U.S. patent application number 12/781027 was filed with the patent office on 2010-09-02 for method of diagnosis of a predisposition to develop thrombotic disease and its uses.
This patent application is currently assigned to SANOFI-AVENTIS DEUTSCHLAND GMBH. Invention is credited to Jean-Francois DELEUZE, Matthias HERRMANN, Detlef KOZIAN, Sandrine MACE, Sylvain RICARD.
Application Number | 20100221738 12/781027 |
Document ID | / |
Family ID | 34878183 |
Filed Date | 2010-09-02 |
United States Patent
Application |
20100221738 |
Kind Code |
A1 |
KOZIAN; Detlef ; et
al. |
September 2, 2010 |
METHOD OF DIAGNOSIS OF A PREDISPOSITION TO DEVELOP THROMBOTIC
DISEASE AND ITS USES
Abstract
The present invention refers to a method of diagnosis of a
predisposition to develop thrombotic disease, to test systems and
their use for the diagnosis of a predisposition to develop
thrombotic disease, to a P.sub.2X.sub.1 promoter variant and its
use for screening for an anti-thrombotic agent, and to methods for
identifying an individual that can be prophylactically or
therapeutically treated with an anti-thrombotic agent, or for
adapting a therapeutic or prophylactic dose of an anti-thrombotic
agent.
Inventors: |
KOZIAN; Detlef;
(Hattersheim, DE) ; HERRMANN; Matthias; (Hofheim,
DE) ; DELEUZE; Jean-Francois; (Combs La Ville,
FR) ; RICARD; Sylvain; (Paris, FR) ; MACE;
Sandrine; (Jouy-En-Josas, FR) |
Correspondence
Address: |
ANDREA Q. RYAN;SANOFI-AVENTIS U.S. LLC
1041 ROUTE 202-206, MAIL CODE: D303A
BRIDGEWATER
NJ
08807
US
|
Assignee: |
SANOFI-AVENTIS DEUTSCHLAND
GMBH
Frankfurt am Main
DE
|
Family ID: |
34878183 |
Appl. No.: |
12/781027 |
Filed: |
May 17, 2010 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10592692 |
May 8, 2007 |
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PCT/EP2005/002761 |
Mar 16, 2005 |
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12781027 |
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60605757 |
Aug 31, 2004 |
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Current U.S.
Class: |
435/6.16 ;
536/24.1; 536/24.31 |
Current CPC
Class: |
C12Q 1/6883 20130101;
C12Q 2600/156 20130101; A61P 7/02 20180101 |
Class at
Publication: |
435/6 ;
536/24.31; 536/24.1 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68; C07H 21/00 20060101 C07H021/00 |
Foreign Application Data
Date |
Code |
Application Number |
Mar 29, 2004 |
EP |
04007511.1 |
Claims
1. A test system comprising at least one nucleic acid probe or
oligonucleotide used for determining the sequence of at least one
allele of the P.sub.2X.sub.1 promoter at position 304, position
764, position 838, or position 1002 of SEQ ID NO:1 in a tissue
sample obtained from an individual.
2. The test system according to claim 1 comprising at least one
oligonucleotide comprising SEQ ID NO:3 or SEQ ID NO:4 for
determining the sequence of the P.sub.2X.sub.1 promoter of at least
one allele at position 304 of SEQ ID NO:1, at least one
oligonucleotide comprising SEQ ID NO:5 or SEQ ID NO:6 for
determining the sequence of the P.sub.2X.sub.1 promoter of at least
one allele at position 764 of SEQ ID NO:1, at least one
oligonucleotide comprising SEQ ID NO:7 or SEQ ID NO:8 for
determining the sequence of the P.sub.2X.sub.1 promoter of at least
one allele at position 838 of SEQ ID NO:1, or at least one
oligonucleotide comprising SEQ ID NO:9 or SEQ ID NO:10 for
determining the sequence of the P.sub.2X.sub.1 promoter of at least
one allele at position 1002 of SEQ ID NO:1.
3. A method for diagnosis of a predisposition to develop peripheral
vascular disease (PVD), stroke, prolonged reversible ischemic
neurological deficit (PRIND), transitory ischemic attack (TIA) or
myocardial infarction comprising: (a) selecting at least one
nucleic acid probe or oligonucleotide from the test system of claim
1, (b) obtaining a tissue sample from an individual, and (c)
determining the sequence of at least one allele of the
P.sub.2X.sub.1 promoter at position 304, position 764, position 838
or position 1002 of SEQ ID NO:1, wherein (i) a Tat position 304, a
C at position 764 or a C at position 1002 indicates a
predisposition to PVD, (ii) a C at position 304 or a G at position
764 indicates a predisposition to stroke, PCD or TIA, or (iii) a T
at position 838 indicates a predisposition to myocardial
infarction.
4. The test system of claim 1 further comprising at least one
anti-P.sub.2X.sub.1 antiserum, anti-P.sub.2X.sub.1 antibody, or
anti-P.sub.2X.sub.1 antibody-fragment for determining the amount of
the P.sub.2X.sub.1 protein in a tissue sample obtained from an
individual.
5. An isolated P.sub.2X.sub.1 promoter variant comprising at least
one T at position 304, C at position 764, T at position 838 or C at
position 1002 of SEQ ID NO:1.
6. The isolated P.sub.2X.sub.1 promoter variant of claim 5, wherein
the promoter variant produces a detectable product.
7. A method of screening for an anti-thrombotic agent, comprising:
(a) providing the P.sub.2X.sub.1 promoter variant according to
claim 6, (b) bringing the P.sub.2X.sub.1 promoter variant into
contact with a test compound, and (c) determining the activity of
the P.sub.2X.sub.1 promoter variant by measuring the detectable
product.
8. A method of screening for an anti-thrombotic agent, wherein the
method comprises the steps of: (a) providing a P.sub.2X.sub.1
promoter variant according to claim 5, (b) bringing the
P.sub.2X.sub.1 promoter variant into contact with a test compound,
and (c) determining the activity of the P.sub.2X.sub.1 promoter
variant.
9. The method according to claim 7 or 8 which is adapted to a
high-throughput screening of test compounds.
Description
[0001] The present invention refers to a method of diagnosis of a
predisposition to develop thrombotic disease, to test systems and
their use for the diagnosis of a predisposition to develop
thrombotic disease, to a P.sub.2X.sub.1 promoter variant and its
use for screening for an anti-thrombotic agent, and to methods for
identifying an individual that can be prophylactically or
therapeutically treated with an anti-thrombotic agent, or for
adapting a therapeutic or prophylactic dose of an anti-thrombotic
agent.
[0002] Thrombotic disease, such as peripheral vascular disease
(PVD), stroke, and myocardial infarction, can be caused by
arteriosclerotic plaques or by blood platelet aggregates. The risk
of an individual to develop thrombotic disease appears to be
influenced, at least in part, by a genetic predisposition. However,
the underlying genetic factors are not yet completely known
(Arterioscler Thromb Vasc Biol 24:1-14, 2004).
[0003] At present, only a small number of diagnostic tests are
available for determining the predisposition of an individual for
thrombotic disease. (Saffroy R, Lemoine A, Haas p, Tindiliere F,
Marion S, Debuire B. Rapid automated simultaneous screening of
(G1691A) Factor V, (G20210A) prothrombin, and (C677T)
methylenetetrahydrofolate reductase variants by multiplex PCR using
fluorescence scanning technology. Genet Test. 2002 Fall;
6(3):233-6).
[0004] However, the known tests all have the problem, that the risk
of thrombotic disease of an individual cannot be reliably
determined. Therefore there is a need for new test systems which
allow to reliably determine the predisposition of an individual of
thrombotic disease, in particular the risk of PVD, of stroke, or of
myocardial infarction.
[0005] It is an object of the present invention to provide more
reliable methods of diagnosis of a predisposition of an individual
to develop thrombotic disease. In particular, it is desirable to
provide a test system for convenient handling of a suitable method
of diagnosis, to provide a method and a test system for screening
for new anti-thrombotic agents, to provide a method of identifying
an anti-thrombotic agent for the prophylactic or therapeutic
treatment of an individual having a predisposition to develop
thrombotic disease, and to provide a method of adapting a
therapeutic or prophylactic dose of an anti-thrombotic agent.
