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From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

Nature volume 466, pages 714–719 (2010)Cite this article

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Abstract

Recent genome-wide association studies (GWASs) have identified a locus on chromosome 1p13 strongly associated with both plasma low-density lipoprotein cholesterol (LDL-C) and myocardial infarction (MI) in humans. Here we show through a series of studies in human cohorts and human-derived hepatocytes that a common noncoding polymorphism at the 1p13 locus, rs12740374, creates a C/EBP (CCAAT/enhancer binding protein) transcription factor binding site and alters the hepatic expression of the SORT1 gene. With small interfering RNA (siRNA) knockdown and viral overexpression in mouse liver, we demonstrate that Sort1 alters plasma LDL-C and very low-density lipoprotein (VLDL) particle levels by modulating hepatic VLDL secretion. Thus, we provide functional evidence for a novel regulatory pathway for lipoprotein metabolism and suggest that modulation of this pathway may alter risk for MI in humans. We also demonstrate that common noncoding DNA variants identified by GWASs can directly contribute to clinical phenotypes.

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Figure 1: Human chromosome 1p13 locus is preferentially associated with very small LDL and liver gene expression.
Figure 2: rs12740374 is responsible for haplotype-specific difference in transcriptional activity.
Figure 3: rs12740374 alters a C/EBP transcription factor binding site.
Figure 4: Overexpression or knockdown of Sort1 in mouse liver alters plasma lipids and lipoproteins.

References

  1. Rader, D. J. et al. Monogenic hypercholesterolemia: new insights in pathogenesis and treatment. J. Clin. Invest. 111, 1795–1803 (2003)

    Article  CAS  Google Scholar 

  2. Brown, M. S. & Goldstein, J. L. Heart attacks: gone with the century? Science 272, 629 (1996)

    Article  ADS  CAS  Google Scholar 

  3. Waters, D. D. et al. Lipid treatment assessment project 2: a multinational survey to evaluate the proportion of patients achieving low-density lipoprotein cholesterol goals. Circulation 120, 28–34 (2009)

    Article  CAS  Google Scholar 

  4. Kathiresan, S. et al. Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. Nature Genet. 40, 189–197 (2008)

    Article  CAS  Google Scholar 

  5. Willer, C. J. et al. Newly identified loci that influence lipid concentrations and risk of coronary artery disease. Nature Genet. 40, 161–169 (2008)

    Article  CAS  Google Scholar 

  6. Wallace, C. et al. Genome-wide association study identifies genes for biomarkers of cardiovascular disease: serum urate and dyslipidemia. Am. J. Hum. Genet. 82, 139–149 (2008)

    Article  CAS  Google Scholar 

  7. Kathiresan, S. et al. Common variants at 30 loci contribute to polygenic dyslipidemia. Nature Genet. 41, 56–65 (2009)

    Article  CAS  Google Scholar 

  8. Aulchenko, Y. S. et al. Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. Nature Genet. 41, 47–55 (2009)

    Article  CAS  Google Scholar 

  9. Sabatti, C. et al. Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. Nature Genet. 41, 35–46 (2009)

    Article  CAS  Google Scholar 

  10. Teslovich, T. M. et al. Biological, clinical and population relevance of 95 loci for blood lipids. Nature 10.1038/nature09270 (this issue)

  11. Samani, N. J. et al. Genomewide association analysis of coronary artery disease. N. Engl. J. Med. 357, 443–453 (2007)

    Article  CAS  Google Scholar 

  12. Myocardial Infarction Genetics Consortium. Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. Nature Genet. 41, 334–341 (2009)

  13. Berneis, K. K. & Krauss, R. M. Metabolic origins and clinical significance of LDL heterogeneity. J. Lipid Res. 43, 1363–1379 (2002)

    Article  CAS  Google Scholar 

  14. Musunuru, K. et al. Ion mobility analysis of lipoprotein subfractions identifies three independent axes of cardiovascular risk. Arterioscler. Thromb. Vasc. Biol. 29, 1975–1980 (2009)

    Article  CAS  Google Scholar 

  15. Siri-Tarino, P. W., Williams, P. T., Fernstrom, H. S., Rawlings, R. S. & Krauss, R. M. Reversal of small, dense LDL subclass phenotype by normalization of adiposity. Obesity (Silver Spring) 17, 1768–1775 (2009)

    Article  CAS  Google Scholar 

  16. Linsel-Nitschke, P. et al. Genetic variation at chromosome 1p13.3 affects sortilin mRNA expression, cellular LDL-uptake and serum LDL levels which translates to the risk of coronary artery disease. Atherosclerosis 208, 183–189 (2010)

    Article  CAS  Google Scholar 

  17. Darlington, G. J., Wang, N. & Hanson, R. W. C/EBP alpha: a critical regulator of genes governing integrative metabolic processes. Curr. Opin. Genet. Dev. 5, 565–570 (1995)

    Article  CAS  Google Scholar 

  18. Osada, S., Yamamoto, H., Nishihara, T. & Imagawa, M. DNA binding specificity of the CCAAT/enhancer-binding protein transcription factor family. J. Biol. Chem. 271, 3891–3896 (1996)

