Atherosclerosis 242 (2015) 630e631
Contents lists available at ScienceDirect
Atherosclerosis journal homepage: www.elsevier.com/locate/atherosclerosis
Discussion
Cardiovascular disease genes come together Aldons J. Lusis UCLA School of Medicine, Los Angeles, CA 90095-1679, USA
a r t i c l e i n f o Article history: Received 12 June 2015 Accepted 15 June 2015 Available online 23 June 2015 Keywords: TGF beta 1 signaling CAD GWAS loci Gene-by-gene interactions
Genome-wide association studies (GWAS) for coronary artery disease (CAD) have identified about 50 significant loci and about 100 suggestive loci [1]. The challenge now is to identify the causal genes (most loci contain multiple genes) and then to connect them in biologic pathways and networks. In this issue of Atherosclerosis Turner and colleagues [2] take an important step in their study of TGFb1 signaling effects on CAD candidate genes. The authors hypothesized that genes at two CAD GWAS loci, containing the COL4A1 and COL4A2 genes on chromosome 13 and
Fig. 1. Epistatic interactions between SMAD3 and COL4A1/COL4A2 polymorphisms in CAD. Panel A: The peak single nucleotide polymorphisms rs12441344 (SNP A) and rs72655775 (SNP B) individually show association with CAD in population studies. To model their effects on CAD (Y), the authors used logistic regression modeling in which b0 is a constant, b1 and b2 are coefficients for the individual gene dosage effects of SNPs A and B, b3 is a coefficient for their joint (epistatic) effect, and ε is the error. The p value for the interaction is obtained under the null hypothesis that the true b3 ¼ 0. Panel B: How might the two genes exhibit a non-additive interaction? There are many possible scenarios but a hypothetical one is illustrated. In this case, the two COL4A alleles show differential responsiveness to TGFb1 (and SMAD3) signaling while the two SMAD3 alleles have differential expression. Thus, among individuals carrying the SMAD A allele, there is little effect of the COL4A alleles on collagen IV levels, while in individuals carrying the SMAD B allele, the COL4A alleles have a large effect.
DOI of original article: http://dx.doi.org/10.1016/j.atherosclerosis.2015.08.008. E-mail address: [email protected]. http://dx.doi.org/10.1016/j.atherosclerosis.2015.06.024 0021-9150/© 2015 Elsevier Ireland Ltd. All rights reserved.
A.J. Lusis / Atherosclerosis 242 (2015) 630e631
the SMAD3 gene on chromosome 15, might be connected through TGFb signaling [1,3]. TGFb1 is synthesized by vascular cells, T cells and monocyte/macrophages, and its expression has previously been associated with protection against atherosclerosis in both human studies and mouse models. TGFb1 is known to upregulate the COL4A1 and COL4A2 genes encoding type IV collagens, and a potential mechanism for the protective effect on CAD is the inhibition of smooth muscle cell proliferation by collagen [4]. SMAD3 is another known target of TGFb1 and the authors tested the possibility that SMAD3 mediates the up-regulation of the collagen genes by TGFb1. Using cultured human aortic smooth muscle cells and a cell line known to express the COL4A1/COL4A2 genes, they carried out studies with pharmacological inhibitors of TGFb1 signaling and siRNA knockdown of the SMADs to show that both SMAD3 and SMAD4, which form heterodimers, are required for the upregulation of COL4A1/COL4A2 by TGFb1. They also provided evidence that the activation of COL4A1/COL4A2 by SMAD3/SMAD4 may not be direct (Fig. 1). Knowing this, they further asked whether there might be a significant gene-by-gene interaction (epistasis) between the loci. That