[0006] According to a first aspect of the present invention, the
object is solved by providing a method of diagnosis of a
predisposition to develop thrombotic disease, wherein the method
comprises: (a) determining the sequence of at least one allele of
the P.sub.2X.sub.1 promoter at least at one of the positions 304,
764, 838, or 1002 of SEQ ID NO:1, and/or (b) determining the amount
of the P.sub.2X.sub.1 protein in a tissue sample obtained from an
individual.
[0007] In the present invention, it has surprisingly been found,
that the P.sub.2X.sub.1 promoter occurs in humans in the form of
P.sub.2X.sub.1 promoter variants comprising sequence variations at
the above-identified positions, which are closely correlated to a
predisposition of their carriers to develop various forms of
thrombotic disease. The present invention is based on the study
performed with 1400 patients, which is, due to the high number of
patients, very meaningful. Therefore, the present invention
provides for the first time a reliable method of diagnosis of a
predisposition to develop thrombotic disease. Preferred embodiments
of the method of diagnosis of the invention refer to the diagnosis
of particular forms of thrombotic disease which are correlated to
the presence of particular P.sub.2X.sub.1 promoter variants.
[0008] The variations of individual nucleotides in the
P.sub.2X.sub.1 promoter as claimed in the present invention occur
with a high frequency in a given population, in particular with a
frequency >1%, and can therefore be classified as so-called
single-nucleotide polymorphisms (SNPs). Therefore, they are well
suited as diagnostic markers of a predisposition of an individual
for developing thrombotic disease.
[0009] The single nucleotide polymorphisms (SNPs) in the
P.sub.2X.sub.1 promoter have an impact on the amount of the
P.sub.2X.sub.1 protein produced in the respective individual.
Therefore, according to the present invention, an altered amount of
the P.sub.2X.sub.1 protein in a tissue sample is the reliable
marker for the predisposition to develop thrombotic disease.
[0010] The P.sub.2X.sub.1 receptor is a member of the so-called
ATP-gated ion channels of the P.sub.2X receptor family. It is found
in a multitude of human tissues and cells, for example in neurons,
smooth muscle cells, and blood platelets (Gene 2001, Vol
269:167-175; Thromb Haemost 1998, Vol 103:858-866). The amino acid
sequence of the P.sub.2X.sub.1 receptor is available under the
Accession Number S71927 at the NCBI protein database.
[0011] In blood platelets, P.sub.2X.sub.1 is involved in the
mobilization of calcium ions and in the initiation of the
aggregation of platelets (J Biol Chem 1998, Vol 273:2024-2029).
Sporadically, mutations in the gene of the P.sub.2X.sub.1 receptor
leading to abnormally strong hemorrhage in their carriers have been
described (J Biol Chem 2002, Vol 275:22611-22614). In smooth muscle
cells the P.sub.2X.sub.1 receptors are responsible for
vasoconstriction. In endothelium cells the activation of
P.sub.2X.sub.1 by ATP leads to the liberation of prostacyclin and
nitrogen monoxide (NO), which exert vasodilatory and
antiproliferative effects on smooth muscle cells (TIPS 1998, Vol
19:99-107).
[0012] Recently, the sequence of the promoter of the P.sub.2X.sub.1
gene and its deletion mutants have been described (Gene 2001, Vol
269:167-175; Accession Number AF177472, NCBI Nucleotide Database).
It has been shown that certain regions of the promoter contribute
pivotally to the transcription of the P.sub.2X.sub.1 mRNA.
Furthermore, it is known that the P.sub.2X.sub.1 protein is
involved in thrombotic processes (J Exp Med 198(4):661-7,
2003).
[0013] In the present invention, reference to positions within the
nucleotide sequence of the P.sub.2X.sub.1 promoter is made
referring to SEQ ID NO:1, which corresponds to the sequence
available under the Accession Number AF177472 at the NCBI
Nucleotide Database. Preferably, the P.sub.2X.sub.1 protein
comprises the amino acid sequence according to SEQ ID NO:2, which
is available under the Accession Number S71927 at the NCBI Protein
Database.
[0014] In the present invention, previously unknown variations of
individual nucleotides in the P.sub.2X.sub.1 promoter have been
observed, which are correlated to the predisposition of an
individual to develop thrombotic disease. These variations comprise
the variation from C to T at position 304, from G to C at position
764, from T to G at position 838, or from T to C at position 1002
of SEQ ID NO:1. The order of citation of the individual
nucleotides, e.g. "from C to T at position 304" indicates the
variation from the more frequently occurring base at a given
position to the less frequently observed base at the same
position.
[0015] According to the present invention, an individual may
comprise 1, 2, 3 or 4 of the variations in the P.sub.2X.sub.1
promoter at the positions 304, 764, 838 or 1002 of SEQ ID NO:1, may
comprise no variation at the positions 304, 764, 838 or 1002 of SEQ
ID NO:1, or may comprise any combination of either the bases C or T
at position 304, G or C at position 764, T or G at position 838, or
T or C at position 1002 of SEQ ID NO:1 on either one or both
alleles of the P.sub.2X.sub.1 promoter.
[0016] In the present invention, diagnosis of a predisposition to
develop thrombotic disease comprises the determination of the risk
of an individual to develop thrombotic disease, and/or the
diagnosis of acute or chronic thrombotic disease. Thrombotic
disease comprises any form of thrombosis, in particular any form of
intravital blood plug formation in arteries or veins and any
associated clinical symptoms in any part of the human or animal
body, in particular in any organ or member. A blood plug comprises
in particular aggregates of blood platelets and/or plaque material
derived from arteriosclerotic plaques. Thrombotic disease
preferably comprises peripheral vascular disease (PVD), myocardial
infarction, preferably early myocardial infarction, and stroke, in
particular comprising transitory ischemic attack (TIA) and/or
prolonged reversible ischemic neurological deficit (PRIND). PVD
comprises in particular a common circulation problem in which the
arteries that carry blood to the legs or arms become narrowed or
clogged, and which is sometimes called peripheral arterial disease,
or PAD. Many people also refer to the condition as "hardening of
the arteries."Early myocardial infarction preferably refers to any
form of myocardial infarction occurring in people or animals at any
age prior to old age.
[0017] The methods of diagnosis of the invention preferably refer
to in vitro methods of diagnosis, wherein a tissue sample is used,
which has been removed from the body of an individual prior to
executing the method of diagnosis of the invention. Further
preferred embodiments of the invention refer to in vivo methods of
diagnosis, preferably wherein a tissue sample located within the
body of an individual is used in in-situ methods of diagnosis.
[0018] In the present invention, a tissue sample comprises
preferably cells, such as blood cells, in particular blood
platelets, red and/or white blood cells, smooth muscle cells,
striated muscle cells, epithelial cells of any epithelium,
connective tissue cells of any connective tissue, neurons, tissue
samples of the skin, mucosal tissue samples, tissue samples of any
organ, and any body fluids, in particular whole blood, or any blood
fraction, liquor, lymph, urine, saliva, and semen.
[0019] In the present invention, an individual comprises any
vertebrate animal, preferably any mammal, preferably a human, of
any age or sex, in particular a new-born, child, adolescent, adult,
or senescent human or animal, any human or animal germ-line cell, a
human or animal oocyte or spermatocyte, a human or animal
fertilized oocyte, any human or animal being prior to birth, in
particular any human or animal embryo or fetus.
[0020] In a preferred embodiment of the method of diagnosis of a
predisposition to develop thrombotic disease, the presence in a
tissue sample from an individual of at least one allele of the
P.sub.2X.sub.1 promoter comprising a variation from C to T at
position 304 of SEQ ID NO:1 is indicative of an increased risk of
peripheral vascular disease (PVD). Preferably, the presence of the
variation from C to T at position 304 on both alleles of the
P.sub.2X.sub.1 promoter is indicative of a further increased risk
of PVD.
[0021] In a further preferred embodiment, the presence in a tissue
sample of at least one allele of the P.sub.2X.sub.1 promoter
comprising a variation from G to C at position 764 of SEQ ID NO:1
is indicative of an increased risk of PVD. Preferably, the presence
of the variation from G to C at position 764 on both alleles of the
P.sub.2X.sub.1 promoter is indicative of a further increased risk
of PVD.
