U, Morgenstern R, Nyren P.
Direct analysis of single-nucleotide polymorphism on
double-stranded DNA by pyrosequencing. Biotechnol Appl Biochem.
2000 Apr. 31 (Pt 2):107-12) Allele Specific Amplification (ASA)
(WO93/22456), Allele Specific Hybridisation, single base extension
(U.S. Pat. No. 4,656,127), ARMS-PCR, Taqman.TM. (U.S. Pat. Nos.
4,683,202; 4,683,195; and 4,965,188), oligo ligation assays,
single-strand conformational analysis ((SSCP) Orita et al PNAS 86
2766-2770 (1989)), Genetic Bit Analysis (WO 92/15712) and RFLP
direct sequencing, mass-spectrometry (MALDI-TOF) and DNA arrays.
The appropriate restriction enzyme, will, of course, be dependent
upon the polymorphism and restriction site, and will include those
known to persons skilled in the art. Analysis of the digested
fragments may be performed using any method in the art, for example
gel analysis, or southern blots.
[0094] There is provided a method of diagnosing, or determining
predisposition to disease or severity of disease, comprising
determining the presence or absence of an allele of a SNP at e.g.
as shown in Table 2c, or at position 185752b4.sub.--2,
185752b5.sub.--2 and/or 4321017b38.sub.--1 of FIG. 5, wherein
presence of a risk allele is diagnostic of disease or
predisposition to disease or severity of disease.
[0095] The present invention is advantageous in that it facilitates
the accurate diagnosis of disease, or the determination of
predisposition to disease or the severity of disease. Thus, by
genotyping, an individual may be identified as having or being
predisposed to disease and the likely severity of the disease. This
helps to identify those individuals who are likely to respond
positively to particular treatments or preventative measures. Thus,
more effective therapies or preventative measures can be
administered.
[0096] The diseases, which are associated with the polymorphisms of
the invention, include atopic diseases, such as asthma, atopy,
hayfever, eczema, atopic dermatitis or allergic rhinitis and
non-atopic asthma. Predisposition to disease in the context of the
present invention means that these individuals are at higher risk
of developing the disease, or a more severe form of the disease, or
a particular form of the disease.
[0097] In the context of the present invention, a risk allele is
the allele of a polymorphism, which is associated with disease or
predisposition to disease. The risk allele may be the wild type or
the variant allele, as defined below.
[0098] The term "polymorphism" refers to the coexistence of
multiple forms of a sequence. Thus, a polymorphic site is the
location at which sequence divergence occurs. The different forms
of the sequence, which exist as a result of the presence of a
polymorphism, are referred to as "alleles". The region comprising a
polymorphic site may be referred to as a polymorphic region.
[0099] Examples of the ways in which polymorphisms are manifested
include restriction fragment length polymorphisms (Botstein et al
Am J Hum Genet 32 314-331 (1980)), variable number of tandem
repeats, hypervariable regions, minisatellites, di- or
multi-nucleotide repeats, insertion elements and nucleotide or
amino acid deletions, additions or substitutions. A polymorphic
site may be as small as one base pair, which may alter a codon thus
resulting in a change in the encoded amino acid sequence.
[0100] Single nucleotide polymorphisms arise due to the
substitution, deletion or insertion of a nucleotide residue at a
polymorphic site. Such variations are referred to as SNPs. SNPs may
occur in protein coding regions, in which case different
polymorphic forms of the sequence may give rise to variant protein
sequences. Other SNPs may occur in non-coding regions. In either
case, SNPs may result in defective proteins or regulation of genes,
thus resulting in disease. Other SNPs may have no phenotypic
effects, but may show linkage to disease states, thus serving as
markers for disease. SNPs typically occur more frequently
throughout the genome than other forms of polymorphism discussed
above, and there is therefore a greater probability of finding a
SNP associated with a particular disease state.
[0101] Linkage disequilibrium is the co-inheritance of two alleles
at greater frequencies than would be expected from the separate
frequencies of each allele. Conversely, alleles are in linkage
equilibrium if they occur together. The expected frequency of two
alleles inherited together is the product of the frequency of each
allele.
[0102] Also provided is a method diagnosing an individual as having
abnormal serum IgE levels, the method comprising demonstrating in
the individual the presence or absence of an allele which is
associated with the SNP marker 185752b4.sub.--2 and optionally any
other SNP in linkage disequilibrium with the marker and a method
for diagnosing an individual as having an STI above 5 mm, the
method comprising demonstrating in the individual the presence or
absence of an allele which is associated with the SNP marker
4321017b38.sub.--1 and optionally any other SNP in linkage
disequilibrium with the marker.
[0103] Where two or more polymorphisms are genotyped, the method
preferably defines determining the presence or absence of a
haplotype, which is indicative of disease or predisposition to
disease. A haplotype is defined herein as a collection of
polymorphic sites in a particular sequence that are inherited in a
group, i.e. are in linkage disequilibrium with each other. The
identification of haplotypes in the diagnosis of disease helps to
reduce the possibility of false positives. The haplotype may be any
particular combination of polymorphisms of Table 1, optionally in
combination with one or more known polymorphisms. A preferred
haplotype is the combination of SNPs as shown in Table 2c; or
positions 185752b4.sub.--2, 185752b5.sub.--3 and 4321017b38.sub.--1
of FIG. 5.
[0104] A method for diagnosing an individual as being atopic, the
method comprising demonstrating in an individual the presence or
absence of alleles associated with the haplotype as shown in Table
2c or the haplotype 185752b4.sub.--2, 185752b5.sub.--3,
4321031b43.sub.--1 and optionally any other SNP in linkage
disequilibrium with any one of these markers is also provided.
[0105] The methods of the sixteenth aspect are preferably carried
out on a sample removed from a subject. Any biological sample
comprising cells containing nucleic acid, preferably that of FIG.
5, is suitable for this purpose. Examples of suitable samples
include whole blood, leukocytes, semen, saliva, tears, buccal, skin
or hair. For analysis of DNA, mRNA or protein, the sample must come
from a tissue in which the sequence of interest is expressed. Blood
is a readily accessible sample. Thus, the method of the sixteenth
aspect preferably includes the steps of obtaining a sample from an
individual, preparing nucleic acid and/or protein from the sample
and analysing the nucleic acid or protein sample for the presence
or absence of a particular allele or gene or combination of genes
of interest or a particular splice variant. Where nucleic acid is
to be analysed, it is preferred that an amplification step be
performed prior to analysis. A preferred amplification technique is
PCR, although any other suitable methods may be employed.
Preferably the method uses a pair of primers which hybridise under
stringent conditions to a region either side of a SNP. The primers
may include an oligonucleotide sequence as shown in Table 4.
[0106] The subject is preferably a mammal, and more preferably a
human. The subject may be an infant, a child or an adult.
Alternatively, the sample may be obtained from the subject
prepartum e.g. by amniocentesis.
[0107] A subject's risk factor for disease may be determined with
reference also to other known genetic factors, and/or clinical,
physiological or dietary factors.
[0108] The above described methods may require amplification of the
DNA sample from the subject, and this can be done by techniques
known in the art, such as PCR (see PCR Technology: Principles and
Applications for DNA Amplification (ed. H. A. Erlich, Freeman
Press, NY 1992; PCR Protocols: A Guide to methods and Applications
(eds. Innis et al., Academic press, San Diego, Calif. 1990);
Mattila et al., Nucleic Acids Res. 19 4967 (1991); Eckert et al.,
PCR Methods and Applications 117 (1991) and U.S. Pat. No.
4,683,202. Other suitable amplification methods include ligase
chain reaction (LCR) (Wu et al., Genomics 4 560 (1989); Landegran
et al., Science 241 1077 (1988)), transcription amplification (Kwoh
et al., Proc Natl Acad Sci USA 86 1173 (1989)), self sustained
sequence replication (Guatelli et al., Proc Natl Acad Sci USA 87
1874 (1990)) and nucleic acid based sequence amplification (NASBA).
The latter two methods both involve isothermal reactions based on
isothermal transcription which produce both single stranded RNA and
double stranded DNA as the amplification products, in a ratio of 30
or 100 to 1, respectively.
[0109] Where it is desirable to analyse multiple samples
simultaneously, it may be preferable to use arrays as described in
WO95/11995. The array may contain a number of probes, each designed
to identify variants of the ANGE, CLLD7 or CLLD8 genes or any
combination of two or more of these genes or any splice variant of
the genes from a sample.
[0110] Where a restriction enzyme is required, it can be selected
according to the nature of the polymorphism and restriction site.
Suitable enzymes will be known to persons skilled in the art.
Analysis of the digested fragments may be performed using any
method in the art, for example gel analysis, or Southern blots.
[0111] Determination of an allele of a polymorphism using the above
methods typically involves the use of anti-sense sequences i.e.
sequences which are complementary to the nucleic acid sequences of
interest, which may include part of the sequence of FIG. 5. Such
sequences are described in the first to eighth aspects of the
invention.
[0112] Where it is desirable to identify the presence of multiple
single nucleotide polymorphisms, or haplotypes, in a sample from a
subject, it may be preferable to use an array. The array may
contain a number of probes, each designed to identify one or more
of the above single nucleotide polymorphisms of the invention.
[0113] An antibody to the ANGE, CLLD7 or CLLD8 genes or any
combination of these genes, or the presence or absence of any
splice variant of the genes as previously described may be used in
the method of the sixteenth aspect. The detection of binding of the
antibody to the antigen in a sample may be assisted by methods
known in the art, such as the use of a secondary antibody, which
binds to the first antibody, or a ligand. Immunoassays including
immunofluorescence assays (IFA) and enzyme linked immunosorbent
assays (ELISA) and immunoblotting may be used to detect the
presence of the antigen. For example, where ELISA is used, the
method may comprise binding the antibody to a substrate, contacting
the bound antibody with the sample containing the antigen,
contacting the above with a second antibody bound to a detectable
moiety (typically an enzyme such as horse radish peroxidase or
alkaline phosphatase), contacting the above with a substrate for
the enzyme, and finally observing the colour change which is
indicative of the presence of the antigen in the sample.
[0114] Any biological sample comprising cells containing nucleic
acid or protein is suitable for this purpose. Examples of suitable
samples include whole blood, semen, saliva, tears, buccal, skin or
hair. For analysis of cDNA, mRNA or protein, the sample must come
from a tissue in which the ANGE, CLLD7 or CLLD8 genes or any
combination of two or more of these genes or any splice variant of
the genes is expressed. Peripheral blood leukocytes are a readily
accessible sample.
[0115] In a seventeenth aspect of the invention, there is provided
a splice variant of ANGE, CLLD8 or CLLD7 for use in a method of
diagnosing an IgE mediated disease, atopy, or a form of atopic
disease or non-atopic asthma, or predicting severity of disease, or
predisposition to disease.
[0116] The splice variant is preferably an RNA, more preferably a
mRNA sequence, encoded by the whole or part of the sequence of ANGE
or CLLD8 or CLLD7. Transcripts of the ANGE gene and splice variants
of the ANGE gene are included as a further aspect of the invention.
The splice variants of the seventeenth aspect include at least one
exon, or fragment of an exon of ANGE, CLLD8 or CLLD7, or a
combination of at least one exon, or fragment of an exon, from at
least two of the ANGE, CLLD8 and CLLD7 genes. In particular, the
splice variants of ANGE may include transcripts having AB011031
exon 1 or AF155105 exon 1; or comprising at least exon 2; lacking
exon 2; comprising at least exon Va or Vb which lies between exons
5 and 6 (FIG. 4G); lacking exon Va or Vb; comprising at least exon
4, 5, 6, 7 and/or 8. The intron/exon map of ANGE is shown in FIG.
3.
[0117] In an eighteenth aspect, there are provided the use of a
splice variant of ANGE and/or CLLD8 and/or CLLD7 in the manufacture
of a diagnostic for use in a method of diagnosing atopy or a form
of atopic disease, or predicting severity of disease, or
predisposition to disease. Alternatively, the splice variant is
provided for use in the manufacture of a medicament for treating
disease or for use in a method of treating disease.
