MicroRNA-148a regulates LDL receptor and ABCA1 expression to control circulating lipoprotein levels

  1. Goedeke, Leigh
  2. Rotllan, Noemi
  3. Canfrán-Duque, Alberto
  4. Aranda, Juan F
  5. Ramírez, Cristina M
  6. Araldi, Elisa
  7. Lin, Chin-Sheng
  8. Anderson, Norma N
  9. Wagschal, Alexandre
  10. de Cabo, Rafael
  11. Horton, Jay D
  12. Lasunción, Miguel A
  13. Näär, Anders M
  14. Suárez, Yajaira
  15. Fernández-Hernando, Carlos
Revista:
Nature Medicine

ISSN: 1078-8956,  1546-170X

Año de publicación: 2015

Volumen: 21

Número: 11

Páginas: 1280-1289

Tipo: Artículo

DOI: 10.1038/NM.3949 GOOGLE SCHOLAR lock_openAcceso abierto editor

Otras publicaciones en: Nature Medicine

Resumen

The hepatic low-density lipoprotein receptor (LDLR) pathway is essential for clearing circulating LDL cholesterol (LDL-C). Whereas the transcriptional regulation of LDLR is well characterized, the post-transcriptional mechanisms that govern LDLR expression are just beginning to emerge. Here we develop a high-throughput genome-wide screening assay to systematically identify microRNAs (miRNAs) that regulate LDLR activity in human hepatic cells. From this screen we identified and characterized miR-148a as a negative regulator of LDLR expression and activity and defined a sterol regulatory element–binding protein 1 (SREBP1)-mediated pathway through which miR-148a regulates LDL-C uptake. In mice, inhibition of miR-148a increased hepatic LDLR expression and decreased plasma LDL-C. Moreover, we found that miR-148a regulates hepatic expression of ATP-binding cassette, subfamily A, member 1 (ABCA1) and circulating high-density lipoprotein cholesterol (HDL-C) levels in vivo. These studies uncover a role for miR-148a as a key regulator of hepatic LDL-C clearance through direct modulation of LDLR expression and demonstrate the therapeutic potential of inhibiting miR-148a to ameliorate an elevated LDL-C/HDL-C ratio, a prominent risk factor for cardiovascular disease.