[0022] In further preferred embodiments, the presence of the
variation from C to T at position 304 of SEQ ID NO:1 on both
alleles of the P.sub.2X.sub.1 promoter, or the presence of the
variation from G to C at position 764 of SEQ ID NO:1 on both
alleles of the P.sub.2X.sub.1 promoter is indicative of a reduced
risk of stroke, in particular of a reduced risk of transitory
ischemic attack (TIA) or of prolonged reversible ischemic
neurological deficit (PRIND).
[0023] In further preferred embodiments, the presence of C at
position 304 of SEQ ID NO:1 instead of a T on at least one allele
of the P.sub.2X.sub.1 promoter, or the presence of G at position
764 of SEQ ID NO:1 instead of C on at least one allele of the
P.sub.2X.sub.1 promoter is indicative of an increased risk of
stroke.
[0024] In a further preferred embodiment, the presence in a tissue
sample of at least one allele of the P.sub.2X.sub.1 promoter
comprising a variation from T to G at position 838 of SEQ ID NO:1
is indicative of a reduced risk of early myocardial infarction.
Furthermore, the presence in a tissue sample of at least one allele
of the P2X1 promoter comprising a T at position 838 of SEQ ID NO:1
is indicative an increased risk of premature myocardial infarction.
Preferably, the presence of the variation from T to G at position
838 on both alleles of the P.sub.2X.sub.1 promoter is indicative of
a further reduced risk of early myocardial infarction.
[0025] In the present invention, the risk of an early myocardial
infarction is preferably the risk of women having less than 55
years of age or of men having less than 60 years of age of
suffering a myocardial infarction.
[0026] In a further preferred embodiment, the presence in a tissue
sample of at least one allele of the P.sub.2X.sub.1 promoter
comprising the variation from T to C at position 1002 of SEQ ID
NO:1 is indicative of an increased risk of PVD. Preferably, the
presence of the variation from T to C at position 1002 on both
alleles of the P.sub.2X.sub.1 promoter is indicative of a further
increased risk of PVD.
[0027] In further preferred embodiments, the sequence of the
P.sub.2X.sub.1 promoter is determined at more than one position,
preferably at two, at three, or at all positions 304, 764, 838, or
1002 of SEQ ID NO:1. Preferably, the sequence of both alleles of
the P.sub.2X.sub.1 promoter is determined at one, two, three or all
positions 304, 764, 838, or 1002 of SEQ ID NO:1.
[0028] Preferably, the sequence of the P.sub.2X.sub.1 promoter or
of fragments thereof comprising at least one of positions 304, 764,
838, or 1002 of SEQ ID NO:1 is determined using any method for the
sequence analysis of nucleic acids, in particular any DNA
sequencing protocol based on the DNA sequencing protocol according
to Sanger (Current Protocols in Molecular Biology, edited by Fred
M. Ausubel, Roger Brent, Robert E. Kingston, David D. Moore, J. G.
Seidman, John A. Smith, Kevin Struhl; Looseleaf: 0-471-650338-X;
CD-ROM: 0-471-30661-4), in particular using radioactively labeled
nucleotides or using nucleotides labeled with a fluorescent dye, in
particular involving a polymerase chain reaction (PCR), or using a
chemical sequencing method (Pyrosequencing: an accurate detection
platform for single nucleotide polymorphisms, Hum Mutat. 2002 May;
19(5):479-85), in particular using pyrosequencing (Pyrosequencing
for SNP genotyping, Methods Mol Biol. 2003; 212:189-95; Comparison
of GenFlex Tag array and Pyrosequencing in SNP genotyping, J Mol
Diagn. 2003 November; 5(4):243-9; Microarrays and genetic
epidemiology: a multipurpose tool for a multifaceted field. Genet
Epidemiol. 2002 June; 23(1):4-20, review), or using mass
spectrometry for the analysis of a nucleic acid sequence (A novel
MALDI-TOF based methodology for genotyping single nucleotide
polymorphisms, Nucleic Acids Res. 2003 Dec. 15; 31(24):e155;
Digital genotyping using molecular affinity and mass spectrometry,
Nat Rev Genet. 2003 December; 4(12):1001-8).
[0029] In addition, the sequence of the P.sub.2X.sub.1 promoter or
of fragments thereof comprising at least one of the positions 304,
764, 838, or 1002 of SEQ ID NO:1 can be determined using any
sequence-specific nucleic acid detection method allowing to detect
single-nucleotide variations, in particular any such method
involving complementary base pairing. For example, the
P.sub.2X.sub.1 promoter variants of the invention can be detected
in a polymerase chain reaction (PCR) using oligonucleotide primers
allowing the amplification of a P.sub.2X.sub.1 promoter fragment
only if either C or T is present at position 304, either G or C is
present at position 764, either T or G is present at position 838,
and/or either T or C is present at position 1002 of SEQ ID NO:1.
Methods for performing PCR are known in the art (Current Protocols
in Molecular biology; edited by Fred M. Ausubel et al., supra).
Further, a so-called TaqMan analysis can be used for the detection
of the P.sub.2X.sub.1 promoter variants of the invention (PNAS USA,
88: 7276-7280; Nucl Acid Res, 21: 3761-3766). Further, a
DNA-microarray allowing the detection of a P.sub.2X.sub.1 promoter
fragment only if either C or T is present at position 304, either G
or C is present at position 764, either T or G is present at
position 838, and/or either T or C is present at position 1002 of
SEQ ID NO:1 can be used, which the skilled person readily provides
(Microarrays and genetic epidemiology: a multipurpose tool for a
multifaceted field, Genet Epidemiol. 2002 June; 23(1):4-20;
High-density genechip oligonucleotide probe arrays, Adv Biochem Eng
Biotechnol. 2002; 77:21-42). Further, Southern hybridization assays
using nucleic acid probes allowing the detection of the
single-nucleotide polymorphisms of the P.sub.2X.sub.1 promoter
variants of the invention may be used.
[0030] Preferably, the sequence of the P.sub.2X.sub.1 promoter is
determined in a DNA sequencing protocol or in a method involving a
polymerase chain reaction, preferably in a TaqMan PCR analysis,
using at least one oligonucleotide comprising SEQ ID NO:3 or SEQ ID
NO:4 for determining the sequence of the P.sub.2X.sub.1 promoter at
position 304 of SEQ ID NO:1, using at least one oligonucleotide
comprising SEQ ID NO:5 or SEQ ID NO:6 for determining the sequence
of the P.sub.2X.sub.1 promoter at position 764 of SEQ ID NO:1,
using at least one oligonucleotide comprising SEQ ID NO:7 or SEQ ID
NO:8 for determining the sequence of the P.sub.2X.sub.1 promoter at
position 838 of SEQ ID NO:1, and/or using at least one
oligonucleotide comprising SEQ ID NO:9 or SEQ ID NO:10 for
determining the sequence of the P.sub.2X.sub.1 promoter at position
1002 of SEQ ID NO:1.
[0031] SEQ ID NO:3 corresponds to position 62490-62507 of the NCBI
sequence AC005940.3.
[0032] SEQ ID NO:4 is the antisense strang to position 472-289 of
SEQ ID NO:1.
[0033] SEQ ID NO:5 corresponds to position 618-635 in SEQ ID
NO:1.
[0034] SEQ ID NO:6 is the antisense strang to position 775-784 of
SEQ ID NO:1.
[0035] SEQ ID NO:7 corresponds to position 818-837 in SEQ ID
NO:1.
[0036] SEQ ID NO:8 is the antisense strang to position 1003-1022 of
SEQ ID NO:1
[0037] SEQ ID NO:9 corresponds to position 818-837 in SEQ ID
NO:1.
[0038] SEQ ID NO:10 is the antisense strang to position 1003-1022
in SEQ ID NO:1.
[0039] In a further preferred embodiment of the method of the
invention of diagnosis of a predisposition to develop thrombotic
disease, an altered amount of the P.sub.2X.sub.1 protein in a
tissue sample is indicative of the predisposition to develop
thrombotic disease.