[0118] In a nineteenth aspect, there is provided a kit comprising a
splice variant according to the seventeenth aspect for use in a
method according to the sixteenth aspect. Preferably, two or more
splice variants are provided, preferably in the form of an array,
or on a chip.
[0119] In a twentieth aspect, there is provided a polynucleotide
sequence comprising the ANGE, CLLD8 or CLLD7 genes, or a
polypeptide encoded by the sequence, or fragment thereof, for use
in a screen for an agent which inhibits or enhances the activity of
ANGE, CLLD8 or CLLD7. Methods of screening for such agents are also
provided.
[0120] In a twenty-first aspect of the invention there is provided
a kit for diagnosis of disease or predisposition to disease,
comprising a means for determining the presence or absence of a
allele of a SNP of Table 1, wherein the allele is diagnostic of
disease, or of predisposition to disease, or of severity of
disease.
[0121] In a preferred embodiment, the kit comprises a means for
determining the presence or absence of one or more risk alleles of
polymorphisms according to the eighth aspect. In particular, the
kit comprises means for determining the presence or absence of a
risk allele of a SNP as shown in Table 2c; or at at position
185752b4.sub.--2, position 185752b5.sub.--3, and/or position
4321017b38.sub.--1 of FIG. 5.
[0122] Preferably the kit will comprise the components necessary to
determine the presence or absence of a risk allele of the eighth
aspect, in accordance with the sixteenth aspect of the invention.
Such components include PCR primers and/or probes, for example
those described above, PCR enzymes, restriction enzymes, and DNA or
RNA purification means. Preferably, the kit will contain at least
one pair of primers, or probes, preferably as described above in
accordance with the eighth aspect of the invention. The primers are
preferably allele specific primers. Other components include
labelling means, buffers for the reactions. In addition, a control
nucleic acid sample may be included, which comprises a wild type or
variant nucleic acid sequence as defined above, or a PCR product of
the same. The kit will usually also comprise instructions for
carrying out the diagnostic method, and a key detailing the
correlation between the results and the likelihood of disease. The
kit may also comprise an agent for the prevention or treatment of
disease.
[0123] In a twenty-second aspect of the invention, there is
provided a method of identifying a compound for treatment of
disease, comprising (a) administration of a compound to tissue
comprising a nucleic acid molecule comprising one or more SNPs at
positions which correspond to a positions of FIG. 5 listed in Table
1; and (b) determining whether the agent modulates an effect of the
SNPs.
[0124] In a preferred embodiment, the isolated nucleic acid
molecule is according to the eighth aspect of the invention, and
most preferably comprises a SNP as shown in Table 2c; or at a
position corresponding to position 185752b4.sub.--2 and/or position
185752b5.sub.--3, and/or position 4321017b38.sub.--1 of FIG. 5.
[0125] In this aspect, a nucleic acid molecule of the invention,
and/or a cell line according to an aforementioned aspect, may be
used to screen for agents, which are capable of modulating the
effect of a SNP.
[0126] Potential agents are those which react differently with a
risk allele and non-risk allele. Putative agents will include those
known to persons skilled in the art, and include chemical or
biological compounds, sense or anti-sense nucleic acid sequence for
example as described above, binding proteins, kinases, and any
other gene or gene product, agonist or antagonist. Preferably, the
agent will be capable of modulating the effects of the disease
causing allele. Most preferably, the agent is one which is capable
of ameliorating the deleterious effects of the risk allele.
[0127] Such agents may be suitable for either prophylactic
administration or after a disease has been diagnosed. The route of
administration is suitably chosen according to the disease or
condition to be treated, however, typical routes of administration
of the agent of the present invention include but are not limited
to oral, rectal, intravenous, parenteral, intramuscular and
sub-cutaneous routes. The invention also provides for agents to be
administered either as DNA or RNA and thus as a form of gene
therapy. The agents may be delivered into cells directly by means
including but not limited to liposomes, viral vectors and coated
particles (gene gun).
[0128] In a twenty-third aspect of the present invention there is
provided an agent or antibody as described above according to the
invention, for use in preventing or treating an IgE mediated
disease such as asthma, atopy, hayfever, eczema, atopic dermatitis
or allergic rhinitis or non-atopic asthma.
[0129] There is also provided an agent capable of influencing
expression of the ANGE and/or CLLD8 and/or CLLD7 genes for use in a
method of treating an IgE-mediated disease e.g. atopy or non-atopic
asthma in an individual. Preferably, the agent is capable of
influencing the activity of the ANGE and/or CLLD8 and/or CLLD7 gene
promoters and/or influencing RNA splicing of the ANGE and/or CLLD8
and/or CLLD7 or ANGE and CLLD7 genes or any combination of two or
more of the genes or of any splice variant. Influencing or
modulating the activity may include either inhibiting or enhancing,
or altering the pattern of activity. Examples of agents according
to the twenty-third aspect include but are not limited to proteins,
such as transcription factors, which may bind to the ANGE/CLLD8
promoter or splice sites; antibodies or binding partners;
ribozymes; and polynucleotide sequences.
[0130] Preferred agents for influencing the expression of the genes
include polynucleotide sequences, which are complementary to the
relevant polynucleotide sequence of FIG. 5. Sequence
complementarity can be determined using conventional techniques
available in the art. Preferred complementary, or antisense,
sequences are those which hybridise under stringent conditions to
the genes. Suitably stringent conditions are those under which
non-specific hybridisation (e.g. to non-ANGE sequences) are
avoided.
[0131] In relation to the present invention, "stringent conditions"
refers to the washing conditions used in a hybridisation protocol.
In general, the washing conditions should be a combination of
temperature and salt concentration so that the denaturation
temperature is approximately 5 to 20.degree. C. below the
calculated T.sub.m of the nucleic acid under study. The T.sub.m of
a nucleic acid probe of 20 bases or less is calculated under
standard conditions (1M NaCl) as [4.degree.
C..times.(G+C)+2.degree. C..times.(A+T)], according to Wallace
rules for short oligonucleotides. For longer DNA fragments, the
nearest neighbour method, which combines solid thermodynamics and
experimental data may be used, according to the principles set out
in Breslauer et al., PNAS 83: 3746-3750 (1986). The optimum salt
and temperature conditions for hybridisation may be readily
determined in preliminary experiments in which DNA samples
immobilised on filters are hybridised to the probe of interest and
then washed under conditions of different stringencies. While the
conditions for PCR may differ from the standard conditions, the
T.sub.m may be used as a guide for the expected relative stability
of the primers. For short primers of approximately 14 nucleotides,
low annealing temperatures of around 44.degree. C. to 50.degree. C.
are used. The temperature may be higher depending upon the base
composition of the primer sequence used.
[0132] Antisense sequences which hybridise under stringent
conditions to the ANGE or CLLD8 or CLLD7 genes may be useful as
primers in any of the aspects of the present invention. Pairs of
primers for amplification of all or part of the ANGE, CLLD8 or
CLLD7 genes, or alleles, or variants thereof, form another aspect
of the invention.
[0133] There is also provided the use of an agent or antibody as
described above in the manufacture of a medicament for use in
preventing or treating an IgE mediated disease such as asthma,
atopy, hayfever, eczema, atopic dermatitis or allergic rhinitis or
non-atopic asthma. The agents of the above aspect, in particular
antisense sequences, may also be useful in diagnosing an individual
as having atopy.
[0134] According to a twenty-fourth aspect of the invention, there
is provided, a pharmaceutical composition or medicament comprising
a nucleic acid or polypeptide sequence as defined above according
to the invention. Alternatively, the pharmaceutical composition may
comprise an agent as defined in relation to the above aspect or an
antibody according to the eleventh aspect of the invention.
[0135] Administration of pharmaceutical compositions is
accomplished by any effective route, e.g. orally or parenterally.
Methods of parental delivery include topical, intra-arterial,
subcutaneous, intramedullary, intravenous, or intranasal
administration. Administration can also be effected by
amniocentesis-related techniques. Oral administration followed by
subcutaneous injection would be the preferred routes of uptake;
also long acting immobilisations would be used. In addition to the
active ingredients, these pharmaceutical compositions may contain
suitable pharmaceutically acceptable carriers comprising excipients
and other compounds that facilitate processing of the active
compounds into preparations which can be used pharmaceutically.
Further details on techniques for formulation and administration
may be found in the latest edition of "REMINGTON'S PHARMACEUTICAL
SCIENCES" (Maack Publishing Co, Easton Pa.).
[0136] Pharmaceutical compositions for oral administration can be
formulated using pharmaceutically acceptable carriers well known in
the art, in dosages suitable for oral administration. Such carriers
enable the pharmaceutical compositions to be formulated as tablets,
pills, dragees, capsules, liquids, gels, syrups, slurries,
suspensions, etc., suitable for ingestion by the patient.
[0137] Pharmaceutical compositions suitable for use in the present
invention include compositions wherein the active ingredients are
contained in an effective amount to achieve the intended purpose.
Thus, a therapeutically effective amount is an amount sufficient to
ameliorate or eradicate the symptoms of the disease being treated.
The amount actually administered will be dependent upon the
individual to which treatment is to be applied, and will preferably
be an optimised amount such that the desired effect is achieved
without significant side-effects. The determination of a
therapeutically effective dose is well within the capability of
those skilled in the art. Of course, the skilled person will
realise that divided and partial doses are also within the scope of
the invention.
[0138] For any compound, the therapeutically effective dose can be
estimated initially either in cell culture assays or in any
appropriate animal model. These assays should take into account
receptor activity as well as downstream processing activity. The
animal model is also used to achieve a desirable concentration
range and route of administration. Such information can then be
used to determine useful doses and routes for administration in
humans.
[0139] A therapeutically effective amount refers to that amount of
agent, which ameliorates the symptoms or condition. Therapeutic
efficacy and toxicity of such compounds can be determined by
standard pharmaceutical procedures, in cell cultures or
experimental animals (e.g. ED.sub.50, the dose therapeutically
effective in 50% of the population; and LD.sub.50, the dose lethal
to 50% of the population). The dose ratio between therapeutic and
toxic effects is the therapeutic index, and it can be expressed as
the ratio ED.sub.50/LD.sub.50. Pharmaceutical compositions, which
exhibit large therapeutic indices, are preferred. The data obtained
from cell culture assays and animal studies is used in formulating
a range of dosage for human use. The dosage of such compounds lies
preferably within a range of circulating concentrations that
include the ED.sub.50 with little or no toxicity. The dosage varies
within this range depending upon the dosage form employed,
sensitivity of the patient, and the route of administration.
[0140] The exact dosage is chosen by the individual physician in
view of the patient to be treated. Dosage and administration are
adjusted to provide sufficient levels of the active moiety or to
maintain the desired effect. Additional factors, which may be taken
into account, include the severity of the disease state. Long
acting pharmaceutical compositions might be administered every 3 to
4 days, every week, or once every two weeks depending on half-life
and clearance rate of the particular formulation. Guidance as to
particular dosages and methods of delivery is provided in the
literature (see, U.S. Pat. Nos. 4,657,760; 5,206,344 and 5,225,212
herein incorporated by reference).
[0141] According to a twenty-fifth aspect of the invention, there
is provided a method of preventing or treating disease in a subject
comprising modulating the activity, expression, half life or
post-translational modification of ANGE and/or CLLD7 and/or CLLD8
or any combination of two or more of these genes or any splice
variant of the genes in the subject.
[0142] In addition, the treatment of individuals having an IgE
mediated disease or non-atopic asthma includes prevention of atopy,
and prophylactic and therapeutic measures.
[0143] Preferably, the method is carried out in a subject who has
been diagnosed as suffering from, or is susceptible to IgE mediated
diseases such as asthma, atopy, hayfever, eczema, atopic dermatitis
or allergic rhinitis, or non-atopic asthma.
[0144] Preferably, the method comprises determining the presence or
absence of a risk allele of a SNP such as one which has an
association with IgE mediated disease e.g. at position
185752b4.sub.--2, 185752b5.sub.--3 and/or 4321017b38.sub.--1 of
FIG. 5; or which has an association with asthma, atopy or a
combination thereof e.g. as shown in Table 2c; and if the risk
allele is present, administering treatment in order to prevent,
delay or reduce the disease.
