A Protein-Truncating HSD17B13 Variant and Protection from Chronic Liver Disease
Noura S Abul-Husn, Xiping Cheng, Alexander H Li, Yurong Xin, Claudia Schurmann, Panayiotis Stevis, Yashu Liu, Julia Kozlitina, Stefan Stender, G Craig Wood, Ann N Stepanchick, Matthew D Still, Shane McCarthy, Colm O'Dushlaine, Jonathan S Packer, Suganthi Balasubramanian, Nehal Gosalia, David Esopi, Sun Y Kim, Semanti Mukherjee, Alexander E Lopez, Erin D Fuller, John Penn, Xin Chu, Jonathan Z Luo, Uyenlinh L Mirshahi, David J Carey, Christopher D Still, Michael D Feldman, Aeron Small, Scott M Damrauer, Daniel J Rader, Brian Zambrowicz, William Olson, Andrew J Murphy, Ingrid B Borecki, Alan R Shuldiner, Jeffrey G Reid, John D Overton, George D Yancopoulos, Helen H Hobbs, Jonathan C Cohen, Omri Gottesman, Tanya M Teslovich, Aris Baras, Tooraj Mirshahi, Jesper Gromada, Frederick E Dewey, Noura S Abul-Husn, Xiping Cheng, Alexander H Li, Yurong Xin, Claudia Schurmann, Panayiotis Stevis, Yashu Liu, Julia Kozlitina, Stefan Stender, G Craig Wood, Ann N Stepanchick, Matthew D Still, Shane McCarthy, Colm O'Dushlaine, Jonathan S Packer, Suganthi Balasubramanian, Nehal Gosalia, David Esopi, Sun Y Kim, Semanti Mukherjee, Alexander E Lopez, Erin D Fuller, John Penn, Xin Chu, Jonathan Z Luo, Uyenlinh L Mirshahi, David J Carey, Christopher D Still, Michael D Feldman, Aeron Small, Scott M Damrauer, Daniel J Rader, Brian Zambrowicz, William Olson, Andrew J Murphy, Ingrid B Borecki, Alan R Shuldiner, Jeffrey G Reid, John D Overton, George D Yancopoulos, Helen H Hobbs, Jonathan C Cohen, Omri Gottesman, Tanya M Teslovich, Aris Baras, Tooraj Mirshahi, Jesper Gromada, Frederick E Dewey
Abstract
Background: Elucidation of the genetic factors underlying chronic liver disease may reveal new therapeutic targets.
Methods: We used exome sequence data and electronic health records from 46,544 participants in the DiscovEHR human genetics study to identify genetic variants associated with serum levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST). Variants that were replicated in three additional cohorts (12,527 persons) were evaluated for association with clinical diagnoses of chronic liver disease in DiscovEHR study participants and two independent cohorts (total of 37,173 persons) and with histopathological severity of liver disease in 2391 human liver samples.
Results: A splice variant (rs72613567:TA) in HSD17B13, encoding the hepatic lipid droplet protein hydroxysteroid 17-beta dehydrogenase 13, was associated with reduced levels of ALT (P=4.2×10-12) and AST (P=6.2×10-10). Among DiscovEHR study participants, this variant was associated with a reduced risk of alcoholic liver disease (by 42% [95% confidence interval {CI}, 20 to 58] among heterozygotes and by 53% [95% CI, 3 to 77] among homozygotes), nonalcoholic liver disease (by 17% [95% CI, 8 to 25] among heterozygotes and by 30% [95% CI, 13 to 43] among homozygotes), alcoholic cirrhosis (by 42% [95% CI, 14 to 61] among heterozygotes and by 73% [95% CI, 15 to 91] among homozygotes), and nonalcoholic cirrhosis (by 26% [95% CI, 7 to 40] among heterozygotes and by 49% [95% CI, 15 to 69] among homozygotes). Associations were confirmed in two independent cohorts. The rs72613567:TA variant was associated with a reduced risk of nonalcoholic steatohepatitis, but not steatosis, in human liver samples. The rs72613567:TA variant mitigated liver injury associated with the risk-increasing PNPLA3 p.I148M allele and resulted in an unstable and truncated protein with reduced enzymatic activity.
Conclusions: A loss-of-function variant in HSD17B13 was associated with a reduced risk of chronic liver disease and of progression from steatosis to steatohepatitis. (Funded by Regeneron Pharmaceuticals and others.).
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References
- Kochanek KD, Murphy SL, Xu J, Tejada-Vera B. Deaths: final data for 2014. Natl Vital Stat Rep 2016;65:1–122.
- Browning JD, Szczepaniak LS, Dobbins R, et al. Prevalence of hepatic steatosis in an urban population in the United States: impact of ethnicity. Hepatology 2004;40:1387–95.
- Lazo M, Hernaez R, Eberhardt MS, et al. Prevalence of nonalcoholic fatty liver disease in the United States: the Third National Health and Nutrition Examination Survey, 1988–1994. Am J Epidemiol 2013;178:38–45.
- Williams CD, Stengel J, Asike MI, et al. Prevalence of nonalcoholic fatty liver disease and nonalcoholic steatohepatitis among a largely middle-aged population utilizing ultrasound and liver biopsy: a prospective study. Gastroenterology 2011;140:124–31.
