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PMID: 20386740 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

Chromosome 9p21 SNPs Associated with Multiple Disease Phenotypes Correlate with ANRIL Expression.

PLoS genetics ·Vol. 6 ·No. 4 ·2010-04-08 ·Pages e1000899

Cunnington MS, Santibanez Koref M, Mayosi BM, Burn J, Keavney B

Abstract

Single nucleotide polymorphisms (SNPs) on chromosome 9p21 are associated with coronary artery disease, diabetes, and multiple cancers. Risk SNPs are mainly non-coding, suggesting that they influence expression and may act in cis. We examined the association between 56 SNPs in this region and peripheral blood expression of the three nearest genes CDKN2A, CDKN2B, and ANRIL using total and allelic expression in two populations of healthy volunteers: 177 British Caucasians and 310 mixed-ancestry South Africans. Total expression of the three genes was correlated (P<0.05), suggesting that they are co-regulated. SNP associations mapped by allelic and total expression were similar (r = 0.97, P = 4.8x10(-99)), but the power to detect effects was greater for allelic expression. The proportion of expression variance attributable to cis-acting effects was 8% for CDKN2A, 5% for CDKN2B, and 20% for ANRIL. SNP associations were similar in the two populations (r = 0.94, P = 10(-72)). Multiple SNPs were independently associated with expression of each gene (P<0.05 after correction for multiple testing), suggesting that several sites may modulate disease susceptibility. Individual SNPs correlated with changes in expression up to 1.4-fold for CDKN2A, 1.3-fold for CDKN2B, and 2-fold for ANRIL. Risk SNPs for coronary disease, stroke, diabetes, melanoma, and glioma were all associated with allelic expression of ANRIL (all P<0.05 after correction for multiple testing), while association with the other two genes was only detectable for some risk SNPs. SNPs had an inverse effect on ANRIL and CDKN2B expression, supporting a role of antisense transcription in CDKN2B regulation. Our study suggests that modulation of ANRIL expression mediates susceptibility to several important human diseases.

MeSH Terms
Alleles Chromosomes, Human, Pair 9 Cyclin-Dependent Kinase Inhibitor p15/genetics,metabolism Cyclin-Dependent Kinase Inhibitor p16/genetics,metabolism Genetic Predisposition to Disease/genetics Genotype Humans Male Middle Aged Phenotype Polymorphism, Single Nucleotide RNA, Untranslated/genetics,metabolism
Chemicals
Cyclin-Dependent Kinase Inhibitor p15 Cyclin-Dependent Kinase Inhibitor p16 RNA, Untranslated
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Cunnington Michael S
Institute of Human Genetics, Newcastle University, Newcastle upon Tyne, United Kingdom.
Santibanez Koref Mauro
Mayosi Bongani M
Burn John
Keavney Bernard
Conflict of Interest

The authors have declared that no competing interests exist.

