EP1100963A2 - Polymorphismes du gene ccr-2 de l'homme - Google Patents

Polymorphismes du gene ccr-2 de l'homme

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Publication number
EP1100963A2
EP1100963A2 EP99934896A EP99934896A EP1100963A2 EP 1100963 A2 EP1100963 A2 EP 1100963A2 EP 99934896 A EP99934896 A EP 99934896A EP 99934896 A EP99934896 A EP 99934896A EP 1100963 A2 EP1100963 A2 EP 1100963A2
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European Patent Office
Prior art keywords
ccr
positions
gene
åhism
polymo
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EP99934896A
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German (de)
English (en)
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John Craig Smith
Rakesh Anand
John Edward Norris Morten
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AstraZeneca AB
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AstraZeneca AB
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Priority claimed from GBGB9816193.8A external-priority patent/GB9816193D0/en
Priority claimed from GBGB9901844.2A external-priority patent/GB9901844D0/en
Application filed by AstraZeneca AB filed Critical AstraZeneca AB
Publication of EP1100963A2 publication Critical patent/EP1100963A2/fr
Withdrawn legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P19/00—Drugs for skeletal disorders
    • A61P19/02—Drugs for skeletal disorders for joint disorders, e.g. arthritis, arthrosis
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P29/00—Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/172—Haplotypes

Definitions

  • This invention relates to polymorphisms in the human CCR-2 gene and corresponding novel allelic polypeptides encoded thereby.
  • the invention also relates to methods and materials for analysing allelic variation in the CCR-2 gene, and to the use of CCR-2 polymorphism in the diagnosis and treatment of CCR-2 ligand mediated diseases such as rheumatoid arthritis and other inflammatory diseases.
  • MCP-1 acts through the CCR-2 receptor (also known as the MCP-1 receptor).
  • MCP- 2 and MCP-3 may also act, at least in part, through the MCP-1 receptor.
  • MCP-1 is a member of the chemokine family of pro-infiammatory cytokines which mediate leukocyte chemotaxis and activation.
  • MCP-1 is a C-C chemokine which is one of the most potent and selective T-cell and monocyte chemoattractant and activating agents known.
  • MCP-1 has been implicated in the pathophysiology of a large number of inflammatory diseases including rheumatoid arthritis, glomerular nephritides, lung fibrosis, restenosis (International Patent Application WO 94/09128), alveolitis (Jones et al., 1992, J. Immunol., 149, 2147) and asthma.
  • Other disease areas where MCP-1 is thought to play a part in their pathology are atherosclerosis (e.g. Koch et al., 1992, J. Clin. Invest., 90, 772-779), psoriasis (Deleuran et al, 1996, J. Dermatological Science, 13,.
  • An MCP-1 inhibitor may also be useful to treat stroke, reperfusion injury, ischemia, myocardial infarction and transplant rejection.
  • CCR-2 polypeptide is known to exist in 2 isoforms, CCR-2A and CCR-2B, which are alternatively spliced variants of a single CCR-2 gene.
  • the reader is referred to the following publications: Organization and differential expression of the Human Monocyte Chemoattractant Protein 1 Receptor Gene: Evidence for the role of the carboxy-terminal tail in receptor trafficking, LM Wong et al J Biol Chem 272,1038-1045 (1997), see Figure 1 therein in particular; and International patent application WO 95/19436, Charo et al.
  • a chemokine receptor CCR2 allele delays HIV-1 disease progression and is associated with a CCR5 promoter mutation, LG Kostrikis et al Nature Medicine 4, 350-353 (1998); and The role of CCR5 and CCR2 polymorphisms in HIV-1 transmission and disease progression, NL Michael et al Nature Medicine 3, 1160-1162 (1997).
  • the CCR-2 gene has been cloned and published as a EMBL Accession number:
  • CCR-2 The genomic sequence of CCR-2 is contained in the B AC (Bacterial Artificial Chromosome) clone, 11 OP 12 (Research Genetics), which is published as EMBL Accession number U95626 (143068 bp). All positions herein of polymorphisms in the promoter region relate to the position therein unless stated or otherwise apparent from the context.
  • B AC Bacterial Artificial Chromosome
  • Point mutations in polypeptides will be referred to as follows: natural amino acid (using 1 or 3 letter nomenclature) , position, new amino acid.
  • natural amino acid using 1 or 3 letter nomenclature
  • position new amino acid.