[0040] In the present invention, determining the amount of the
P.sub.2X.sub.1 protein in a tissue sample preferably comprises
determining its amount or determining its presence in a tissue
sample. Preferably, determining the amount of the P.sub.2X.sub.1
protein in a tissue sample comprises any method of detecting an
individual protein, for example a Western analysis or an ELISA
assay using an anti-P.sub.2X.sub.1 antiserum or an
anti-P.sub.2X.sub.1 antibody, in particular using a monoclonal
anti-P.sub.2X.sub.1 antibody or an anti-P.sub.2X.sub.1 antibody
fragment, in particular P.sub.2X.sub.1 protein in a tissue sample
using a single-chain antibody or an enzymatically or recombinantly
produced antibody fragment (Current Protocols in Immunology; edited
by: John E. Coligan, Ada M. Kruisbeek, David H. Margulies, Ethan M.
Shevach, Waren Strober; Looseleaf: 0-471-52276-7; CD-ROM:
0371-30660-6). The invention encompasses the use of any
anti-P.sub.2X.sub.1 antiserum or anti-P.sub.2X.sub.1 antibody, in
particular any monoclonal anti-P.sub.2X.sub.1 antibody or an
anti-P.sub.2X.sub.1 antibody fragment, in particular any
single-chain antibody or enzymatically or recombinantly produced
antibody fragment in the methods and test systems of the
invention.
[0041] In preferred embodiments, the amount of the P.sub.2X.sub.1
mRNA is indicative of the amount of the P.sub.2X.sub.1 protein.
Preferably, the amount of the P.sub.2X.sub.1 protein is determined
by measuring the amount of the P.sub.2X.sub.1 mRNA. Preferably, the
presence of the P.sub.2X.sub.1 mRNA is indicative of the presence
of the P.sub.2X.sub.1 protein. Preferably, the P.sub.2X.sub.1 mRNA
in the sense as used herein comprises the complementary sequence to
at least part of the P.sub.2X.sub.1 promoter and/or encompasses at
least part of the coding region of the P.sub.2X.sub.i gene.
Preferably, the amount of a precursor mRNA or of the mature mRNA or
of a fragment thereof is determined. Preferably, the amount or
presence of the mRNA is determined in a Northern analysis (Current
Protocols in Molecular Biology; edited by Fred M. Ausubel et al.,
supra), in a PCR analysis comprising an initial step of reverse
transcribing the RNA molecule, in a differential display analysis
(Comparative gene-expression analysis; Trends Biotechnol. 1999
February; 17(2):73-8), or in a representational difference analysis
(Comparative gene-expression analysis; Trends Biotechnol. 1999,
supra).
[0042] In further preferred embodiments, the activity of the
P.sub.2X.sub.1 protein in a tissue sample is indicative of its
amount. Preferably, the activity of the P.sub.2X.sub.1 protein is
determined in a P.sub.2X.sub.1 activity assay (Journal Biol.
Chemistry, published Dec. 29, 2003 ahead of publishing as
Manuscript No M308964200). Preferably, the activity of the
P.sub.2X.sub.1 protein is determined in a human or animal cell.
[0043] According to a further aspect of the present invention, the
variations in the P.sub.2X.sub.1 promoter of the present invention
allow to provide a test system for the convenient determination of
a predisposition to develop thrombotic disease. Thus, a further
aspect of the present invention refers to a test system comprising
at least one nucleic acid probe or oligonucleotide for determining
the sequence of the P.sub.2X.sub.1 promoter at position 304,
preferably for detecting either C or T at position 304, for
determining the sequence of the P.sub.2X.sub.1 promoter at position
764, preferably for detecting either G or C at position 764, for
determining the sequence of the P.sub.2X.sub.1 promoter at position
838, preferably for detecting either T or G at position 838, or for
determining the sequence of the P.sub.2X.sub.1 promoter at position
1002, preferably for detecting either T or C at position 1002 of
SEQ ID NO:1 in a tissue sample obtained from an individual.
[0044] Preferably, the oligonucleotide is at least one PCR primer,
preferably a set of PCR primers is provided, which allows to
amplify a P.sub.2X.sub.1 promoter fragment only if either C or T is
present at position 304, either G or C is present at position 764,
either T or G is present at position 838, and/or either T or C is
present at position 1002 of SEQ ID NO:1. The skilled person readily
provides such an oligonucleotide or set of PCR primers (Current
Protocols in Molecular Biology; edited by Fred M. Ausubel et al.,
supra).
[0045] In a preferred embodiment, the test system comprises at
least one oligonucleotide comprising SEQ ID NO:3 or SEQ ID NO:4 for
determining the sequence of the P.sub.2X.sub.1 promoter at position
304 of SEQ ID NO:1, at least one oligonucleotide comprising SEQ ID
NO:5 or SEQ ID NO:6 for determining the sequence of the
P.sub.2X.sub.1 promoter at position 764 of SEQ ID NO:1, at least
one oligonucleotide comprising SEQ ID NO:7 or SEQ ID NO:8 for
determining the sequence of the P.sub.2X.sub.1 promoter at position
838 of SEQ ID NO:1, and/or at least one oligonucleotide comprising
SEQ ID NO:9 or SEQ ID NO:10 for determining the sequence of the
P.sub.2X.sub.1 promoter at position 1002 of SEQ ID NO:1.
[0046] In a further preferred embodiment, the test system comprises
a DNA-microarray, which preferably allows the detection of a
P.sub.2X.sub.1 promoter fragment only if C is present at position
304, only if T is present at position 304, only if G is present at
position 764, only if C is present at position 764, only if T is
present at position 838, only if G is present at position 838, only
if T is present at position 1002 and/or only if C is present at
position 1002 of SEQ ID NO:1, which the skilled person readily
provides (Microarrays and genetic epidemiology: a multipurpose tool
for a multifaceted field, Genet Epidemiol. 2002 June; 23(1):4-20;
High-density genechip oligonucleotide probe arrays, Adv Biochem Eng
Biotechnol. 2002; 77:21-24).
[0047] In a further preferred embodiment, the test system comprises
a labeled nucleic acid probe for use in a Southern hybridization
assay, which allows the detection of a P.sub.2X.sub.1 promoter
fragment only if C is present at position 304, only if T is present
at position 304, only if G is present at position 764, only if C is
present at position 764, only if T is present at position 838, only
if G is present at position 838, only if T is present at position
1002 and/or only if C is present at position 1002 of SEQ ID NO:1.
The skilled person is able to perform such experiments (Current
Protocols in Molecular Biology; edited by Fred M. Ausubel et al.,
supra).
[0048] Preferably, the nucleic acid probe is radioactively labeled,
fluorescently labeled, or is immunologically detectable, in
particular is digoxygenin-labeled (Roche Diagnostics GmbH,
Mannheim).
[0049] Still a further aspect of the present invention refers to
the use of the above-mentioned test system comprising at least one
nucleic acid probe or oligonucleotide for the diagnosis of a
predisposition to develop thrombotic disease. With respect to the
use of the test system, the embodiments defined above for the
method of the invention of diagnosis of a predisposition to develop
thrombotic disease also apply.
[0050] A further aspect of the present invention refers to a test
system comprising at least one anti-P.sub.2X.sub.1 antiserum,
anti-P.sub.2X.sub.1 antibody, or anti-P.sub.2X.sub.1
antibody-fragment for determining the presence, preferably the
amount, of the P.sub.2X.sub.1 protein in a tissue sample obtained
from an individual.
[0051] Preferably the test system comprises at least one monoclonal
anti-P.sub.2X.sub.1 antibody or an anti-P.sub.2X.sub.1 antibody
fragment, in particular a single-chain antibody or an antibody
fragment, preferably an enzymatically or recombinantly produced
single-chain antibody or an antibody fragment (references).
Preferably, the test system of the invention encompasses any
anti-P.sub.2X.sub.1 antiserum or anti-P.sub.2X.sub.1 antibody, in
particular any monoclonal anti-P.sub.2X.sub.1 antibody or any
anti-P.sub.2X.sub.1 antibody fragment, preferably any enzymatically
or recombinantly produced single-chain antibody or an antibody
fragment.