is, do the polymorphisms at the loci each contribute to CAD independently, such that the combined effect on CAD is simply the sum of their individual effects, or do they act in a more complex, non-additive manner? They addressed this question using logistic regression to test the model shown in Fig. 1. To have sufficient power and replicate the findings, they carried out meta-analysis on 5 independent cohorts totaling 4956 cases and 2774 controls. The evidence for an interaction was highly significant (Bonferroni e adjusted p value 6.9 103). The study is important for two reasons. First, it provides strong evidence for the role of a pathway, rather than simply a gene, in CAD. All the genes in the pathway now become potential targets for intervention and for further biochemical and genetic studies. Second, this study provides one of very few examples of epistatic interactions in common human diseases. Whether epistatic interactions play a large role in CAD and other common diseases is unclear [5e7], but the issue is of considerable interest. In addition
631
to providing mechanistic information, an understanding of epistasis is relevant to the puzzle of missing heritability [8]. Acknowledgments This work is supported by grants HL28481, HL30568, HL126753, and the Leducq Foundation. References [1] H. Schunkert, I.R. Konig, S. Kathiresan, M.P. Reilly, T.L. Assimes, H. Holm, et al., Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease, Nat. Genet. 43 (4) (2011) 333e338. Epub 2011/03/08. doi: 10.1038/ng.784. PubMed PMID: 21378990; PubMed Central PMCID: PMC3119261. [2] A.W. Turner, M. Nikpay, A. Silva, P. Lau, A. Martinuk, T.A. Linseman, et al., Functional interaction between COL4A1/COL4A2 and SMAD risk loci for coronary artery disease, Atherosclerosis 242 (2) (2015) 543e552. [3] N.J. Samani, J. Erdmann, A.S. Hall, C. Hengstenberg, M. Mangino, B. Mayer, et al., Genomewide association analysis of coronary artery disease, N. Engl. J. Med. 357 (5) (2007) 443e453. Epub 2007/07/20. doi: 10.1056/NEJMoa072366. PubMed PMID: 17634449; PubMed Central PMCID: PMC2719290. [4] A.W. Orr, M.Y. Lee, J.A. Lemmon, A. Yurdagul Jr., M.F. Gomez, P.D. Bortz, et al., Molecular mechanisms of collagen isotype-specific modulation of smooth muscle cell phenotype, Arterioscler. Thromb. Vasc. Biol. 29 (2) (2009) 225e231. Epub 2008/11/22. doi: 10.1161/ATVBAHA.108.178749. PubMed PMID: 19023090; PubMed Central PMCID: PMC2692987. [5] J.S. Bloom, I.M. Ehrenreich, W.T. Loo, T.L. Lite, L. Kruglyak, Finding the sources of missing heritability in a yeast cross, Nature 494 (7436) (2013) 234e237. Epub 2013/02/05. doi: 10.1038/nature11867. PubMed PMID: 23376951; PubMed Central PMCID: PMC4001867. [6] G. Hemani, K. Shakhbazov, H.J. Westra, T. Esko, A.K. Henders, A.F. McRae, et al., Detection and replication of epistasis influencing transcription in humans, Nature 508 (7495) (2014) 249e253. Epub 2014/02/28. doi: 10.1038/nature13005. PubMed PMID: 24572353; PubMed Central PMCID: PMC3984375. [7] H. Shao, L.C. Burrage, D.S. Sinasac, A.E. Hill, S.R. Ernest, W. O'Brien, et al., Genetic architecture of complex traits: large phenotypic effects and pervasive epistasis, Proc. Natl. Acad. Sci. U. S. A. 105 (50) (2008) 19910e19914. Epub 2008/12/11. doi: 10.1073/pnas.0810388105. PubMed PMID: 19066216; PubMed Central PMCID: PMC2604967. [8] O. Zuk, E. Hechter, S.R. Sunyaev, E.S. Lander, The mystery of missing heritability: genetic interactions create phantom heritability, Proc. Natl. Acad. Sci. U. S. A. 109 (4) (2012) 1193e1198. Epub 2012/01/10. doi: 10.1073/pnas.1119675109. PubMed PMID: 22223662; PubMed Central PMCID: PMC3268279.