  • D25K or “Asp25Lys” means that at position 25 an aspartic acid (D) has been changed to lysine (K).
  • K lysine
  • the present invention is based on the discovery of two single nucleotide polymorphisms (SNPs) in the coding sequence of the CCR-2 gene and 11 SNPs in the promoter sequence of the CCR-2 gene.
  • SNPs single nucleotide polymorphisms
  • a method for the diagnosis of a single nucleotide polymorphism in CCR-2 in a human comprises determining the sequence of the nucleic acid of the human at one or more of positions 2385 and 2649 in the coding sequence of the CCR-2 gene as defined by the positions in EMBL ACCESSION NO.
  • human includes both a human having or suspected of having a CCR-2 ligand mediated disease and an asymptomatic human who may be tested for predisposition or susceptibility to such disease. At each position the human may be homozygous for an allele or the human may be a heterozygote.
  • single nucleotide polymorphism includes single nucleotide substitution, nucleotide insertion and nucleotide deletion which in the case of insertion and deletion includes insertion or deletion of one or more nucleotides at a position of a gene.
  • the method for diagnosis described herein is one in which the single nucleotide polymorphism at position 2385 is presence of C and/or T.
  • the method for diagnosis described herein is one in which the single nucleotide polymorphism at position 2649 is presence of G and/or A. In another embodiment of the invention preferably the method for diagnosis described herein is one in which the single nucleotide polymorphism at position 40915 is presence of A and/or T.
  • the method for diagnosis described herein is one in which the single nucleotide polymorphism at position 41047 is the presence or absence of an insertion of AC A.
  • the method for diagnosis described herein is one in which the single nucleotide polymorphism at position 41058 is the presence of C and/or A. In another embodiment of the invention preferably the method for diagnosis described herein is one in which the single nucleotide polymorphism at position 41507 is the presence of C and/or A.
  • the method for diagnosis described herein is one in which the single nucleotide polymo ⁇ hism at position 41768 is the presence of A and/or T.
  • the method for diagnosis described herein is one in which the single nucleotide polymorphism at position 42401 is the presence of A and/or G.
  • the method for diagnosis described herein is one in which the single nucleotide polymorphism at position 42598 is presence or absence or an insertion of T.
  • the method for diagnosis described herein is one in which the single nucleotide polymorphism at position 42673 is the presence of G and/or A. In another embodiment of the invention preferably the method for diagnosis described herein is one in which the single nucleotide polymo ⁇ hism at position 42723 is the presence of C and/or A.
  • the method for diagnosis described herein is one in which the single nucleotide polymo ⁇ hism at position 42874 is the presence of A and/or G.
  • the method for diagnosis described herein is one in which the single nucleotide polymo ⁇ hism at position 43018 is the presence of A and/or T.
  • the method for diagnosis is preferably one in which the sequence is determined by a method selected from amplification refractory mutation system and restriction fragment length polymo ⁇ hism.
  • Allelic variation at position 2385 consists of a single base substitution from C (the published base), preferably to T.
  • Allelic variation at position 2649 consists of a single base substitution from G (the published base), preferably to A.
  • Allelic variation at position 40915 consists of a single base substitution from A (the published base), preferably to T.
  • Allelic variation at position 41047 consists of the absence of insertion (the published case), preferably to the insertion of AC A.
  • Allelic variation at position 41058 consists of a single base substitution from C (the published base), preferably to A.
  • Allelic variation at position 41507 consists of a single base substitution from C (the published base), preferably to A.
  • Allelic variation at position 41768 consists of a single base substitution from A (the published base), preferably to T.
  • Allelic variation at position 42401 consists of a single base substitution from A (the published base), preferably to G.
  • Allelic variation at position 42598 consists of a single base substitution from the absence of insertion (the published case), preferably to the insertion of T.
  • Allelic variation at position 42673 consists of a single base substitution from G (the published base), preferably to A.
  • Allelic variation at position 42723 consists of a single base substitution from C (the published base), preferably to A.
  • Allelic variation at position 42874 consists of a single base substitution from A (the published base), preferably to G.
  • Allelic variation at position 43018 consists of a single base substitution from A (the published base), preferably to T.
  • the status of the individual may be determined by reference to allelic variation at any one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve or thirteen positions.
