A T-cell-related signature for prognostic stratification and immunotherapy response in hepatocellular carcinoma based on transcriptomics and single-cell sequencing

BMC Bioinformatics

Research

Yinghui Song¹  Ranzhiqiang Yang²  Bo Sun²  Bai Ding²  Yuhang Li²  Xu Chen²  Yu Chen²  Sulai Liu²  Chuang Peng² 

[1] Central Laboratory of Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, 410005, Changsha, Hunan, China;Department of Hepatobiliary Surgery, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, 410005, Changsha, Hunan, China;

关键词: T-cell marker genes;    Single-cell RNA sequencing;    Immunotherapy;    Hepatocellular carcinoma;    Prognostic signature;   

DOI  :  10.1186/s12859-023-05344-7

 received in 2023-03-09, accepted in 2023-05-18,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundHepatocellular carcinoma (HCC) is the fifth most frequently diagnosed malignancy and the third leading cause of cancer death globally. T cells are significantly correlated with the progression, therapy and prognosis of cancer. Limited systematic studies regarding the role of T-cell-related markers in HCC have been performed.MethodsT-cell markers were identified with single-cell RNA sequencing (scRNA-seq) data from the GEO database. A prognostic signature was developed with the LASSO algorithm in the TCGA cohort and verified in the GSE14520 cohort. Another three eligible immunotherapy datasets, GSE91061, PRJEB25780 and IMigor210, were used to verify the role of the risk score in the immunotherapy response.ResultsWith 181 T-cell markers identified by scRNA-seq analysis, a 13 T-cell-related gene-based prognostic signature (TRPS) was developed for prognostic prediction, which divided HCC patients into high-risk and low-risk groups according to overall survival, with AUCs of 1 year, 3 years, and 5 years of 0.807, 0.752, and 0.708, respectively. TRPS had the highest C-index compared with the other 10 established prognostic signatures, suggesting a better performance of TRPS in predicting the prognosis of HCC. More importantly, the TRPS risk score was closely correlated with the TIDE score and immunophenoscore. The high-risk score patients had a higher percentage of SD/PD, and CR/PR occurred more frequently in patients with low TRPS-related risk scores in the IMigor210, PRJEB25780 and GSE91061 cohorts. We also constructed a nomogram based on the TRPS, which had high potential for clinical application.ConclusionOur study proposed a novel TRPS for HCC patients, and the TRPS could effectively indicate the prognosis of HCC. It also served as a predictor for immunotherapy.

【 授权许可】

CC BY   
© The Author(s) 2023

【 图 表 】

41116_2023_36_Article_IEq269.gif

Fig. 1

41116_2023_36_Article_IEq230.gif

41116_2023_36_Article_IEq228.gif

Fig. 1

41116_2023_36_Article_IEq191.gif

Fig. 1

41116_2023_36_Article_IEq178.gif

41116_2023_36_Article_IEq163.gif

40517_2023_256_Article_IEq264.gif

41116_2023_36_Article_IEq124.gif

Fig. 1