Research Paper Volume 9, Issue 1 pp 26—40

Transcriptional regulation of PNPLA3 and its impact on susceptibility to nonalcoholic fatty liver Disease (NAFLD) in humans

Wanqing Liu1, , Quentin M Anstee2, , Xiaoliang Wang1,3, , Samer Gawrieh4, , Eric R. Gamazon5,6, , Shaminie Athinarayanan1, , Yang-Lin Liu2, , Rebecca Darlay7, , Heather J Cordell7, , Ann K Daly2, , Chris P Day2, , Naga Chalasani4, ,

  • 1 Department of Medicinal Chemistry and Molecular Medicine, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA
  • 2 Liver Research Group, Institute of Cellular Medicine, The Medical School, Newcastle University, Newcastle upon Tyne, UK
  • 3 Department of General Surgery, Shanghai Jiaotong University Affiliated First People's Hospital, Shanghai, P. R. China
  • 4 Division of Gastroenterology and Hepatology, Indiana Fatty Liver Disease Research Group, Indiana University School of Medicine, Indianapolis, IN 46202, USA
  • 5 Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60627, USA
  • 6 Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN 37235, USA
  • 7 Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
  • 8 FLIP Investigator group members: Guruprasad P. Aithal (Nottingham, UK), Mike Allison (Cambridge, UK), Karine Clement (Paris, France), Jean-Francois Dufour, Felix Stickel (Bern, Switzerland), Sven Francque (Antwerp, Belgium), Luc Van Gaal (Antwerp, Belgium) and Vlad Ratziu (Paris, France).
  • 9 Fatty Liver Proteomic and Genomic Project (FLPGP) Investigators group members: Michael Olivier and Harald H. H. Göring (San Antonio, TX); James Wallace, Mathew Goldblatt, and Richard Komorowski (Milwaukee, WI).
* Equal contribution

Received: June 15, 2016       Accepted: September 28, 2016       Published: October 13, 2016
How to Cite

Copyright: © 2016 Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


The increased expression of PNPLA3148M leads to hepatosteatosis in mice. This study aims to investigate the genetic control of hepatic PNPLA3 transcription and to explore its impact on NAFLD risk in humans. Through a locus-wide expression quantitative trait loci (eQTL) mapping in two human liver sample sets, a PNPLA3 intronic SNP, rs139051 A>G was identified as a significant eQTL (p = 6.6×10-8) influencing PNPLA3 transcription, with the A allele significantly associated with increased PNPLA3 mRNA. An electrophoresis mobility shift assay further demonstrated that the A allele has enhanced affinity to nuclear proteins than the G allele. The impact of this eQTL on NAFLD risk was further tested in three independent populations. We found that rs139051 did not independently affect the NAFLD risk, whilst rs738409 did not significantly modulate PNPLA3 transcription but was associated with NAFLD risk. The A-G haplotype associated with higher transcription of the disease-risk rs738409 G allele conferred similar risk for NAFLD compared to the G-G haplotype that possesses a lower transcription level. Our study suggests that the pathogenic role of PNPLA3148M in NAFLD is independent of the gene transcription in humans, which may be attributed to the high endogenous transcription level of PNPLA3 gene in human livers.


eQTL: expression quantitative trait loci; NAFLD: nonalcoholic fatty liver disease; PNPLA3: patatin-like phospholipase domain-containing protein 3; SNP: single nucleotide polymorphism; mRNA: messenger ribosomal nucleic acid; EMSA: electrophoretic mobility shift assay; HCC: hepatocellular carcinoma; GWAS: Genome-wide association studies; NASH: nonalcoholic steatohepatitis; FDR: false discovery rate; NAS: NAFLD Activity Score; ChIP-seq: chromatin immunoprecipitation-sequencing; FLIP: Fatty Liver Inhibition of Progression.