[0052] In the present invention, the P.sub.2X.sub.1 protein
preferably comprises the amino acid sequence according to SEQ ID
NO:2, which is available under the Accession Number S71927 at the
NCBI protein database.
[0053] Preferably, the amount of the P.sub.2X.sub.1 protein in a
tissue sample is determined using any method of detecting the
presence or measuring the amount of an individual protein, for
example in a Western analysis or in an ELISA assay.
[0054] A further aspect of the invention refers to the use of the
test system comprising at least one anti-P.sub.2X.sub.1 antiserum,
anti-P.sub.2X.sub.1 antibody, or anti-P.sub.2X.sub.1
antibody-fragment for the diagnosis of a predisposition to develop
thrombotic disease.
[0055] Further aspects of the present invention refer to the
detection of new prophylactic and therapeutic compounds for
thrombotic disease, with the help of the P.sub.2X.sub.1 promoter
variants of the invention.
[0056] A further aspect of the present invention refers to a
P.sub.2X.sub.1 promoter variant comprising a DNA fragment
comprising at least one of the positions 304, 764, 838, and/or 1002
of SEQ ID NO:1. Preferably, the P.sub.2X.sub.1 promoter variant
comprises T or C at position 304, C or G at position 764, T at
position 838, and/or C at position 1002 of SEQ ID NO:1. Preferably,
the P.sub.2X.sub.1 promoter variant comprises the regions of the
P.sub.2X.sub.1 promoter, which have been shown to contribute to the
transcription of the P.sub.2X.sub.1 mRNA (Gene 2001, Vol
269:167-175).
[0057] A further aspect of the present invention refers to a test
system comprising the P.sub.2X.sub.1 promoter variant of the
invention, wherein the promoter variant directs the synthesis of a
detectable product.
[0058] A further aspect of the present invention refers to the use
of the test system comprising the P.sub.2X.sub.1 promoter variant
of the invention for screening for an anti-thrombotic agent.
Preferably, an anti-thrombotic agent is identified by its ability
to counteract the effect of a given P.sub.2X.sub.1 promoter variant
as compared to a wild type P.sub.2X.sub.1 promoter.
[0059] According to a further aspect of the invention referring to
the detection of new prophylactic and therapeutic compounds for
thrombotic disease, wherein the P.sub.2X.sub.1 promoter variants of
the invention are used with advantage, a method of screening for an
anti-thrombotic agent is provided.
[0060] A further aspect of the present invention refers to a method
of screening for an anti-thrombotic agent, wherein the method
comprises the steps of: (a) providing a P.sub.2X.sub.1 promoter
variant of the invention, preferably a P.sub.2X.sub.1 promoter
variant comprising T or C at position 304, C or G at position 764,
T at position 838, or C at position 1002 of SEQ ID NO:1, (b)
bringing the P.sub.2X.sub.1 promoter variant into contact with a
test compound, and (c) determining the activity of the
P.sub.2X.sub.1 promoter variant.
[0061] Preferably, an anti-thrombotic agent is an active agent for
the prophylaxis or the treatment of thrombotic disease, preferably
of PVD, stroke, preferably TIA, PRIND, and/or myocardial
infarction, preferably early myocardial infarction.
[0062] In further preferred embodiments, the method of screening is
adapted to a high-throughput screening of test compounds.
[0063] Preferably, the method involves determining the activity of
the P.sub.2X.sub.1 promoter variant in the presence of a test
compound, and comparing it to the activity of the P.sub.2X.sub.1
promoter variant in the absence of the test compound. Preferably,
the method involves the use of the test system of the invention for
screening for an anti-thrombotic agent, as described herein.
[0064] A test compound is preferably a small molecule which is a
candidate for an effector molecule enhancing or inhibiting the
activity of a component of the transcriptional apparatus of a cell,
and in particular a candidate for a small molecule effector
interacting with a component of the basal transcription apparatus,
in particular interacting with the general or basal transcription
factors involved in the mechanics of binding to DNA and initiating
transcription. Preferably, the test compound is any chemical
compound, such as a naturally occurring compound or a chemically
synthesized compound that is identical or similar to a naturally
occurring compound, or any chemically synthesized compound that
does not occur in nature.
[0065] A naturally occurring compound is preferably a compound that
can be detected in or isolated from a multicellular or single-cell
organism, in particular in an animal, a plant, a fungus, a yeast, a
bacterium, or any other cell-containing organism, or in a virus. A
chemically synthesized compound that does not occur in nature is
preferably synthesized by combinatorial chemistry. Preferably, it
comprises a lead structure derived from a naturally occurring
compound, preferably from a candidate for an effector molecule
which can bind to a transcription factor or component of the basal
transcriptional apparatus of a cell.
[0066] Preferably, the test compound is a biochemical or chemical
test compound, e.g. in the form of a chemical compound library.
According to the present invention the term "chemical compound
library" refers to a plurality of chemical compounds that have been
assembled from any of multiple sources, including chemically
synthesized molecules and natural products, or that have been
generated by combinatorial chemistry techniques. Preferably, the
test compound is any low-molecular weight compound.
[0067] Advantageously, a chemical compound library is especially
suitable for high throughput screening. It may be comprised of
chemical compounds of a particular structure or compounds of a
particular creature such as a plant.
[0068] In a preferred embodiment, the activity of the
P.sub.2X.sub.1 promoter comprising T at position 304 of SEQ ID
NO:1, in particular in a cell comprising T on one or both alleles
of the P.sub.2X.sub.1 promoter, is determined and compared to the
activity of the P.sub.2X.sub.1 promoter comprising C at position
304, and an anti-thrombotic agent is identified as a test compound
which reverses the effect of T at position 304 on the activity of
the P.sub.2X.sub.1 promoter. Preferably, the thus identified
anti-thrombotic agent can be used for the prevention or the therapy
of peripheral vascular disease (PVD).
[0069] In a further preferred embodiment, the activity of the
P.sub.2X.sub.1 promoter comprising C at position 304 of SEQ ID
NO:1, in particular in a cell comprising C on one or both alleles
of the P.sub.2X.sub.1 promoter, is determined and compared to the
activity of the P.sub.2X.sub.1 promoter comprising T at position
304, and an anti-thrombotic agent is identified as a test compound
which reverses the effect of C at position 304 on the activity of
the P.sub.2X.sub.1 promoter. Preferably, the thus identified
anti-thrombotic agent can be used for the prevention or the therapy
of stroke, preferably of TIA or PRIND.
[0070] In a further preferred embodiment, the activity of the
P.sub.2X.sub.1 promoter comprising C at position 764 of SEQ ID
NO:1, in particular in a cell comprising C on one or both alleles
of the P.sub.2X.sub.1 promoter, is determined and compared to the
activity of the P.sub.2X.sub.1 promoter comprising G at position
764, and an anti-thrombotic agent is identified as a test compound
which reverses the effect of C at position 764 on the activity of
the P.sub.2X.sub.1 promoter. Preferably, the thus identified
anti-thrombotic agent can be used for the prevention or the therapy
of PVD.
[0071] In a further preferred embodiment, the activity of the
P.sub.2X.sub.1 promoter comprising G at position 764 of SEQ ID
NO:1, in particular in a cell comprising G on one or both alleles
of the P.sub.2X.sub.1 promoter, is determined and compared to the
activity of the P.sub.2X.sub.1 promoter comprising C at position
764, and an anti-thrombotic agent is identified as a test compound
which reverses the effect of G at position 764 on the activity of
the P.sub.2X.sub.1 promoter. Preferably, the thus identified
anti-thrombotic agent can be used for the prevention or the therapy
of stroke, preferably of TIA or PRIND.
[0072] In a further preferred embodiment, the activity of the
P.sub.2X.sub.1 promoter comprising T at position 838 of SEQ ID
NO:1, in particular in a cell comprising T on one or both alleles
of the P.sub.2X.sub.1 promoter, is determined and compared to the
activity of the P.sub.2X.sub.1 promoter comprising G at position
838, and an anti-thrombotic agent is identified as a test compound
which reverses the effect of T at position 838 on the activity of
the P.sub.2X.sub.1 promoter. Preferably, the thus identified
anti-thrombotic agent can be used for the prevention or the therapy
of myocardial infarction, preferably of early myocardial
infarction.