[0145] Preferably, the step of determining the presence or absence
of a risk allele is carried out in accordance with the sixteenth
aspect, and therefore also comprises determining the presence or
absence of risk alleles of SNPs of Table 1, or any combination
thereof, for example as described above.
[0146] There is also provided a method of preventing or treating an
IgE mediated disease or of non-atopic asthma in an individual, the
method comprising modulating the expression of the CLLD8 and/or
ANGE and/or CLLD7 genes or any combination of two or more of the
genes or of any splice variant of the genes. Preferably, the method
modulates the production of a gene product according to the first
to eighth aspects of the invention. In particular, the twenty-fifth
aspect may be achieved by modulating the activity of the CLLD8
promoter, or modulating the splicing of the CLLD8 and/or ANGE
genes.
[0147] By modulating or influencing is meant inhibiting, enhancing
or otherwise altering the expression.
[0148] The prevention or treatment of disease according to the
twenty-fifth aspect may include the administration of any agent
capable of modulating the effects of the ANGE, CLLD7 or CLLD8 genes
or any combination of two or more of these genes or fragments of
these genes or any splice variant of the genes or of an allele
which has an association with disease. Preferably, the agent is one
which is capable of ameliorating the deleterious effects of the
risk allele. The methods include, but are not limited to, gene
therapy techniques. Gene therapy techniques typically involve
replacing the nucleic acid sequence comprising the risk allele, or
otherwise down regulating the effects of the risk allele. The
nucleic acid sequences of the first to eighth aspect, or sequences
anti-sense thereto, will be useful in gene therapy.
[0149] By modulating is meant inhibiting or increasing the activity
of the gene or gene product. Preferably, the activity is inhibited.
The activity of the gene or gene product includes any aspect of its
production or function, including transcription and translation of
nucleic acid sequences, and assembly of the protein,
post-translational modification of the protein and downstream
interactions with other factors.
[0150] The activity of the ANGE, CLLD7 or CLLD8 gene or any
combination of two or more of these genes or any splice variant of
the genes can be modulated in a number of ways. For example, the
expression of the gene may be inhibited through the use of
antisense sequences, such as those of the first to eighth aspects
of the invention or by the production of antisense RNA sequences.
Such sequences when introduced into a subject by gene therapy will
hybridise to the ANGE, CLLD7 or CLLD8 gene or to any transcript
which is a combination of two or more of these genes or to any
splice variant of the genes or to RNA transcribed from the gene or
genes, and inhibit its transcription or translation. This method
may be particularly useful where it is desirable to modulate the
function or expression of certain splice variants of ANGE, CLLD7 or
CLLD8 or certain combinations of these genes whilst not affecting
others.
[0151] Introduction of a nucleic acid sequence may use gene therapy
methods including those known in the art. In general, a nucleic
acid sequence will be introduced into the target cells of a
subject, usually in the form of a vector and preferably in the form
of a pharmaceutically acceptable carrier. Any suitable delivery
vehicle may be used, including viral vectors, such as retroviral
vector systems, which can package a recombinant genome. The
retrovirus could then be used to infect and deliver the
polynucleotide to the target cells. Other delivery techniques are
also widely available, including the use of adenoviral vectors,
adeno-associated vectors, lentiviral vectors, pseudotyped
retroviral vectors and pox or vaccinia virus vectors. Liposomes may
also be used, including commercially available liposome
preparations such as Lipofectin.RTM., Lipofectamine.RTM.,
(GIBCO-BRL, Inc. Gaitherburg, Md.), Superfect.RTM. (Qiagen Inc,
Hilden, Germany) and Transfectam.RTM. (Promega Biotec Inc, Madison
Wis.).
[0152] Other means to modulate a biological activity of the ANGE,
CLLD7 or CLLD8 gene or any combination of two or more of these
genes or any splice variant of the genes includes using agents
which may affect interaction of ANGE, CLLD7 or CLLD8 or any
combination of two or more of these genes or any splice variant of
the genes with downstream factors with which they interact.
[0153] Also provided is an agent capable of influencing expression
of the ANGE, CLLD8 or CLLD7 gene, for use in a method of preventing
or treating an IgE mediated disease or non-atopic asthma in an
individual. Preferably the agent is capable of influencing the
activity of the ANGE. CLLD8 or CLLD7 gene promoters or any
combination of two or more of the gene promoters. Preferably the
agent is capable of influencing RNA splicing of the ANGE, CLLD8 or
CLLD7 gene or of any combination of two or more of the transcripts
of the genes.
[0154] Agents include nucleic acid sequences of the first to eighth
aspects, polypeptide sequences of the tenth aspect, antibodies of
the eleventh aspect, and any other agent defined herein, preferably
those which are capable of modulating the activity of ANGE, CLLD7
or CLLD8 or any combination of two or more of these genes or any
splice variant of the genes.
[0155] The subject may be any animal, preferably a mammal, and more
preferably human.
[0156] Also provided is the use of an agent as defined above in the
manufacture of a medicament for use in the prevention or treatment
of an IgE mediated disease or non-atopic asthma, as defined above,
in a subject.
[0157] According to a twenty-sixth aspect of the invention, there
is provided a number of screens. A first screen provides for
identifying an agent, which modulates the activity of the ANGE,
CLLD7 or CLLD8 gene or any combination of two or more of these
genes or any splice variant of the genes comprising:
[0158] providing a polypeptide sequence as claimed in the tenth
aspect of the invention;
[0159] providing a substrate;
[0160] providing an agent to be tested;
[0161] measuring whether the agent to be tested modulates the
activity of the polypeptide by measuring processing of the
substrate.
[0162] The components of the screen are combined, in any optional
order, more than 1 substrate or polypeptide may be included in the
assay.
[0163] In the screening assay the polypeptide may be any
polypeptide according to the tenth aspect of the invention.
Fragments of the ANGE, CLLD7 or CLLD8 genes or any combination of
two or more of the genes or any splice variant of the genes may be
used. Also, the ANGE, CLLD7 or CLLD8 genes or any combination of
these genes or any splice variant of the genes which comprise one
or more SNP nucleic acid sequences of the present invention, such
as described in the first to eighth aspects may be used. The
polypeptide may be purified or non-purified. The polypeptide may be
soluble. It may comprise one or more of the domains.
[0164] The agent being tested is being identified for use in the
prevention or treatment of an IgE mediated disease or disorder or
in non-atopic asthma. IgE mediated diseases or disorders include:
asthma, atopy, hayfever, eczema, atopic dermatitis or allergic
rhinitis.
[0165] The substrate may be any which is processed by a polypeptide
according to the tenth aspect of the invention. By processed is
meant any changes which can be measured. These substrates may be
fluorescently labelled or modified to allow easy detection of
processing. Such labelling or modification is known to the person
skilled in the art.
[0166] In a preferred embodiment, the assay is any means of
measuring histone methyl transferase activity or nucleotide
exchange factor activity known to the person skilled in the art.
For example Hama et al J. Biol. Chem., 274: 15284-15291 1999.
[0167] The present invention further provides a screen for
identifying an agent which modulates the activity of the ANGE,
CLLD7 or CLLD8 genes or any combination of two or more of these
genes or any splice variant of the genes comprising:
[0168] providing a polypeptide according to the tenth aspect of the
invention;
[0169] providing an agent to be tested;
[0170] providing a cell; and
[0171] measuring whether the agent to be tested modulates the
activity of the polypeptide by measuring adhesion of the cell to a
surface.
[0172] Such a screen can be referred to as a cell adhesion screen
(or assay). The components of the screen are combined, in any
optional order.
[0173] Typically cells used in the cell adhesion assay may be
maintained in suspension where adhesion is measured by aggregation
of the cells due to intercellular adhesion molecule interactions.
Alternatively, adhesion to a surface may be measured. The surface
may be a non-biological molecule e.g. tissue culture plastic or it
may be a biological molecule, which is cellular or non-cellular.
Examples of a non-cellular molecule include extracellular matrix
components such as fibronectin, collagen and such like. One or more
cells or other biological non-cellular molecules may be attached to
a surface such as a tissue culture surface or an extracellular
matrix component-coated surface. Adhesion is determined by
measuring the adhesion of a cell to a surface. Modulation in cell
adhesion may be either an increase in cell adhesion or a decrease
in cell adhesion. An agent is considered to be a modulator of the
polypeptide of the tenth aspect if it affects the activity or
expression of the polypeptide, this may be either at the level of
expression of the ANGE, CLLD7 or CLLD8 genes or of the expression
of any combination of two or more of the genes or any splice
variant of the genes or by altering the half life of any of the
ANGE, CLLD7 or CLLD8 mRNA or polypeptide molecules or of any
combination of two or more of the genes, or of any splice variant
of the genes or by affecting the post-translation modification
status of the ANGE, CLLD7 or CLLD8 polypeptides or the polypeptide
encoded by any combination of two or more of these genes or the
polypeptide encoded by any splice variant of the genes.
[0174] The cell may be the host cell of the fourteenth aspect of
the invention comprising the vector of the ninth aspect. The
twenty-sixth aspect also includes the use of the host cell in
screens to identify an agent.
[0175] Yet a further aspect of the invention provides a screen for
identifying an agent which modulates the activity of the ANGE,
CLLD7 or CLLD8 genes or the activity of any combination of two or
more of the genes or the activity of any splice variant of the
genes comprising:
[0176] providing a polypeptide according to the tenth aspect of the
invention;
[0177] providing an agent to be tested;
[0178] providing a cell;
[0179] measuring a change in differentiation or proliferation of
the cell.
[0180] The components of the screen are combined, in any optional
order.
[0181] Typically, differentiation may be measured by any means
known to the persons skilled in the art for example in the case of
a B-lymphocyte, the change in differentiation can be B-cell
activation. The cell may express one or more of the polypeptides of
the tenth aspect or be the host cell of the fourteenth aspect. In
the case of other cell types it may be the induction or prevention
of production of a cell signalling factor such as an
immunomodulator e.g. a cytokine or growth factor. The cell
signalling factor may be secreted. The immunomodulator may be a
peptide regulatory factor or may be any other biological substance
which expression is altered by an agent which modulates the ANGE,
CLLD7 or CLLD8 gene or any combination of two or more of these
genes or any splice variant of the genes. Typically this assay is
performed in vitro for example in tissue or organ culture and the
cell may be cultured following removal from a patient or animal or
the transgenic animal of the fifteenth aspect.
[0182] The change in phenotype may be any. It may involve a change
in B-cell phenotype.
[0183] Such a screen provides an in vitro model for identifying an
agent which modulates the activity of the ANGE, CLLD7 or CLLD8 gene
or any combination of two or more of these genes or any splice
variant of the genes.
[0184] Yet a further aspect of the invention provides a screen for
identifying an agent which modulates the activity of the ANGE,
CLLD7 or the CLLD8 gene or any combination of two or more of the
genes or any splice variant of the genes comprising:
[0185] providing a transgenic animal according to the fifteenth
aspect of the invention;
[0186] providing an agent to be tested;
[0187] contacting the transgenic animal with the agent to be
tested;
[0188] detecting a change in the transgenic animals phenotype.
[0189] The components of the screen are combined, in any optional
order.
[0190] The cell against which the agent is tested may be in
suspension, tissue culture, as part of an organ or as part of an
animal. Preferably the animal is a laboratory animal, such as a
rat, rabbit, mouse or other rodent.
[0191] A change in phenotype includes a change in gene expression
or in the production of RNA or protein or in cell morphology or
behaviour.
[0192] Yet a further aspect of the invention provides a screen for
detecting a side effect associated with the use of an agent which
modulates the activity of the ANGE, CLLD7 or CLLD8 gene or any
combination of two or more of the genes or any splice variant of
the genes comprising:
[0193] providing a cell which does not substantially express the
nucleic acid sequence of the first to eighth aspects of the
invention or the polypeptide of the tenth aspect of the
invention;
[0194] providing an agent to be tested;
[0195] contacting the agent to be tested with the cell; and
[0196] measuring any side effect produced by the agent on the
cell.