Contents lists available at ScienceDirect
Atherosclerosis journal homepage: www.elsevier.com/locate/atherosclerosis
Discussion
Cardiovascular disease genes come together Aldons J. Lusis UCLA School of Medicine, Los Angeles, CA 90095-1679, USA
a r t i c l e i n f o Article history: Received 12 June 2015 Accepted 15 June 2015 Available online 23 June 2015 Keywords: TGF beta 1 signaling CAD GWAS loci Gene-by-gene interactions
Genome-wide association studies (GWAS) for coronary artery disease (CAD) have identified about 50 significant loci and about 100 suggestive loci [1]. The challenge now is to identify the causal genes (most loci contain multiple genes) and then to connect them in biologic pathways and networks. In this issue of Atherosclerosis Turner and colleagues [2] take an important step in their study of TGFb1 signaling effects on CAD candidate genes. The authors hypothesized that genes at two CAD GWAS loci, containing the COL4A1 and COL4A2 genes on chromosome 13 and
Fig. 1. Epistatic interactions between SMAD3 and COL4A1/COL4A2 polymorphisms in CAD. Panel A: The peak single nucleotide polymorphisms rs12441344 (SNP A) and rs72655775 (SNP B) individually show association with CAD in population studies. To model their effects on CAD (Y), the authors used logistic regression modeling in which b0 is a constant, b1 and b2 are coefficients for the individual gene dosage effects of SNPs A and B, b3 is a coefficient for their joint (epistatic) effect, and ε is the error. The p value for the interaction is obtained under the null hypothesis that the true b3 ¼ 0. Panel B: How might the two genes exhibit a non-additive interaction? There are many possible scenarios but a hypothetical one is illustrated. In this case, the two COL4A alleles show differential responsiveness to TGFb1 (and SMAD3) signaling while the two SMAD3 alleles have differential expression. Thus, among individuals carrying the SMAD A allele, there is little effect of the COL4A alleles on collagen IV levels, while in individuals carrying the SMAD B allele, the COL4A alleles have a large effect.
DOI of original article: http://dx.doi.org/10.1016/j.atherosclerosis.2015.08.008. E-mail address: [email protected]. http://dx.doi.org/10.1016/j.atherosclerosis.2015.06.024 0021-9150/© 2015 Elsevier Ireland Ltd. All rights reserved.
A.J. Lusis / Atherosclerosis 242 (2015) 630e631
the SMAD3 gene on chromosome 15, might be connected through TGFb signaling [1,3]. TGFb1 is synthesized by vascular cells, T cells and monocyte/macrophages, and its expression has previously been associated with protection against atherosclerosis in both human studies and mouse models. TGFb1 is known to upregulate the COL4A1 and COL4A2 genes encoding type IV collagens, and a potential mechanism for the protective effect on CAD is the inhibition of smooth muscle cell proliferation by collagen [4]. SMAD3 is another known target of TGFb1 and the authors tested the possibility that SMAD3 mediates the up-regulation of the collagen genes by TGFb1. Using cultured human aortic smooth muscle cells and a cell line known to express the COL4A1/COL4A2 genes, they carried out studies with pharmacological inhibitors of TGFb1 signaling and siRNA knockdown of the SMADs to show that both SMAD3 and SMAD4, which form heterodimers, are required for the upregulation of COL4A1/COL4A2 by TGFb1. They also provided evidence that the activation of COL4A1/COL4A2 by SMAD3/SMAD4 may not be direct (Fig. 1). Knowing this, they further asked whether there might be a significant gene-by-gene interaction (epistasis) between the loci. That is, do the polymorphisms