Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma

TLDR

Identifying hepatocellular carcinoma patients at greatest risk of recurrence after curative treatment is challenging, yet high‑risk patients could benefit from novel interventions, and progress has been hindered by the lack of a method to profile genomewide expression in formalin‑fixed, paraffin‑embedded tissue. The study aimed to demonstrate the feasibility of profiling over 6,000 genes in formalin‑fixed, paraffin‑embedded hepatocellular carcinoma tissues. The authors applied this high‑quality profiling method to 307 patients across four series, successfully generating data from 90 % of samples, including those archived for more than 24 years, to discover and validate a survival‑associated gene‑expression signature. While tumor tissue expression profiles showed no survival association, gene signatures from adjacent non‑tumoral liver tissue were strongly correlated with survival in a Japanese training set and validated in an independent cohort of 225 patients (P = 0.04), confirming a reproducible prognostic signature in peritumoral liver tissue.

Abstract

It is a challenge to identify patients who, after undergoing potentially curative treatment for hepatocellular carcinoma, are at greatest risk for recurrence. Such high-risk patients could receive novel interventional measures. An obstacle to the development of genome-based predictors of outcome in patients with hepatocellular carcinoma has been the lack of a means to carry out genomewide expression profiling of fixed, as opposed to frozen, tissue.We aimed to demonstrate the feasibility of gene-expression profiling of more than 6000 human genes in formalin-fixed, paraffin-embedded tissues. We applied the method to tissues from 307 patients with hepatocellular carcinoma, from four series of patients, to discover and validate a gene-expression signature associated with survival.The expression-profiling method for formalin-fixed, paraffin-embedded tissue was highly effective: samples from 90% of the patients yielded data of high quality, including samples that had been archived for more than 24 years. Gene-expression profiles of tumor tissue failed to yield a significant association with survival. In contrast, profiles of the surrounding nontumoral liver tissue were highly correlated with survival in a training set of tissue samples from 82 Japanese patients, and the signature was validated in tissues from an independent group of 225 patients from the United States and Europe (P=0.04).We have demonstrated the feasibility of genomewide expression profiling of formalin-fixed, paraffin-embedded tissues and have shown that a reproducible gene-expression signature correlated with survival is present in liver tissue adjacent to the tumor in patients with hepatocellular carcinoma.