References (78)
78 references, click to expand
  1. Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes.
    PLoS Comput Biol. 2007 Apr 20;3(4):e72 PMID: 17447839
  2. DNA damage, vascular senescence and atherosclerosis.
    J Mol Med (Berl). 2008 Sep;86(9):1033-43 PMID: 18563380
  3. Regulation of p16CDKN2 expression and its implications for cell immortalization and senescence.
    Mol Cell Biol. 1996 Mar;16(3):859-67 PMID: 8622687
  4. Linkage and association study of late-onset Alzheimer disease families linked to 9p21.3.
    Ann Hum Genet. 2008 Nov;72(Pt 6):725-31 PMID: 18761660
  5. A survey of genetic and epigenetic variation affecting human gene expression.
    Physiol Genomics. 2004 Jan 15;16(2):184-93 PMID: 14583597
  6. Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility.
    Nat Genet. 2009 Aug;41(8):905-8 PMID: 19578366
  7. Strong association of common variants in the CDKN2A/CDKN2B region with type 2 diabetes in French Europids.
    Diabetologia. 2008 May;51(5):821-6 PMID: 18368387
  8. Association of single-nucleotide polymorphisms in the cell cycle genes with breast cancer in the British population.
    Carcinogenesis. 2008 Feb;29(2):333-41 PMID: 18174243
  9. The same sequence variant on 9p21 associates with myocardial infarction, abdominal aortic aneurysm and intracranial aneurysm.
    Nat Genet. 2008 Feb;40(2):217-24 PMID: 18176561
  10. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA.
    Nature. 2008 Jan 10;451(7175):202-6 PMID: 18185590
  11. Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations.
    PLoS One. 2008;3(12):e4105 PMID: 19116668
  12. Expression of p16(INK4a) in peripheral blood T-cells is a biomarker of human aging.
    Aging Cell. 2009 Aug;8(4):439-48 PMID: 19485966
  13. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes.
    Genome Biol. 2002 Jun 18;3(7):RESEARCH0034 PMID: 12184808
  14. In vitro assays fail to predict in vivo effects of regulatory polymorphisms.
    Hum Mol Genet. 2007 Aug 15;16(16):1931-9 PMID: 17566082
  15. Hypoplasia of endocrine and exocrine pancreas in homozygous transgenic TGF-beta1.
    Mol Cell Endocrinol. 2005 Jan 14;229(1-2):175-84 PMID: 15607541
  16. INK4/ARF transcript expression is associated with chromosome 9p21 variants linked to atherosclerosis.
    PLoS One. 2009;4(4):e5027 PMID: 19343170
  17. Primer3 on the WWW for general users and for biologist programmers.
    Methods Mol Biol. 2000;132:365-86 PMID: 10547847
  18. A common allele on chromosome 9 associated with coronary heart disease.
    Science. 2007 Jun 8;316(5830):1488-91 PMID: 17478681
  19. Aurora-A and p16 polymorphisms contribute to an earlier age at diagnosis of pancreatic cancer in Caucasians.
    Clin Cancer Res. 2007 May 15;13(10):3100-4 PMID: 17505013
  20. African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping.
    Annu Rev Genomics Hum Genet. 2008;9:403-33 PMID: 18593304
  21. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants.
    Science. 2007 Jun 1;316(5829):1341-5 PMID: 17463248
  22. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.
    Nat Genet. 2008 May;40(5):638-45 PMID: 18372903
  23. Sequence variants on chromosome 9p21.3 confer risk for atherosclerotic stroke.
    Ann Neurol. 2009 May;65(5):531-9 PMID: 19475673
  24. A single nucleotide polymorphism in the 3'untranslated region of the CDKN2A gene is common in sporadic primary melanomas but mutations in the CDKN2B, CDKN2C, CDK4 and p53 genes are rare.
    Int J Cancer. 2001 Nov 20;95(6):388-93 PMID: 11668523
  25. Selection of reference genes for gene expression studies in human neutrophils by real-time PCR.
    BMC Mol Biol. 2005 Feb 18;6:4 PMID: 15720708
  26. Promoter SNPs in G1/S checkpoint regulators and their impact on the susceptibility to childhood leukemia.
    Blood. 2007 Jan 15;109(2):683-92 PMID: 17008550
  27. Long non-coding RNAs: insights into functions.
    Nat Rev Genet. 2009 Mar;10(3):155-9 PMID: 19188922
  28. CDKN2A common variants and their association with melanoma risk: a population-based study.