[0197] The components of the screen are combined, in any optional
order.
[0198] The side effect to be measured may be any, and may depend on
whether the cell is part of a larger tissue or animal. It may
involve a change in cell differentiation, or cell proliferation.
The side effect may be a measure of the change of phenotype of an
organ or animal.
[0199] Yet a further aspect of the invention provides a screen for
identifying an agent which modulates the activity of a
polynucleotide according to the first to eighth aspects of the
invention or a polypeptide according to the tenth aspect of the
invention comprising:
[0200] providing an isolated nucleic acid according to the first to
eighth aspects of the invention or a polypeptide according to the
tenth aspect of the invention;
[0201] providing an agent to be tested;
[0202] measuring whether the agent to be tested modulates the
activity of the isolated nucleic acid or polypeptide by measuring
the interaction of the agent with the sample of nucleic acid or
polypeptide.
[0203] Preferably this screen is an in vitro transcription assay,
measuring transcription of the ANGE, CLLD7 or CLLD8 gene or any
combination of two or more of these genes or any splice variant of
the genes.
[0204] Alternatively, an agent may be identified by the use of
theoretical or model characteristics of the ANGE, CLLD7 or CLLD8
gene or of a transcript produced by a combination of two or more of
these genes or any splice variant of the genes. The functional or
structural characteristics may be of the protein itself or of a
computer generated model, a physical two- or three-dimensional
model or an electrical (e.g. computer) generated primary, secondary
or tertiary structure, as well as the pharmacaphore (three
dimensional electron density map) or its X ray crystal
structure.
[0205] Putative agents will include those known to persons skilled
in the art or new substances, and include chemical or biological
compounds, such as anti-sense nucleotide sequences, polyclonal or
monoclonal antibodies which bind to a polypeptide sequence of the
tenth aspect.
[0206] According to a twenty-seventh aspect of the invention, there
is provided the use of a nucleic acid sequence or polypeptide
sequence as defined above in a screen for an agent which modulates
the activity of the ANGE, CLLD7 or CLLD8 gene or of any combination
of two or more of the genes or of any splice variant of the
genes.
[0207] The method preferably comprises contacting a putative agent
with a nucleic acid or polypeptide sequence according to an
aforementioned aspect of the present invention and monitoring
expression and/or activity of the nucleotide or polypeptide
sequence. Potential agents are those which alter the activity or
expression of the polynucleotide or polypeptide sequence compared
to the activity or expression in the absence of the agent. The
present method may be carried out by contacting a putative agent
with a host cell, tissue culture, or transgenic non-human animal
comprising a nucleotide or polypeptide according to the invention,
and displaying inflammatory disease.
[0208] Also provided are agents identified by the methods of the
twenty-sixth aspect.
[0209] Preferred features for the second and subsequent aspects of
the invention are as for the first aspect mutatis mutandis.
[0210] FIG. 1 shows a Linkage Disequilibrium map of the atopy
locus.
[0211] a) Linkage Disequilibrium Map of the Atopy Locus
[0212] A GOLD plot.sup.28 of colour coded pair-wise disequilibrium
statistics (D') between markers is shown. The locus extends from
the bottom left of the figure to the top right. Red and yellow
indicate areas of strong LD. LD is approximately divided into four
regions. The scale bar at the bottom indicates a distance of 200
Kb.
[0213] b) Detail of LD Around the ANGE (NY-REN-34) Gene Complex
[0214] Association to IgE levels is shown above the figure. Genes
are shown as black arrows, pointing in the direction of
transcription. The scale bar at the bottom indicates a distance of
100 Kb
[0215] FIG. 2 shows the extent of linkage disequilibrium between
SNPs on chromosome 13q14.
[0216] FIG. 3
[0217] a) shows the schematic structure of the gene ANGE
[0218] b) Detail of structure of ANGE promoter and alternate
exons
[0219] c) Pile up of transcripts by amplification between
alternative Exon I and Exon III
[0220] d) shows transcription of ANGE to immune tissue from
alternate Exon 1.
[0221] FIG. 4 shows splice variation in ANGE.
[0222] a) PCR Amplification of Exons 1-3 in Multiple Tissue cDNA
Panels
[0223] The presence of a smaller band indicating absence of exon 2
is observed in all tissues.
[0224] b) PCR Amplification of Exons 4-6 in Multiple Tissue cDNA
Panels
[0225] The presence of additional bands indicating retention of a
additional exons (Va and Vb) is observed in lung and immune
tissues. The band is present in cDNAs from unactivated lymphocytes,
and absent in activated lymphocytes.
[0226] c) PCR Amplification of Exons 7-8 in Multiple Tissue cDNA
Panels
[0227] The presence of additional bands, indicating retention of
exon 7 is observed in lung liver, kidney and pancreas, and immune
tissues. The band is most highly expressed in cDNAs from resting T
and B cells.
[0228] FIG. 5 shows the nucleotide sequence of the ANGE 1 gene
(NY-REN-34) as nucleotides 313649-346509 the nucleotide sequence of
CLLD8 as nucleotides 294727-309803 and the sequence of CLLD8 as
nucleotides 349634-410846 of BAC bA103J18.03548.
[0229] FIG. 5a shows the following sequences for the ANGE gene:
[0230] (i) Exon sequences;
[0231] (ii) Protein sequence;
[0232] FIG. 5b shows the following sequences for the NY-REN-34
gene:
[0233] (i) mRNA sequence;
[0234] (ii) Protein sequence;
[0235] (iii) Alternative protein sequence;
[0236] FIG. 5c shows the following sequences for the CLLD7
gene:
[0237] (i) Exon sequences;
[0238] (ii) Protein sequence.
[0239] FIG. 5d shows the following sequences for the CLLD8
gene:
[0240] (i) Exon structure and nucleic acid sequence;
[0241] (ii) Protein sequence.
[0242] FIG. 6 shows the nucleotide sequence of BAC
bA101d11.01116.
[0243] FIG. 7 shows the nucleotide sequence of BAC bA236
m15.00303.
[0244] FIG. 8 shows domain architectures of CLLD8, ANGE and related
proteins, drawn approximately to scale.
[0245] Proteins are described in the text. The SET domains of CLLD8
and ESET are bifurcated due to the presence of large insertions.
The IL-5 promoter REII-region-binding protein, that arises from an
mRNA initiated within a middle intron of the WHSC1/MMSET
gene.sup.46, is shown.
[0246] Domain symbols: AT, AT-hook DNA-binding motif; B,
bromodomain; C (white-on-black), cysteine-rich regions flanking SET
domains; C, FYRC domain; C.sub.5HCH, zinc finger domain; CpG,
methyl-CpG-binding domains; CXXC, CXXC-type zinc finger; HMG, high
mobility group domains; N, FYRN domain; P, PHD domains with two
(blue rectangle) and one (yellow rectangle) Zn2+-coordinating
groups; PW, PWWP domains; SET, Su(var)3-9, Enhancer-of-zeste,
trithorax methyltransferase domains; and, T, tudor domains.
[0247] FIG. 9 shows co-expression of the CLLD8/ANGE gene
complex.
[0248] FIG. 10 shows Northern Blots of the gene for ANGE
(NY-REN-34) and CLLD8. The presence of large bands and differential
splicing in PBMC is apparent.
[0249] The figures show alternative probings of the same Northern
blot. The expected transcript size of approximately 1.6 Kb for ANGE
is seen in all tissues. A 3.0 Kb band is prominent in lymph node
and thymus, and polymorphic higher molecular weight bands between
6.0 and 8.0 Kb are visible in immune tissues. The expected 4.0 Kb
band is seen for CLLD8 in all tissues. Additional higher molecular
weight bands may also been seen, but their distribution does not
coincide with that of ANGE.
[0250] FIG. 11--Western blot of Cos-7 cells lysates after transient
transfection with pcDNA4 expression vectors.
[0251] 3.times.10.sup.5 cells were transfected with 1 .mu.g
pcDNA4His/MaxLacZ only (lane 1) or with 1 .mu.g pcDNA4His/MaxLacZ
plus 6 .mu.g pcDNA4His/Max-CLLD7 (lane 2), 6 .mu.g
pcDNA4His/Max-CLLD8 (lane 3), 6 .mu.g pcDNA4His[Max-REN34 (lane 4)
and 6 .mu.g pcDNA4His/Max-ANGE (lane 5). Cells were harvested 24
hours post-transfection and whole cell lysates run on a 10%
polyacrylamide gel. Proteins were transferred to PVDF membrane,
which was probed with an anti-polyhistidine antibody.
[0252] FIG. 12--HMT radioactive assay using nuclear extracts from
Cos7 cells transfected with pcDNA CLLD8.
[0253] Cells were harvested either 24 or 48 hrs post-transfection
with nuclear extracts being tested for HBT activity. The control
extracts were treated with Fugene only. All Cos7 extracts
equivalent to 11 ug total protein. Positive control=bacterial
SUV39H1(82412) 10 ug; negative control=no protein.
[0254] FIG. 13 shows examples of results obtained with each of the
DNA probes containing a potentially functional SNP.
[0255] FIG. 14 shows the results of such immunolocalisation
experiments. CLLD7 (a) and ANGE (b) have a punctate cytoplasmic
localisation whereas CLLD8 (c) appears to be restricted to the
nucleus of the COS-7 cells.
[0256] TABLE 1 shows associations between LnIgE and the identified
SNPs in BAC bA103J18.03548, BAC bA101d11.0116 and BAC bA236
m15.00303.
[0257] The position is in base pairs from the beginning of the
reference sequence from the BAC/PAC contig.
[0258] TABLE 2 shows association of common
b4.sub.--2.b5.sub.--3.b43.sub.-- -1 haplotypes to total IgE in
subject panels.
[0259] a) SNP/marker associations with total serum IgE.
[0260] b) Association of common b42.b5.sub.--3.b43.sub.--1
haplotypes to total IgE in subject panels.
[0261] c) Association with categorical traits (asthma and
atopy).
[0262] TABLE 3 shows the full length cDNAs isolated from a 1 mb
region of FIG. 5.
[0263] TABLE 4 shows the primer pairs used in the identification of
the SNPs.
[0264] a) SNPS identified in region.
[0265] b) Shows the primer pairs used in RFLP assays.
[0266] c) SNP sequences.
[0267] PCR amplification between exon XII of CLLD8 and exon III of
ANGE. Three bands are observed (A, B and C) and their splice
structure is depicted in the insert. Band B, which lacks ANGE exon
II, has an open reading frame that continues from CLLD8 through to
ANGE. The highest molecular weight band arises from priming from a
homologous sequence within the IgGFc locus.
[0268] TABLE 5 shows peptide sequences used to generate
antibodies.
[0269] TABLE 6 shows putative functional promoter SNPs tested by
EMSAs.
EXAMPLE 1
[0270] Subjects
[0271] The primary mapping was carried out on 364 subjects in 80
nuclear families sub-selected from a population sample of 230
families from the rural town of Busselton in Western
Australia.sup.3,51 (The AUS1 panel). Families in the panel included
both atopic and non-atopic members, and sibships of three or
greater were not exclusively atopic or non-atopic. The AUS2 panel
consisted of the remaining 150 nuclear families from the population
sample. The UK2 panel consisted of 87 nuclear families recruited
through a child attending an asthma clinic in the Oxford region.
The families contained 216 offspring (148 sibling pairs). The ECZ
panel consisted of 150 nuclear families recruited from the
dermatology clinics at the Great Ormond Street Hospital for
Children, through a child or children with active AD, as previously
described.sup.30.
[0272] Phenotypes
[0273] Skin tests to House Dust Mite (HDM) and mixed grass pollen
(less the response of negative controls), specific IgE titres to
HDM and Timothy Grass, and the total serum IgE were measured as
previously described (Hill, M. R., James, A. L., Faux, J. A. &
et al British Medical Journal 311, 776-9 (1995)). A "Skin Test
Index (STI)" was calculated as the sum of the prick skin test
results to HDM and grass mix (95% of individuals in this population
who were atopic reacted either to HDM, or to grass pollen or both).
