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Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease

Nature Genetics volume 46, pages 352–356 (2014)Cite this article

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Abstract

Nonalcoholic fatty liver disease (NAFLD) is the most common form of liver disease. To elucidate the molecular basis of NAFLD, we performed an exome-wide association study of liver fat content. Three variants were associated with higher liver fat levels at the exome-wide significance level of 3.6 × 10−7: two in PNPLA3, an established locus for NAFLD, and one (encoding p.Glu167Lys) in TM6SF2, a gene of unknown function. The TM6SF2 variant encoding p.Glu167Lys was also associated with higher circulating levels of alanine transaminase, a marker of liver injury, and with lower levels of low-density lipoprotein–cholesterol (LDL-C), triglycerides and alkaline phosphatase in 3 independent populations (n > 80,000). When recombinant protein was expressed in cultured hepatocytes, 50% less Glu167Lys TM6SF2 protein was produced relative to wild-type TM6SF2. Adeno-associated virus–mediated short hairpin RNA knockdown of Tm6sf2 in mice increased liver triglyceride content by threefold and decreased very-low-density lipoprotein (VLDL) secretion by 50%. Taken together, these data indicate that TM6SF2 activity is required for normal VLDL secretion and that impaired TM6SF2 function causally contributes to NAFLD.

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Figure 1: Exome-wide association with HTGC in the Dallas Heart Study (DHS).
Figure 2: Expression of TM6SF2 in cultured hepatocytes.
Figure 3: Knockdown of Tm6sf2 expression in mouse liver is associated with increased HTGC.
Figure 4: Sucrose feeding in Tm6sf2 knockdown mice.

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Acknowledgements

We thank F. Xu for excellent technical assistance. This work was supported by grants from the US National Institutes of Health (HL20948, 1HL092550 and DK090066) and the National Center for Advancing Translational Sciences (UL1TR001105). T.F.V. acknowledges the contributions of G. Gao (University of Massachusetts) for advice and assistance with AAV vector production.

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Author notes

  1. Julia Kozlitina and Eriks Smagris: These authors contributed equally to this work.

Authors and Affiliations

  1. McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA

    Julia Kozlitina, Eriks Smagris, Helen H Hobbs & Jonathan C Cohen

  2. Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

    Stefan Stender & Anne Tybjærg-Hansen

  3. Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

    Børge G Nordestgaard & Anne Tybjærg-Hansen

  4. Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

    Børge G Nordestgaard

  5. Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen University Hospital and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

    Børge G Nordestgaard & Anne Tybjærg-Hansen

  6. Merck Research Laboratories, Kenilworth, New Jersey, USA

    Heather H Zhou & Thomas F Vogt

  7. Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA

    Helen H Hobbs

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Contributions

The manuscript was prepared by all of the authors. E.S. and H.H.Z. performed the experiments. J.K. and S.S. performed the genetic analysis and association studies. T.F.V., A.T.-H., B.G.N., J.C.C. and H.H.H. provided experimental design and coordination.

Corresponding authors

Correspondence to Helen H Hobbs or Jonathan C Cohen.

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The authors declare no competing financial interests.

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Supplementary Figure 1 Short hairpin RNA–mediated knockdown of Tm6sf2 in mice.

(a) AAV vector alone or AAV expressing an shRNA against mouse Tm6sf2 mRNA were injected into the tail veins of 8-week-old chow-fed C57Bl/6J male mice (n = 5/group). After 2 weeks, the mice were killed and the liver, white adipose tissue (WAT) and small intestine were harvested. Levels of Tm6sf2 mRNA were measured using real-time PCR and normalized to m36B4 levels. The differences in mean expression levels were compared using a two-sample t test. (b) AAV expressing three different shRNAs or AAV vector alone were injected intravenously into 8-week-old chow-fed C57Bl/6J male mice (n = 6/group). All three shRNAs were directed against mouse Tm6sf2, but only shRNA8 knocked down the levels of Tm6sf2 mRNA with high efficiency in cultured cells. Two weeks after the injection, mice were fasted for 4 h, the livers were harvested, and the levels of Tm6sf2 mRNA were measured using real-time PCR. Values were normalized to m36B4 and expressed relative to the mean value of the AAV-only treated mice. Plasma was collected in the same experiment, and triglyceride and cholesterol levels were measured as described in the Online Methods. Differences in mean expression levels were compared using two-sample t tests. Ct, cycle threshold value.

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Kozlitina, J., Smagris, E., Stender, S. et al. Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease. Nat Genet 46, 352–356 (2014). https://doi.org/10.1038/ng.2901

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