We report a multi-ancestry genome-wide association study on liver cirrhosis and its associated endophenotypes, alanine aminotransferase (ALT) and γ-glutamyl transferase. Using data from 12 cohorts, including 18,265 cases with cirrhosis, 1,782,047 controls, up to 1 million individuals with liver function tests and a validation cohort of 21,689 cases and 617,729 controls, we identify and validate 14 risk associations for cirrhosis. Many variants are located near genes involved in hepatic lipid metabolism. One of these, PNPLA3 p.Ile148Met, interacts with alcohol intake, obesity and diabetes on the risk of cirrhosis and hepatocellular carcinoma (HCC). We develop a polygenic risk score that associates with the progression from cirrhosis to HCC. By focusing on prioritized genes from common variant analyses, we find that rare coding variants in GPAM associate with lower ALT, supporting GPAM as a potential target for therapeutic inhibition. In conclusion, this study provides insights into the genetic underpinnings of cirrhosis.

Background and Aims: Inherited short telomeres are associated with a risk of liver disease, whereas longer telomeres predispose to cancer. The association between telomere length and risk of HCC and cholangiocarcinoma remains unknown. Approach and Results: We measured leukocyte telomere length using multiplex PCR in 63,272 individuals from the Danish general population. Telomere length and plasma ALT concentration were not associated (β = 4 ×10⁻⁶, p-value = 0.06) in a linear regression model, without any signs of a nonlinear relationship. We tested the association between telomere length and risk of cirrhosis, HCC, and cholangiocarcinoma using Cox regression. During a median follow-up of 11 years, 241, 76, and 112 individuals developed cirrhosis, HCC, and cholangiocarcinoma, respectively. Telomere length and risk of cirrhosis were inversely and linearly associated (p-value = 0.004, p for nonlinearity = 0.27). Individuals with telomeres in the shortest vs. longest quartile had a 2.25-fold higher risk of cirrhosis. Telomere length and risk of HCC were nonlinearly associated (p-value = 0.009, p-value for nonlinearity = 0.01). This relationship resembled an inverted J-shape, with the highest risk observed in individuals with short telomeres. Individuals with telomeres in the shortest versus longest quartile had a 2.29-fold higher risk of HCC. Telomere length was inversely and linearly associated with the risk of cholangiocarcinoma. Individuals with telomeres in the shortest versus longest quartile had a 1.86-fold higher risk of cholangiocarcinoma. Conclusions: Shorter telomere length is associated with a higher risk of cirrhosis, HCC, and cholangiocarcinoma.

Cirrhosis and hepatocellular carcinoma (HCC) are long-term complications of chronic liver disease (CLD). In this large multi-ancestry genome-wide association study of all-cause cirrhosis (35,481 cases, 2.36M controls) and HCC (6,680 cases, 1.76M controls), we identified 27 loci associated with cirrhosis (10 novel) and 11 with HCC (three novel). Three novel cirrhosis loci were replicated in independent cohorts (e.g. FGF21, RPTOR, and IFNL3/4). Fifteen cirrhosis loci exhibited differential effects on cirrhosis risk via underlying etiologies, and six HCC loci influenced HCC risk indirectly via cirrhosis. In a gene-burden analysis of rare variants from whole-genome sequencing data in the VA Million Veteran Program (n=102,677), we identified GSTA5 as a novel cirrhosis-associated gene, while APOB and ATP9B were associated with and replicated for HCC. A high genetic risk score for cirrhosis was associated with a nearly doubled risk of CLD progressing to cirrhosis (HR=1.94, P=2×10⁻⁶⁸) and of cirrhosis progressing to HCC (HR=1.65, P=7×10⁻⁰⁸). Finally, among individuals with chronic hepatitis C who underwent antiviral therapy, cirrhosis risk was modified by variants in PNPLA3, IFNL3/4, and CD81 following pegylated interferon-α therapy, and by APOE lead variant following direct-acting antiviral therapy. These findings provide new insights into the complex genetic architecture of CLD progression with potential clinical and therapeutic implications.

Background & Aims: While cirrhosis is a primary risk factor for hepatocellular carcinoma (HCC), a significant proportion of HCC cases attributed to metabolic dysfunction‐associated steatotic liver disease (MASLD) develop in the absence of cirrhosis. MASLD is strongly linked to obesity, a known risk factor for multiple cancers. Whether the effect of obesity on HCC is mediated via cirrhosis or other factors is unknown. Methods: We used univariable Mendelian randomization (MR) to test the total effect of a higher body mass index (BMI), a proxy for obesity, on HCC, and multivariable MR to test the direct effect. Results: We estimated that the effect of BMI was a 1.65‐fold higher risk of HCC per standard deviation increase (95% confidence interval (CI): 1.28–2.12, p ‐value = 1.0 × 10 ⁻⁵ ). The BMI effect became indistinguishable from zero when taking liability to cirrhosis into account with multivariable MR (odds ratio = 1.12, 95% CI: 0.84–1.50, p ‐value = 0.44). We investigated additional potential pathways linking BMI to HCC—such as inflammation and type 2 diabetes—and explored the direct effect of childhood obesity on the risk of HCC. We found no direct effect of inflammation or type 2 diabetes ( p ‐values > 0.05). Childhood body size increased the risk of HCC (odds ratio = 1.78, 95% CI: 1.27–2.49, p ‐value = 8 × 10 ⁻⁴ ), but the effect disappeared when we took adult body size into account using multivariable MR. Conclusions: Cirrhosis liability is the primary mediator of the causal effect of obesity on HCC.