Review
Functional genomics of the CDKN2A/B locus in cardiovascular and metabolic disease: what have we learned from GWASs?

https://doi.org/10.1016/j.tem.2015.01.008Get rights and content

Highlights

  • 9p21.3 SNP variants were tagged by a genome-wide association study (GWAS) as a hot spot associated with cardiovascular disease (CVD) and type 2 diseases.

  • It is not clear why this chromosome region is a vital genetic region, or by which pathways this locus might influence cardio-metabolic susceptibility.

  • The function of cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) gene products may mechanistically link the 9p21.3 risk locus with CVD and type 2 diabetes (T2D).

  • In addition to direct vascular and immune-modulatory roles of CDKN2A/B, this locus may influence cardio-metabolic diseases by affecting metabolic functions.

Genome-wide association studies (GWASs) provide an unprecedented opportunity to examine, on a large scale, the association of common genetic variants with complex diseases like type 2 diabetes (T2D) and cardiovascular disease (CVD), thus allowing the identification of new potential disease loci. Using this approach, numerous studies have associated SNPs on chromosome 9p21.3 situated near the cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) locus with the risk for coronary artery disease (CAD) and T2D. However, identifying the function of the nearby gene products (CDKN2A/B and ANRIL) in the pathophysiology of these conditions requires functional genomic studies. We review the current knowledge, from studies using human and mouse models, describing the function of CDKN2A/B gene products, which may mechanistically link the 9p21.3 risk locus with CVD and diabetes.

Introduction

T2D patients display increased risk for CVDs (see Glossary). The prevalence of both pathologies is increasing despite intense efforts in prevention and disease treatment. The pathogenesis of CVD and T2D involves the interaction of environmental and genetic factors. Identification of the pathophysiological mechanisms and risk factors, allowing lifestyle intervention and pharmacological therapies, is paramount to curb the epidemic propagation of these diseases.

Although T2D and CVD are often clinically linked and share obvious risk factors such as life style, the existence of shared genetic signatures has remained elusive for a long time. In recent years, GWASs focusing on CVD and T2D have provided a wealth of new information allowing the identification of biological pathways not associated with conventional risk factors. GWASs have identified a common susceptibility locus on chromosome 9p21.3 for both T2D and CVD, with the sequence variants rs10757278-G and rs10811661-T, respectively, associated with CAD and T2D [1].

Discovered in 2007 by three independent GWASs 2, 3, 4 and replicated since in several other studies, the chromosome 9p21.3 locus is, to date, one of the most robust genetic markers of CAD and myocardial infarction (MI) in Caucasian [5], Korean, and Japanese populations 6, 7. This locus also associates with atherosclerosis severity, with a substantially higher risk allele frequency in subjects with multivessel disease [8]. Furthermore, an association of rs10757278-G was also demonstrated with abdominal aortic and intracranial aneurysms [9], suggesting a more general impact of this locus on vascular function and remodeling. The strongest association of 9p21.3 variants is with the risk of first rather than subsequent CHD events [10], suggesting an action of this locus on the burden of CAD, rather than on MI due to plaque instability/rupture and thrombosis.

The 9p21.3 locus, spanning a >50-kb genomic region, contains multiple SNPs associated with CVD that are in strong linkage disequilibrium (LD), defining a core risk haplotype robustly associated with CVD [11]. T2D is a well-established risk factor for CVD and especially for atherosclerosis, raising thus the possibility that the region on 9p21.3 predisposes to both CVD and T2D through shared biological mechanisms. However, the CVD SNP rs10757278 and T2D SNP rs10811661 (Figure 1) are in adjacent LD blocks, and the two SNPs are not associated (r2<0.01) in the HapMap of Utah residents with northern and western European ancestry (CEU) data [9]. Moreover, despite the clear genetic signal at this locus, the underlying biological mechanisms are still poorly understood. The genome region containing the SNPs on chromosome 9p21.3 harbors no known protein-coding genes, but expresses the long noncoding RNA ANRIL (antisense noncoding RNA in the inhibitor of CDK4 (INK4) locus). The closest adjacent protein-coding genes including the cyclin-dependent kinase (CDK) inhibitors CDKN2A and CDKN2B, known as tumor suppressors, are considered as potential functional candidates. Moreover, it must be kept in mind that rs10757278 and rs10811661 are separated by <10 kb from CDKN2A and CDKN2B. Candidate gene approaches have also reported variants in this locus associated with ovarian cancer, acute lymphoblastic leukemia, glioma, malignant melanoma, breast cancer, pancreatic cancer, nasopharyngeal neoplasm, and glaucoma [12], showing that this chromosomal area harbors genes involved in a number of different pathophysiological processes. It should be noted that the link with cancer is more expected than with T2D and CVD, considering the well-known function of the CDKN2A/B gene products in cell cycle control (Box 1).