  • test sample of nucleic acid is conveniently a sample of blood, bronchoalveolar lavage fluid, sputum, or other body fluid or tissue obtained from an individual. It will be appreciated that the test sample may equally be a nucleic acid sequence corresponding to the sequence in the test sample, that is to say that all or a part of the region in the sample nucleic acid may firstly be amplified using any convenient technique e.g. PCR, before analysis of allelic variation.
  • allelic variation requires a mutation discrimination technique, optionally an amplification reaction and optionally a signal generation system.
  • Table 1 lists a number of mutation detection techniques, some based on the PCR. These may be used in combination with a number of signal generation systems, a selection of which is listed in Table 2. Further amplification techniques are listed in Table 3. Many current methods for the detection of allelic variation are reviewed by Nollau et al, Clin. Chem.
  • Fluorescence Fluorescence: FRET, Fluorescence quenching, Fluorescence polarisation - United Kingdom Patent No. 2228998 (Zeneca Limited)
  • Preferred mutation detection techniques include ARMSTM, ALEXTM, COPS, Taqman, Molecular Beacons, RFLP, and restriction site based PCR and FRET techniques.
  • Particularly preferred methods include ARMSTM and RFLP based methods.
  • ARMSTM is an especially preferred method.
  • the diagnostic methods of the invention are used to assess the efficacy of therapeutic compounds in the treatment of CCR-2 ligand mediated diseases.
  • Assays for example reporter-based assays, may be devised to detect whether one or more of the above polymo ⁇ hisms affect transcription levels and/or message stability.
  • allelic variants of the CCR-2 gene may therefore exhibit differences in their ability to regulate protein biosynthesis under different physiological conditions and will display altered abilities to react to different diseases.
  • differences in protein regulation arising as a result of allelic variation may have a direct effect on the response of an individual to drug therapy.
  • the diagnostic methods of the invention may be useful both to predict the clinical response to such agents and to determine therapeutic dose.
  • the diagnostic methods of the invention are used to assess the predisposition and/or susceptibility of an individual to diseases mediated by CCR-2 ligands. This may be particularly relevant in the development of rheumatoid arthritis and cardiovascular disease and the present invention may be used to recognise individuals who are particularly at risk from developing these conditions.
  • the diagnostic methods of the invention are used in the development of new drug therapies which selectively target one or more allelic variants of the CCR-2 gene. Identification of a link between a particular allelic variant and predisposition to disease development or response to drug therapy may have a significant impact on the design of new drugs. Drugs may be designed to regulate the biological activity of variants implicated in the disease process whilst minimising effects on other variants. In a further diagnostic aspect of the invention the presence or absence of variant nucleotides is detected by reference to the loss or gain of, optionally engineered, sites recognised by restriction enzymes. In the accompanying Example 2 we provide details of convenient engineered restriction enzyme sites that are lost or gained as a result of a polymo ⁇ hism of the invention.
  • a human CCR2 gene or its complementary strand comprising a polymo ⁇ hism corresponding with one or more of positions 2385 and 2649 as defined by the positions in EMBL ACCESSION NO. U 80924 and in which there is a T at position 2385 and an A at position 2649 or a fragment thereof of at least 20 bases comprising at least one of the polymo ⁇ hisms. Fragments are at least 17 bases, more preferably at least 20 bases, more preferably at least
  • a human CCR2 gene or its complementary strand comprising a polymo ⁇ hism corresponding with one or more positions 40915, 41047, 41058, 41507, 41768, 42401, 42598, 42673, 42723, 42874 and 43018 in the promoter sequence of the CCR-2 gene as defined by the positions in the EMBL
  • ACCESSION NO. U95626 and in which there is a T at position 40915, an insertion of ACA at position 41047, an A at position 41058, an A at position 41507, a T at position 41768, a G at 42401, the insertion of a T at position 42598, an A at position 42673, an A at position 42723, a G at position 42874 ,or a T at position 43018 or a fragment thereof of at least 20 bases comprising at least one polymo ⁇ hism.
  • Fragments are at least 17 bases, more preferably at least 20 bases, more preferably at least 30 bases.
  • nucleotide sequence comprising a human CCR2 gene or its complementary strand or an antisense sequence thereto comprising a polymo ⁇ hism at one or more of: positions 2385 and 2649 as defined by the positions in EMBL ACCESSION NO. U 80924 and in which there is a T at position 2385 and an A at position 2649; or positions 40915, 41047, 41058, 41507, 41768, 42401, 42598, 42673, 42723, 42874 and 43018 in the promoter sequence of the CCR-2 gene as defined by the positions in the EMBL ACCESSION NO.
