Single-cell mapping of N6-methyladenosine in esophageal squamous cell carcinoma and exploration of the risk model for immune infiltration

Yuanliu Nie; Guangyue Yao; Xiaoying Xu; Yi Liu; Ke Yin; Jingjiang Lai; Qiang Li; Fengge Zhou; Zhe Yang

doi:10.3389/fendo.2023.1155009

Single-cell mapping of N6-methyladenosine in esophageal squamous cell carcinoma and exploration of the risk model for immune infiltration

Front Endocrinol (Lausanne). 2023 Mar 21:14:1155009. doi: 10.3389/fendo.2023.1155009. eCollection 2023.

Authors

Yuanliu Nie¹, Guangyue Yao¹, Xiaoying Xu², Yi Liu³, Ke Yin⁴, Jingjiang Lai⁵, Qiang Li⁶, Fengge Zhou⁶, Zhe Yang^{1

6}

Affiliations

¹ Tumor Research and Therapy Center, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China.
² Shandong First Medical University, College of Basic Medicine, Shandong First Medical University-Shandong Academy of Medical Sciences, Jinan, Shandong, China.
³ Department of Computer Science and Technology, Ocean University of China, Qingdao, China.
⁴ Department of Pathology, Shandong Provincial Hospital, Shandong University, Jinan, China.
⁵ Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.
⁶ Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.

Abstract

Background: N6-methyladenosine (m6A) modification is the most common RNA modification, but its potential role in the development of esophageal cancer and its specific mechanisms still need to be further investigated.

Methods: Bulk RNA-seq of 174 patients with esophageal squamous carcinoma from the TCGA-ESCC cohort, GSE53625, and single-cell sequencing data from patients with esophageal squamous carcinoma from GSE188900 were included in this study. Single-cell analysis of scRNA-seq data from GSE188900 of 4 esophageal squamous carcinoma samples and calculation of PROGENy scores. Demonstrate the scoring of tumor-associated pathways for different cell populations. Cell Chat was calculated for cell populations. thereafter, m6A-related differential genes were sought and risk models were constructed to analyze the relevant biological functions and impact pathways of potential m6A genes and their impact on immune infiltration and tumor treatment sensitivity in ESCC was investigated.

Results: By umap downscaling analysis, ESCC single-cell data were labelled into clusters of seven immune cell classes. Cellchat analysis showed that the network interactions of four signaling pathways, MIF, AFF, FN1 and CD99, all showed different cell type interactions. The prognostic risk model constructed by screening for m6A-related differential genes was of significant value in the prognostic stratification of ESCC patients and had a significant impact on immune infiltration and chemotherapy sensitivity in ESCC patients.

Conclusion: In our study, we explored a blueprint for the distribution of single cells in ESCC based on m6A methylation and constructed a risk model for immune infiltration analysis and tumor efficacy stratification in ESCC on this basis. This may provide important potential guidance for revealing the role of m6A in immune escape and treatment resistance in esophageal cancer.

Keywords: N6-Methyladenosine; bioinfomatics; esophageal squamous cell carcinoma; immune infiltration; single-gene sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adenosine
Cell Communication
Esophageal Neoplasms* / genetics
Esophageal Squamous Cell Carcinoma* / genetics
Humans

Substances

Adenosine

Grants and funding

This study is supported by Beijing Xisike Clinical Oncology Research Foundation [grant number Y-2019AZMS-0522]; the Natural Science Foundation of Shandong Province [grant number ZR2020MH229] and the Xisike - 2019 Qilu Oncology Research Fund Project [grant number Y-QL2019-0149].