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Identification of the CD8 T-cell exhaustion signature of hepatocellular carcinoma for the prediction of prognosis and immune microenvironment by integrated analysis of bulk- and single-cell RNA sequencing data.

作者信息

Fan Jianhui, Zhang Qinghua, Huang Tiancong, Li Haitao, Fang Guoxu

机构信息

Department of Infectious Disease, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China.

Department of Minimally Invasive Surgery, Fuzhou Hospital of Traditional Chinese Medicine Affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou, China.

出版信息

Transl Cancer Res. 2024 Nov 30;13(11):5856-5872. doi: 10.21037/tcr-24-650. Epub 2024 Nov 20.


DOI:10.21037/tcr-24-650
PMID:39697729
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11651828/
Abstract

BACKGROUND: Hepatocellular carcinoma (HCC) is a prevalent type of cancer with high incidence and mortality rates. It is the third most common cause of cancer-related deaths. CD8 T cell exhaustion (TEX) is a progressive decline in T cell function due to sustained T cell receptor stimulation from continuous antigen exposure. Studies have shown that CD8 TEX plays an important role in the anti-tumor immune process and is significantly correlated with patient prognosis. The aim of the research is to establish a reliable CD8 TEX-based signature using single-cell RNA sequencing (scRNA-seq) and high-throughput RNA sequencing (RNA-seq), providing a new approach to evaluate HCC patient prognosis and immune microenvironment. METHODS: The RNA-seq data of HCC patients were download from three different databases: The Cancer Genome Atlas (TCGA), the Gene Expression Omnibus (GEO), and the International Cancer Genome Consortium (ICGC). HCC's 10× scRNA data were acquired from GSE149614. Based on single-cell sequencing data, CD8 TEX-related genes were identified using uniform manifold approximation and projection (UMAP) algorithm, singleR, and marker gene methods. Afterwards, we proceeded to construct CD8 TEX signature using differential gene analysis, univariate Cox regression analysis, least absolute shrinkage and selection operator (LASSO) regression, and multivariate Cox regression analysis. We also validated the CD8 TEX signature in GEO and ICGC external cohorts and investigated clinical characteristics, chemotherapy sensitivity, mutation landscape, functional analysis, and immune cell infiltration in different risk groups. RESULTS: The CD8 TEX signature, consisting of 13 genes (, , , , , , , , , , , ), was found to have a strong predictive effect on the prognosis of HCC. The Kaplan-Meier (KM) analysis showed that the overall survival (OS) rate of patients in the low-risk group was higher than that of patients in the high-risk group across different datasets and specific populations. The research findings suggested that the risk score was an independent predictor of HCC prognosis. The model based on clinical features and risk score has a strong predictive effect. We observed significant differences among various risk groups in terms of clinical characteristics, functional analysis, mutation landscape, chemotherapy sensitivity, and immune cell infiltration. CONCLUSIONS: We constructed a CD8 TEX signature to predict the survival probability of patients with HCC. We also found that the model could predict the sensitivity of targeted drugs and immune cell infiltration, and the risk score was negatively correlated with CD8 T cell infiltration. In summary, the CD8 TEX signature of HCC was constructed for the prediction of prognosis and immune microenvironment by integrated analysis of bulk and scRNA-seq data.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/488928972e35/tcr-13-11-5856-f12.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/f6bc7e929ff7/tcr-13-11-5856-f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/70b649be63ac/tcr-13-11-5856-f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/6d25356e5db3/tcr-13-11-5856-f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/6fb60fb3c963/tcr-13-11-5856-f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/7c72904ebe57/tcr-13-11-5856-f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/9f1d1a384fa4/tcr-13-11-5856-f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/709b964396e3/tcr-13-11-5856-f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/c8dfb9943ead/tcr-13-11-5856-f8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/308fed2a30f1/tcr-13-11-5856-f9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/c84fa3c16f10/tcr-13-11-5856-f10.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/a3468e95c52a/tcr-13-11-5856-f11.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/488928972e35/tcr-13-11-5856-f12.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/f6bc7e929ff7/tcr-13-11-5856-f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/70b649be63ac/tcr-13-11-5856-f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/6d25356e5db3/tcr-13-11-5856-f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/6fb60fb3c963/tcr-13-11-5856-f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/7c72904ebe57/tcr-13-11-5856-f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/9f1d1a384fa4/tcr-13-11-5856-f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/709b964396e3/tcr-13-11-5856-f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/c8dfb9943ead/tcr-13-11-5856-f8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/308fed2a30f1/tcr-13-11-5856-f9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/c84fa3c16f10/tcr-13-11-5856-f10.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/a3468e95c52a/tcr-13-11-5856-f11.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f66/11651828/488928972e35/tcr-13-11-5856-f12.jpg

相似文献

[1]
Identification of the CD8 T-cell exhaustion signature of hepatocellular carcinoma for the prediction of prognosis and immune microenvironment by integrated analysis of bulk- and single-cell RNA sequencing data.

Transl Cancer Res. 2024-11-30

[2]
T-cell exhaustion signatures characterize the immune landscape and predict HCC prognosis integrating single-cell RNA-seq and bulk RNA-sequencing.

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[3]
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[4]
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J Transl Med. 2023-3-27

[5]
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[6]
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Curr Med Chem. 2024

[7]
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[8]
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Eur J Med Res. 2024-7-5

[9]
Identification of a Novel CD8 T cell exhaustion-related gene signature for predicting survival in hepatocellular carcinoma.

BMC Cancer. 2023-12-4

[10]
New HCC Subtypes Based on CD8 Tex-Related lncRNA Signature Could Predict Prognosis, Immunological and Drug Sensitivity Characteristics of Hepatocellular Carcinoma.

J Hepatocell Carcinoma. 2024-7-5

本文引用的文献

[1]
Identification of a Novel CD8 T cell exhaustion-related gene signature for predicting survival in hepatocellular carcinoma.

BMC Cancer. 2023-12-4

[2]
T-cell exhaustion signatures characterize the immune landscape and predict HCC prognosis integrating single-cell RNA-seq and bulk RNA-sequencing.

Front Immunol. 2023

[3]
Global Epidemiology and Genetics of Hepatocellular Carcinoma.

Gastroenterology. 2023-4

[4]
Natural Killer Cells Induce CD8 T Cell Dysfunction Galectin-9/TIM-3 in Chronic Hepatitis B Virus Infection.

Front Immunol. 2022

[5]
Multi-Scale Spatial Analysis of the Tumor Microenvironment Reveals Features of Cabozantinib and Nivolumab Efficacy in Hepatocellular Carcinoma.

Front Immunol. 2022

[6]
Neoadjuvant Cabozantinib and Nivolumab Converts Locally Advanced HCC into Resectable Disease with Enhanced Antitumor Immunity.

Nat Cancer. 2021-9

[7]
Hepatocellular carcinoma.

Nat Rev Dis Primers. 2021-1-21

[8]
Immunotherapy for hepatocellular carcinoma.

Cancer Lett. 2019-12-4

[9]
RNA sequencing: the teenage years.

Nat Rev Genet. 2019-7-24

[10]
Maftools: efficient and comprehensive analysis of somatic variants in cancer.

Genome Res. 2018-10-19

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