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Multicenter Study
. 2020 Sep;73(3):505-515.
doi: 10.1016/j.jhep.2020.04.003. Epub 2020 Apr 13.

Genome-wide association study of non-alcoholic fatty liver and steatohepatitis in a histologically characterised cohort☆

Quentin M Anstee  1 , Rebecca Darlay  2 , Simon Cockell  3 , Marica Meroni  4 , Olivier Govaere  5 , Dina Tiniakos  6 , Alastair D Burt  7 , Pierre Bedossa  5 , Jeremy Palmer  5 , Yang-Lin Liu  5 , Guruprasad P Aithal  8 , Michael Allison  9 , Hannele Yki-Järvinen  10 , Michele Vacca  11 , Jean-Francois Dufour  12 , Pietro Invernizzi  13 , Daniele Prati  4 , Mattias Ekstedt  14 , Stergios Kechagias  14 , Sven Francque  15 , Salvatore Petta  16 , Elisabetta Bugianesi  17 , Karine Clement  18 , Vlad Ratziu  19 , Jörn M Schattenberg  20 , Luca Valenti  4 , Christopher P Day  5 , Heather J Cordell  2 , Ann K Daly  21 ; EPoS Consortium Investigators
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Free article
Multicenter Study

Genome-wide association study of non-alcoholic fatty liver and steatohepatitis in a histologically characterised cohort☆

Quentin M Anstee et al. J Hepatol. 2020 Sep.
Free article

Erratum in

Abstract

Background & aims: Genetic factors associated with non-alcoholic fatty liver disease (NAFLD) remain incompletely understood. To date, most genome-wide association studies (GWASs) have adopted radiologically assessed hepatic triglyceride content as the reference phenotype and so cannot address steatohepatitis or fibrosis. We describe a GWAS encompassing the full spectrum of histologically characterised NAFLD.

Methods: The GWAS involved 1,483 European NAFLD cases and 17,781 genetically matched controls. A replication cohort of 559 NAFLD cases and 945 controls was genotyped to confirm signals showing genome-wide or close to genome-wide significance.

Results: Case-control analysis identified signals showing p values ≤5 × 10-8 at 4 locations (chromosome [chr] 2 GCKR/C2ORF16; chr4 HSD17B13; chr19 TM6SF2; chr22 PNPLA3) together with 2 other signals with p <1 × 10-7 (chr1 near LEPR and chr8 near IDO2/TC1). Case-only analysis of quantitative traits showed that the PNPLA3 signal (rs738409) had genome-wide significance for steatosis, fibrosis and NAFLD activity score and a new signal (PYGO1 rs62021874) had close to genome-wide significance for steatosis (p = 8.2 × 10-8). Subgroup case-control analysis for NASH confirmed the PNPLA3 signal. The chr1 LEPR single nucleotide polymorphism also showed genome-wide significance for this phenotype. Considering the subgroup with advanced fibrosis (≥F3), the signals on chr2, chr19 and chr22 maintained their genome-wide significance. Except for GCKR/C2ORF16, the genome-wide significance signals were replicated.

Conclusions: This study confirms PNPLA3 as a risk factor for the full histological spectrum of NAFLD at genome-wide significance levels, with important contributions from TM6SF2 and HSD17B13. PYGO1 is a novel steatosis modifier, suggesting that Wnt signalling pathways may be relevant in NAFLD pathogenesis.

Lay summary: Non-alcoholic fatty liver disease is a common disease where excessive fat accumulates in the liver and may result in cirrhosis. To understand who is at risk of developing this disease and suffering liver damage, we undertook a genetic study to compare the genetic profiles of people suffering from fatty liver disease with genetic profiles seen in the general population. We found that particular sequences in 4 different areas of the human genome were seen at different frequencies in the fatty liver disease cases. These sequences may help predict an individual's risk of developing advanced disease. Some genes where these sequences are located may also be good targets for future drug treatments.

Keywords: Fibrosis; GCKR; GWAS; HSD17B13; NAFLD; NASH; PNPLA3; SNP; TM6SF2.

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Conflict of interest statement

Conflict of interest Quentin Anstee reports grants from European Commission during the conduct of the study; other from Acuitas Medical, grants, personal fees and other from Allergan/Tobira, other from E3Bio, other from Eli Lilly & Company Ltd, other from Galmed, grants, personal fees and other from Genfit SA, personal fees and other from Gilead, other from Grunthal, other from Imperial Innovations, grants and other from Intercept Pharma Europe Ltd, other from Inventiva, other from Janssen, personal fees from Kenes, other from MedImmune, other from NewGene, grants and other from Pfizer Ltd, other from Raptor Pharma, grants from GlaxoSmithKline, grants and other from Novartis Pharma AG, grants from AbbVie, personal fees from BMS, grants from GSK, other from NGMBio, other from Madrigal, other from Servier, outside the submitted work; Dina Tiniakos reports consultation fees from Intercept Pharmaceuticals Inc, Allergan, Cirius Therapeutics and an educational grant from Histoindex Pte Ltd; Guruprasad P. Aithal reports institutional consultancy income outside the scope of this study from GSK and Pfizer; Michael Allison reports consultancy/advisory with MedImmune/Astra Zeneca, E3Bio, honoraria from Intercept, Grant support from GSK, Takeda; Jean-Francois Dufour reports advisory committees with AbbVie, Bayer, BMS, Falk, Genfit, Genkyotex, Gilead Science, HepaRegenix, Intercept, Lilly, Merck, Novartis and speaking and teaching with Bayer, BMS, Intercept, Genfit, Gilead Science, Novartis; Pietro Invernizzi reports grants from Intercept, Gilead and Bruschettini; Mattias Ekstedt reports personal fees from AbbVie, AstraZeneca, Albireo, Diapharma, Gilead and non-financial support from Echosens (through LITMUS IMI project); Karine Clement has no personal honoraria but has consultancy and scientific collaboration activity for LNC therapeutics, Confotherapeutics and Danone Research; Jörn M. Schattenberg reports grants from Gilead and Boehringer Ingelheim and fees from Gilead, Boehringer Ingelheim, Galmed, Genfit, Intercept, Novartis, Pfizer and AbbVie outside the submitted work. All other authors report no conflicts of interest. Please refer to the accompanying ICMJE disclosure forms for further details.

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