Section snippets

CDKN2A/B gene products and ANRIL expression in human samples

The CDKN2A locus encodes the CDK inhibitor protein (CDKI) p16INK4a and the p53 regulatory protein p14ARF (p19ARF in mice), whereas the CDKN2B gene encodes another CDKI, p15INK4b. All these proteins are involved in cell cycle regulation, aging, senescence, and apoptosis 13, 14.

The protein products of the CDKN2A/B locus, that is, p16INK4a, p14ARF, and p15INK4b, are expressed in normal and atherosclerotic human coronary arteries [15]. In atherosclerotic lesions, these proteins localize to a subset

CDKN2A/B genes in the control of metabolism

Systemic metabolic risk factors for CVD, such as observed in dyslipidemia and diabetes, are rising rapidly worldwide due to the obesity epidemic. CVD complications account for more than 70% of the morbidity associated with these diseases. eQTL studies for CDKN2B have associated the CVD-risk region with reduced CDKN2B expression in human subcutaneous adipose tissue (SAT) and circulating leukocytes [53]. CDKN2B appears to play a significant role in regulating SAT expandability, determinant of

Concluding remarks and future perspectives

9p21.3 SNP variants were tagged by GWASs as a hot spot associated with cardio-metabolic diseases. Although GWAS findings are not yet translated into clinical application for personalized health care of individual patients, they constitute nevertheless a first step towards an improved understanding of disease etiology. Several studies tried to decipher the function of the CDKN2A/B gene products in cardio-metabolic diseases (Figure 2). Nonetheless, even with the progress made, we are far from

Glossary

Cardiovascular disease (CVD)
includes all the diseases of the heart and circulation including coronary heart disease (angina and myocardial infarction), heart failure, congenital heart disease, and ischemic stroke.
Coronary heart diseases (CHDs)
are a set of complex, prevalent, and related conditions including coronary artery disease (CAD) and myocardial infarction (MI). CHD begins as atherosclerosis, an inflammatory disease that is influenced by multiple environmental and genetic factors. It

References (90)

  • C. Cudejko

    p16INK4a deficiency promotes IL-4-induced polarization and inhibits proinflammatory signaling in macrophages

    Blood

    (2011)
  • P-A. Svensson

    CDKN2B expression and subcutaneous adipose tissue expandability: possible influence of the 9p21 atherosclerosis locus

    Biochem. Biophys. Res. Commun.

    (2014)
  • J-A. Kim

    The inhibition of T-cells proliferation by mouse mesenchymal stem cells through the induction of p16INK4A-cyclin D1/cdk4 and p21waf1, p27kip1-cyclin E/cdk2 pathways

    Cell. Immunol.

    (2007)
  • J. Bies

    Myeloid-specific inactivation of p15Ink4b results in monocytosis and predisposition to myeloid leukemia

    Blood

    (2010)
  • M. Moritani

    Hypoplasia of endocrine and exocrine pancreas in homozygous transgenic TGF-beta1

    Mol. Cell. Endocrinol.

    (2005)
  • L. Fajas

    E2Fs regulate adipocyte differentiation

    Dev. Cell

    (2002)
  • M. Ruas et al.

    The p16INK4a/CDKN2A tumor suppressor and its relatives

    Biochim. Biophys. Acta

    (1998)
  • M. Dauriz et al.