    Cancer Res. 2005 Feb 1;65(3):835-9 PMID: 15705881
  29. Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family: identification of ANRIL, an antisense noncoding RNA whose expression coclusters with ARF.
    Cancer Res. 2007 Apr 15;67(8):3963-9 PMID: 17440112
  30. Genome-wide association study identifies five susceptibility loci for glioma.
    Nat Genet. 2009 Aug;41(8):899-904 PMID: 19578367
  31. Functional analysis of the chromosome 9p21.3 coronary artery disease risk locus.
    Arterioscler Thromb Vasc Biol. 2009 Oct;29(10):1671-7 PMID: 19592466
  32. Polymorphisms of p16, p27, p73, and MDM2 modulate response and survival of pancreatic cancer patients treated with preoperative chemoradiation.
    Ann Surg Oncol. 2009 Feb;16(2):431-9 PMID: 19020940
  33. An integrated genomic analysis of human glioblastoma multiforme.
    Science. 2008 Sep 26;321(5897):1807-12 PMID: 18772396
  34. Features associated with germline CDKN2A mutations: a GenoMEL study of melanoma-prone families from three continents.
    J Med Genet. 2007 Feb;44(2):99-106 PMID: 16905682
  35. Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN.
    Nucleic Acids Res. 2003 Jul 1;31(13):3651-3 PMID: 12824386
  36. Tagging single nucleotide polymorphisms in cell cycle control genes and susceptibility to invasive epithelial ovarian cancer.
    Cancer Res. 2007 Apr 1;67(7):3027-35 PMID: 17409409
  37. Whole genome analyses suggest ischemic stroke and heart disease share an association with polymorphisms on chromosome 9p21.
    Stroke. 2008 May;39(5):1586-9 PMID: 18340101
  38. A common variant of the p16(INK4a) genetic region is associated with physical function in older people.
    Mech Ageing Dev. 2007 May-Jun;128(5-6):370-7 PMID: 17459456
  39. PROMO: detection of known transcription regulatory elements using species-tailored searches.
    Bioinformatics. 2002 Feb;18(2):333-4 PMID: 11847087
  40. Genomewide association analysis of coronary artery disease.
    N Engl J Med. 2007 Aug 2;357(5):443-53 PMID: 17634449
  41. Association of interindividual differences in p14ARF promoter methylation with single nucleotide polymorphism in primary colorectal cancer.
    Cancer. 2008 Apr 15;112(8):1699-707 PMID: 18327804
  42. An expectation-maximization algorithm for the analysis of allelic expression imbalance.
    Am J Hum Genet. 2006 Sep;79(3):539-43 PMID: 16909391
  43. Significant impact of promoter hypermethylation and the 540 C>T polymorphism of CDKN2A in cutaneous melanoma of the vertical growth phase.
    Am J Pathol. 2002 Jul;161(1):229-37 PMID: 12107107
  44. Worldwide patterns of haplotype diversity at 9p21.3, a locus associated with type 2 diabetes and coronary heart disease.
    Genome Med. 2009 May 12;1(5):51 PMID: 19463184
  45. CDKN2A-positive breast cancers in young women from Poland.
    Breast Cancer Res Treat. 2007 Jul;103(3):355-9 PMID: 17061045
  46. miRBase: tools for microRNA genomics.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8 PMID: 17991681
  47. The UCSC Genome Browser database: update 2010.
    Nucleic Acids Res. 2010 Jan;38(Database issue):D613-9 PMID: 19906737
  48. The human ARF cell cycle regulatory gene promoter is a CpG island which can be silenced by DNA methylation and down-regulated by wild-type p53.
    Mol Cell Biol. 1998 Nov;18(11):6457-73 PMID: 9774662
  49. Transforming growth factor beta activates the promoter of cyclin-dependent kinase inhibitor p15INK4B through an Sp1 consensus site.
    J Biol Chem. 1995 Nov 10;270(45):26750-3 PMID: 7592908
  50. Susceptibility to coronary artery disease and diabetes is encoded by distinct, tightly linked SNPs in the ANRIL locus on chromosome 9p.
    Hum Mol Genet. 2008 Mar 15;17(6):806-14 PMID: 18048406
  51. Population genomics of human gene expression.
    Nat Genet. 2007 Oct;39(10):1217-24 PMID: 17873874
  52. A common variant of CDKN2A (p16) predisposes to breast cancer.
    J Med Genet. 2005 Oct;42(10):763-5 PMID: 15879498
  53. p16(INK4a) translation suppressed by miR-24.
    PLoS One. 2008 Mar 26;3(3):e1864 PMID: 18365017
