Reply to: HCC and liver disease risk in homozygous PNPLA3 p.I148M carriers approach monogenic inheritance
Authors: Quentin M. Anstee, Yang-Lin Liu, Christopher P. Day, Helen L. Reeves
Journal: Journal of Hepatology (2015)

HCC and liver disease risks in homozygous PNPLA3 p.I148M carriers approach monogenic inheritanceJournal of HepatologyVol. 62Issue 4PreviewThe study published in the Journal of Hepatology by Liu et al. [1] has robustly validated a strong genetic association between the common PNPLA3 variant p.I148M and the risk of developing hepatocellular carcinoma (HCC), in patients with non-alcoholic fatty liver disease (NAFLD), also reported previously [2]. The association study [1] comprised 100 individuals with NAFLD-associated HCC and 1,476 controls and showed that homozygous carriers of the p.148M mutation carry a 12-fold increased HCC risk (odds ratio [OR] = 12.19, 95% confidence interval = 6.89–21.58, p <0.0001) as compared to p.I148 homozygotes. Full-Text PDF Open AccessCarriage of the PNPLA3 rs738409 C >G polymorphism confers an increased risk of non-alcoholic fatty liver disease associated hepatocellular carcinomaJournal of HepatologyVol. 61Issue 1PreviewSubtle inter-patient genetic variation and environmental factors combine to determine disease progression in non-alcoholic fatty liver disease (NAFLD). Carriage of the PNPLA3 rs738409 c.444C >G minor allele (encoding the I148M variant) has been robustly associated with advanced NAFLD. Although most hepatocellular carcinoma (HCC) is related to chronic viral hepatitis or alcoholic liver disease, the incidence of NAFLD-related HCC is increasing. We examined whether rs738409 C >G was associated with HCC-risk in patients with NAFLD. Full-Text PDF We read with interest the thought-provoking letter from Krawczyk et al. [[1]Krawczyk M. Stokes C.S. Romeo S. Lammert F. HCC and liver disease risk in homozygous PNPLA3 p. I148M carriers approach monogenic inheritance.J Hepatol. 2015; 62: 980-981Abstract Full Text Full Text PDF PubMed Scopus (26) Google Scholar] in response to our recent publication in the Journal of Hepatology describing the strong genetic association between the PNPLA3 rs738409 (C>G, p.I148M) variant and the development of NAFLD-associated hepatocellular carcinoma (HCC) [[2]Liu Y.L. Patman G.L. Leathart J.B. Piguet A.C. Burt A.D. Dufour J.F. et al.Carriage of the PNPLA3 rs738409 C>G polymorphism confers an increased risk of non-alcoholic fatty liver disease associated hepatocellular carcinoma.J Hepatol. 2014; 61: 75-81Abstract Full Text Full Text PDF PubMed Scopus (310) Google Scholar]. We agree that the observed magnitude of effect is striking: comparison of genotype frequencies between a NAFLD-HCC patient cohort and an unselected UK general population sample (the MRC/Wellcome Trust UK 1958 Birth Cohort) demonstrated a 12-fold increased risk of HCC [OR 12.19; 95% CI 6.89–21.58; p <0.0001] for rs738409 minor (G) allele homozygotes relative to C-allele homozygotes [[2]Liu Y.L. Patman G.L. Leathart J.B. Piguet A.C. Burt A.D. Dufour J.F. et al.Carriage of the PNPLA3 rs738409 C>G polymorphism confers an increased risk of non-alcoholic fatty liver disease associated hepatocellular carcinoma.J Hepatol. 2014; 61: 75-81Abstract Full Text Full Text PDF PubMed Scopus (310) Google Scholar]. Krawczyk et al. compare the effect of PNPLA3 to the monogenic condition, hereditary haemochromatosis due to HFE rs1800562 (A>G, p.C282Y). As their detailed comparison demonstrates, carriage of either variant confers a similar risk of HCC [[1]Krawczyk M. Stokes C.S. Romeo S. Lammert F. HCC and liver disease risk in homozygous PNPLA3 p. I148M carriers approach monogenic inheritance.J Hepatol. 2015; 62: 980-981Abstract Full Text Full Text PDF PubMed Scopus (26) Google Scholar]. Although statistical techniques to assess proportion of variability explained by genetic variations are imperfect [[3]Witte J.S. Visscher P.M. Wray N.R. The contribution of genetic variants to disease depends on the ruler.Nat Rev Genet. 2014; 15: 765-776Crossref PubMed Scopus (96) Google Scholar], our data indicates a Population Attributable Risk (PAR) of PNPLA3 rs738409 for HCC of 55% and an AUROC of 0.68 attributable to this variant [[2]Liu Y.L. Patman G.L. Leathart J.B. Piguet A.C. Burt A.D. Dufour J.F. et al.Carriage of the PNPLA3 rs738409 C>G polymorphism confers an increased risk of non-alcoholic fatty liver disease associated hepatocellular carcinoma.J Hepatol. 2014; 61: 75-81Abstract Full Text Full Text PDF PubMed Scopus (310) Google Scholar]. Further supporting the independent role of PNPLA3 rs738409 as a risk factor for HCC, it is telling that other genetic variants that are strong modifiers of NAFLD severity and fibrosis progression such as TM6SF2 [4Liu Y.L. Reeves H.L. Burt A.D. Tiniakos D. McPherson S. Leathart J.B. et al.TM6SF2 rs58542926 influences hepatic fibrosis progression in patients with non-alcoholic fatty liver disease.Nat Commun. 