Bronchial responsiveness to methacholine was measured as previously
described: the maximum dose administered was 12 .mu.mol. The slope
of the dose-response curve was calculated as (pre-dose forced
expiratory volume in one second (FEV1)-- last FEV1), the cumulative
dose of methacholine. A constant of 0.01 was added to each
measurement, to allow log.sub.c transformation when Slope was 0.
Eosinophils in peripheral blood were Coulter-counted and the values
log.sub.c transformed before analysis.
[0274] "Atopy" was defined as a STI>5 mm, or a RAST score to HDM
and Timothy Grass>2, or a total serum 1 gE> the 7.sup.th
decile of the age-corrected population. "Normal" was defined as a
STI of 0 and a RAST Index of 0, and a total serum IgE< the
7.sup.th decile of the age and sex-matched population. Intermediate
phenotypes were classified as unknown. The subjects were
administered a modified British MRC questionnaire as previously
described. "Asthma" was defined as a positive answer to the
questions "Have you ever had an attack of asthma?" and "If yes, has
this happened on more than one occasion?".
[0275] SNP Discovery and Typing
[0276] Discovery of SNPs was performed through direct sequencing of
non-repetitive DNA fragments that were greater than 1000 Bp in
length. For each sequence reaction, primers designed covering
500-600 bps genomic sequence. Five individual samples and one
pooled DNA panel of 32 individuals were sequenced. Traces were
assembled by the Polyphred/Phrap programmes. Following this random
SNP discovery, sequencing of all exons with 250 bp leading and
trailing DNA was carried out for all potential candidate genes from
the region.
[0277] SNP typing was by PCR and restriction digestion. In the
absence of a natural restriction site, one primer was modified to
generate a restriction site. PCR was carried out in 10 .mu.l
reaction which contained 1) 5 .mu.l 10 ng/.mu.l individual DNA; 2)
5 pmol forward and reverse primers; 3) 0.08 u TaqGold; 4) 1.5-3 mM
Mg.sup.2+. PCR carried at 94.degree. C. for 15 minutes then 35
cycles for 1) 94.degree. C. 30 s; 2) 50-60.degree. C. 30 s; 3)
72.degree. C. 45 s. After finishing PCR, the plates were tested for
checking if the PCR worked, then 5 .mu.l digestion solution which
contained 1-2 u restriction enzyme added to each reaction. Samples
were run in 24% agrose gels after 3-5 hours digestion. Total 40
SNPs were typed in the Busselton and UK1 family sets.
[0278] Statistical Analysis of Association
[0279] Errors in SNP typing were detected by testing for Mendelian
errors and by the MERLIN computer program
(http://bioinformatics.well.ox.ac.uk/M- erlin), which identifies
improbable recombination events from dense SNP maps. SNP haplotypes
were generated by MERLIN and recoded as individual alleles.
[0280] Tests of association to quantitative traits were carried out
by the QTDT program, which allowed use of markers and phenotypes as
covariates in analyses.sup.29. Association to asthma and
categorical traits was examined by the Monks test routine of
QTDT.sup.29,31.
[0281] Sequence Analyses
[0282] Genomic sequence was analysed using a modification of HPREP
(G. Micklem, unpublished); screening for repeat elements in
RepBase.sup.52 using REPEATMASKER (Smit, A. F. and Green, P.
http://repeatmasker.genome.- washington.edu); for matches to human,
rodent, EST, STS and other DNA databases, SWISSPROT, TREMBL and
TREMBLNEW peptide databases, CpG islands using CPG.sup.53,
transcription factor elements and putative promoter regions using
PROMOTERSCAN.sup.54, and exon predictions using GRAIL.sup.55,
GENSCAN.sup.56, GENEPARSER.sup.57 and MZEF58. Annotations were
collated using ACeDB (http://www.acedb.or/). Known genes were
identified using BLASTN.sup.59 against the EMBL DNA database. The
peptide databases SWISSPROT, TREMBL and TREMBLNEW were searched
using BLASTX.sup.59 for homologues to transcripts of unknown
function. Putative roles for remaining transcripts were established
using PSI-BLAST.sup.59 and SMART.sup.60.
[0283] IMAGE Clone Sequence and Extension
[0284] IMAGE clones mapping to the region were obtained from
Research Genetics and sequenced on a 377 DNA sequencer using ABI
Prism Big Dye Terminator (PE Applied Biosystems). Consensus
sequences for each IMAGE clone was aligned by the GCG program.
Marathon-Ready.TM. cDNA RACE libraries were obtained form CLONTECH
to extend 5' and 3' cDNA ends of the IMAGE clones. Two
gene-specific primers(GSP) were designed for each direction for
each consensus. Distinct bands from RACE PCR were cut from gels and
purified. The bands were cloned with ZERO Blunt.TM. PCR Cloning kit
from Invitrogen. The inserts were sequenced using Big Dye
Terminator, and integrated into consensus sequences with GCG.
[0285] Tissue Expression
[0286] Human Multiple Tissue Northern (MTN.TM.) Blots and Human
Immune System MTN blots were obtained from CLONTECH. Human Multiple
Tissue, Human Immune System and Human Blood Fractions Multiple
Tissues cDNA Panels from CLONTECH were used for expression analysis
by PCR amplification of target sequences.
[0287] Systematic investigation of the exonic and intronic
structure of the splice variants of ANGE was carried out by
selective PCR, gel separation of products, cloning with ZERO
Blunt.TM. PCR Cloning kit, and Big Dye Terminator sequencing.
EXAMPLE 2
[0288] A saturation genetic map of chromosome 13q14 identified a
one lod support unit for the location of the atopy locus within a
7.5 cM region centred on D13S161.sup.17. A 1.5 Mb BAC and PAC
contig was constructed, centring on D13S273. A positive association
between the total serum IgE and alleles of the microsatellite
USA724GI in two panels of families.sup.4 was found.
[0289] The limit of detection of linkage disequilibrium (LD)
between a disease and a marker given our sample size is likely to
be less than 100 Kb.sup.18,19, suggesting that the atopy gene was
within 100 Kb in either direction of USA724G]. This region of
chromosome 13q14 is commonly deleted in B-cell chronic lymphocytic
leukaemia (BCLL).sup.20.
[0290] Scaffold sequence tag sites (STSs) from our BAC/PAC contig
were then used to prioritise genomic sequencing of the central 1 Mb
of the locus. These STSs were mapped on to BAC contigs built by a
combination of Hind m digest fingerprinting and STS
content.sup.23,24. An overlapping set of clones from the RPCI-11
BAC library.sup.25 was sequenced using a hierarchical shotgun
sequencing strategy.sup.26. The sequence of the region (in the form
of 3 BACs) is shown in FIGS. 5, 6 and 7.
[0291] Linkage Disequilibrium Mapping
[0292] SNPs were detected by sequencing repeat-free contigs than
1.5 Kb in length in 5 unrelated atopic subjects and 5 unrelated
controls, together with a pool of DNA from 32 unrelated
individuals.
[0293] Association to Quantitative Traits
[0294] Forty-seven SNPs and a 15 bp deletion-insertion polymorphism
were identified with minor allele frequencies $ 20%. These were
genotyped in our primary panel of 364 individuals in 80 nuclear
families.sup.34. Error checking and haplotype generation was
carried out by the MERLIN computer program 27. Linkage
disequilibrium (ID) between markers was assessed by estimation of
D' from the parental haplotypes.sup.18 and portrayed by the GOLD
program.sup.28. LD was roughly distributed into three major and one
minor islands (A, Aii, B and C)(FIG. 1a), defining regions in which
association to disease could be localised.
[0295] Association was sought between the Loge(IgE concentration)
(LnIgE) and the SNPs by variance components analyses.sup.29 (Table
1).
[0296] Association to LnIgE clustered around the 185752b4.sub.--2
SNP and extended for approximately 100 Kb within the A and Aii
islands of LD (Table 1). Association to the STI was less well
defined, but seemed to be centred around 4321017b38.sub.--1 and
extend for 150 kb. The distance between the two peaks was
approximately 160 kb.
[0297] In order to test if these peaks corresponded to distinct
QTLs, associations to the LnIgE were tested with the STI as a
covariate and vice versa (Table 1). Associations were similarly
tested with 185752b4.sub.--2 and as covariates. In each case the
LnIgE/185752b4.sub.--2 complex appeared as distinct from the
STI/4321017b38.sub.--1 complex.
[0298] The region of association to LnIgE extended across 3 genes
(Table 1)(FIG. 1b). The identification of the genes is described
below. Inclusion of markers in the first or third genes as
covariates (b1.sub.--1 or 44593.sub.--15) did not abolish the
association within the middle gene, whereas the use of a marker in
this gene as a covariate (b4.sub.--2) removed the evidence for
association in the outer regions. These results suggested that the
QTL is contained within the centre of markers, which show
association to the LnIgE.
[0299] In order to test for replication, six markers (b11.sub.--2,
b4.sub.--2, b5.sub.--3, b43.sub.--1, b38.sub.--1 and b28.sub.--2)
were typed in other panels of subjects. In order to minimise the
numbers of comparisons, the markers were assembled into 3-marker
haplotypes, and multi-allelic tests of association were performed
before examining individual haplotypes. The b4.sub.--2, b5.sub.--3,
b43.sub.--1 haplotype showed consistent association to the LnIgE in
each of the panels tested (Table 2). Two haplotypes containing the
b4.sub.--2*2 and the b5.sub.--3*1 alleles (A and D, Table 2) showed
negative association with the LnIgE, although they differed at the
b43.sub.--1 locus. Positive association was observed with the C
haplotype (containing b4.sub.--2*1 and b5.sub.--3*2) in a panel of
families with atopic dermatitis.sup.30. These results further
suggest that the polymorphism influencing IgE levels is nearest to
b4.sub.--2 and b5.sub.--3.
[0300] The combined panel of Busselton families (AUS1 and AUS2) may
be taken to be representative of the general population.
Association was seen to asthma in these subjects with the
b4.sub.--2 and b5.sub.--3 markers (p=0.024 and p=0.017
respectively) using a transmission disequilibrium test.sup.31.
[0301] Association to Categorical Traits
[0302] Gene Identification and Domain Homologies
[0303] Unfinished BAC sequence of the region was assembled and
annotated. Systematic identification of expressed sequences was
carried out by examination of EST databases and from a cDNA
selection experiment.sup.4. Partial sequences from these sources
were consolidated into cDNA contigs, and further extended these by
3' and 5' RACE and Northern blotting was carried out to determine
transcript sizes, and to examine tissue expression of the
genes.
[0304] Six full length cDNAs were identified from the 1 Mb region
of genomic sequence (Table 3).
[0305] Four other sequences were found in the EST databases, but
did not have open reading frames (ORFs) or a splice structure and
were likely to be genomic contaminants (UniGene clusters Hs.58452,
Hs.268773, and Hs.212161).
[0306] Physical mapping of the chromosome 13q14 BCLL locus cell has
recently identified 5 of these genes.sup.22. Three were considered
novel candidate genes for leukemogenesis and were named as CLLD6,
CLLD7, and CLLD8. The other genes are karyopherin-.A-inverted.3
(KPNA3) and the gene corresponding to the NY-REN-34 antigen (ANGE).
The sixth gene is Emopamil-binding related protein (EBRP).
[0307] Sequence homologies for the three distal genes do not
suggest an obvious role in atopy or asthma: EBRP may act as a D8-D7
sterol isomerase in cholesterol biosynthesis, the sequence of KPNA3
suggests that it is involved in the nuclear transport
system.sup.32, and CLLD6 contains a SPRY domain, suggesting
possible microtubule-binding. The three remaining genes form a
tight cluster which contains the region of association to LnIgE
levels (Table 1)(FIG. 1b).
[0308] CLLD8
[0309] The most proximal gene, CLLD8, contains both a
methyl-CpG-binding domain (MBD) and a SET domain.sup.22 (FIG. 8).