[0073] In a preferred embodiment, the activity of the
P.sub.2X.sub.1 promoter comprising C at position 1002 of SEQ ID
NO:1, in particular in a cell comprising Con one or both alleles of
the P.sub.2X.sub.1 promoter, is determined and compared to the
activity of the P.sub.2X.sub.1 promoter comprising T at position
1002, and an anti-thrombotic agent is identified as a test compound
which reverses the effect of C at position 1002 on the activity of
the P.sub.2X.sub.1 promoter. Preferably, the thus identified
anti-thrombotic agent can be used for the prevention or the therapy
of PVD.
[0074] A further aspect of the present invention refers to a method
for the manufacture of a medicament comprising at least one
anti-thrombotic agent for the prophylaxis or treatment of
thrombotic disease, preferably of PVD, stroke, in particular TIA or
PRIND, and or of myocardial infarction, preferably of early
myocardial infarction, wherein the anti-thrombotic agent is
detected using the P.sub.2X.sub.1 promoter variants of the
invention, preferably wherein the anti-thrombotic agent is detected
in the method of the invention of screening for an anti-thrombotic
agent.
[0075] A further aspect of the present invention refers to a method
of identifying an anti-thrombotic agent which can be used for the
prophylactic or therapeutic treatment of an individual having a
predisposition to develop thrombotic disease, comprising the steps
of: (a) identifying an individual having a predisposition to
develop thrombotic disease, using the method of the present
invention for identifying an individual having a predisposition to
develop thrombotic disease, and (b) identifying an anti-thrombotic
agent for the treatment of said individual, using the method of the
invention of screening for an anti-thrombotic agent.
[0076] Another aspect of the present invention refers to a method
of adapting a therapeutic or prophylactic dose of an
anti-thrombotic agent, comprising the steps of: (a) identifying an
individual having a predisposition to develop thrombotic disease,
using the method of the present invention for identifying an
individual having a predisposition to develop thrombotic disease,
(b) identifying an anti-thrombotic agent for the treatment of said
individual, using the method of the present invention of screening
for an anti-thrombotic agent, and (c) selecting a therapeutically
or prophylactically effective dose of said anti-thrombotic agent
for said individual.
[0077] In addition, the invention refers to any further uses of the
P.sub.2X.sub.1 promoter variants of the invention, wherein
thrombotic diseases or their predisposition is diagnosed, or
treatments are provided.
[0078] A further aspect of the present invention refers to the use
of the P.sub.2X.sub.1 promoter variants of the invention for the
development of a method or test system for the diagnosis of a
predisposition to develop thrombotic disease, a method or test
system for screening for an anti-thrombotic agent, a method or test
system for identifying an individual which can be treated with an
anti-thrombotic agent, or a method or test system for adapting a
therapeutic or prophylactic dose of an anti-thrombotic agent.
[0079] In the following, the invention is described in more detail
with reference to amino acid sequences, nucleic acid sequences and
the examples. Yet, no limitation of the invention is intended by
the details of the examples. Rather, the invention pertains to any
embodiment which comprises details which are not explicitly
mentioned in the examples herein, but which the skilled person
finds without undue effort.
Description of the Sequences
[0080] SEQ ID NO:1 comprises the DNA sequence of the P.sub.2X.sub.1
promoter available under the Accession No. AF177472 at the NCBI
Nucleotide Database. [0081] SEQ ID NO:2 comprises the amino acid
sequence of the P.sub.2X.sub.1 protein, available under the
Accession No. S71927 at the NCBI Protein Database. [0082] SEQ ID
NO:3 comprises the sequence of a first oligonucleotide for
determining the sequence of the P.sub.2X.sub.1 promoter at position
304 of SEQ ID NO:1. SEQ ID NO:3 corresponds to position 62490-62507
of the NCBI sequence AC005940.3. [0083] SEQ ID NO:4 comprises the
sequence of a second oligonucleotide for determining the sequence
of the P.sub.2X.sub.1 promoter at position 304 of SEQ ID NO:1,
which is located in the 3'-direction relative to SEQ ID NO:3 on the
complementary strand. SEQ ID NO:4 is the antisense strang to
position 472-289 of SEQ ID NO:1. [0084] SEQ ID NO:5 comprises the
sequence of a first oligonucleotide for determining the sequence of
the P.sub.2X.sub.1 promoter at position 764 of SEQ ID NO:1. SEQ ID
NO:5 corresponds to position 618-635 in SEQ ID NO:1. [0085] SEQ ID
NO:6 comprises the sequence of a second oligonucleotide for
determining the sequence of the P.sub.2X.sub.1 promoter at position
764 of SEQ ID NO:5, which is located in the 3'-direction relative
to SEQ ID NO:5 on the complementary strand. SEQ ID NO:6 is the
antisense strang to position 775-784 of SEQ ID NO:1. [0086] SEQ ID
NO:7 comprises the sequence of a first oligonucleotide for
determining the sequence of the P.sub.2X.sub.1 promoter at position
838 of SEQ ID NO:1. SEQ ID NO:7 corresponds to position 818-837 in
SEQ ID NO:1. [0087] SEQ ID NO:8 comprises the sequence of a second
oligonucleotide for determining the sequence of the P.sub.2X.sub.1
promoter at position 838 of SEQ ID NO:1, which is located in the
3'-direction relative to SEQ ID NO:7 on the complementary strand.
SEQ ID NO:8 is the antisense strang to position 1003-1022 of SEQ ID
NO:1. [0088] SEQ ID NO:9 comprises the sequence of a first
oligonucleotide for determining the sequence of the P.sub.2X.sub.1
promoter at position 1002 of SEQ ID NO:1. SEQ ID NO:9 corresponds
to position 818-837 in SEQ ID NO:1. [0089] SEQ ID NO:10 comprises
the sequence of a second oligonucleotide for determining the
sequence of the P.sub.2X.sub.1 promoter at position 1002 of SEQ ID
NO:1, which is located in the 3'-direction relative to SEQ ID NO:9
on the complementary strand. SEQ ID NO:10 is the antisense strang
to position 1003-1022 in SEQ ID NO:1.
DESCRIPTION OF THE EXAMPLES
Abbreviations Used for the P.sub.2X.sub.1 Promoter Variants
[0090] The following abbreviations are used, wherein the indicated
positions refer to the positions of the nucleotides in SEQ ID NO:1:
[0091] P.sub.2X.sub.1 C3040 refers to a group of persons carrying a
cytidine (C) at position 304 on both alleles of the P.sub.2X.sub.1
gene. These persons are homocygous for this P.sub.2X.sub.1 variant.
[0092] P.sub.2X.sub.1 C304T refers to a group of persons carrying a
cytidine (C) at position 304 on one allele of the P.sub.2X.sub.1
gene and a thymidine (T) at position 304 on the other allele of the
P.sub.2X.sub.1 gene. These persons are heterocygous for this
P.sub.2X.sub.1 variant. [0093] P.sub.2X.sub.1 T304T refers to a
group of persons carrying a thymidine (T) at position 304 on both
alleles of the P.sub.2X.sub.1 gene. These persons are homocygous
for this P.sub.2X.sub.1 variant. [0094] P.sub.2X.sub.1 G764G refers
to a group of persons carrying a guanosine (G) at position 764 on
both alleles of the P.sub.2X.sub.1 gene. These persons are
homocygous for this P.sub.2X.sub.1 variant. [0095] P.sub.2X.sub.1
G764G refers to a group of persons carrying a cytidine (C) at
position 764 on one allele of the P.sub.2X.sub.1 gene and carrying
a guanosine (G) at position 764 on the other allele of the
P.sub.2X.sub.1 gene. These persons are heterocygous for this
P.sub.2X.sub.1 variant. [0096] P.sub.2X.sub.1 C764C refers to a
group of persons carrying a cytidine (C) at position 764 on both
alleles of the P.sub.2X.sub.1 gene. These persons are homocygous
for this P.sub.2X.sub.1 variant. [0097] P.sub.2X.sub.1 T838T refers
to a group of persons carrying a thymidine (T) at position 838 on
both alleles of the P.sub.2X.sub.1 gene. These persons are
homocygous for this P.sub.2X.sub.1 variant. [0098] P.sub.2X.sub.1
T838G refers to a group of persons carrying a thymidine (T) at
position 838 on one allele of the P.sub.2X.sub.1 gene and a
guanosine (G) at position 838 on the other allele of the
P.sub.2X.sub.1 gene. These persons are heterocygous for this
P.sub.2X.sub.1 variant. [0099] P.sub.2X.sub.1 G838G refers to a
group of persons carrying a guanosine (G) at position 838 on both
alleles of the P.sub.2X.sub.1 gene. These persons are homocygous
for this P.sub.2X.sub.1 variant. [0100] P.sub.2X.sub.1 T1002T
refers to a group of persons carrying a thymidine (T) at position
1002 on both alleles of the P.sub.2X.sub.1 gene. These persons are
homocygous for this P.sub.2X.sub.1 variant. [0101] P.sub.2X.sub.1
T1002C refers to a group of persons carrying a thymidine (T) at
position 1002 on one allele of the P.sub.2X.sub.1 gene and a
cytidine (C) at position 1002 on the other allele of the
P.sub.2X.sub.1 gene. These persons are heterocygous for this
P.sub.2X.sub.1 variant. [0102] P.sub.2X.sub.1 C1002C refers to a
group of persons carrying a cytidine (C) at position 1002 on both
alleles of the P.sub.2X.sub.1 gene. These persons are homocygous
for this P.sub.2X.sub.1 variant.
