Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma

N Engl J Med 2008;359:1995-2004. Published: 2008.10.14

Yujin Hoshida, Augusto Villanueva, Masahiro Kobayashi, Judit Peix, Derek Y. Chiang, Amy Camargo, Supriya Gupta, Jamie Moore, Matthew J. Wrobel, Jim Lerner, Michael Reich, Jennifer A. Chan, Jonathan N. Glickman, Kenji Ikeda, Masaji Hashimoto, Goro Watanabe, Maria G. Daidone, Sasan Roayaie, Myron Schwartz, Swan Thung, Helga B. Salvesen, Stacey Gabriel, Vincenzo Mazzaferro, Jordi Bruix, Scott L. Friedman, Hiromitsu Kumada, Josep M. Llovet, Todd R. Golub

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Background: It is a challenge to identify those patients who, after undergoing potentially curative treatments for hepatocellular carcinoma, are at greatest risk of 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, tissues. Methods: 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. Results: 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tissue was highly effective: samples from 90% of the patients yielded data of high quality, including samples that had been archived for more than 24 years.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 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). Conclusions: We have demonstrated the feasibility of genomewide expression profiling of formalin-fixed, paraffin-embedded tissues and have shown that a reproducible gene-expression signature correlating with survival is present in liver tissue adjacent to the tumor in patients with hepatocellular carcinoma.


Supplemental Data

Description Link/Filename
Datasets_used_for_informative_gene_selection.xls (15 KB)
Train_HCC.gct (5810 KB)
Train_Liver.gct (5953 KB)
Validation_Liver.gct (16155 KB)
Training_HCC_all.txt (13 KB)
Train_Liver.txt (9 KB)
Validation_Liver.txt (26 KB)
HCC_samples_used_for_outcome_prediction.txt (1 KB)
IlluminaDASL Pipeline ( GenePattern Public Server)