- Younossi ZM, Stepanova M, Afendy M, et al. Changes in the prevalence of the most common causes of chronic liver diseases in the United States from 1988 to 2008. Clin Gastroenterol Hepatol 2011;9(6): 524–530.e1.
- Cohen JC, Horton JD, Hobbs HH. Human fatty liver disease: old questions and new insights. Science 2011;332:1519–23.
- Romeo S, Kozlitina J, Xing C, et al. Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease. Nat Genet 2008;40:1461–5.
- Rotman Y, Koh C, Zmuda JM, Kleiner DE, Liang TJ. The association of genetic variability in patatin-like phospholipase domain-containing protein 3 (PNPLA3) with histological severity of nonalcoholic fatty liver disease. Hepatology 2010;52: 894–903.
- Sookoian S, Castaño GO, Burgueño AL, Gianotti TF, Rosselli MS, Pirola CJ. A nonsynonymous gene variant in the adiponutrin gene is associated with nonalcoholic fatty liver disease severity. J Lipid Res 2009;50:2111–6.
- Trépo E, Romeo S, Zucman-Rossi J, Nahon P. PNPLA3 gene in liver diseases. J Hepatol 2016;65:399–412.
- 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 2014;46:352–6.
- Liu YL, Reeves HL, Burt AD, et al. TM6SF2 rs58542926 influences hepatic fibrosis progression in patients with nonalcoholic fatty liver disease. Nat Commun 2014;5:4309.
- Sookoian S, Castaño GO, Scian R, et al. Genetic variation in transmembrane 6 superfamily member 2 and the risk of nonalcoholic fatty liver disease and histological disease severity. Hepatology 2015;61:515–25.
- Smagris E, Gilyard S, BasuRay S, Cohen JC, Hobbs HH. Inactivation of Tm6sf2, a gene defective in fatty liver disease, impairs lipidation but not secretion of very low density lipoproteins. J Biol Chem 2016;291:10659–76.
- Mahdessian H, Taxiarchis A, Popov S, et al. TM6SF2 is a regulator of liver fat metabolism influencing triglyceride secretion and hepatic lipid droplet content. Proc Natl Acad Sci U S A 2014; 111:8913–8.
- Huang Y, Cohen JC, Hobbs HH. Expression and characterization of a PNPLA3 protein isoform (I148M) associated with nonalcoholic fatty liver disease. J Biol Chem 2011;286:37085–93.
- Pirazzi C, Adiels M, Burza MA, et al. Patatin-like phospholipase domain-containing 3 (PNPLA3) I148M (rs738409) affects hepatic VLDL secretion in humans and in vitro. J Hepatol 2012;57:1276–82.
- Dewey FE, Murray MF, Overton JD, et al. Distribution and clinical impact of functional variants in 50,726 whole-exome sequences from the DiscovEHR study. Science 2016;354:aaf6814.
- Brantly M, Nukiwa T, Crystal RG. Molecular basis of alpha-1-antitrypsin deficiency. Am J Med 1988;84:6A:13–31.
- Kitamoto T, Kitamoto A, Yoneda M, et al. Genome-wide scan revealed that polymorphisms in the PNPLA3, SAMM50, and PARVB genes are associated with development and progression of nonalcoholic fatty liver disease in Japan. Hum Genet 2013;132:783–92.
- Feitosa MF, Wojczynski MK, North KE, et al. The ERLIN1-CHUK-CWF19L1 gene cluster influences liver fat deposition and hepatic inflammation in the NHLBI Family Heart Study. Atherosclerosis 2013; 228:175–80.
- Chambers JC, Zhang W, Sehmi J, et al. Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma. Nat Genet 2011;43: 1131–8.
- Liu S, Huang C, Li D, et al. Molecular cloning and expression analysis of a new gene for short-chain dehydrogenase/reductase 9. Acta Biochim Pol 2007;54:213–8.
- Su W, Wang Y, Jia X, et al. Comparative proteomic study reveals 17β-HSD13 as a pathogenic protein in nonalcoholic fatty liver disease. Proc Natl Acad Sci U S A 2014;111:11437–42.
- Donati B, Motta BM, Pingitore P, et al. The rs2294918 E434K variant modulates patatin-like phospholipase domain-containing 3 expression and liver damage. Hepatology 2016;63:787–98.
- Moeller G, Adamski J. Integrated view on 17beta-hydroxysteroid dehydrogenases. Mol Cell Endocrinol 2009;301:7–19.
- Kampf C, Mardinoglu A, Fagerberg L, et al. The human liver-specific proteome defined by transcriptomics and antibodybased profiling. FASEB J 2014;28:2901–14.
- Li P, Oh DY, Bandyopadhyay G, et al. LTB4 promotes insulin resistance in obese mice by acting on macrophages, hepatocytes and myocytes. Nat Med 2015; 21:239–47.
- Buch S, Stickel F, Trepo E, et al. A genome-wide association study confirms PNPLA3 and identifies TM6SF2 and MBOAT7 as risk loci for alcohol-related cirrhosis. Nat Genet 2015;47:1443–8.
- Mancina RM, Dongiovanni P, Petta S, et al. The MBOAT7-TMC4 variant rs641738 increases risk of nonalcoholic fatty liver disease in individuals of European descent. Gastroenterology 2016;150(5):1219–1230.e6.
Source: PubMed