[0103] The four single-nucleotide polymorphisms (SNPs) identified
in the P.sub.2X.sub.i promoter regions were investigated in a group
of 1404 patients, in order to determine the association of these
genetic variations with the clinical symptoms of these
patients.
Detection of Single-Nucleotide Polymorphisms (SNPS) by DNA Sequence
Analysis
[0104] Genomic regions within the promoter of the P.sub.2X.sub.i
gene were amplified using the following oligonucleotide primers:
[0105] For the detection of the nucleotide variation from C to T at
position 304 in the P.sub.2X.sub.1 promoter sequence, the following
primers were used, which are derived from the sequence AC005940.3:
[0106] AC005940.3 is the number of a sequence deposited in the NCBI
database of a genomic clone, which comprises sequences upstream of
the P.sub.2X.sub.1 promoter. Based on that sequence, it is possible
to design an oligonucleotide which can be used for the
amplification of that region which allows identification of
P.sub.2X.sub.1 promoter variants at position 304. In contrast,
AF177472.1 is the number of that sequence of the P.sub.2X.sub.1
gene which has been deposited in the NCBI database and which
comprises the promoter region and parts of the coding region.
TABLE-US-00001 [0106] 5'-GAAAAGCCCATGACACCC-3'
5'-CAACACGGGACAGAGAAC-3'
[0107] 2. For the detection of the nucleotide variation from G to C
at position 764 in the P.sub.2X.sub.1 promoter sequence, the
following primers were used, which were derived from SEQ ID
NO:1:
TABLE-US-00002 [0107] 5'-GATGTGGTGCTGGTCTTG-3'
5'-GCTGGCATCTCTATCCCCCA-3'
[0108] 3. For the detection of the nucleotide variation from T to G
at position 838 in the P.sub.2X.sub.1 promoter sequence, the
following primers were used, which were derived from SEQ ID
NO:1:
TABLE-US-00003 [0108] 5'-GGAACTCAGAGCCTCCTTCC-3'
5'-GGCAAGATGGAGCTCTGGCC-3'
[0109] 4. For the detection of the nucleotide variation from T to C
at position 1002 in the P.sub.2X.sub.1 promoter sequence, the
following primers were used, which were derived from SEQ ID
NO:1:
TABLE-US-00004 [0109] 5'-GGAACTCAGAGCCTCCTTCC-3'
5'-GGCAAGATGGAGCTCTGGCC-3'
[0110] The genomic regions were amplified using the
above-identified oligonucleotide primers in the PCR protocol
indicated below.
[0111] The reagents used were from Applied Biosystems (Foster City,
USA): 20 ng genomic DNA; 1 unit TaqGold DNA polymerase; 1.times.Taq
polymerase buffer; 500 .mu.M dNTPs; 2.5 mM MgCl.sub.2; 200 nM of
each amplification primer pair (sequences under 1. and 2.);
H.sub.2O ad 5 .mu.l.
PCR amplification program for genotyping 1 cycle comprising:
95.degree. C. for 10 min; followed by 2 cycles, each comprising:
95.degree. C. for 30 sec, followed by 70.degree. C. for 30 sec;
followed by 2 cycles, each comprising: 95.degree. C. for 30 sec,
followed by 65.degree. C. for 30 sec;
[0112] followed by 2 cycles, each comprising: 95.degree. C. for 30
sec, followed by 60.degree. C. for 30 sec; followed by 40 cycles,
each comprising: 95.degree. C. for 30 sec, followed by 56.degree.
C. for 30 sec, followed by 72.degree. C. for 30 sec; followed by 1
cycle comprising: 72.degree. C. for 10 min, followed by 4.degree.
C. for 30 sec.
[0113] PCR Amplification Program for Sequencing [0114] 1 cycle
comprising: 96.degree. C. for 2 min; [0115] followed by 30 cycles,
each comprising: 96.degree. C. for 10 sec, followed by 55.degree.
C. for 10 sec, followed by 65.degree. C. for 4 min; [0116] followed
by 1 cycle comprising: 72.degree. C. for 7 min, followed by
4.degree. C. for 30 sec.
Analysis of the Sequencing Products
[0117] The sequences were first analyzed using the Sequence
Analysis Software (Applied Biosystems, Foster City, USA) in order
to obtain crude data. The crude data were processed using Phred,
Phrap, Polyphred and Consed. Phred, Phrap, Polyphred and Consed are
software written by Phil Green of the Washington University
(http://www.genome.washington.edu).
Example
Results Obtained with a Group of 1404 Patients
[0118] Table 1 indicates the characteristics of the group of
patients in which the genetic variants at the positions 304, 764,
838 and 1002 of SEQ ID NO:1 in the promoter region of the
P.sub.2X.sub.1 were analyzed.
TABLE-US-00005 TABLE 1 n % Total 1404 Gender Female 406 28.9 Male
998 71.1 Age* 62.7 (30.0-90.7) BMI* 27.8 (Body Mass (16.7-57.1)
Index) High blood 834 59.4 pressure Smokers 923 65.7 Angina
pectoris 210 62.7 Diabetics (ADA) 445 31.7 Cardiac 579 41.0
infarction CAD (>20% 1087 78.8 stenosis) Stroke 106 7.5 *Medians
and Quartiles (Q1-Q3)
[0119] Table 2 indicates the distribution of P.sub.2X.sub.1
variants in the analyzed group of patients referring to the
indicated positions according to SEQ ID NO:1 in the P.sub.2X.sub.1
promoter region.
TABLE-US-00006 TABLE 2 not P.sub.2X.sub.1 C304C P.sub.2X.sub.1
C304T P.sub.2X.sub.1 T304T determined Patients (n) 674 596 119 15
P.sub.2X.sub.1 G764G P.sub.2X.sub.1 G764C P.sub.2X.sub.1 C764C
Patients (n) 685 595 119 5 P.sub.2X.sub.1 T838T P.sub.2X.sub.1
T838G P.sub.2X.sub.1 G838G Patients (n) 1128 243 17 16
P.sub.2X.sub.1 P.sub.2X.sub.1 P.sub.2X.sub.1 T1002T T1002C C1002C
Patients (n) 410 669 299 17
[0120] Table 3 indicates the association of the indicated
P.sub.2X.sub.1 variants according to SEQ ID NO:1 with the clinical
endpoints in the analyzed group of patients. The number of patients
in which the indicated clinical endpoint was observed is given in
percent.
