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

Nature 466, 714–719 (05 August 2010) | Download Citation

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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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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

    • Kiran Musunuru
    • , Alanna Strong
    • , Sekar Kathiresan
    •  & Daniel J. Rader

    These authors contributed equally to this work.

Affiliations

  1. Cardiovascular Research Center and Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, 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, Massachusetts 02142, 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, Maryland 21287, 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, Pennsylvania 19104, USA

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

  5. Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, 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. Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA

    • Brian Muchmore
    •  & Ludmila Prokunina-Olsson

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

    • Jennifer L. Hall

  9. Sage Bionetworks, Seattle, Washington 98109, USA

    • Eric E. Schadt

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

    • Carlos R. Morales

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

    • Sissel Lund-Katz
    •  & Michael C. Phillips

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

    • Marju Orho-Melander
    •  & Olle Melander

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

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.

Corresponding authors

Correspondence to Sekar Kathiresan or Daniel J. Rader.

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DOI

https://doi.org/10.1038/nature09266

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