scRNA-seq determines the characteristics of T cell marker genes to predict the prognosis of esophageal cancer

  • Fang Meng 1 ,
  • Jiaru Hu 2 ,
  • Jinhu Qiang 1 ,
  • Qifeng Shi 3 ,
  • Jing Ji 3 ,
  • Zhenyu Li 4 ,
  • Lu Li 2 ,
  • Lei Lv , 5 ,
  • Shiqiang Zhang , 1
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  • 1. Department of Oncology & Hematology, Xishan People's Hospital of Wuxi City, Wuxi, China
  • 2. The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
  • 3. Department of Pathology, Xishan People's Hospital of Wuxi City, Wuxi, China
  • 4. Graduate School of Wannan Medical College, Wannan Medical College, Wuhu, China
  • 5. Department of Cancer Epigenetics Program, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
lvlei@ustc.edu.cn
zhangshiqiang711@163.com

Received date: 21 Oct 2023

Revised date: 27 Feb 2024

Accepted date: 12 Mar 2024

Copyright

2024 2024 The Authors. Precision Medical Sciences published by John Wiley & Sons Australia, Ltd on behalf of Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital.

Abstract

Esophageal cancer (EC) mainly includes two histological subtypes, esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma, which is of high morbidity and mortality. With the continuous development of medical technology, the treatment of EC has been greatly improved, but its prognosis is still unfavorable. Recent single-cell RNA-sequencing (scRNA-seq) is expected to bring breakthroughs in the treatment of EC. First, we identified T cell marker genes and generated signature by analyzing scRNA-seq data from Expression Omnibus (GEO) database and TCGA database. Then, an immune prognostic model was constructed using the least absolute shrinkage and selection operator. We found that the survival rate of ESCC varied significantly among the low- and high-risk groups. Two genes from T cell signature, DCPS and CYB5R3, were expressed in ESCC cells. Collectively, our study proposed a novel prognostic signature for ESCC patients based on T cell marker genes.

Cite this article

Fang Meng , Jiaru Hu , Jinhu Qiang , Qifeng Shi , Jing Ji , Zhenyu Li , Lu Li , Lei Lv , Shiqiang Zhang . scRNA-seq determines the characteristics of T cell marker genes to predict the prognosis of esophageal cancer[J]. Precision Medical Sciences, 2024 , 13(2) : 107 -117 . DOI: 10.1002/prm2.12130

1
He S, Xu J, Liu X, Zhen Y. Advances and challenges in the treatment of esophageal cancer. Acta Pharm Sin B. 2021;11:3379-3392.

DOI

2
Abnet CC, Arnold M, Wei WQ. Epidemiology of esophageal squamous cell carcinoma. Gastroenterology. 2018;154:360-373.

DOI

3
Lin Y, Totsuka Y, He Y, et al. Epidemiology of esophageal cancer in Japan and China. J Epidemiol. 2013;23:233-242.

DOI

4
Codipilly DC, Qin Y, Dawsey SM, et al. Screening for esophageal squamous cell carcinoma: recent advances. Gastrointest Endosc. 2018;88:413-426.

DOI

5
Liang L, Yu J, Li J, et al. Integration of scRNA-seq and bulk RNA-seq to analyse the heterogeneity of ovarian cancer immune cells and establish a molecular risk model. Front Oncol. 2021;11:711020.

DOI

6
Katzenelenbogen Y, Sheban F, Yalin A, et al. Coupled scRNA-seq and intracellular protein activity reveal an immunosuppressive role of TREM2 in cancer. Cell. 2020;182:872-885.e819.

DOI

7
Ranzoni AM, Tangherloni A, Berest I, et al. Integrative single-cell RNA-seq and ATAC-seq analysis of human developmental hematopoiesis. Cell Stem Cell. 2021;28:472-487.e477.

DOI

8
Combe M, Garijo R, Geller R, Cuevas JM, Sanjuán R. Single-cell analysis of RNA virus infection identifies multiple genetically diverse viral genomes within single infectious units. Cell Host Microbe. 2015;18:424-432.

DOI

9
Golumbeanu M, Cristinelli S, Rato S, et al. Single-cell RNA-seq reveals transcriptional heterogeneity in latent and reactivated HIV-infected cells. Cell Rep. 2018;23:942-950.

DOI

10
Zhang TQ, Xu ZG, Shang GD, Wang JW. A single-cell RNA sequencing profiles the developmental landscape of Arabidopsis root. Mol Plant. 2019;12:648-660.