2014; 5: 4309Crossref PubMed Scopus (387) Google Scholar, 5Dongiovanni P. Petta S. Maglio C. Fracanzani A.L. Pipitone R. Mozzi E. et al.TM6SF2 gene variant disentangles nonalcoholic steatohepatitis from cardiovascular disease.Hepatology. 2014; Google Scholar], do not appear to confer an additional, independent increased risk of HCC [[4]Liu Y.L. Reeves H.L. Burt A.D. Tiniakos D. McPherson S. Leathart J.B. et al.TM6SF2 rs58542926 influences hepatic fibrosis progression in patients with non-alcoholic fatty liver disease.Nat Commun. 2014; 5: 4309Crossref PubMed Scopus (387) Google Scholar]. We agree with Krawczyk et al. that PNPLA3 is an important genetic risk factor for liver disease. For the moment, we would however caution against a move towards considering "PNPLA3-associated NAFLD", or by extension "PNPLA3-associated HCC", as distinct, monogenic conditions analogous to HFE in haemochromatosis but rather suggest that PNPLA3 should be considered a strong modifier within a complex, polygenic disease trait that is subject both to genetic and substantial environmental influence (e.g. due to dietary factors and the intestinal microbiota [[6]Anstee Q.M. Targher G. Day C.P. Progression of NAFLD to diabetes mellitus, cardiovascular disease or cirrhosis.Nat Rev Gastroenterol Hepatol. 2013; 10: 330-344Crossref PubMed Scopus (1033) Google Scholar]). Given the mounting evidence of an association between PNPLA3 and HCC [7Burza M.A. Pirazzi C. Maglio C. Sjoholm K. Mancina R.M. Svensson P.A. et al.PNPLA3 I148M (rs738409) genetic variant is associated with hepatocellular carcinoma in obese individuals.Dig Liver Dis. 2012; 44: 1037-1041Abstract Full Text Full Text PDF PubMed Scopus (79) Google Scholar, 8Trepo E. Nahon P. Bontempi G. Valenti L. Falleti E. Nischalke H.D. et al.Association between the PNPLA3 (rs738409 C>G) variant and hepatocellular carcinoma: evidence from a meta-analysis of individual participant data.Hepatology. 2014; 59: 2170-2177Crossref PubMed Scopus (173) Google Scholar], it is timely to consider the clinical utility of PNPLA3 genotyping to assist in patient risk stratification. It has been suggested that, assuming a sensitivity of 80%, an odds ratio of >50 is required to control false-positive rates to an acceptable level of <10% [[9]Manolio T.A. Bringing genome-wide association findings into clinical use.Nat Rev Genet. 2013; 14: 549-558Crossref PubMed Scopus (253) Google Scholar]. A re-analysis of the data from Liu et al. [[2]Liu Y.L. Patman G.L. Leathart J.B. Piguet A.C. Burt A.D. Dufour J.F. et al.Carriage of the PNPLA3 rs738409 C>G polymorphism confers an increased risk of non-alcoholic fatty liver disease associated hepatocellular carcinoma.J Hepatol. 2014; 61: 75-81Abstract Full Text Full Text PDF PubMed Scopus (310) Google Scholar] to assess sensitivity/specificity is shown in Table 1. Based on these data, the use of PNPLA3 genotyping alone to positively predict risk of HCC is unlikely to be tenable. However, even in this HCC-enriched dataset, the negative predictive value was substantially greater, both within the NAFLD vs. NAFLD-HCC comparison and the NAFLD-HCC vs. unselected background population comparison, and so it may be that knowledge of PNPLA3 rs738409 genotype has utility to select out those individuals least likely to develop HCC and therefore least likely to benefit from surveillance. As Krawczyk et al. suggest, studies addressing the interaction between PNPLA3 and HFE in determining HCC risk would be of great interest. Given the increasing prevalence of NAFLD-HCC and consequent clinical need for improved risk-stratification care pathways [[10]Dyson J. Jaques B. Chattopadyhay D. Lochan R. Graham J. Das D. et al.Hepatocellular cancer: the impact of obesity, type 2 diabetes and a multidisciplinary team.J Hepatol. 2014; 60: 110-117Abstract Full Text Full Text PDF PubMed Scopus (1) Google Scholar], we would also suggest that large, prospective studies are needed urgently to validate our findings and to determine the utility and health-economic merits of a multi-factorial risk stratification that incorporates PNPLA3 rs738409 genotype along with other recognised risk factors for HCC.Table 1Reanalysis of the data from Liu et al. [2]Liu Y.L. Patman G.L. Leathart J.B. Piguet A.C. Burt A.D. Dufour J.F. et al.Carriage of the PNPLA3 rs738409 C>G polymorphism confers an increased risk of non-alcoholic fatty liver disease associated hepatocellular carcinoma.J Hepatol. 2014; 61: 75-81Abstract Full Text Full Text PDF PubMed Scopus (310) Google Scholar focusing on clinical utility of PNPLA3 genotype testing in HCC risk prediction.PPV/NPV will alter according to the underlying prevalence of HCC in population assessed.∗PPV, positive predictive value; NPV, negative predictive value. Open table in a new tab PPV/NPV will alter according to the underlying prevalence of HCC in population assessed. ∗PPV, positive predictive value; NPV, negative predictive value. The authors declared that they do not have anything to disclose regarding funding or conflict of interest with respect to this manuscript.