Copyright
©The Author(s) 2025. Published by Baishideng Publishing Group Inc. All rights reserved.
Uncovering immune cell heterogeneity in hepatocellular carcinoma by combining single-cell RNA sequencing with T-cell receptor sequencing
Xin-Yu Gu, Shuang-Lin Gu, Zi-Yi Chen, Jin-Long Tong, Xiao-Yue Li, Hui Dong, Cai-Yun Zhang, Wen-Xian Qian, Xiu-Chang Ma, Chang-Hua Yi, Yong-Xiang Yi
Xin-Yu Gu, Jin-Long Tong, Xiao-Yue Li, Yong-Xiang Yi, Department of Infectious Diseases, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, Jiangsu Province, China
Xin-Yu Gu, Department of General Surgery, Changshu Hospital Affiliated to Nanjing University of Chinese Medicine, Changshu 215500, Jiangsu Province, China
Shuang-Lin Gu, Hui Dong, Cai-Yun Zhang, Wen-Xian Qian, Xiu-Chang Ma, Chang-Hua Yi, Department of Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, Jiangsu Province, China
Zi-Yi Chen, Genetic Center, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410078, Hunan Province, China
Chang-Hua Yi, College of Medical Technology, Shaoyang University, Shaoyang 422000, Hunan Province, China
Yong-Xiang Yi, Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu Province, China
Co-first authors: Xin-Yu Gu and Shuang-Lin Gu.
Co-corresponding authors: Chang-Hua Yi and Yong-Xiang Yi.
Author contributions: Gu XY and Li XY conducted all the experiments; Gu XY collected the samples; Gu SL and Chen ZY contributed to the data analyses and generated the figures; Gu XY, Gu SL, and Chen ZY wrote the manuscript; Gu XY and Gu SL contributed equally as co-first authors; Yi CH revised the manuscript, provided financial support for this project, led the overall outline of the topic, and made major decisions about the article; Yi CH and Yi YX contributed equally as co-corresponding authors; Gu XY, Gu SL, Chen ZY, Tong JL, Li XY, Dong H, Zhang CY, Qian WX, Ma XC, Yi CH, and Yi YX have read and agreed to the published version of the manuscript.
Supported by the Scientific Research Topic of Jiangsu Provincial Health Care Commission, No. M2021017; the High-level Talent Research Project of the Second Hospital of Nanjing, No. 0313504; and the Nanjing Second Hospital Academic Leader Program, No. 0313506.
Institutional review board statement: This study was approved by Medical Research Ethics Committee at the Second Hospital of Nanjing (No. 2022-LS-ky034). The patients provided their written informed consent to participate in this study.
Conflict-of-interest statement: All the authors report no relevant conflicts of interest for this article.
Data sharing statement: The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive of the National Genomics Data Center, China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences (GSA-Human: HRA003731), which are publicly accessible at
https://ngdc.cncb.ac.cn/gsa-human.
Open Access: This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See:
https://creativecommons.org/Licenses/by-nc/4.0/ Corresponding author: Yong-Xiang Yi, MD, PhD, Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Gulou District, Nanjing 210008, Jiangsu Province, China.
ian0126@126.com
Received: July 12, 2024
Revised: November 13, 2024
Accepted: December 31, 2024
Published online: February 27, 2025
Processing time: 222 Days and 12.4 Hours
BACKGROUND
Understanding the status and function of tumor-infiltrating immune cells is essential for improving immunotherapeutic effects and predicting the clinical response in human patients with carcinoma. However, little is known about tumor-infiltrating immune cells, and the corresponding research results in hepatocellular carcinoma (HCC) are limited.
AIM
To investigate potential biomarker genes that are important for the development of HCC and to understand how immune cell subsets react throughout this process.
METHODS
Using single-cell RNA sequencing and T-cell receptor sequencing, the heterogeneity and potential functions of immune cell subpopulations from HCC tissue and normal tissue adjacent to carcinoma, as well as their possible interactions, were analyzed.
RESULTS
Eight T-cell clusters from patients were analyzed and identified using bioinformatics, including six typical major T-cell clusters and two newly identified T-cell clusters, among which Fc epsilon receptor 1G+ T cells were characterized by the upregulation of Fc epsilon receptor 1G, tyrosine kinase binding protein, and T cell receptor delta constant, whereas metallothionein 1E+ T cells proliferated significantly in tumors. Differentially expressed genes, such as regulator of cell cycle, cysteine and serine rich nuclear protein 1, SMAD7 and metallothionein 1E, were identified as significantly upregulated in tumors and have potential as biomarkers. In association with T-cell receptor analysis, we inferred the clonal expansion characteristics of each T-cell cluster in HCC patients.
CONCLUSION
We identified lymphocyte subpopulations and potential biomarker genes critical for HCC development and revealed the clonal amplification of infiltrating T cells. These data provide valuable resources for understanding the response of immune cell subsets in HCC.
Core Tip: In this study, the heterogeneity of immune cell subpopulations, their potential functions, and their possible interactions in hepatocellular carcinoma (HCC) tissues and cancer-adjacent normal tissues were analyzed using single-cell RNA sequencing and T-cell receptor sequencing. Genes that may serve as biomarkers were identified by characterizing the major T-cell populations and 2 newly identified T-cell populations. In combination with the T-cell receptor analysis, we also inferred the clonal expansion characteristics of each T-cell cluster in HCC patients. In conclusion, we identified lymphocyte subpopulations and potential biomarker genes critical for HCC development and revealed the clonal expansion of infiltrating T cells.
