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Needles in the genetic haystack of lipid disorders: single nucleotide polymorphisms in the microRNA regulome

2013; Elsevier BV; Volume: 54; Issue: 5 Linguagem: Inglês

10.1194/jlr.r035766

1539-7262

Praveen Sethupathy,

RNA modifications and cancer

In recent years, microRNAs (miRNA) have emerged as important posttranscriptional regulators of gene expression in a wide variety of biological pathways. Since the discovery of the liver-specific miRNA-122 (miR-122) and its critical role in hepatic function, numerous additional miRNAs have been implicated in lipid metabolism. It is now apparent that lipid homeostasis is governed in part by an intricate web of miRNA activity. miRNAs are thought to confer robustness against environmental changes, such as diet modifications. Therefore, naturally occurring genetic variation that perturbs miRNA expression and/or function is likely to contribute to interindividual variability in lipid phenotypes. Although the field is still in its infancy, this review describes the growing evidence for miRNA-related genetic variation as etiological factors in lipid disorders. Specific examples, including a variant in a miRNA transcriptional control element that leads to dyslipidemia as well as a variant in a miRNA target site that modulates the effect of diet on plasma lipid levels, are discussed. Finally, the utility of recent systems genetics approaches to uncover hidden miRNA-related genetic associations with lipid disorders are considered, thereby illuminating the needles in the genetic haystack. In recent years, microRNAs (miRNA) have emerged as important posttranscriptional regulators of gene expression in a wide variety of biological pathways. Since the discovery of the liver-specific miRNA-122 (miR-122) and its critical role in hepatic function, numerous additional miRNAs have been implicated in lipid metabolism. It is now apparent that lipid homeostasis is governed in part by an intricate web of miRNA activity. miRNAs are thought to confer robustness against environmental changes, such as diet modifications. Therefore, naturally occurring genetic variation that perturbs miRNA expression and/or function is likely to contribute to interindividual variability in lipid phenotypes. Although the field is still in its infancy, this review describes the growing evidence for miRNA-related genetic variation as etiological factors in lipid disorders. Specific examples, including a variant in a miRNA transcriptional control element that leads to dyslipidemia as well as a variant in a miRNA target site that modulates the effect of diet on plasma lipid levels, are discussed. Finally, the utility of recent systems genetics approaches to uncover hidden miRNA-related genetic associations with lipid disorders are considered, thereby illuminating the needles in the genetic haystack. Non-coding RNA (ncRNA) is a diverse class of regulatory molecules involved in the control of gene expression (1Esteller M. Non-coding RNAs in human disease.Nat. Rev. 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Moreover, miRNAs have been demonstrated to be i) stable plasma biomarkers of physiological status (4Mitchell P.S. Parkin R.K. Kroh E.M. Fritz B.R. Wyman S.K. Pogosova-Agadjanyan E.L. Peterson A. Noteboom J. O舗Briant K.C. Allen A. et al.Circulating microRNAs as stable blood-based markers for cancer detection.Proc. Natl. Acad. Sci. USA. 2008; 105: 10513-10518Crossref PubMed Scopus (6419) Google Scholar, 5Karolina D.S. Tavintharan S. Armugam A. Sepramaniam S. Pek S.L. Wong M.T. Lim S.C. Sum C.F. Jeyaseelan K. Circulating miRNA profiles in patients with metabolic syndrome.J. Clin. Endocrinol. Metab. 2012; 97: E2271-E2276Crossref PubMed Scopus (303) Google Scholar), ii) novel intercellular signaling molecules (6Vickers K.C. Remaley A.T. Lipid-based carriers of microRNAs and intercellular communication.Curr. Opin. Lipidol. 2012; 23: 91-97Crossref PubMed Scopus (249) Google Scholar), iii) etiological factors in complex diseases (7Couzin J. 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Modulation of hepatitis C virus RNA abundance by a liver-specific microRNA.Science. 