RNA-seq data for tumor and adjacent non-tumor tissues from hepatocellular carcinoma patients with anti-PD-1 therapy

Immune checkpoint inhibitors elicit durable antitumor effects in multiple cancers, yet not all patients respond. Here, we aimed to develop and validate a molecular classification of hepatocellular carcinoma (HCC) patients based on 42 fatty acid degradation genes and demonstrate its predictive ability in the clinical response of anti-PD1 therapy in HCC patients. We studied global mRNA expression profiles from 41 primary tumor tissues and 25 nontumor tissues derived from 41 HCC patients. 17 patients received anti-PD1 therapy and were available with clinical response. 63 samples were also sent for lipidomics analysis. Methods for the study included gene expression analysis, consensus clustering analysis, pathway enrichment analysis, and Single-Sample Gene Set Enrichment Analysis (ssGSEA). This study identified and validated a novel molecular classification based on fatty acid degradation that predicts clinical response to anti-PD-1 therapy in hepatocellular carcinoma. Overall design: In total, 69 samples from hepatocellular carcinoma tumors and adjacent non-tumor liver tissue have been obtained from 44 patients who underwent radical resection between January 2019 and June 2021 in Nanjing Drum Tower Hospital. Three samples didn't pass the quality control for RNA-seq and 6 samples didn't pass the quality control for lipidomics analysis due to tissue degradation or limited tissue amount, thus being ruled out from the study. Seventeen patients received anti-PD1 therapy and were available with clinical response. The study was approved by the Research Ethics Committee of Drum Tower hospital, and written informed consent was obtained from each patient. Each sample was assigned a new research ID, and the patient's name or medical record number used during hospitalization was de-identified.