DOI

11
Dinh HQ, Pan F, Wang G, et al. Integrated single-cell transcriptome analysis reveals heterogeneity of esophageal squamous cell carcinoma microenvironment. Nat Commun. 2021;12:7335.

DOI

12
Caushi JX, Zhang J, Ji Z, et al. Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers. Nature. 2021;596:126-132.

DOI

13
Winer H, Rodrigues GOL, Hixon JA, et al. IL-7: comprehensive review. Cytokine. 2022;160:156049.

DOI

14
Barata JT, Durum SK, Seddon B. Flip the coin: IL-7 and IL-7R in health and disease. Nat Immunol. 2019;20:1584-1593.

DOI

15
Song B, Shen S, Fu S, Fu J. HSPA6 and its role in cancers and other diseases. Mol Biol Rep. 2022;49:10565-10577.

DOI

16
Zhang L, Zhuo HQ, Hong ZJ, Hou JJ, Cheng J, Cai J. HSPA6, a novel prognostic and therapeutic biomarker, associated with Ming classification in gastric cancer. J Clin Lab Anal. 2023;37:e24763.

DOI

17
Wang L, Hou J, Wang J, et al. Regulatory roles of HSPA6 in Actinidia chinensis planch. Root extract (acRoots)-inhibited lung cancer proliferation. Clin Transl Med. 2020;10:e46.

DOI

18
Lu J, Peng Y, Huang R, et al. Elevated TYROBP expression predicts poor prognosis and high tumor immune infiltration in patients with low-grade glioma. BMC Cancer. 2021;21:723.

DOI

19
Jiang J, Ding Y, Wu M, et al. Identification of TYROBP and C1QB as two novel key genes with prognostic value in gastric cancer by network analysis. Front Oncol. 2020;10:1765.

DOI

20
Yang CS, Chen XL. Research on esophageal cancer: with personal perspectives from studies in China and Kenya. Int J Cancer. 2021;149:264-276.

DOI

21
Gabrilovich DI, Ostrand-Rosenberg S, Bronte V. Coordinated regulation of myeloid cells by tumours. Nat Rev Immunol. 2012;12:253-268.

DOI

22
Li R, Mukherjee MB, Lin J. Coordinated regulation of myeloid-derived suppressor cells by cytokines and chemokines. Cancers(Basel). 2022;14(5):1236.

DOI

23
Goswami S, Anandhan S, Raychaudhuri D, Sharma P. Myeloid cell-targeted therapies for solid tumours. Nat Rev Immunol. 2023;23:106-120.

DOI

24
De Leo A, Ugolini A, Veglia F. Myeloid cells in glioblastoma microenvironment. Cells. 2020;10(1):18.

DOI

25
Dysthe M, Parihar R. Myeloid-derived suppressor cells in the tumor microenvironment. Adv Exp Med Biol. 2020;1224:117-140.

DOI

26
Anand P, Guillaumet-Adkins A, Dimitrova V, et al. Single-cell RNA-seq reveals developmental plasticity with coexisting oncogenic states and immune evasion programs in ETP-ALL. Blood. 2021;137:2463-2480.

DOI

27
Jerby-Arnon L, Shah P, Cuoco MS, et al. A cancer cell program promotes T cell exclusion and resistance to checkpoint blockade. Cell. 2018;175:984-997.e924.

DOI

28
Xu K, Zhang W, Wang C, et al. Integrative analyses of scRNA-seq and scATAC-seq reveal CXCL14 as a key regulator of lymph node metastasis in breast cancer. Hum Mol Genet. 2021;30:370-380.

DOI

29
Wang G, Qiu M, Xing X, et al. Lung cancer scRNA-seq and lipidomics reveal aberrant lipid metabolism for early-stage diagnosis. Sci Transl Med. 2022;14:eabk2756.

DOI

30
Maynard A, McCoach CE, Rotow JK, et al. Therapy-induced evolution of human lung cancer revealed by single-cell RNA sequencing. Cell. 2020;182:1232-1251.e1222.

DOI

31
Li X, Sun Z, Peng G, et al. Single-cell RNA sequencing reveals a pro-invasive cancer-associated fibroblast subgroup associated with poor clinical outcomes in patients with gastric cancer. Theranostics. 2022;12:620-638.

DOI

32
Zhang P, Yang M, Zhang Y, et al. Dissecting the single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer. Cell Rep. 2019;27:1934-1947.e1935.

DOI

33
Wang B, Zhang Y, Qing T, et al. Comprehensive analysis of metastatic gastric cancer tumour cells using single-cell RNA-seq. Sci Rep. 2021;11:1141.

DOI

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