2005; 309: 1577-1581Crossref PubMed Scopus (2128) Google Scholar). Subsequently, it was demonstrated that inhibition of miR-122 by a locked nucleic acid (LNA) antisense oligonucleotide diminishes HCV viremia in chimpanzees (17Lanford R.E. Hildebrandt-Eriksen E.S. Petri A. Persson R. Lindow M. Munk M.E. Kauppinen S. Orum H. Therapeutic silencing of microRNA-122 in primates with chronic hepatitis C virus infection.Science. 2010; 327: 198-201Crossref PubMed Scopus (1464) Google Scholar). The anti-miR-122 LNA molecule (known as Miravirsen) has since advanced to phase II human clinical trials for hepatitis C treatment, and it appears to induce a potent antiviral effect in the absence of evident liver or cardiac toxicities (18Lindow M. Kauppinen S. Discovering the first microRNA-targeted drug.J. Cell Biol. 2012; 199: 407-412Crossref PubMed Scopus (230) Google Scholar). miR-122 was also the first miRNA identified as a regulator of lipid metabolism (19Esau C. Davis S. Murray S.F. Yu X.X. Pandey S.K. Pear M. Watts L. Booten S.L. Graham M. McKay R. et al.miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting.Cell Metab. 2006; 3: 87-98Abstract Full Text Full Text PDF PubMed Scopus (1771) Google Scholar). In 2006, antisense oligonucleotide-mediated inhibition of miR-122 (ASO-miR-122) in mice reduced plasma cholesterol levels, decreased hepatic lipid synthesis, and enhanced hepatic fatty acid oxidation (19Esau C. Davis S. Murray S.F. Yu X.X. Pandey S.K. Pear M. Watts L. Booten S.L. Graham M. McKay R. et al.miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting.Cell Metab. 2006; 3: 87-98Abstract Full Text Full Text PDF PubMed Scopus (1771) Google Scholar). Moreover, the ASO-miR-122 was also able to reverse the effects of diet-induced obesity by reducing hepatic steatosis. Consistent with these findings, Miravirsen (anti-miR-122 LNA) has been shown to reduce plasma cholesterol levels in humans as well (18Lindow M. Kauppinen S. Discovering the first microRNA-targeted drug.J. Cell Biol. 2012; 199: 407-412Crossref PubMed Scopus (230) Google Scholar). Recently, miR-122 was also demonstrated to be a critical regulator of hepatic circadian rhythm (20Gatfield D. Le Martelot G. Vejnar C.E. Gerlach D. Schaad O. Fleury-Olela F. Ruskeepaa A.L. Oresic M. Esau C.C. Zdobnov E.M. et al.Integration of microRNA miR-122 in hepatic circadian gene expression.Genes Dev. 2009; 23: 1313-1326Crossref PubMed Scopus (302) Google Scholar), inflammation (21Hsu S.H. Wang B. Kota J. Yu J. Costinean S. Kutay H. Yu L. Bai S. La Perle K. Chivukula R.R. et al.Essential metabolic, anti-inflammatory, and anti-tumorigenic functions of miR-122 in liver.J. Clin. 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Moreover, they demonstrated that many miRNAs, including miR-145, miR-27b, miR-30d, and miR-34a, are more significantly altered in NASH than miR-122. Very recently, several of these miRNAs, such as miR-27b (28Vickers K.C. Shoucri B.M. Levin M.G. Wu H. Pearson D.S. Osei-Hwedieh D. Collins F.S. Remaley A.T. Sethupathy P. MicroRNA-27b is a regulatory hub in lipid metabolism and is altered in dyslipidemia.Hepatology. 2013; 57: 533-542Crossref PubMed Scopus (176) Google Scholar) and miR-34a (34Lee J. Kemper J.K. Controlling SIRT1 expression by microRNAs in health and metabolic disease.Aging (Albany NY). 2010; 2: 527-534Crossref PubMed Scopus (87) Google Scholar), and a growing number of others, including miR-125a, miR-33, miR-370, miR-378, miR-613, and miR-758, have been directly implicated in the regulation of lipid synthesis, transport, storage, and metabolism. Given these findings, which have been summarized in several recent review articles (35Rayner K.J. Fernandez-Hernando C. Moore K.J. MicroRNAs regulating lipid metabolism in atherogenesis.Thromb. Haemost. 2012; 107: 642-647Crossref PubMed Google Scholar, 36Moore K.J. Rayner K.J. Suarez Y. Fernandez-Hernando C. The role of microRNAs in cholesterol efflux and hepatic lipid metabolism.Annu. Rev. Nutr. 2011; 31: 49-63Crossref PubMed Scopus (124) Google Scholar, 37Fernandez-Hernando C. Suarez Y. Rayner K.J. Moore K.J. MicroRNAs in lipid metabolism.Curr. Opin. Lipidol. 2011; 22: 86-92Crossref PubMed Scopus (246) Google Scholar, 38Sacco J. Adeli K. MicroRNAs: emerging roles in lipid and lipoprotein metabolism.Curr. Opin. Lipidol. 