The MBD appears to lack amino acids required to bind methylated
CpG.sup.33,34, but remains likely to bind DNA. SET domains modulate
gene expression epigenetically through histone H3
methylation.sup.35-37. CLLD8 is likely to be a H3 methyltransferase
since it contains both active site and flanking cysteine residues
that are important for catalytic activity.sup.37.
[0310] Histone Methyl Transferases
[0311] The expression of genes in eukaryotic organisms is dependent
on DNA accessibility. In its natural state, DNA is packaged around
a set of histones, H2A, H.sub.2B, H3 and H4. Further higher order
compaction is facilitated by the interaction with H1 histone and
other non-histone proteins. In this condensed state, chromatin is
inaccessible to the transcription machinery and thus genes
contained within it are silent. Histone methyl transferases play a
critical role in the regulation of gene expression. In mammalian
cells, these enzymes are known to methylate histones H3 and H4 at
specific lysine residues. The most widely studied member of this
protein family is SUV39H1, which selectively methylates histone H3
at lysine residue 9 (K9). The catalytic domain of this enzyme is
contained within a highly conserved sequence known as the SET
domain. This sequence is required in combination with two flanking
cysteine-rich sequences (Pre-SET and Post-SET) to facilitate
histone methylation. Thus the PreSET-SET-PostSET domain is regarded
as a characteristic signature of histone methyltransferase
proteins. CLLD8 contains an expanded SET domain and a methyl
binding domain, a structure that is capable of recognising
methylated DNA.
[0312] Reference: Kouzarides, T. "Histone Methylation in
transcriptional control" (2002) Curr Opin Genet and Devel
12:198-209.
[0313] ANGE (NY-REN-34)
[0314] The next gene is approximately 4 Kb distal to the 3' end of
CLLD8 and is transcribed in the same direction. It encodes
NY-REN-34 antigen which was identified by serological analyses of
cDNA products from four patients with renal cell carcinoma.sup.38.
Transcripts of the gene are also highly represented in stomach,
tonsil and in B-cells (UniGene cluster 279799). The gene product
contains two PHD (plant homeo domain) zinc fingers, which suggest
its involvement in chromatin-mediated transcriptional
regulation.sup.39 (FIG. 8). PHD fingers normally posses two
Zn.sup.2+ co-ordinating groups which contain cysteine and histidine
residues. The N-terminal (5') of the NY-REN-34 finger pair however
lacks one of the two coordinating groups.
[0315] The arrangement of PHD fingers in NY-REN-34 is
characteristic of human proteins such as ALL-1 and AF10 whose genes
are fused in some cases of acute lymphoblastic leukaemia.sup.40
(FIG. 8). Analogy to AF10.sup.41 and ALL.sup.42 PHD fingers
suggests that the NY-REN-34 PHD finger pair is likely to possess a
homodimerisation or a protein-binding role or both. NY-REN-34 has
also been called BCAP (BRCA1-C terminus associated protein)(EMBL
accession AB011031) and is likely to interact with the BRCT domains
of BRCA1. These domains are capable of stimulating transcription,
remodelling chromatin and interacting with histone-modifying
enzymes such as the histone acetyltransferase p300 and the human
histone deacetylase, HDAC.sup.43.
[0316] CLLD7
[0317] CLLD7 follows only 3 Kb from the end of ANGE, but is
transcribed in the opposite direction. It shows strong protein
sequence similarity to RLG and RCC1 (regulator of chromatin
condensation 1). RCC1 binds to DNA and to histones H2A and H2B44.
CLLD7 contains a BTB/POZ domain, which classically form homophilic
and heterophilic dimers.
[0318] Remodelling of chromatin structure is important in
transcriptional regulation of genes influencing IgE
production.sup.45, so CLLD8, ANGE and CLLD7 may all be considered
candidates for influencing atopic processes. However, CLLD8 and
ANGE both contain domain homologies to the IL-5 promoter
REII-region-binding protein (RE-IIBP).sup.46, as well as to genes
found in leukaemia (ALL).sup.40 and multiple myeloma
(MMSET).sup.46,47 (FIG. 8). This suggests a role in immune
regulation and immunoglobulin production.
[0319] CLLD8 and ANGE (NY-REN-34) Co-Expression
[0320] The close genomic proximity of CLLD8 and ANGE raises the
possibility of co-ordinate expression of both genes, or expression
of a combined gene product that would be similar to RE-IIBP.sup.46.
PCR between exon XII of CLLD8 and exon III of ANGE identified three
bands (A, B and C) which were expressed in most tissues (FIG. 10).
Each band contained a specific splice structure (FIG. 3), but our
sequence did not identify an extended open reading frame in any of
the bands. Despite the absence of an open reading frame, the
non-random splice structure suggests a function, which may be
regulatory.
[0321] Tissue Expression and Splice Variation
[0322] We examined northern blots of CLLD8, ANGE and CLLD7. The
northern for ANGE showed polymorphic high molecular weight bands
(FIG. 10). High molecular weight bands were also seen with CLLD8,
but these did not match the tissues in which similar bands were
seen with ANGE (FIG. 2). CLLD6 and the other genes from the contig
showed the expected size bands with a uniform and ubiquitous tissue
distribution.
[0323] The ANGE gene contains 10 exons. Examination of the public
databases identified a number of alternative first exons with
alternative start methionines for protein translation
(EMBL:AF155105, AL552215, B1463029, BG759124). We have been able to
identify all of these variants by sequencing of specific PCR
products from cDNA panels (data not shown). In addition, versions
of the cDNA show skipping of exon II were found (ESTHUM: BF662927
and BE787177, EMBL:AL552215). The AL552215 variant results in an
incomplete first PHD domain, that would not be anticipated to be
functional.
[0324] Exon-specific PCR of cDNA from multiple tissue panels
identified exon II skipping variants to be present at approximately
the same concentration in all tissues (FIG. 4a).
[0325] Highly tissue-specific splice variants were found which
contained additional exons between exons V and VI (named exon Va
and Vb). These variants differed by 54 bps, and were present in
lung and peripheral blood leucocytes (PBL) (FIG. 4b). Examination
of PBL fractions showed that the splice variants were present in
unactivated CD4+, CD8+ and CD19+ cells, but absent in activated
cells. Both exons result in a premature stop codon. Alternative
splicing with a premature stop codon has previously been identified
as mechanism for negative control of transcription.sup.48, and a
negative role for these variants is consistent with their
expression in inactive T and B Cells.
[0326] A splice variant in which intron VII was retained between
exons VII and VIII (ESTHUM: BE141730), which was most strongly
expressed in active CD4+ and CD8+ leukocytes was observed (FIG.
4c). This variant also results in a premature stop codon.
[0327] ANGE
[0328] The identification of ANGE (NY-REN-34) by positional cloning
rests on three lines of evidence: genetic localisation, tissue
expression, and inferred or demonstrated gene function. In the
present case, although the region of association to the total serum
IgE concentration extends across three genes, our analysis suggests
that this is attributable to polymorphism within the gene for ANGE
(FIG. 1, Table 1, and Table 2). Domains from CLLD8 and ANGE have
homologies with known B-Cell transcription factors. Only one gene,
ANGE, has differential expression in immune cells and tissues, and
is likely to be responsible for atopy at this locus.
[0329] We have carried out further sequencing of ANGE and CLLD8 for
5' regions, all exons, and non-repetitive areas of introns. One
conservative coding (Glu-Gly) variant was found in CLLD8, and
showed only weak association with the IgE(p<0.01). One non
conservative (Pro-Ser) variant was found in ANGE
(ANGE1.times.3C148T). A non conservative coding (Val-Ala) variant
was found in CLLD7 (CLD703).
[0330] The SNPs within the A island of LID were in strong
disequilibrium. Control regions for genes may extend for 100
Kb.sup.49, and we have observed at least two haplotypes with
different effects on serum IgE levels. Our results indicate that
loci underlying complex traits will contain several polymorphisms
with different functional consequences.sup.50.
EXAMPLE 3
[0331] Sequence Analyses
[0332] DNA sequence from overlapping, unfinished BACs was assembled
to form larger contigs using contigwalk, a systematic comparison
and extension tool using BLASTN (S. J. Broxholme, unpublished). A
framework map of the region of interest was prepared using vector
scores of STS markers from the critical region in the Genebridge4
Radiation Hybrid panel and the Radiation Hybrid mapping software
RHMAPPER (Stein, L., Kruglyak, L., Slonim, D., Lander, E. (1995)
http://www.genome.wi.mit.edu/- ftp/pub/software/rhmapper.) RHMAPPER
was then used to find markers in RHDB (Rodriguez-Tome, P. &
Lijnzaad, P Nucleic Acids Res 29, 165-6. (2001)) that could be
placed within this framework.
[0333] For each RHDB entry placed within the framework, the
accession number was found from its annotation, and ESTs were
selected for the next stage. TIGR Assembler (Sutton G. G., White
O., Adams, M. D. and Kerlavage, A. R. (1995) Genome Science &
Technology, 1, 9-19) was used to make a non-redundant set of
sequences.
[0334] Genomic sequence was analysed using a modification of hprep
(G. Micklem, unpublished); screening for repeat elements in RepBase
(Jurka, J. Trends Genet 16, 418-20. (2000)) using RepeatMasker
(Smit, A. F. A. and Green, P.
http://repeatmasker.genome.washington.edu); for matches to human,
rodent, EST, STS and other DNA databases, SWISSPROT, TREMBL and
TREMBLNEW peptide databases, CPG islands using cpg (Larsen, F.,
Gundersen, G., Lopez, R. & Prydz, H. Genomics 13, 1095-107.
(1992)), transcription factor elements and putative promoter
regions using promoterscan (Prestridge, D. S J Mol Biol 249,
923-32. (1995)), and exon predictions using GRAIL (Xu, Y., Mural,
R. J. & Uberbacher, E. C. Comput Appl Biosci 10, 613-23.
(1994)), GENSCAN (Burge, C. & Karlin, S. J Mol Biol 268, 78-94.
(1997)), geneparser (Snyder, E. E. & Stormo, G. D. Nucleic
Acids Res 21, 607-13. (1993)) and MZEF (Zhang, M. Q. Proc Natl Acad
Sci USA 94, 565-8. (1997)). Annotations were collated using ACeDB
(http://www.acedb.org/).
[0335] Known genes were identified using BLASTN (Altschul, S. F. et
al. Nucleic Acids Res 25, 3389-402. (1997)) against the EMBL DNA
database. The peptide databases SWISSPROT, TREMBL and TREMBLNEW
were searched using BLASTX (Altschul et al., supra) for homologues
to transcripts of unknown function. Putative roles for remaining
transcripts were established using PSI-BLAST (Altschul et al.,
supra) and SMART (Schultz, J., Copley, R. R., Doerks, T., Ponting,
C. P. & Bork, P Nucleic Acids Res 28, 2314. (2000)).
[0336] IMAGE Clone Sequence and Extension
[0337] IMAGE clones mapping to the region were obtained from
Research Genetics and sequenced on a 377 DNA sequencer using ABI
Prism Big Dye Terminator (PE Applied Biosystems). The reaction
contained 2 .mu.l Bigdye, 2 .mu.l Half Bigdye, 1 .mu.l primer (5
pmol/.mu.l), 1-4 .mu.l plasmid DNA (400 ng) and 14-1 .mu.l
dsH.sub.2O. The sequence reactions were performed in MJ thermal
cycler. 1); 95.degree. C.-1 min; 2) 95.degree. C.--1 is; 3)
50.degree. C.--10s; 4) 60.degree. C.--4 mins; 5) repeated step 2 to
4 for 24 cycles [25 cycles total]; 6) 15.degree. C.--hold.
Consensus sequences for each IMAGE clone was aligned by the GCG
program.
[0338] Marathon-Ready.TM. cDNA RACE libraries were obtained form
CLONTECH to extend 5' and 3' cDNA ends of the IMAGE clone
sequences. Two gene-specific primers(GSP) were designed for each
direction for each consensus. There were about 150-200 bps
overlapping sequence between the two GSP primers. GSP primers were
designed to have 25-28 bps, 50-70% GC and Tm 65.degree. C.
