Rare germline variants in key pathways contribute to hepatocellular carcinoma risk in Hispanics

Background: Hepatocellular carcinoma (HCC) is the sixth most common cancer and the third leading cause of cancer-related death. The primary cause of HCC is shifting from viral hepatitis infections to metabolic dysfunction-associated steatotic liver disease (MASLD). In the U.S., Hispanics have the highest incidence of HCC. Furthermore, MASLD-related HCC occurs more frequently in Hispanics compared to non-Hispanic Whites and Blacks. These disparities suggest population-specific genetic mechanisms underlying HCC development. While genome-wide association studies have uncovered genetic risk factors for HCC, most studies have focused on East Asian and European ancestry populations and common variants, which often confer small effect sizes. Rare variants can exert larger effects than common variants and may provide novel biological insights, particularly in underrepresented Hispanics. Methods: We performed whole-exome sequencing on blood samples from 719 Hispanic individuals, including 455 HCC cases and 264 controls. Analyses focused on 576 genes previously implicated in HCC and MASLD. We prioritized rare, protein-altering variants with minor allele frequency ≤ 0.01 in both our controls and the Admixed American (AMR, primarily Hispanic/Latino ancestry) population from the Genome Aggregation Database (gnomAD). Only variants present in ≥ 3 HCC cases and predicted to be deleterious (with a scaled Combined Annotation Dependent Depletion (CADD) score ≥ 15) were considered. Associations were evaluated using single-variant allelic analysis and gene-based burden tests. Allele counts from gnomAD AMR population controls (n = 30,019) were integrated into the analysis to improve the estimation of odds rations (ORs) and 95% confidence intervals (CIs). Results: Among 576 genes examined, we identified 27 rare deleterious variant candidates across 24 genes significantly enriched in HCC cases. Top candidate variants included those in immune response genes such as HLA-DRB1 (W38X; OR 15.13, 95% CI 4.91-39.90) and in cell growth genes such as SIK3 (A1272V; OR 7.19, 95% CI 1.85-20.11). Several lipid metabolism genes also showed enrichment, including PLB1 V417L (OR 21.95, 95% CI 3.81-88.18), ADAMTS9 S1638L (OR 3.09, 95% CI 0.98-7.47), TM6SF2 R138W (OR 2.66, 95% CI 1.55-4.28). These genes also showed significant aggregation of rare variants in the burden test. Notably, TM6SF2 R138W significantly enriched in HCC cases born in the US and in HCC cases with alcohol liver disease and MASLD etiologies (OR = 3.30, 95% CI: 0.98-14.27, P = 0.040). Conclusion: These results highlight that rare, deleterious variants across immune, cell-regulatory, and lipid-metabolic pathways contribute to elevated HCC risk in Hispanics. These findings further suggest potential gene-environment interactions that may underlie HCC disparities and provide a genetic basis for future targeted prevention strategies in high-risk populations.