2012; 23: 220-225Crossref PubMed Scopus (91) Google Scholar, 39Moore K.J. Rayner K.J. Suarez Y. Fernandez-Hernando C. microRNAs and cholesterol metabolism.Trends Endocrinol. Metab. 2010; 21: 699-706Abstract Full Text Full Text PDF PubMed Scopus (121) Google Scholar, 40Rotllan N. Fernandez-Hernando C. MicroRNA regulation of cholesterol metabolism.Cholesterol. 2012; 2012: 847849Crossref PubMed Scopus (64) Google Scholar, 41Rottiers V. Naar A.M. MicroRNAs in metabolism and metabolic disorders.Nat. Rev. Mol. Cell Biol. 2012; 13: 239-250Crossref PubMed Scopus (880) Google Scholar), it is apparent that the activity of numerous miRNAs contributes to lipid homeostasis. miRNA loci are transcribed predominantly by RNA Polymerase II (42Schanen B.C. Li X. Transcriptional regulation of mammalian miRNA genes.Genomics. 2011; 97: 1-6Crossref PubMed Scopus (123) Google Scholar), which yields primary transcripts (pri-miRNA) that range from a few kilobases to a few hundred kilobases in length (43Saini H.K. Enright A.J. Griffiths-Jones S. Annotation of mammalian primary microRNAs.BMC Genomics. 2008; 9: 564Crossref PubMed Scopus (113) Google Scholar). Pri-miRNAs harbor one or more hairpin-like secondary structures, termed precursor miRNAs (pre-miRNA), which are cleaved and shuttled to the cytoplasm, where they are processed further into ∼22 bp double-stranded RNA duplexes (44Kim V.N. Han J. Siomi M.C. Biogenesis of small RNAs in animals.Nat. Rev. Mol. Cell Biol. 2009; 10: 126-139Crossref PubMed Scopus (2581) Google Scholar). One of the strands, referred to as the mature miRNA, is loaded onto the RNA-induced silencing complex (RISC). The miRNA guides and tethers the RISC to specific target sites within RNA molecules in order to regulate their stability and/or translation (3Bartel D.P. MicroRNAs: target recognition and regulatory functions.Cell. 2009; 136: 215-233Abstract Full Text Full Text PDF PubMed Scopus (15858) Google Scholar). The canonical pathway for miRNA biogenesis and targeting is shown in Fig. 1. The miRNA regulome is defined as the compendium of regulatory elements that either regulate miRNA expression (transcriptional control elements and pre-miRNAs) or are regulated by miRNA activity (RNA target sites). Genetic variation in the miRNA regulome can perturb miRNA expression and/or function, potentially contributing to a wide variety of lipid-related phenotypes (45Sethupathy P. Collins F.S. MicroRNA target site polymorphisms and human disease.Trends Genet. 2008; 24: 489-497Abstract Full Text Full Text PDF PubMed Scopus (285) Google Scholar, 46Borel C. Antonarakis S.E. Functional genetic variation of human miRNAs and phenotypic consequences.Mamm. Genome. 2008; 19: 503-509Crossref PubMed Scopus (71) Google Scholar, 47Mishra P.J. Bertino J.R. MicroRNA polymorphisms: the future of pharmacogenomics, molecular epidemiology and individualized medicine.Pharmacogenomics. 2009; 10: 399-416Crossref PubMed Scopus (235) Google Scholar). Transcriptional control elements can be classified as either proximal (i.e., promoter) or distal (i.e., long-range regulatory elements; LRE). Both classes of elements recruit transcriptional factor (TF) complexes that enhance or silence the expression of one or more genes (48Maston G.A. Evans S.K. Green M.R. Transcriptional regulatory elements in the human genome.Annu. Rev. Genomics Hum. Genet. 2006; 7: 29-59Crossref PubMed Scopus (576) Google Scholar). Genetic mutations within these elements can alter the binding affinity for one or more TFs, and the resulting effect on transcription could directly influence lipid metabolic pathways. For example, several single nucleotide polymorphisms (SNP) in the core promoter region of the low-density lipoprotein receptor (LDLR) gene have been shown to abolish binding of the transcription factor Sp1 (49Usifo E. Leigh S.E. Whittall R.A. Lench N. Taylor A. Yeats C. Orengo C.A. Martin A.C. Celli J. Humphries S.E. 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Ahfeldt T. Sachs K.V. Li X. Li H. Kuperwasser N. Ruda V.M. et al.From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus.Nature. 