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Identification of differentially expressed genes in lung adenocarcinoma cells using single-cell RNA sequencing not
Zhencong Chen1, Mengnan Zhao1, Ming Li1
1Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, 200032, Shanghai, China.
Abstract:
Lung adenocarcinoma (LUAD) is the leading cause of cancer-related deaths worldwide. Traditional RNA sequencing data fails to detect the exact cellular and molecular changes in tumor cells as they make up only a small proportion of tumor tissue. 10× genomics single-cell RNA sequencing (10× scRNA-seq) and gene expression data of LUAD patients was obtained from the Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, ArrayExpress, TCGA, and GEO databases. Differentially expressed genes (DEGs) were identified in LUAD and alveolar cells (DEGs-scRNA-cancer_cell), tumor- and normal tissue-derived cells (DEGs-scRNA-sample), and normal and LUAD patients (DEGs-Bulk). Flow cytometry and qRT-PCR were performed to validate the significantly differentially expressed ligand-receptor pairs. We selected 159,219 cells and 594 samples in the scRNA-seq data and traditional RNA sequencing, respectively. A total of 1042 DEGs-scRNA-cancer_cell, 788 DEGs-scRNA-sample, and 2510 DEGs-Bulk were identified in this study. We also identified 57 DEGs that were only detected in DEGs-scRNA-cancer_cell (only-DEGs-scRNA-cancer_cell). To explore the relationship between only-DEGs-scRNA-cancer_cell and survival in LUAD, 14 and 22 only-DEGs-scRNA-cancer_cell, which were closely related with survival in TCGA and GEO cohorts were identified. Functional enrichment analyses showed these DEGs-scRNA-cancer_cells were mainly related to cell proliferation and immunoregulation. Our study detected and compared DEGs at different levels and revealed genes that may regulate tumor development. Our results provide a potential new protocol to determine the contribution of DEGs to cancer progression and to help identify potential therapeutic targets.
Insights
Single-cell RNA sequencing reveals novel genes in lung adenocarcinoma (LUAD) that impact cell proliferation and immune regulation, offering potential therapeutic targets for this deadly cancer.
Area of Science:
- Oncology
- Genomics
- Bioinformatics
Background:
- Lung adenocarcinoma (LUAD) is a leading cause of cancer mortality.
- Traditional RNA sequencing struggles to identify molecular changes in the small fraction of tumor cells within tissue.
- Single-cell RNA sequencing (scRNA-seq) offers higher resolution for cellular and molecular analysis.
Purpose of the Study:
- To identify differentially expressed genes (DEGs) in LUAD using scRNA-seq and bulk RNA sequencing.
- To compare DEGs identified at different cellular and sample levels.
- To explore the prognostic value of LUAD-specific DEGs and their functional roles.
Main Methods:
- Acquired and analyzed 10× scRNA-seq and bulk RNA sequencing data from LUAD patients.
- Identified DEGs in cancer cells versus alveolar cells, tumor versus normal tissue, and LUAD versus normal patients.
- Validated differentially expressed ligand-receptor pairs using flow cytometry and qRT-PCR.
- Performed functional enrichment analysis on identified DEGs.
Main Results:
- Identified 1042 DEGs between LUAD and alveolar cells, 788 DEGs between tumor and normal tissue cells, and 2510 DEGs between LUAD and normal patients.
- Discovered 57 DEGs exclusively in LUAD cancer cells (only-DEGs-scRNA-cancer_cell).
- Found 14 and 22 only-DEGs-scRNA-cancer_cell associated with survival in TCGA and GEO cohorts, respectively.
- Enrichment analysis linked these DEGs to cell proliferation and immunoregulation.
Conclusions:
- scRNA-seq provides a more precise method for detecting DEGs in LUAD.
- Specific DEGs identified solely in cancer cells hold prognostic significance and are linked to key cancer processes.
- This study offers a framework for understanding DEG contributions to LUAD progression and identifies potential therapeutic targets.
