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Identification of differentially expressed genes in lung adenocarcinoma cells using single-cell RNA sequencing not detected using traditional RNA sequencing and microarray.
- Source :
-
Laboratory investigation; a journal of technical methods and pathology [Lab Invest] 2020 Oct; Vol. 100 (10), pp. 1318-1329. Date of Electronic Publication: 2020 Apr 23. - Publication Year :
- 2020
-
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.
- Subjects :
- Adenocarcinoma of Lung mortality
Biomarkers, Tumor genetics
Gene Expression Profiling
Gene Expression Regulation, Neoplastic
Gene Regulatory Networks
Genetic Markers
Humans
Kaplan-Meier Estimate
Lung Neoplasms mortality
Multigene Family
Oligonucleotide Array Sequence Analysis
Prognosis
Adenocarcinoma of Lung genetics
Lung Neoplasms genetics
RNA-Seq methods
Single-Cell Analysis methods
Subjects
Details
- Language :
- English
- ISSN :
- 1530-0307
- Volume :
- 100
- Issue :
- 10
- Database :
- MEDLINE
- Journal :
- Laboratory investigation; a journal of technical methods and pathology
- Publication Type :
- Academic Journal
- Accession number :
- 32327726
- Full Text :
- https://doi.org/10.1038/s41374-020-0428-1