2010; 466: 714-719Crossref PubMed Scopus (808) Google Scholar, 55Marian A.J. Genome-wide association studies complemented with mechanistic biological studies identify sortilin 1 as a novel regulator of cholesterol trafficking.Curr. Atheroscler. Rep. 2011; 13: 190-192Crossref PubMed Scopus (4) Google Scholar). Until recently, attempts to map disease-associated genetic variants to miRNA transcriptional control elements have been severely hindered by poor annotation of miRNA promoters and LREs. Conventional methods for the identification of a gene promoter, such as 5′ rapid amplification of cDNA ends (5′-RACE), require access to the full-length primary transcript of the gene. However, the primary transcripts of miRNAs are often too rapidly processed and degraded, which renders these traditional approaches less reliable for miRNA promoter identification (56Lee Y. Kim M. Han J. Yeom K.H. Lee S. Baek S.H. Kim V.N. MicroRNA genes are transcribed by RNA polymerase II.EMBO J. 2004; 23: 4051-4060Crossref PubMed Scopus (3240) Google Scholar). In the last few years, several conceptual and technological advances in the field of epigenomics have allowed for the detection of miRNA promoter regions by analyzing chromatin structure (57Kouzarides T. Chromatin modifications and their function.Cell. 2007; 128: 693-705Abstract Full Text Full Text PDF PubMed Scopus (8034) Google Scholar, 58Park P.J. ChIP-seq: advantages and challenges of a maturing technology.Nat. Rev. Genet. 2009; 10: 669-680Crossref PubMed Scopus (1305) Google Scholar). Active promoters are characterized by a nucleosome-free site (open chromatin) that is flanked by regions enriched for specific chromatin marks, including histone H3 lysine 27 mono-acetylation (H3K27ac), histone H3 lysine 4 tri-methylation (H3K4me3), and histone H3 lysine 79 di-methylation (H3K79me2). In the last few years, the application of epigenome-wide chromatin profiling strategies has led to a comprehensive set of annotations for mammalian miRNA promoters (42Schanen B.C. Li X. Transcriptional regulation of mammalian miRNA genes.Genomics. 2011; 97: 1-6Crossref PubMed Scopus (123) Google Scholar). Largely due to the relatively recent annotation of miRNA promoters, disease-causing variants in miRNA transcriptional control elements have not yet been extensively investigated. However, one illustrative example is that of a functional SNP (rs57095329) in the promoter of miR-146a that confers significant risk for systemic lupus erythematosus (SLE) (59Luo X. Yang W. Ye D.Q. Cui H. Zhang Y. Hirankarn N. Qian X. Tang Y. Lau Y.L. de Vries N. et al.A functional variant in microRNA-146a promoter modulates its expression and confers disease risk for systemic lupus erythematosus.PLoS Genet. 2011; 7: e1002128Crossref PubMed Scopus (229) Google Scholar). The rs57095329 minor allele reduces the binding affinity for the transcriptional activator Ets1, which in turn reduces miR-146a expression (59Luo X. Yang W. Ye D.Q. Cui H. Zhang Y. Hirankarn N. Qian X. Tang Y. Lau Y.L. de Vries N. et al.A functional variant in microRNA-146a promoter modulates its expression and confers disease risk for systemic lupus erythematosus.PLoS Genet. 2011; 7: e1002128Crossref PubMed Scopus (229) Google Scholar). SLE is associated with dyslipoproteinemia (60Borba E.F. Carvalho J.F. Bonfa E. Mechanisms of dyslipoproteinemias in systemic lupus erythematosus.Clin. Dev. Immunol. 2006; 13: 203-208Crossref PubMed Scopus (61) Google Scholar, 61Chung C.P. Oeser A. Solus J. Avalos I. Gebretsadik T. 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Furthermore, viral administration of miR-146a to lupus-prone mice was found to inhibit the progression of SLE (63Pan Y. Jia T. Zhang Y. Zhang K. Zhang R. Li J. Wang L. MS2 VLP-based delivery of microRNA-146a inhibits autoantibody production in lupus-prone mice.Int. J. Nanomedicine. 2012; 7: 5957-5967Crossref PubMed Scopus (74) Google Scholar). Therefore, the overexpression of miR-146a may represent a novel preventative and/or therapeutic strategy for immune-related lipid disorders. Bona fide miRNA target sites are distributed across the entire transcriptome (64Chi S.W. Zang J.B. Mele A. Darnell R.B. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps.Nature. 2009; 460: 479-486Crossref PubMed Scopus (1409) Google Scholar, 65Hafner M. Landthaler M. Burger L. Khorshid M. Hausser J. Berninger P. Rothballer A. Ascano Jr, M. Jungkamp A.C. 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