    Current insights into the joint genetic basis of type 2 diabetes and coronary heart disease

    Curr. Cardiovasc. Risk Rep.

    (2014)
  • A. Helgadottir

    A common variant on chromosome 9p21 affects the risk of myocardial infarction

    Science

    (2007)
  • P.R. Burton

    Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls

    Nature

    (2007)
  • R. McPherson

    A common allele on chromosome 9 associated with coronary heart disease

    Science

    (2007)
  • R. Roberts et al.

    9p21 and the genetic revolution for coronary artery disease

    Clin. Chem.

    (2012)
  • K. Hinohara

    Replication of the association between a chromosome 9p21 polymorphism and coronary artery disease in Japanese and Korean populations

    J. Hum. Genet.

    (2008)
  • G-Q. Shen

    Four SNPs on chromosome 9p21 in a South Korean population implicate a genetic locus that confers high cross-race risk for development of coronary artery disease

    Arterioscler. Thromb. Vasc. Biol.

    (2008)
  • A. Helgadottir

    The same sequence variant on 9p21 associates with myocardial infarction, abdominal aortic aneurysm and intracranial aneurysm

    Nat. Genet.

    (2008)
  • W.D. Foulkes

    The CDKN2A (p16) gene and human cancer

    Mol. Med.

    (1997)
  • J. Gil et al.

    Regulation of the INK4b–ARF–INK4a tumour suppressor locus: all for one or one for all

    Nat. Rev. Mol. Cell Biol.

    (2006)
  • O. Jarinova

    Functional analysis of the chromosome 9p21.3 coronary artery disease risk locus

    Arterioscler. Thromb. Vasc. Biol.

    (2009)
  • G.K. Hansson et al.

    The immune response in atherosclerosis: a double-edged sword

    Nat. Rev. Immunol.

    (2006)
  • Y. Zhang

    Premature senescence of highly proliferative endothelial progenitor cells is induced by tumor necrosis factor-alpha via the p38 mitogen-activated protein kinase pathway

    FASEB J.

    (2009)
  • Y. Liu

    INK4/ARF transcript expression is associated with chromosome 9p21 variants linked to atherosclerosis

    PLoS ONE

    (2009)
  • L. Folkersen

    Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants

    PLoS ONE

    (2009)
  • L.M. Holdt

    ANRIL expression is associated with atherosclerosis risk at chromosome 9p21

    Arterioscler. Thromb. Vasc. Biol.

    (2010)
  • M.S. Cunnington

    Chromosome 9p21 SNPs associated with multiple disease phenotypes correlate with ANRIL expression

    PLoS Genet.

    (2010)
  • A.P. Pilbrow

    The chromosome 9p21.3 coronary heart disease risk allele is associated with altered gene expression in normal heart and vascular tissues

    PLoS ONE

    (2012)
  • A. Motterle

    Functional analyses of coronary artery disease associated variation on chromosome 9p21 in vascular smooth muscle cells

    Hum. Mol. Genet.

    (2012)
  • N.A. Almontashiri

    Abstract 15730: serum interferon alpha 21 is a biomarker of the 9p21.3 risk locus for coronary artery disease

    Circulation

    (2011)
  • A. Congrains

    ANRIL: molecular mechanisms and implications in human health

    Int. J. Mol. Sci.

    (2013)
  • H.M. Broadbent

    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)
  • Y. Kotake

    Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15INK4B tumor suppressor gene

    Oncogene

    (2011)
  • E. Pasmant

    ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWAS

    FASEB J.

    (2011)
  • O. Harismendy

    9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response

    Nature

    (2011)
  • A. Gschwendtner

    Sequence variants on chromosome 9p21.3 confer risk of atherosclerotic stroke

    Ann. Neurol.

    (2009)
  • T. Minamino

    Ras induces vascular smooth muscle cell senescence and inflammation in human atherosclerosis

    Circulation

    (2003)
  • J.B. Kim

    The effect of 9p21.3 coronary artery disease locus neighboring genes on atherosclerosis in mice

    Circulation

    (2012)
  • Cited by (123)

    View all citing articles on Scopus
    View full text