The dynamic dysregulated network identifies stage-specific markers during lung adenocarcinoma malignant progression and metastasis

Li Wang; Wangyang Liu; Kailai Liu; Lixia Wang; Xiangzhe Yin; Lin Bo; Haotian Xu; Shihua Lin; Ke Feng; Xinyu Zhou; Lin Lin; Meiting Fei; Caiyu Zhang; Shangwei Ning; Hongying Zhao

Molecular Therapy: Nucleic Acids (Dec 2022)

The dynamic dysregulated network identifies stage-specific markers during lung adenocarcinoma malignant progression and metastasis

Li Wang,
Wangyang Liu,
Kailai Liu,
Lixia Wang,
Xiangzhe Yin,
Lin Bo,
Haotian Xu,
Shihua Lin,
Ke Feng,
Xinyu Zhou,
Lin Lin,
Meiting Fei,
Caiyu Zhang,
Shangwei Ning,
Hongying Zhao

Affiliations

Li Wang: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; Corresponding author Li Wang, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Wangyang Liu: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
Kailai Liu: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
Lixia Wang: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
Xiangzhe Yin: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
Lin Bo: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
Haotian Xu: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
Shihua Lin: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
Ke Feng: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
Xinyu Zhou: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
Lin Lin: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
Meiting Fei: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
Caiyu Zhang: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
Shangwei Ning: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; Corresponding author Shangwei Ning, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Hongying Zhao: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; Corresponding author Hongying Zhao, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.

Journal volume & issue: Vol. 30
pp. 633 – 647

Abstract

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Brain metastasis occurs in approximately 30% of patients with lung adenocarcinoma (LUAD) and is closely associated with poor prognosis, recurrence, and death. However, dynamic gene regulation and molecular mechanism driving LUAD progression remain poorly understood. In this study, we performed a comprehensive single-cell transcriptome analysis using data from normal, early stage, advanced stage, and brain metastasis LUAD. Our single-cell-level analysis reveals the cellular composition heterogeneity at different stages during LUAD progression. We identified stage-specific risk genes that could contribute to LUAD progression and metastasis by reprogramming immune-related and metabolic-related functions. We constructed an early advanced metastatic dysregulated network and revealed the dynamic changes in gene regulations during LUAD progression. We identified 6 early advanced (HLA-DRB1, HLA-DQB1, SFTPB, SFTPC, PLA2G1B, and FOLR1), 8 advanced metastasis (RPS15, RPS11, RPL13A, RPS24, HLA-DRB5, LYPLA1, KCNJ15, and PSMA3), and 2 common risk genes in different stages (SFTPD and HLA-DRA) as prognostic markers in LUAD. Particularly, decreased expression of HLA-DRA, HLA-DRB1, HLA-DQB1, and HLA-DRB5 refer poor prognosis in LUAD by controlling antigen processing and presentation and T cell activation. Increased expression of PSMA3 and LYPLA1 refer poor prognosis by reprogramming fatty acid metabolism and RNA catabolic process. Our findings will help further understanding the pathobiology of brain metastases in LUAD.

Published in Molecular Therapy: Nucleic Acids

ISSN: 2162-2531 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Medicine: Therapeutics. Pharmacology
Website: https://www.cell.com/molecular-therapy-family/nucleic-acids/latest-content

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