    Article  CAS  Google Scholar 

  19. Olive, M., Williams, S. C., Dezan, C., Johnson, P. F. & Vinson, C. Design of a C/EBP-specific, dominant-negative bZIP protein with both inhibitory and gain-of-function properties. J. Biol. Chem. 271, 2040–2047 (1996)

    Article  CAS  Google Scholar 

  20. Ahn, S. et al. A dominant-negative inhibitor of CREB reveals that it is a general mediator of stimulus-dependent transcription of c-fos. Mol. Cell. Biol. 18, 967–977 (1998)

    Article  CAS  Google Scholar 

  21. Miller, M., Shuman, J. D., Sebastian, T., Dauter, Z. & Johnson, P. F. Structural basis for DNA recognition by the basic region leucine zipper transcription factor CCAAT/enhancer-binding protein alpha. J. Biol. Chem. 278, 15178–15184 (2003)

    Article  CAS  Google Scholar 

  22. Si-Tayeb, K. et al. Highly efficient generation of human hepatocyte-like cells from induced pluripotent stem cells. Hepatology 51, 297–305 (2010)

    Article  CAS  Google Scholar 

  23. Petersen, C. M. et al. Molecular identification of a novel candidate sorting receptor purified from human brain by receptor-associated protein affinity chromatography. J. Biol. Chem. 272, 3599–3605 (1997)

    Article  CAS  Google Scholar 

  24. Nielsen, M. S. et al. The sortilin cytoplasmic tail conveys Golgi-endosome transport and binds the VHS domain of the GGA2 sorting protein. EMBO J. 20, 2180–2190 (2001)

    Article  CAS  Google Scholar 

  25. Nykjaer, A. et al. Sortilin is essential for proNGF-induced neuronal cell death. Nature 427, 843–848 (2004)

    Article  ADS  CAS  Google Scholar 

  26. Shi, J. & Kandror, K. V. Sortilin is essential and sufficient for the formation of Glut4 storage vesicles in 3T3–L1 adipocytes. Dev. Cell 9, 99–108 (2005)

    Article  CAS  Google Scholar 

  27. Kitajima, K. et al. Complete prevention of atherosclerosis in apoE-deficient mice by hepatic human apoE gene transfer with adeno-associated virus serotypes 7 and 8. Arterioscler. Thromb. Vasc. Biol. 26, 1852–1857 (2006)

    Article  CAS  Google Scholar 

  28. Tanigawa, H. et al. Expression of cholesteryl ester transfer protein in mice promotes macrophage reverse cholesterol transport. Circulation 116, 1267–1273 (2007)

    Article  CAS  Google Scholar 

  29. Soutschek, J. et al. Therapeutic silencing of an endogenous gene by systemic administration of modified siRNAs. Nature 432, 173–178 (2004)

    Article  ADS  CAS  Google Scholar 

  30. Frank-Kamenetsky, M. et al. Therapeutic RNAi targeting PCSK9 acutely lowers plasma cholesterol in rodents and LDL cholesterol in nonhuman primates. Proc. Natl Acad. Sci. USA 105, 11915–11920 (2008)

    Article  ADS  CAS  Google Scholar 

  31. Akinc, A. et al. A combinatorial library of lipid-like materials for delivery of RNAi therapeutics. Nature Biotechnol. 26, 561–569 (2008)

    Article  CAS  Google Scholar 

  32. Zeng, J., Racicott, J. & Morales, C. R. The inactivation of the sortilin gene leads to a partial disruption of prosaposin trafficking to the lysosomes. Exp. Cell Res. 315, 3112–3124 (2009)

    Article  CAS  Google Scholar 

  33. Keebler, M. E. et al. Association of blood lipids with common DNA sequence variants at 19 genetic loci in the multiethnic United States National Health and Nutrition Examination Survey III. Circ. Cardiovasc. Genet. 2, 238–243 (2009)

    Article  CAS  Google Scholar 

  34. Reiner, A. P. et al. Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1α are associated with C-reactive protein. Am. J. Hum. Genet. 82, 1193–1201 (2008)

    Article  CAS  Google Scholar 

  35. Musunuru, K. et al. Candidate Gene Association Resource (CARe): design, methods, and proof of concept. Circ. Cardiovasc. Genet. 3, 267–275 (2010)