at the loci each contribute to CAD independently, such that the combined effect on CAD is simply the sum of their individual effects, or do they act in a more complex, non-additive manner? They addressed this question using logistic regression to test the model shown in Fig. 1. To have sufficient power and replicate the findings, they carried out meta-analysis on 5 independent cohorts totaling 4956 cases and 2774 controls. The evidence for an interaction was highly significant (Bonferroni e adjusted p value 6.9 103). The study is important for two reasons. First, it provides strong evidence for the role of a pathway, rather than simply a gene, in CAD. All the genes in the pathway now become potential targets for intervention and for further biochemical and genetic studies. Second, this study provides one of very few examples of epistatic interactions in common human diseases. Whether epistatic interactions play a large role in CAD and other common diseases is unclear [5e7], but the issue is of considerable interest. In addition
631
to providing mechanistic information, an understanding of epistasis is relevant to the puzzle of missing heritability [8]. Acknowledgments This work is supported by grants HL28481, HL30568, HL126753, and the Leducq Foundation. References [1] H. Schunkert, I.R. Konig, S. Kathiresan, M.P. Reilly, T.L. Assimes, H. Holm, et al., Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease, Nat. Genet. 43 (4) (2011) 333e338. Epub 2011/03/08. doi: 10.1038/ng.784. PubMed PMID: 21378990; PubMed Central PMCID: PMC3119261. [2] A.W. Turner, M. Nikpay, A. Silva, P. Lau, A. Martinuk, T.A. Linseman, et al., Functional interaction between COL4A1/COL4A2 and SMAD risk loci for coronary artery disease, Atherosclerosis 242 (2) (2015) 543e552. [3] N.J. Samani, J. Erdmann, A.S. Hall, C. Hengstenberg, M. Mangino, B. Mayer, et al., Genomewide association analysis of coronary artery disease, N. Engl. J. Med. 357 (5) (2007) 443e453. Epub 2007/07/20. doi: 10.1056/NEJMoa072366. PubMed PMID: 17634449; PubMed Central PMCID: PMC2719290. [4] A.W. Orr, M.Y. Lee, J.A. Lemmon, A. Yurdagul Jr., M.F. Gomez, P.D. Bortz, et al., Molecular mechanisms of collagen isotype-specific modulation of smooth muscle cell phenotype, Arterioscler. Thromb. Vasc. Biol. 29 (2) (2009) 225e231. Epub 2008/11/22. doi: 10.1161/ATVBAHA.108.178749. PubMed PMID: 19023090; PubMed Central PMCID: PMC2692987. [5] J.S. Bloom, I.M. Ehrenreich, W.T. Loo, T.L. Lite, L. Kruglyak, Finding the sources of missing heritability in a yeast cross, Nature 494 (7436) (2013) 234e237. Epub 2013/02/05. doi: 10.1038/nature11867. PubMed PMID: 23376951; PubMed Central PMCID: PMC4001867. [6] G. Hemani, K. Shakhbazov, H.J. Westra, T. Esko, A.K. Henders, A.F. McRae, et al., Detection and replication of epistasis influencing transcription in humans, Nature 508 (7495) (2014) 249e253. Epub 2014/02/28. doi: 10.1038/nature13005. PubMed PMID: 24572353; PubMed Central PMCID: PMC3984375. [7] H. Shao, L.C. Burrage, D.S. Sinasac, A.E. Hill, S.R. Ernest, W. O'Brien, et al., Genetic architecture of complex traits: large phenotypic effects and pervasive epistasis, Proc. Natl. Acad. Sci. U. S. A. 105 (50) (2008) 19910e19914. Epub 2008/12/11. doi: 10.1073/pnas.0810388105. PubMed PMID: 19066216; PubMed Central PMCID: PMC2604967. [8] O. Zuk, E. Hechter, S.R. Sunyaev, E.S. Lander, The mystery of missing heritability: genetic interactions create phantom heritability, Proc. Natl. Acad. Sci. U. S. A. 109 (4) (2012) 1193e1198. Epub 2012/01/10. doi: 10.1073/pnas.1119675109. PubMed PMID: 22223662; PubMed Central PMCID: PMC3268279.