Referencias bibliográficas

  • Glass, C.K. & Witztum, J.L. Atherosclerosis. the road ahead. Cell 104, 503–516 (2001).
  • Lusis, A.J. Atherosclerosis. Nature 407, 233–241 (2000).
  • Brown, M.S. & Goldstein, J.L. The SREBP pathway: regulation of cholesterol metabolism by proteolysis of a membrane-bound transcription factor. Cell 89, 331–340 (1997).
  • Zelcer, N., Hong, C., Boyadjian, R. & Tontonoz, P. LXR regulates cholesterol uptake through Idol-dependent ubiquitination of the LDL receptor. Science 325, 100–104 (2009).
  • Hua, X. et al. SREBP-2, a second basic-helix-loop-helix–leucine zipper protein that stimulates transcription by binding to a sterol regulatory element. Proc. Natl. Acad. Sci. USA 90, 11603–11607 (1993).
  • Tontonoz, P., Kim, J.B., Graves, R.A. & Spiegelman, B.M. ADD1: a novel helix-loop-helix transcription factor associated with adipocyte determination and differentiation. Mol. Cell. Biol. 13, 4753–4759 (1993).
  • Yokoyama, C. et al. SREBP-1, a basic-helix-loop-helix–leucine zipper protein that controls transcription of the low density lipoprotein receptor gene. Cell 75, 187–197 (1993).
  • Goldstein, J.L. & Brown, M.S. Regulation of the mevalonate pathway. Nature 343, 425–430 (1990).
  • Walker, A.K. et al. A conserved SREBP-1–phosphatidylcholine feedback circuit regulates lipogenesis in metazoans. Cell 147, 840–852 (2011).
  • Horton, J.D. et al. Combined analysis of oligonucleotide microarray data from transgenic and knockout mice identifies direct SREBP target genes. Proc. Natl. Acad. Sci. USA 100, 12027–12032 (2003).
  • Maxwell, K.N., Soccio, R.E., Duncan, E.M., Sehayek, E. & Breslow, J.L. Novel putative SREBP and LXR target genes identified by microarray analysis in liver of cholesterol-fed mice. J. Lipid Res. 44, 2109–2119 (2003).
  • Beaven, S.W. & Tontonoz, P. Nuclear receptors in lipid metabolism: targeting the heart of dyslipidemia. Annu. Rev. Med. 57, 313–329 (2006).
  • Ambros, V. The functions of animal microRNAs. Nature 431, 350–355 (2004).
  • Bartel, D.P. MicroRNAs: target recognition and regulatory functions. Cell 136, 215–233 (2009).
  • Filipowicz, W., Bhattacharyya, S.N. & Sonenberg, N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat. Rev. Genet. 9, 102–114 (2008).
  • Rayner, K.J. et al. MiR-33 contributes to the regulation of cholesterol homeostasis. Science 328, 1570–1573 (2010).
  • Najafi-Shoushtari, S.H. et al. MicroRNA-33 and the SREBP host genes cooperate to control cholesterol homeostasis. Science 328, 1566–1569 (2010).
  • Jeon, T.I. et al. An SREBP-responsive microRNA operon contributes to a regulatory loop for intracellular lipid homeostasis. Cell Metab. 18, 51–61 (2013).
  • Rayner, K.J. et al. Antagonism of miR-33 in mice promotes reverse cholesterol transport and regression of atherosclerosis. J. Clin. Invest. 121, 2921–2931 (2011).
  • Rayner, K.J. et al. Inhibition of miR-33a/b in nonhuman primates raises plasma HDL and lowers VLDL triglycerides. Nature 478, 404–407 (2011).
  • Rottiers, V. et al. Pharmacological inhibition of a microRNA family in nonhuman primates by a seed-targeting 8-mer antimiR. Sci. Transl. Med. 5, 212ra162 (2013).
  • de Aguiar Vallim, T.Q. et al. MicroRNA-144 regulates hepatic ABCA1 and plasma HDL following activation of the nuclear receptor FXR. Circ. Res. 112, 1602–1612 (2013).
  • Ramírez, C.M. et al. Control of cholesterol metabolism and plasma HDL levels by miRNA-144. Circ. Res. 112, 1592–1601 (2013).
  • Vickers, K.C. et al. MicroRNA-223 coordinates cholesterol homeostasis. Proc. Natl. Acad. Sci. USA 111, 14518–14523 (2014).
  • Elmén, J. et al. LNA-mediated microRNA silencing in nonhuman primates. Nature 452, 896–899 (2008).
  • Elmén, J. et al. Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to upregulation of a large set of predicted target mRNAs in the liver. Nucleic Acids Res. 36, 1153–1162 (2008).
  • Esau, C. et al. miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting. Cell Metab. 3, 87–98 (2006).
  • Soh, J., Iqbal, J., Queiroz, J., Fernandez-Hernando, C. & Hussain, M.M. MicroRNA-30c reduces hyperlipidemia and atherosclerosis in mice by decreasing lipid synthesis and lipoprotein secretion. Nat. Med. 19, 892–900 (2013).
  • Brown, M.S., Dana, S.E. & Goldstein, J.L. Regulation of 3-hydroxy-3-methylglutaryl coenzyme A reductase activity in human fibroblasts by lipoproteins. Proc. Natl. Acad. Sci. USA 70, 2162–2166 (1973).
  • Goldstein, J.L., Basu, S.K., Brunschede, G.Y. & Brown, M.S. Release of low-density lipoprotein from its cell surface receptor by sulfated glycosaminoglycans. Cell 7, 85–95 (1976).
  • Zhang, J.H., Chung, T.D. & Oldenburg, K.R. A simple statistical parameter for use in evaluation and validation of high-throughput screening assays. J. Biomol. Screen. 4, 67–73 (1999).
  • Birmingham, A. et al. Statistical methods for analysis of high-throughput RNA interference screens. Nat. Methods 6, 569–575 (2009).
  • Barad, O. et al. MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res. 14, 2486–2494 (2004).
  • Landgraf, P. et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129, 1401–1414 (2007).
  • Vickers, K.C. et al. MicroRNA-27b is a regulatory hub in lipid metabolism and is altered in dyslipidemia. Hepatology 57, 533–542 (2013).
  • Arora, A. & Simpson, D.A. Individual mRNA expression profiles reveal the effects of specific microRNAs. Genome Biol. 9, R82 (2008).
  • Do, R. et al. Common variants associated with plasma triglycerides and risk for coronary artery disease. Nat. Genet. 45, 1345–1352 (2013).