TABLE-US-00007 TABLE 3 P.sub.2X.sub.1 genotype P.sub.2X.sub.1 C304C
P.sub.2X.sub.1 C304T P.sub.2X.sub.1 T304T PVD 7.27% 9.90% 13.45%
Stroke/PRIND/TIA 7.27% 8.89% 2.52% P.sub.2X.sub.1 G764G
P.sub.2X.sub.1 G764C P.sub.2X.sub.1 C764C PVD 7.01% 10.08% 13.45%
Stroke/PRIND/TIA 7.30% 8.91% 2.52% P.sub.2X.sub.1 T838T
P.sub.2X.sub.1 T838G P.sub.2X.sub.1 G838G Early myocardial 20.12%
13.99% 5.88% infarction P.sub.2X.sub.1 T1002T P.sub.2X.sub.1 T1002C
P.sub.2X.sub.1 C1002C PVD 5.73% 9.72% 11.04%
[0121] In the analyzed group of patients an increased risk of PVD
was observed, depending on the presence and the number of alleles
comprising a T at position 304 or, respectively, the presence and
the number of alleles comprising a C at position 764 in the
promoter of the P.sub.2X.sub.1 gene. In addition, a reduced risk of
stroke/PRIND/TIA was observed in patients carrying P.sub.2X.sub.1
T304T or P.sub.2X.sub.1 C764C. An increased risk for the occurrence
of an early myocardial infarction (defined as myocardial infarction
in women <55 years and men <60 years) depends on the presence
and the number of alleles comprising a T at position 838 in the
promoter of the P.sub.2X.sub.1 gene. Further, an increased risk for
the occurrence of PVD depends on the presence and the number of
alleles comprising a C at position 1002 in the promoter of the
P.sub.2X.sub.1 gene. On the basis of these association analyses it
can be concluded that genetic variations in the promoter region of
the P.sub.2X.sub.1 gene have an important impact on the occurrence
and the frequency of cardiovascular and thrombotic diseases.
Sequence CWU 1
1
1011506DNAHomo sapiens 1ggattgatta attgacaagg agagactgac ctgggtgctg
gaaggggcca tgggcagcct 60tctgtgggtg acccccattc agacaggctg ccgggattcc
cagccccagg gcctggctcc 120tgcccagagc acttccagct catggctcgc
cagcaagaag actccttatc agccttaagg 180gtggggcggc tccgacgaca
gggccgtggg ggctcgccag ggaggcccct gcttccagct 240tgaacctcca
gtaccacccc gggtgagctt gggcaactca tttctcttct ctgagcttgg
300tttcctcatc ttcaaaacga ggggtggggc tggggaggcc tccagctctg
aggagccaac 360gtgggaccct ctgcccaccc caaacccctg tgttcagggc
ccgagctggg ggtgggaagg 420gaaggcaggg actgcagagg tgctgtgccc
ccgactcatt gggggcctcc agttctctgt 480cccgagttgc tgagacccat
cccctgtgag cctcgaccta gaaggaacag cccttattac 540cccaatttac
agatgaggca acaggctcgg agaggcaagg tgacacccag cccccacagc
600caagaagtgg cagagccagg gatctccgag gtcaggctct ctcggctggt
cttgggcccc 660ccatggcacc ggtgacggat gtggtgctgg tcttggctgg
gcacctgcca cctctctccc 720tctgatggtg gcccccggca ggacagacag
tgggagagga gaggtggggg atagagatgc 780cagctcagca ccgaggttga
ccgggcacgg ccaggctgga actcagagcc tccttcctct 840ctgccttgct
cgctgcagac ccccagggac gaagcagcca accctggtgg gggagggtgg
900agggtggtgg atggggctgg ggatggaggt ctcattttgg cagtggaggg
gagtcgcggg 960gagtccccta atctgaggag actccagctt cccccaggcc
ctggccagag ctccatcttg 1020ccaggttttg gggggaggat aacttgagga
gtcgactgag agctttatct ttgcccctgt 1080gacgggtggc ctgtggtttc
ctgccaacaa ctcctgtttc cggaggccca acaaggccca 1140cgcagagcca
ggaggggcag tggggctggg cctgggtggc cccaccagcc ccgccccatc
1200tatctttggg aatttatttg tccatgggcg aggctggcct gcagtctgtt
gccttccagg 1260ggccaagagc tgctctgatc acccagggat tctctctcca
acccaagtgc ctccagctga 1320cctctggctc ctgtcctctg gctccacctg
caccgccctg ctcttcctaa ggggccagga 1380agcccccaga agctctacca
tcgacgtggg tggtggcacc cggctcaccc tgagagcaga 1440ggccgtgcag
ggggctcagt tctgagcccc agccggccca ccatggcacg gcggttccag 1500gaggag
15062399PRTHomo sapiens 2Met Ala Arg Arg Phe Gln Glu Glu Leu Ala
Ala Phe Leu Phe Glu Tyr1 5 10 15Asp Thr Pro Arg Met Val Leu Val Arg
Asn Lys Lys Val Gly Val Ile 20 25 30Phe Arg Leu Ile Gln Leu Val Val
Leu Val Tyr Val Ile Gly Trp Val 35 40 45Phe Leu Tyr Glu Lys Gly Tyr
Gln Thr Ser Ser Gly Leu Ile Ser Ser 50 55 60Val Ser Val Lys Leu Lys
Gly Leu Ala Val Thr Gln Leu Pro Gly Leu65 70 75 80Gly Pro Gln Val
Trp Asp Val Ala Asp Tyr Val Phe Pro Ala Gln Gly 85 90 95Asp Asn Ser
Phe Val Val Met Thr Asn Phe Ile Val Thr Pro Lys Gln 100 105 110Thr
Gln Gly Tyr Cys Ala Glu His Pro Glu Gly Gly Ile Cys Lys Glu 115 120
125Asp Ser Gly Cys Thr Pro Gly Lys Ala Lys Arg Lys Ala Gln Gly Ile
130 135 140Arg Thr Gly Lys Cys Val Ala Phe Asn Asp Thr Val Lys Thr
Cys Glu145 150 155 160Ile Phe Gly Trp Cys Pro Val Glu Val Asp Asp
Asp Ile Pro Arg Pro 165 170 175Ala Leu Leu Arg Glu Ala Glu Asn Phe
Thr Leu Phe Ile Lys Asn Ser 180 185 190Ile Ser Phe Pro Arg Phe Lys
Val Asn Arg Arg Asn Leu Val Glu Glu 195 200 205Val Asn Ala Ala His
Met Lys Thr Cys Leu Phe His Lys Thr Leu His 210 215 220Pro Leu Cys
Pro Val Phe Gln Leu Gly Tyr Val Val Gln Glu Ser Gly225 230 235
240Gln Asn Phe Ser Thr Leu Ala Glu Lys Gly Gly Val Val Gly Ile Thr
245 250 255Ile Asp Trp His Cys Asp Leu Asp Trp His Val Arg His Cys
Arg Pro 260 265 270Ile Tyr Glu Phe His Gly Leu Tyr Glu Glu Lys Asn
Leu Ser Pro Gly 275 280 285Phe Asn Phe Arg Phe Ala Arg His Phe Val
Glu Asn Gly Thr Asn Tyr 290 295 300Arg His Leu Phe Lys Val Phe Gly
Ile Arg Phe Asp Ile Leu Val Asp305 310 315 320Gly Lys Ala Gly Lys
Phe Asp Ile Ile Pro Thr Met Thr Thr Ile Gly 325 330 335Ser Gly Ile
Gly Ile Phe Gly Val Ala Thr Val Leu Cys Asp Leu Leu 340 345 350Leu
Leu His Ile Leu Pro Lys Arg His Tyr Tyr Lys Gln Lys Lys Phe 355 360
365Lys Tyr Ala Glu Asp Met Gly Pro Gly Ala Ala Glu Arg Asp Leu Ala
370 375 380Ala Thr Ser Ser Thr Leu Gly Leu Gln Glu Asn Met Arg Thr
Ser385 390 395318DNAHomo sapiens 3gaaaagccca tgacaccc 18418DNAHomo
sapiens 4caacacggga cagagaac 18518DNAHomo sapiens 5gatgtggtgc
tggtcttg 18620DNAHomo sapiens 6gctggcatct ctatccccca 20720DNAHomo
sapiens 7ggaactcaga gcctccttcc 20820DNAHomo sapiens 8ggcaagatgg
agctctggcc 20920DNAHomo sapiens 9ggaactcaga gcctccttcc
201020DNAHomo sapiens 10ggcaagatgg agctctggcc 20
* * * * *
References