Touchdown PCRs were used for the RACE the ends as: 1) 94.degree. C.
for 30 s, 2) 25-30 cycles at 94.degree. C. for 5 s, 68-72.degree.
C. for 4 min.
[0339] Distinct bands from RACE PCR were cut from gels and
purified. The bands were cloned with ZERO Blunt.TM. PCR Cloning kit
from Invitrogen. The inserts were sequenced using Big Dye
Terminator, and integrated into consensus sequences with GCG.
[0340] Northern Blot Analysis
[0341] Human Multiple Tissue Northern (MTN.TM.) Blots and Human
Immune System MTN blots were obtained from CLONTECH. The Human MTN
Blot contained RNA from: heart, brain (Whole), placenta, lung,
liver, skeletal muscle, kidney and pancreas. The Human Immune
System MTN contained: spleen, lymph node, thymus, peripheral blood
leukocyte, bone marrow and fetal liver. The Blots were hybridised
with probes generated from cDNA colon or tissue cDNA solution. The
average size of probes was 500-1000 bps. For gene i154016, the
probe was 1180 bps from exon 1 to exon 10. The probes were
radioactively labelled with [.sup.32P]dATP using random primer
method. All probes were hybridised at 42.degree. C. overnight in
Hybridisation solution (10% Dextran sulphate; 4.times.SSC; 50 mM
sodium phosphate buffer pH7.2; 1 mM EDTA pH 8.0; 10.times.
Denhardts; 50 mg/ml herring DNA sonicated; 1% SDS).
[0342] PCR Screening of MTC Panels
[0343] Human Multiple Tissue cDNA Panels and Human Immune System
Multiple Tissues cDNA Panels from CLONTECH were used for expression
analysis. The Human Multiple Tissues cDNA panel contained cDNA
from: heart, brain, placenta, lung, liver, skeletal muscle, kidney
and pancreas. The Human Immune System Multiple Tissues contained
cDNA from: spleen, lymph node, thymus, tonsil, leukocyte, marrow
and fetal liver. MTC panels were examined in all cDNA consensus
sequence over the five BACs genomic sequence. PCRs were carried out
in 50 .mu.l which contained: 1).sub.36 .mu.l deionised H.sub.2O; 2)
5 .mu.l PCR buffer; 3) 1 .mu.l advanTaq Plus; 4) 5 .mu.l 8 mM dNTP
and 5) 4 .mu.l 5 pmol forward and reverse primers. PCR was
performed as 1) 30 s at 94.degree. C.; 2)22-38 cycles at 94.degree.
C. for 30 s, 68.degree. C. for 2 min; 3) 68.degree. C. for 5 min.
In order to observe the abundance of the particular target, a total
5 .mu.l sample each time was removed from the reactions at 22, 26,
30, 34 and 38 cycles.
[0344] For ANGE (NY-REN-34), the CLONETECH Human Blood Fractions
MTC panel was also tested as above.
[0345] Systematic investigation of the exonic and intronic
structure of the splice variants of ANGE was carried out by
selective PCR, gel separation of products, cloning with ZERO
Blunt.TM. PCR Cloning kit, and Big Dye Terminator sequencing.
[0346] Results
[0347] We then investigated the genes within the region of
association. Unfinished BAC sequence of the region was assembled
and annotated. Systematic identification of expressed sequences was
carried out by examination of EST databases and from a cDNA
selection experiment (G. Anderson. DPhil Thesis, Oxford University
2001). Partial sequences from these sources were consolidated into
cDNA contigs and were further extended by 3' and 5' RACE. Northern
blotting was carried out to determine transcript sizes, and to
examine tissue expression of the genes.
[0348] Six full length cDNAs were eventually identified from the
lMb region of genomic sequence (Table 3). Five other sequences were
found in the EST databases, but did not have open reading frames
(ORFS) or a splice structure and were likely to be genomic
contaminants (i274117, i46536, i513822, i143317 and i447262).
Physical mapping of the chromosome 13q14 BCLL locus cell has
recently identified three of the genes we found, which were named
as CLLD6 (i2350400), CLLD7 (i44593), and CLLD8 (i626548) (Mabuchi,
H. et al. Cancer Res 61, 2870-7. (2001)). These genes were
considered novel candidate genes for leukemogenesis. Our analysis
of the domain content of these genes agrees with the assessment of
Mabuchi et al that CLLD7 might be involved in cell cycle regulation
by chromatin remodelling and that CLLD8, which contains a SET
domain, might be associated with methylation-mediated
transcriptional repression. We have observed a SPRY domain in
CLLD6, which might be involved in microtubule-binding. CLLD6 seems
to be beyond the region of association to LnIgE or the STI.
[0349] The gene corresponding to image clone i154016 has been
previously recognised to code for NY-REN-34 antigen, which was
identified by serological analyses of cDNA from four patients with
renal cell carcinoma (Scanlan, M. J. et al. Int J Cancer 83,
456-64. (1999)). Transcripts of the gene have also been
consistently found in breast carcinoma and in tonsil. The gene
contains two PHD domains, one of which is complete and the second
of which is N-terminal (5') to the first and is missing one of its
two zinc co-ordinating residue groups (mostly Cys). These two PHD
domains are very similar to pairs of PHD domains in
Drosophila/human trithorax and human ALL-1, suggesting that the
gene for NY-REN-34 antigen is involved in chromatin-mediated
transcriptional regulation (Aasland, R., Gibson, T. J. &
Stewart, A. F. Trends Biochem Sci 20, 56-9. (1995)).
[0350] Image clone i1895799 is Emopamil-binding related protein,
which acts as a D8-D7 sterol isomerase. Image clone i626789 is
karyopherin alpha 3, with homologies that suggest that it may be
involved in the nuclear transport system (Takeda, S. et al.
Cytogenet Cell Genet 76, 87-93 (1997)).
[0351] Chromatin structure is important in transcriptional
regulation of genes influencing IgE production (Lavender, P.,
Cousins, D., Smith, P. & Lee, T. Presentation at the National
Asthma Campaign International Congress, June 1999. Clin Exp Allergy
30, 1697-708. (2000)) so that the SET domain and PHD
domain-containing proteins (CLLD8 and NY-REN-34) are prime
candidates for influencing atopic processes.
[0352] Mapping of the transcribed sequences back onto the SNP/LD
map showed that three of the genes were contained under the peak of
association to the LnIgE and STI (FIG. 1). These genes were
NY-REN-34, CLLD7 and the D8-D7 sterol isomerase.
[0353] Further examination of the genes was based on their tissue
expression. Northern blots of CLLD8 and CLLD7 and
Karyophern--showed ubiquitous expression of a single sized
transcript, as previously described. However, NY-REN-34 showed
differential splicing, with higher molecular weight bands present
in immune tissues (FIG. 2).
[0354] This gene was therefore examined in more detail. It consists
of 10 exons, and an alternative exon 1 has been seen in W tissue
(FIG. 3). Only one of these exons has a promoter (FIG. 3). We could
only identify PCR products that contained the promoter-associated
exon from multiple cDNA (MTC) panels. Further exon-specific PCR
amplification of cDNA from the panels showed a number of unexpected
bands (FIG. 4) in tissues. An alternative version within and
without exon two was seen, and was present at approximately the
same concentration in all tissues (FIG. 4a). We observed further
additional bands when amplifying exons 4-6. These bands were highly
tissue-specific, being present in lung and peripheral blood
leucocytes (PBL) (FIG. 4b). Examination of PBL fractions showed
that the splice variants were present in unactivated CD4+, CD8+ and
CD19+ cells, but absent in activated cells. Sequencing of the
splice variant band revealed the presence of an additional exon
between exons 5 and 6. This resulted in an immature stop codon.
Further splice variants were seen with amplification of exons 7-8
(FIG. 4c), which were specific to leukocytes.
[0355] The evidence therefore suggested that the gene for NY-REN-34
is responsible for atopy at this locus. It is situated at the peak
of association to the LnIgE and the STI, its sequence homology
suggests that it acts as a regulatory factor, and is differentially
spliced in the specific tissues known to be involved in the
regulation of IgE and the allergic response. We therefore have
named the NY-REN-34 gene ANGE (atopy new gene).
[0356] There are many cell types and phenotypic readouts which can
be measured to assess the contribution of these genes to the
disease phenotype, including cell-cell interactions, inflammatory
cell recruitment, inflammatory mediator release, and effector
functions. We primarily used B cell lines as the model system for
the cell based assays and IgE promoter activity as the main readout
of B cell function.
EXAMPLE 4
[0357] It is of interest that CLLD8 is in close proximity
(approximately 4 Kb) to ANGE, that ANGE has an alternate first exon
without a promoter, and that high molecular weight bands were
observed on Northern Blots of ANGE. In order to establish if
CLLD8-ANGE may on occasion form a single gene product, PCR was
performed between CLLD8 and ANGE exons in placental cDNA. A band
was observed, indicating the presence with a gene with the domain
structure CpGBD-PreSET-SET-PostSET-PHD-PHD. A similar domain
structure has been observed in IL-5 promoter REII-region-binding
protein (Garlisi, C. G. et al. Am J Respir Cell Mol Biol 24, 90-98.
(2001)).
[0358] Mutations associated with 13q14 have not been identified in
any of the genes mapped to this locus. However, the recognition
that CLLD8/ANGE form a single transcript with differential splicing
(FIG. 9) suggests that this gene may cause atopy.
EXAMPLE 5
[0359] Mammalian Cell Electroporation
[0360] Below is the protocol for the transfection of B cells by
electroporation used in the IgE-luciferase reporter assay. These
electroporation conditions have been optimised for B cells by
measuring .beta.-galactosidase activity after transfection with
pcDNA4/HisMax-LacZ. The conditions used in the optimisation
experiments are given in the Results section.
[0361] The human Burkitt lymphoma cell line DG-75 (DSMZ) was
cultured in fresh RPMI plus 10% FCS 24 hours before transfection.
The cells were harvested by centrifugation at 1000 rpm for 10
minutes and washed once in cold RPMI. 5.times.10.sup.6 cells were
resuspended in 400 .mu.l cold RPMI and transferred to a 0.4 cm gap
electroporation cuvette (BioRad) containing 10 .mu.g pGL2 reporter
vector, 10 .mu.g pcDNA4/HisMax expression vector, and 1 .mu.g
pRL-TK (Promega) for normalisation of data to account for
differences in transfection efficiency. A pulse was delivered at
100 .mu.F and 250V at room temperature using a Gene Pulser II
Electroporator (Bio-Rad). Immediately after transfection 600 .mu.l
warm RPMI plus 10% FCS was added to the cells which were
transferred to 1 ml warm RPMI plus 10% FCS in a 6-well plate. The
cells were cultured at 37.degree. C. for up to 24 hours in the
presence or absence of human recombinant I14 (Sigma).
Measurement of .beta.-galactosidase Activity in
pcDNA4His/MaxLacZ-Transfec- ted Cells
[0362] 24 hours post-electroporation the transfection of B-cells
was monitored by measuring .beta.-galactosidase activity in cell
lysates. Cells were harvested by centrifugation, washed twice in
PBS and resuspended in Reporter Lysis Buffer (Promega). After
incubating at room temperature for 15 minutes the lysates were
centrifuged at 14,000 rpm for 10 minutes and the supernatants added
to an equal volume of 2.times..beta.-galactosidase assay buffer
(200 mM sodium phosphate pH7.3, 2 mM MgCl.sub.2, 100 mM
.beta.-mercaptoethanol, 1.33 mg/ml ONPG). The reactions were
incubated at room temperature or 37.degree. C. until a yellow
coloration had developed. 1 ml of 1M NaCO.sub.3 was added and the
absorbance read immediately at 420 nm.
X-gal Staining of pcDNA4His/MaxLacZ-Transfected Cells
[0363] Transfected cells were harvested by centrifugation, washed
twice in PBS and fixed in 3.7% formaldehyde in PBS for 15 minutes
at room temperature. After washing three times with PBS the cells
were incubated in X-gal solution (0.2% X-gal, 2 mM MgCl.sub.2, 5 mM
K.sub.4Fe(CN).sub.6.3H.sub.2O, 5 mM K.sub.3Fe(CN).sub.6) for 2-16
hours at 37.degree. C.