  • an example antisense expression construct can be readily constructed for instance using the pREPlO vector (Invitrogen Co ⁇ oration).
  • Transcripts are expected to inhibit translation of the gene in cells transfected with this type construct.
  • Antisense transcripts are effective for inhibiting translation of the native gene transcript, and capable of inducing the effects (e.g., regulation of tissue physiology) herein described.
  • Oligonucleotides which are complementary to and hybridizable with any portion of novel gene mRNA disclosed herein are contemplated for therapeutic use.
  • Expression vectors containing random oligonucleotide sequences derived from previously known polynucleotides are transformed into cells. The cells are then assayed for a phenotype resulting from the desired activity of the oligonucleotide. Once cells with the desired phenotype have been identified, the sequence of the oligonucleotide having the desired activity can be identified.
  • Identification may be accomplished by recovering the vector or by polymerase chain reaction (PCR) amplification and sequencing the region containing the inserted nucleic acid material.
  • nucleotide molecules can be synthesized for antisense therapy. These antisense molecules may be DNA, stable derivatives of DNA such as phosphorothioates or methylphosphonates, RNA, stable derivatives of RNA such as 2'-O- alkylRNA, or other oligonucleotide mimetics.
  • Antisense molecules may be introduced into cells by microinjection, liposome encapsulation or by expression from vectors harboring the antisense sequence.
  • a computer readable medium comprising at least one novel polynucleotide sequence of the invention stored on the medium.
  • the computer readable medium may be used, for example, in homology searching, mapping, haplotyping, genotyping or pharmacogenetic analysis or any other bioinformatic analysis.
  • the reader is referred to Bioinformatics, A practical guide to the analysis of genes and proteins, Edited by A D Baxevanis & B F F Ouellette, John Wiley & Sons, 1988.
  • Any computer readable medium may be used, for example, compact disk, tape, floppy disk, hard drive or computer chips.
  • polynucleotide sequences of the invention or parts thereof, particularly those relating to and identifying the single nucleotide polymo ⁇ hisms identified herein represent a valuable information source, for example, to characterise individuals in terms of haplotype and other sub- groupings, such as investigation of susceptibility to treatment with particular drugs. These approaches are most easily facilitated by storing the sequence information in a computer readable medium and then using the information in standard bioinformatics programs or to search sequence databases using state of the art searching tools such as "GCC". Thus, the polynucleotide sequences of the invention are particularly useful as components in databases useful for sequence identity and other search analyses.
  • sequence information in a computer readable medium and use in sequence databases in relation to ' polynucleotide or polynucleotide sequence of the invention' covers any detectable chemical or physical characteristic of a polynucleotide of the invention that may be reduced to, converted into or stored in a tangible medium, such as a computer disk, preferably in a computer readable form.
  • a tangible medium such as a computer disk
  • chromatographic scan data or peak data photographic scan or peak data
  • mass spectrographic data sequence gel (or other) data.
  • the invention provides a computer readable medium having stored thereon one or a more polynucleotide sequences of the invention.
  • a computer readable medium comprising and having stored thereon a member selected from the group consisting of: a polynucleotide comprising the sequence of a polynucleotide of the invention, a polynucleotide consisting of a polynucleotide of the invention, a polynucleotide which comprises part of a polynucleotide of the invention, which part includes at least one of the polymo ⁇ hisms of the invention, a set of polynucleotide sequences wherein the set includes at least one polynucleotide sequence of the invention, a data set comprising or consisting of a polynucleotide sequence of the invention or a part thereof comprising at least one of the polymo ⁇ hisms identified herein.
  • a computer based method for performing sequence identification, said method comprising the steps of providing a polynucleotide sequence comprising a polymo ⁇ hism of the invention in a computer readable medium; and comparing said polymo ⁇ hism containing polynucleotide sequence to at least one other polynucleotide or polypeptide sequence to identify identity (homology), i.e. screen for the presence of a polymo ⁇ hism.
  • the invention further provides nucleotide primers which can detect the polymo ⁇ hisms of the invention.
  • an allele specific primer capable of detecting a CCR-2 gene polymo ⁇ hism at one or more of positions 2385 and 2649 in the CCR-2 gene as defined by the positions in EMBL ACCESSION NO. U 80924, and/or one or more of positions 40915, 41047, 41058, 41507, 41768, 42401, 42598, 42673,
  • An allele specific primer is used, generally together with a constant primer, in an amplification reaction such as a PCR reaction, which provides the discrimination between alleles through selective amplification of one allele at a particular sequence position e.g. as used for ARMSTM assays.