  54. Widespread monoallelic expression on human autosomes.
    Science. 2007 Nov 16;318(5853):1136-40 PMID: 18006746
  55. Oncogenic activity of Cdc6 through repression of the INK4/ARF locus.
    Nature. 2006 Mar 30;440(7084):702-6 PMID: 16572177
  56. A common variant on chromosome 9p21 affects the risk of myocardial infarction.
    Science. 2007 Jun 8;316(5830):1491-3 PMID: 17478679
  57. The prevalence of CDKN2A germ-line mutations and relative risk for cutaneous malignant melanoma: an international population-based study.
    Cancer Epidemiol Biomarkers Prev. 2006 Aug;15(8):1520-5 PMID: 16896043
  58. Characterization of regulatory elements on the promoter region of p16(INK4a) that contribute to overexpression of p16 in senescent fibroblasts.
    J Biol Chem. 2001 Dec 28;276(52):48655-61 PMID: 11598130
  59. Trans-ethnic fine mapping of a quantitative trait locus for circulating angiotensin I-converting enzyme (ACE).
    Hum Mol Genet. 2001 May 1;10(10):1077-84 PMID: 11331618
  60. A genome-wide association study of global gene expression.
    Nat Genet. 2007 Oct;39(10):1202-7 PMID: 17873877
  61. The regulation of INK4/ARF in cancer and aging.
    Cell. 2006 Oct 20;127(2):265-75 PMID: 17055429
  62. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
    Nature. 2007 Jun 7;447(7145):661-78 PMID: 17554300
  63. p16INK4a induces an age-dependent decline in islet regenerative potential.
    Nature. 2006 Sep 28;443(7110):453-7 PMID: 16957737
  64. Genome-wide association study identifies three loci associated with melanoma risk.
    Nat Genet. 2009 Aug;41(8):920-5 PMID: 19578364
  65. p16(CDKN2) gene polymorphism: association with histologic subtypes of epithelial ovarian cancer in China.
    Int J Gynecol Cancer. 2008 Jan-Feb;18(1):30-5 PMID: 17466040
  66. Comprehensive genomic characterization defines human glioblastoma genes and core pathways.
    Nature. 2008 Oct 23;455(7216):1061-8 PMID: 18772890
  67. Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants.
    PLoS One. 2009 Nov 02;4(11):e7677 PMID: 19888323
  68. Extreme clonality in lymphoblastoid cell lines with implications for allele specific expression analyses.
    PLoS One. 2008 Aug 13;3(8):e2966 PMID: 18698422
  69. Genetics of gene expression surveyed in maize, mouse and man.
    Nature. 2003 Mar 20;422(6929):297-302 PMID: 12646919
  70. Cis-acting regulatory variation in the human genome.
    Science. 2004 Oct 22;306(5696):647-50 PMID: 15499010
  71. A HapMap harvest of insights into the genetics of common disease.
    J Clin Invest. 2008 May;118(5):1590-605 PMID: 18451988
  72. Clinical course of bladder neoplasms and single nucleotide polymorphisms in the CDKN2A gene.
    Int J Cancer. 2003 Mar 10;104(1):98-103 PMID: 12532425
  73. Regulation of the INK4b-ARF-INK4a tumour suppressor locus: all for one or one for all.
    Nat Rev Mol Cell Biol. 2006 Sep;7(9):667-77 PMID: 16921403
  74. Germline p16 mutations in familial melanoma.
    Nat Genet. 1994 Sep;8(1):15-21 PMID: 7987387
  75. The proximal GC-rich region of p16(INK4a) gene promoter plays a role in its transcriptional regulation.
    Mol Cell Biochem. 2007 Jul;301(1-2):259-66 PMID: 17333389
  76. Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human.
    Nat Methods. 2009 Aug;6(8):613-8 PMID: 19620972
  77. Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes.
    Science. 2007 Jun 1;316(5829):1336-41 PMID: 17463249
  78. Vascular cell senescence: contribution to atherosclerosis.
    Circ Res. 2007 Jan 5;100(1):15-26 PMID: 17204661
Article Info
Journal
PLoS genetics
Abbr.
PLoS Genet
ISSN
1553-7404
DOI
10.1371/journal.pgen.1000899
Published
2010-04-08
Epub
2010-00-08
Pages
e1000899
Language
English
Region
United States
NLM ID
101239074
PMCID
PMC2851566
Subset
IM
Grants
British Heart Foundation · RG/08/012/25941 · United Kingdom
British Heart Foundation · CH/07/001 · United Kingdom
External Links
PubMed source DOI: 10.1371/journal.pgen.1000899 PMC Full Text View journal details
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