    Article  CAS  Google Scholar 

  36. Schadt, E. E. et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol. 6, e107 (2008)

    Article  Google Scholar 

Download references

Acknowledgements

We thank D. Altshuler, E. Fisher and J. Maraganore for advice and guidance, and A. Akinc, J. Billheimer, R. Brown, R. Camahort, D. Cromley, E. Eduoard, I. Fuki, C. Geaney, G. Hinkle, I. Kohaar, S. Kuchimanchi, W. Lagor, F. Lau, D. Lum, M. Maier, D. Marchadier, R. Meyers, J. Millar, S. Milstein, D. Nguyen, D. Perez, D. Peters, V. Redon, A. Rigamonti, R. Schinzel, M.-S. Sun, S.-A. Toh, A. Wilson and K. Wojnoonski for assistance and suggestions. We acknowledge the National Heart, Lung, and Blood Institute (NHLBI) Gene Therapy Resource Program for providing support for viral vector production as well as the Vector Core laboratory of the University of Pennsylvania for producing the vectors. We acknowledge the members of the NHLBI Candidate Gene Association Resource (CARe) lipids working group for the contribution of association data in African Americans. This work was supported in part by a T32 grant in Cell and Molecular Training for Cardiovascular Biology from the United States National Institutes of Health (NIH), K99-HL098364 from the NIH, and the Clinician Scientist Program of the Harvard Stem Cell Institute (K.M.); a Medical Scientist Training Program grant from the NIH (A.S.); the intramural research program of the Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH (L.P.-O.); the Swedish Medical Research Council, Heart-Lung Foundation, and Påhlsson Foundation (M.O.-M., O.M.); U01-HL069757 from the NIH and research support from Quest Diagnostics, Inc. (R.M.K.); RC2-HL101864 from the NIH (S.K.); and P01-HL059407 and RC2-HL101864 from the NIH and a “Freedom to Discover” Unrestricted Cardiovascular Research Grant from Bristol-Myers Squibb (D.J.R.).

Author information

Author notes

  1. Kiran Musunuru, Alanna Strong, Sekar Kathiresan and Daniel J. Rader: These authors contributed equally to this work.

Authors and Affiliations

  1. Cardiovascular Research Center and Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA

    Kiran Musunuru, Noemi E. Lee, Tim Ahfeldt, Nicolas Kuperwasser, Vera M. Ruda, James P. Pirruccello, Kenechi G. Ejebe, Chad A. Cowan & Sekar Kathiresan

  2. Broad Institute, Cambridge, 02142, Massachusetts, USA

    Kiran Musunuru, James P. Pirruccello, Jennifer L. Hall, Kenechi G. Ejebe, Chad A. Cowan & Sekar Kathiresan

  3. Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, 21287, Maryland, USA

    Kiran Musunuru

  4. Institute for Translational Medicine and Therapeutics, Institute for Diabetes, Obesity and Metabolism, and Cardiovascular Institute, University of Pennsylvania School of Medicine, Philadelphia, 19104, Pennsylvania, USA

    Alanna Strong, Katherine V. Sachs, Xiaoyu Li, Hui Li & Daniel J. Rader

  5. Alnylam Pharmaceuticals, Inc., Cambridge, 02142, Massachusetts, USA

    Maria Frank-Kamenetsky, Jamie Wong, William Cantley, Timothy Racie, Victor Koteliansky & Kevin Fitzgerald

  6. Department of Biochemistry and Molecular Biology II: Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany

    Tim Ahfeldt

  7. Division of Cancer Epidemiology and Genetics, Laboratory of Translational Genomics, National Cancer Institute, National Institutes of Health, Bethesda, 20892, Maryland, USA

    Brian Muchmore & Ludmila Prokunina-Olsson

  8. Program in Cardiovascular Translational Genomics, Lillehei Heart Institute, University of Minnesota, Minneapolis, 55455, Minnesota, USA

    Jennifer L. Hall

  9. Sage Bionetworks, Seattle, 98109, Washington, USA

    Eric E. Schadt

  10. Department of Anatomy and Cell Biology, McGill University, Montreal, H3A 2B2, Quebec, Canada

    Carlos R. Morales

  11. The Children’s Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, 19104, Pennsylvania, USA

    Sissel Lund-Katz & Michael C. Phillips

  12. Department of Clinical Sciences, Skania University Hospital, Lund University, Malmö, SE-20502, Sweden

    Marju Orho-Melander & Olle Melander

  13. Children’s Hospital Oakland Research Institute, Oakland, 94609, California, USA

    Ronald M. Krauss

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Contributions

K.M., A.S., M.F.-K., N.E.L., T.A., K.V.S., X.L., H.L., N.K., V.M.R., J.J.P., B.M., L.P.-O., J.L.H., E.E.S., C.R.M., S.L.-K., M.C.P., J.W., W.C., T.R., K.G.E., M.O.-M., O.M. and R.M.K. carried out experimental work and/or performed data analysis. V.K., K.F., C.A.C., S.K. and D.J.R. supervised the study. K.M., A.S., S.K. and D.J.R. conceived and designed the study. K.M. wrote the manuscript.

Corresponding authors

Correspondence to Sekar Kathiresan or Daniel J. Rader.

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Competing interests

Competing interests: M.F.-K., J.W., W.C., T.R., V.K. and K.F. are employees of Alnylam Pharmaceuticals. R.M.K. has received research support from Quest Diagnostics related to work presented in this manuscript The other authors declare no competing financial interests.

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Musunuru, K., Strong, A., Frank-Kamenetsky, M. et al. From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature 466, 714–719 (2010). https://doi.org/10.1038/nature09266

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