  • the allele specific primer is preferably 17- 50 nucleotides, more preferably about 17-35 nucleotides, more preferably about 17-30 nucleotides.
  • An allele specific primer preferably corresponds exactly with the allele to be detected but derivatives thereof are also contemplated wherein about 6-8 of the nucleotides at the 3' terminus correspond with the allele to be detected and wherein up to 10, such as up to 8, 6, 4, 2, or 1 of the remaining nucleotides may be varied without significantly affecting the properties of the primer.
  • Primers may be manufactured using any convenient method of synthesis. Examples of such methods may be found in standard textbooks, for example "Protocols for Oligonucleotides and Analogues; Synthesis and Properties," Methods in Molecular Biology Series; Volume 20; Ed. Sudhir Agrawal, Humana ISBN: 0-89603-247-7; 1993; 1st Edition. If required the primer(s) may be labelled to facilitate detection.
  • an allele-specific oligonucleotide probe capable of detecting a CCR-2 gene polymo ⁇ hism at one or more of positions 2385 and 2649 in the CCR-2 gene as defined by the positions in EMBL ACCESSION NO. U 80924, and/or one or more positions 40915, 41047, 41058, 41507, 41768, 42401, 42598, 42673, 42723, 42874 , 43018 and in the promoter sequence of the CCR-2 gene as defined by the positions in the EMBL ACCESSION NO. U95626.
  • the allele-specific oligonucleotide probe is preferably 17- 50 nucleotides, more preferably about 17-35 nucleotides, more preferably about 17-30 nucleotides.
  • probes will be apparent to the molecular biologist of ordinary skill.
  • Such probes are of any convenient length such as up to 50 bases, up to 40 bases, more conveniently up to 30 bases in length, such as for example 8-25 or 8-15 bases in length.
  • such probes will comprise base sequences entirely complementary to the corresponding wild type or variant locus in the gene.
  • one or more mismatches may be introduced, provided that the discriminatory power of the oligonucleotide probe is not unduly affected.
  • the probes of the invention may carry one or more labels to facilitate detection.
  • a diagnostic kit comprising an allele specific oligonucleotide probe of the invention and/or an allele-specific primer of the invention.
  • the diagnostic kits may comprise appropriate packaging and instructions for use in the methods of the invention. Such kits may further comprise appropriate buffer(s) and polymerase(s) such as thermostable polymerases, for example taq polymerase.
  • the single nucleotide polymo ⁇ hisms of this invention may be used as genetic markers in linkage studies. This particularly applies to the polymo ⁇ hisms at 2385, 41047, 41507 and 42723 because of their relatively high frequency (see below).
  • the CCR-2 gene has been mapped to chromosome 3p21.3-p24 (Samson et al (1996), Genomics 36, 522-526). Low frequency polymo ⁇ hisms may be particularly useful for haplotyping as described below.
  • a haplotype is a set of alleles found at linked polymo ⁇ hic sites (such as within a gene) on a single (paternal or maternal) chromosome. If recombination within the gene is random, there may be as many as 2" haplotypes, where 2 is the number of alleles at each SNP and n is the number of SNPs.
  • One approach to identifying mutations or polymo ⁇ hisms which are correlated with clinical response is to carry out an association study using all the haplotypes that can be identified in the population of interest. The frequency of each haplotype is limited by the frequency of its rarest allele, so that SNPs with low frequency alleles are particularly useful as markers of low frequency haplotypes.
  • low frequency SNPs may be particularly useful in identifying these mutations (for examples see: Linkage disequilibrium at the cystathionine beta synthase (CBS) locus and the association between genetic variation at the CBS locus and plasma levels of homocysteine.
  • CBS cystathionine beta synthase
  • a method of treating a human in need of treatment with a CCR-2 ligand antagonist drug comprises: i) diagnosis of a single nucleotide polymo ⁇ hism in CCR-2 gene in the human, which diagnosis comprises determining the sequence of the nucleic acid at one or more of positions 2385 and 2649 in the CCR-2 gene as defined by the positions in EMBL ACCESSION NO.
  • Preferably determination of the status of the human is clinically useful. Examples of
  • CCR-2 ligand antagonist drugs have been disclosed in the following publications: US patent 5707815, University of California; International patent application WO 98/06703, Warner Lambert; and Japanese patent application JP 09309877-A, Teijin Limited.