[0364] Dual Luciferase Assay
[0365] 800 .mu.l of transfected-cell suspension was centrifuged at
300 rpm for 10 minutes and washed with 1 ml PBS. The cell pellet
was resuspended in 50 .mu.l passive lysis buffer and incubated for
20 minutes at room temperature on a rotating wheel. The lysates
were briefly centrifuged at 14,000 rpm and dual luciferase activity
was measured in 201 .mu.l of the supernatant using the
Dual-Luciferase Reporter System (Promega) according to the
manufacturer's instructions.
[0366] WST-1 Proliferation Assay
[0367] U20S cells were seeded in a 96-well plate at
3.times.10.sup.3 cells per well and cultured at 37.degree. C. for
24 hours in DMEM plus 10% FCS. Transfections were performed in
triplicate using 300 ng pcDNA4/HisMax expressing CLLD7, CLLD8,
REN34 or ANGE and 0.21 .mu.l FuGENE 6 transfection reagent mixed in
201 .mu.l Optimem, as described in section a. The cells were
cultured for 24, 48, or 72 hours before adding 10 .mu.l per well of
WST-1 cell proliferation reagent. Absorbance was measured at
450/690 nm after a one-hour incubation at 37.degree. C.
[0368] Histone Methyltransferase Assay
[0369] 10 .mu.g of SUV39H1(82412)-GST protein (1 mg/ml) was added
to 5 .mu.g biotinylated H3 peptide (first 21 amino acids of Histone
H3 with a Biotin label on the CO.sub.2H terminus from Upstate
Biotechnology) in MAB (methylation activity buffer as described in
Regulation of chromatin structure by site specific Histone H3
methyltransferases, Rea et al. Nature 406, 593-599, 2000. but using
Tris-Ci pH 8.0) and water to a final volume of 100 .mu.l, allowing
for the addition of 600nCi of .sup.14C s-adenosyl methionine as the
radioactive substrate to initiate the reaction. This was incubated
at 30.degree. C. for 90 minutes. 30-50%1 of PBS washed Streptavidin
Agarose beads (Sigma) were added at room temperature for 30 minutes
with gentle agitation, to bind all biotinylated H3 peptide. Unbound
reaction components were removed by washing beads in at least 10
volumes of PBS, spinning at low speed (.about.5000 rpm) and
removing supernatant to aqueous waste, taking care not to remove
any Agarose beads. The beads were then resuspended in 100 .mu.l of
PBS and added to 3 ml of scintillant fluid for counting of .sup.14C
labelled methylated H3 peptide.
[0370] Screening Methods for Modulators of Methyltransferase
Activity are disclosed in Patent WO 01/94621. The screening methods
in this patent relate to modulators of murine
SUV39H2-methyltransferase.
[0371] Screening for modulators of Suv39h2 Mtase activity (from WO
01/94621).
[0372] All steps are automated and the position of the different
compounds being tested are registered on computer for later
reference. Compounds being tested for modulating activity are
aliquoted into 384 well plates in duplicate. 20-200 nmol of
recombinant GST tagged human SUV39H2 in MAB buffer, is then added
to the reaction. 20 nmol of branched peptide
([TARKST].sub.4-K.sub.2-K-cys) which has been labelled with
europium is then added, followed by 100 nmol of S-adenosyl
methionine. This reaction is left at room temperature for 40 mins,
then transferred onto a second plate to which the .alpha.-methH3-K9
antibody has been coated. This reaction is then left at room
temperature for 40 mins to allow the antibody to bind methylated
substrate. Following capture of methylated substrate, unbound
non-methylated substrate is washed off in 50 mM tris pH 8.5. The
europium label is then cleaved from the peptide in 50 .mu.l pH 4.5
enhancement solution for 25 mins. The chelated europium molecules
are then excited at 360 nm and the level of emitted fluorescence at
620 nm is then calculated using time-resolved fluorescence in a
PolarStar plate reader. The results are then automatically
graphed.
[0373] The level of fluorescence is directly related to the level
of MTase activity. The effect of the different compounds on the
MTase activity can be clearly seen on the graph when compared to
control reactions with no compounds added or with no enzyme added.
The principle of the screening method is as follows:
[0374] a) Suv39h2 is incubated with S-Adenosyl Methionine (SAM) and
a chromogenically labelled unmodified peptide substrate (e.g.
branched peptide [TARKST]4-K2-K-cys).
[0375] Following methylation of this substrate the substrate
becomes an epitope for a Lys9-methyl specific antibody which has
been immobilised on a microtiter plate. The level of bound peptide
can then be quantified by the level of fluorescence of from the
chromogenic label.
[0376] b) In the presence of a modulator (e.g. an inhibitor, I) the
transfer of methyl groups by the MTase will be affected
(decreased), this in turn will affect the amount of substrate
captured by the immobilised antibody, which is quantified by the
level of fluorescence. A compound with inhibitory effects will
result in a decrease in fluorescence signal, whereas a compound
with inhibitory effects will result in a decrease in fluorescent
signal, whereas a compound with enhancing effects will result in an
increase in fluorescent signal.
[0377] A truncated SUV39H1 (82-412), without the Chromo domain, was
amplified by PCR from a Jurkat cDNA library and cloned into
pGEX-2T. Histone methyl transferase activity of truncated protein
was confirmed by radioactive assay.
[0378] Cloning of cDNAs into bacterial expression plasmids.
[0379] All genes, CLLD7, CLLD8 and ANGE, were successfully
amplified from I.M.A.G.E. consortium clones and cloned into the
appropriate vectors: pET28a, pGE.times.4T and pGE.times.6P.
[0380] Expression of Proteins in Mammalian Cells
[0381] Full-length cDNAs for CLLD7, CLLD8, and ANGE 1 were cloned
into pcDNA4His/Max plasmid (Invitrogen) for use in over-expression
studies in B cells. Whole cell lysates were prepared 24 hours
post-transfection and protein expression was detected by western
blotting using an anti-polyhistidine monoclonal antibody. The bands
that were detected in the western blot migrated at approximately
the expected sizes for the recombinant proteins; CLLD7, 58 kDa;
CLLD8, 82 kDa; REN34, 22 kDa; ANGE, 37 kDa (FIG. 11). This
indicates that pcDNA4His/Max constructs are functional and express
the genes of interest. Confirmation of these results was obtained
by probing transfected Cos-7 cell lysates with an antibody to the
Express Epitope (Invitrogen) for detection of ANGE and with
specific antibodies to CLLD8 and ANGE.
[0382] IgE Reporter Assays
[0383] The human germline IgE promoter was cloned into the
luciferase reporter vector pGL-2 Basic (Promega) in both forward
and reverse orientations. pGL-2 Control, in which the luciferase
gene is under the control of the SV40 promoter (Promega), was used
as a positive control for luciferase activity. For normalisation of
data due to differences in transfection efficiency, cells were
co-transfected with pRL-TK (Promega).
[0384] The effect of over-expression of CLLD7 on IgE promoter
activity was measured. Cells were co-transfected with the IgE
reporter construct +/-pcDNA4-CLLD7. Luciferase activity was
measured 24-hours post-transfection and IgE promoter activity
expressed as a ratio of firefly luciferase to renilla luciferase
activity.
[0385] Histone Methyltransferase Assays
[0386] Histone methyltransferases (HMT) are chromatin-modifying
enzymes functioning mainly in the nucleus but could have a role in
the cytoplasmic compartment. Therefore, both nuclear and
cytoplasmic extracts were purified from transfected Cos7 cells, for
use in the HMT assay. Human SUV39H1 (used as a positive control in
the assay) is a Lysine specific Histone methyltransferase that
specifically methylates lysine 9 of Histone H3. Methylation of H3
has been shown to recruit HPI protein resulting in formation of
heterochromatin and may thus be involved in gene regulation/gene
silencing (Rea et al.).
[0387] Nuclear extracts from Cos7 cells transfected with pcDNA
CLLD8 were tested for HMT activity. In experiments transfected Cos
cells showed increased HMT activity relative to the untransfected
control (see FIG. 12).
EXAMPLE 6
[0388] Identification of SNPs that alter the function of a gene is
of importance when the SNP is in a genomic region, which is known
to be associated with the disease. This example describes one
approach to functionally validate a SNP in a putative gene
regulatory region such as a promoter or enhancer. Alterations in
the normal function of these genomic regions influences the levels
of transcription of the gene potentially affecting the levels of
protein, the consequence of which leads to a disease state. The
ability of proteins to bind to DNA with or without the SNP was
demonstrated by electromobility shift assays (EMSAs). An alteration
in the shifting pattern or intensity when comparing the wildtype
and mutant DNA is indicative of differential binding of
transcription factors. This differential effect potentially will
result in differing expression patterns of the gene.
[0389] SNPs Tested
[0390] Four SNPs were identified by in-silico analysis using DB and
Celera SNP databases which lay within predicted regions of the
CLLD7, CLLD8 and ANGE gene promoters. The description of the SNP,
oligonucleotide probes and potential transcription factor binding
sites are shown in Table 7.
[0391] Labelling of Oligos
[0392] The DNA target was produced by 3' biotin end labelling of
complementary oligos with or without the SNP then incubated
together to allow annealing to form a double stranded target
DNA.
[0393] EMSA
[0394] Optimisation of double stranded oligo probe and nuclear
extract was performed as demonstrated in the table. After
incubation at room temperature, the samples were run on 5%
polyacrylamide gels, electroblotted onto Biodyne charged membrane
and the position of the biotin labelled oligos identified using the
LightShift chemiluminescent EMSA kit (Pierce) as described by the
manufacturers instructions and visualised by exposure to film or
CCD camera.
[0395] Results
[0396] NR1 Oligos, hcv9873896, FIG. 13a
[0397] The results showed a difference in protein binding to the
wild-type and the mutant oligos for NR1. There was an increase in
the migration distance for the DNA-protein complex with the mutant
oligo. This is possibly due to a decrease in affinity for the
mutant oligo, the protein could be dissociating ot it is possible
that a different protein from the nuclear extract could be binding
to the DNA.
[0398] NR2 Oligos, clld7.times.1a295t, FIG. 13b
[0399] There was protein-DNA complex formation for both the
wild-type and the mutant oligos but there did not appear to be any
difference between the two.
[0400] NR3 Oligos, clld7prom1a351g, FIG. 13c
[0401] There was evidence of protein binding with the NR3 wild-type
oligo but there was no binding detected with the mutant oligo.
[0402] NR4 Oligos, clld8.times.1a384g, FIG. 13d
[0403] There was a very strong affinity for the protein by both the
wild-type and the mutant oligos.
[0404] There did not appear to be any difference in the affinity
between the wild-type and the mutant oligo.
EXAMPLE 6a
[0405] In order to identify the cellular localisation of the CLLD7,
CLLD8 and ANGE proteins we generated mammalian expression
constructs which when transfected into cells have the ability to
express the recombinant protein. Using antibodies specific to an
epitope tag fused in frame with the protein of interest allows for
visualisation of the protein within the cell.
[0406] Expression Cloning
[0407] The open reading frames of CLLD7 (1590 bp), CLLD8 (2157 bp)
and ANGE (993 bp) were generated by PCR using full-length EST
clones and the PCR product cloned into pcDNA-His.Max-TOPO
(Invitrogen).
[0408] The frame and integrity of the orf was verified by double
stranded sequencing of the insert. The plasmid expression construct
was grown in bulk and purified ready for transfection of COS-7
cells.
[0409] Transfection and Analysis
[0410] Each purified plasmid clone was then transfected into the
COS-7 cells using Fugene transfection reagent (Roche). Prior to
transfection the COS-7 cells were cultured on cover slips overnight
at 0.5.times.10.sup.5 per well in a 24 well plate. Cover slips were
then fixed and labelled with Xpress antibody (Invitrogen) and
detected using the anti-mouse Cy3 antibody. Images were obtained by
immunofluorescence microscopy (FIG. 14a, b, c).
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