  • Global Lipids Genetics Consortium. et al. Discovery and refinement of loci associated with lipid levels. Nat. Genet. 45, 1274–1283 (2013).
  • Huan, T. et al. Genome-wide identification of microRNA expression quantitative trait loci. Nat. Commun. 6, 6601 (2015).
  • Trajkovski, M. et al. MicroRNAs 103 and 107 regulate insulin sensitivity. Nature 474, 649–653 (2011).
  • Mercer, J. et al. RNAi screening reveals proteasome- and Cullin3-dependent stages in vaccinia virus infection. Cell Rep. 2, 1036–1047 (2012).
  • John, B. et al. Human MicroRNA targets. PLoS Biol. 2, e363 (2004).
  • Lewis, B.P., Burge, C.B. & Bartel, D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15–20 (2005).
  • Dweep, H., Gretz, N. & Sticht, C. miRWalk database for miRNA-target interactions. Methods Mol. Biol. 1182, 289–305 (2014).
  • Huang, D.W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).
  • Szklarczyk, D. et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 39, D561–D568 (2011).
  • Thomas, P.D. et al. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 13, 2129–2141 (2003).
  • Down, T.A. & Hubbard, T.J. Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res. 12, 458–461 (2002).
  • Saini, H.K., Griffiths-Jones, S. & Enright, A.J. Genomic analysis of human microRNA transcripts. Proc. Natl. Acad. Sci. USA 104, 17719–17724 (2007).
  • Ernst, J. & Kellis, M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat. Biotechnol. 28, 817–825 (2010).
  • Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43–49 (2011).
  • Kent, W.J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002).
  • Shimomura, I., Bashmakov, Y. & Horton, J.D. Increased levels of nuclear SREBP-1c associated with fatty livers in two mouse models of diabetes mellitus. J. Biol. Chem. 274, 30028–30032 (1999).
  • Shimomura, I., Shimano, H., Horton, J.D., Goldstein, J.L. & Brown, M.S. Differential expression of exons 1a and 1c in mRNAs for sterol regulatory element binding protein-1 in human and mouse organs and cultured cells. J. Clin. Invest. 99, 838–845 (1997).
  • Horton, J.D., Bashmakov, Y., Shimomura, I. & Shimano, H. Regulation of sterol regulatory element binding proteins in livers of fasted and refed mice. Proc. Natl. Acad. Sci. USA 95, 5987–5992 (1998).
  • Peet, D.J. et al. Cholesterol and bile acid metabolism are impaired in mice lacking the nuclear oxysterol receptor LXR alpha. Cell 93, 693–704 (1998).
  • Yoshikawa, T. et al. Identification of liver X receptor-retinoid X receptor as an activator of the sterol regulatory element-binding protein 1c gene promoter. Mol. Cell. Biol. 21, 2991–3000 (2001).
  • Dietschy, J.M., Turley, S.D. & Spady, D.K. Role of liver in the maintenance of cholesterol and low density lipoprotein homeostasis in different animal species, including humans. J. Lipid Res. 34, 1637–1659 (1993).
  • Oram, J.F. & Vaughan, A.M. ABCA1-mediated transport of cellular cholesterol and phospholipids to HDL apolipoproteins. Curr. Opin. Lipidol. 11, 253–260 (2000).
  • Yang, M. et al. Identification of miR-185 as a regulator of de novo cholesterol biosynthesis and low density lipoprotein uptake. J. Lipid Res. 55, 226–238 (2014).
  • Ramírez, C.M. et al. MicroRNA 33 regulates glucose metabolism. Mol. Cell. Biol. 33, 2891–2902 (2013).
  • Dávalos, A. et al. miR-33a/b contribute to the regulation of fatty acid metabolism and insulin signaling. Proc. Natl. Acad. Sci. USA 108, 9232–9237 (2011).
  • Suárez, Y., Fernandez-Hernando, C., Pober, J.S. & Sessa, W.C. Dicer-dependent microRNAs regulate gene expression and functions in human endothelial cells. Circ. Res. 100, 1164–1173 (2007).
  • Goedeke, L. et al. A regulatory role for microRNA 33* in controlling lipid metabolism gene expression. Mol. Cell. Biol. 33, 2339–2352 (2013).
  • Allen, R.M., Marquart, T.J., Jesse, J.J. & Baldan, A. Control of very low–density lipoprotein secretion by N-ethylmaleimide–sensitive factor and miR-33. Circ. Res. 115, 10–22 (2014).
  • Calvo, D., Gomez-Coronado, D., Suarez, Y., Lasuncion, M.A. & Vega, M.A. Human CD36 is a high-affinity receptor for the native lipoproteins HDL, LDL and VLDL. J. Lipid Res. 39, 777–788 (1998).
  • Suárez, Y. et al. Synergistic upregulation of low-density lipoprotein receptor activity by tamoxifen and lovastatin. Cardiovasc. Res. 64, 346–355 (2004).
  • Chamorro-Jorganes, A., Araldi, E., Rotllan, N., Cirera-Salinas, D. & Suarez, Y. Autoregulation of glypican-1 by intronic microRNA-149 fine tunes the angiogenic response to FGF2 in human endothelial cells. J. Cell Sci. 127, 1169–1178 (2014).
  • Ramirez, C.M. et al. MicroRNA-758 regulates cholesterol efflux through post-transcriptional repression of ATP-binding cassette transporter A1. Arterioscler. Thromb. Vasc. Biol. 31, 2707–2714 (2011).
  • Wang, W. et al. Radixin is required to maintain apical canalicular membrane structure and function in rat hepatocytes. Gastroenterology 131, 878–884 (2006).
  • Mattison, J.A. et al. Resveratrol prevents high fat/sucrose diet-induced central arterial wall inflammation and stiffening in nonhuman primates. Cell Metab. 20, 183–190 (2014).
  • Goedeke, L. et al. Long-term therapeutic silencing of miR-33 increases circulating triglyceride levels and hepatic lipid accumulation in mice. EMBO Mol. Med. 6, 1133–1141 (2014).
  • Miller, A.M. et al. MiR-155 has a protective role in the development of non-alcoholic hepatosteatosis in mice. PLoS ONE 8, e72324 (2013).