  • a CCR-2 ligand antagonist drug in preparation of a medicament for treating a CCR-2 ligand mediated disease in a human diagnosed as having a single nucleotide polymo ⁇ hism at one or more of positions 2385 and 2649 in CCR-2 gene as defined by the positions in EMBL ACCESSION NO. U 80924, and/or at one or more positions 40915, 41047, 41058, 41507, 41768, 42401, 42598,
  • a pharmaceutical pack comprising a CCR-2 ligand antagonist drug and instructions for administration of the drug to humans diagnostically tested for a single nucleotide polymo ⁇ hism at one or more of positions
  • AMPLITAQTM available from Perkin-Elmer Cetus, is used as the source of thermostable DNA polymerase.
  • Electropherograms were obtained in a standard manner: data was collected by ABI377 data collection software and the wave form generated by ABI Prism sequencing analysis (2.1.2).
  • DNA was prepared from frozen blood samples collected in EDTA following protocol I (Molecular Cloning: A Laboratory Manual, p392, Sambrook, Fritsch and Maniatis, 2nd Edition, Cold Spring Harbor Press, 1989) with the following modifications.
  • the thawed blood was diluted in an equal volume of standard saline citrate instead of phosphate buffered saline to remove lysed red blood cells.
  • Samples were extracted with phenol, then phenol/chloroform and then chloroform rather than with three phenol extractions.
  • the DNA was dissolved in deionised water.
  • Template Preparation Templates were prepared by PCR using the oligonucleotide primers and annealing temperatures set out below. The extension temperature was 72° and denaturation temperature 94°. Generally 50 ng of genomic DNA was used in each reaction and subjected to 35 cycles of PCR and primary fragment was diluted 1/200 before amplification of secondary fragments. PCR was performed in two stages (primary fragment then secondary fragment) to ensure specific amplification of the desired target sequence.
  • Dye-primer sequencing using Ml 3 forward and reverse primers was as described in the ABI protocol P/N 402114 for the ABI PrismTM dye primer cycle sequencing core kit with "AMPLITAQTMFS" DNA polymerase, modified in that the annealing temperature was 45° and DMSO was added to the cycle sequencing mix to a final concentration of 5 %.
  • the allele frequencies were based on analysis of 20 individuals.
  • Example 2 10 Diagnostic assays for polymorphisms within the coding region of the CCR2 gene
  • the CCR2 gene has been cloned and published (EMBL Accession Number U80924 5471 bp) and all positions herein relate to the position therein unless stated otherwise or apparent from the context. 15 Methods: DNA preparation and Template preparation were performed as described above.
  • the size of full length, uncut PCR product is 380 bp (homozygous wild type), digestion of the PCR product from a homozygous variant will generate products of 275 bp and 105 bp, while digestion of the PCR product from a heterozygote will generate products of 380 bp, 275 bp and 105 bp.
  • the diagnostic primer contains a single mismatch from the wild type sequence at the 3 ' residue 20 (C->G).
  • the human BAC (Bacterial Artificial Chromosome) clone 11 OP 12 contains the CCR2 gene.
  • the complete sequence of clone 11 OP 12 has been published (EMBL Accession Number U95626, 143068 bp) and all positions herein relate to the position therein unless stated otherwise or apparent from the context.
  • Variation at position 42673 modifies an Sphl recognition site (GCATGC).
  • the PCR product (443 bp) containing the wild type sequence will be cleaved by Sphl (New England Biolabs) to generate products of 189 bp and 254 bp.
  • the homozygous variant product will be uncut (443 bp) while digestion of the heterozygote variant sequence will generate products of 189 bp, 254 bp and 443 bp.
  • T-C nucleotide 40917
  • GATC Sau3A site
  • GTTC variant sequence
  • AACGTT Acl I site
  • C/A polymo ⁇ hic variation at position 41507
  • PCR product (230 bp) containing the wild type sequence Digestion of the PCR product (230 bp) containing the wild type sequence with Acl I (New England Biolabs) will generate products of 208 bp and 22 bp.
  • PCR products containing the homozygous variant sequence will be uncut while digestion of hererozygous products will generate products of 230 bp., 208 bp and 22 bp.
  • G-C Engineering of position 41766 creates an Nhe I recognition sequence (GCTAGC) and polymo ⁇ hism (A/T) at position 41768 will modify this recognition sequence.
  • the wild type sequence (GCTAGC) will be cleaved while the variant sequence (GCTTGC) is not.
  • Nhe I (New England Biolabs) will generate products of 22 bp and 220 bp.
  • PCR products containing the variant sequence (GCTTGC) will be uncut while digestion of heterozygote products will generate products of 242 bp,220 bp and 22 bp.
  • PCR products containing the variant sequence (AAGTTT) will be uncut while digestion of heterozygote products will generate products of 301 bp, 278 bp and 23 bp.
  • Constant Primer 42541-42561 5' CCAATGTACAATGTTCCTGAC SEQ ID No: 12 Digestion of a PCR product (203 bp) containing the wild type sequence will generate products of 22 bp and 181 bp. Products containing the variant sequence are uncut while digestion of heterozygote products will generate products of 203 bp, 181 bp and 22 bp.
  • TGTACA Bsr GI recognition sequence
  • a PCR (197 bp) product containing the wild type sequence will not be cleaved by the restriction enzyme Bsr GI (New England Biolabs). Digestion of a PCR product containing the variant sequence will generate products of 172 bp and 25 bp, digestion of a heterozygote product will generate products of 197 bp, 172 bp and 25 bp.
  • a double ARMSTM assay on the polymo ⁇ hisms at 41507 (C/A) and 42673 (G/A) has generated haplotypes at these 2 positions as set out below.

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Abstract

La présente invention concerne des polymorphismes du gène CCR-2 de l'homme. L'invention concerne plus particulièrement 2 polymorphismes de la séquence codante du gène CCR-2 et 11 polymorphismes dans la séquence promotrice du gène CCR-2. L'invention concerne également, d'une part des procédés et du matériel permettant d'analyser les écarts d'allélisme affectant le gène CCR-2, et d'autre part l'utilisation du polymorphisme de CCR-2 pour le diagnostic et le traitement d'affections à médiation d'un ligand de CCR-2, et notamment la polyarthrite rhumatoïde et autres maladies inflammatoires.
EP99934896A 1998-07-25 1999-07-20 Polymorphismes du gene ccr-2 de l'homme Withdrawn EP1100963A2 (fr)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
GBGB9816193.8A GB9816193D0 (en) 1998-07-25 1998-07-25 Chemical compounds
GB9816193 1998-07-25
GB9901844 1999-01-28
GBGB9901844.2A GB9901844D0 (en) 1999-01-28 1999-01-28 Chemical compounds
PCT/GB1999/002341 WO2000006769A2 (fr) 1998-07-25 1999-07-20 Polymorphismes du gene ccr-2 de l'homme

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EP1100963A2 true EP1100963A2 (fr) 2001-05-23

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EP (1) EP1100963A2 (fr)
JP (1) JP2002521063A (fr)
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GB0004183D0 (en) * 2000-02-22 2000-04-12 Smithkline Beecham Plc New use
DE10049549A1 (de) * 2000-10-06 2002-05-02 Markus Hecker Modulation der Transkription pro-inflammatorischer Genprodukte
RU2180922C1 (ru) * 2001-03-14 2002-03-27 Ромащенко Аида Герасимовна Способ определения аллелей гена хемокинового рецептора ccr2 по полиморфному сайту v64i
DE60232442D1 (de) * 2001-03-30 2009-07-09 Shunichi Shiozawa An rheumatischer arthritis beteiligte genomische dnas, diagnoseverfahren dafür, verfahren zur beurteilung der ausbruchsgefahr davon und diagnostischer kit zum nachweis davon
CA2510895A1 (fr) 2002-12-20 2004-07-15 Applera Corporation Polymorphismes genetiques associes a la stenose, procedes de detection, et utilisations

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ATE347594T1 (de) * 1994-01-13 2006-12-15 Univ California Monocyten protein rezeptoren aus säugern, mit chemoattraktion auslösender wirkung
JPH09238688A (ja) * 1996-03-11 1997-09-16 Takeda Chem Ind Ltd ヒトｍｃｐ−１レセプタータンパク質の製造法および用途
WO1997040462A2 (fr) * 1996-04-19 1997-10-30 Spectra Biomedical, Inc. Formes polymorphes en correlation au niveau de phenotypes multiples

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Title
See references of WO0006769A2 *

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JP2002521063A (ja) 2002-07-16
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AU5052999A (en) 2000-02-21

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