Identification of key genes and pathway related to chemoresistance of small cell lung cancer through an integrative bioinformatics analysis

Fan-Rui Zeng; Xu-Yang Zhou; Ling-Ge Zeng; Jian-Cong Sun; Fen He; Wei Mo; Yang Wen; Shu-Yu Wang; Qin Liu; Lin-Lang Guo

doi:10.21037/atm-22-3642

Identification of key genes and pathway related to chemoresistance of small cell lung cancer through an integrative bioinformatics analysis

Ann Transl Med. 2022 Sep;10(18):968. doi: 10.21037/atm-22-3642.

Authors

Fan-Rui Zeng¹, Xu-Yang Zhou², Ling-Ge Zeng², Jian-Cong Sun¹, Fen He¹, Wei Mo¹, Yang Wen², Shu-Yu Wang², Qin Liu³, Lin-Lang Guo²

Affiliations

¹ Department of Radiation Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
² Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
³ Department of Radiology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.

Abstract

Background: Small cell lung cancer (SCLC), the most malignant of all the lung cancer subtypes, is characterized by drug resistance. This study sought to explore the key genes and pathways associated with the chemoresistance of SCLC.

Methods: The drug sensitivity of chemosensitive and chemoresistance SCLC cell lines was measured by Cell Counting Kit-8 assays. The total RNA from chemosensitive cell line H69 and chemoresistance cell line H69AR cells was extracted and subjected to messenger RNA (mRNA) and long non-coding RNA (lncRNA) microarray analyses. The differentially expressed genes (DEGs) and the differentially expressed lncRNAs (DELs) were screened out with a threshold of a |log fold change | ≥1 and an adjusted P value <0.05. A protein-protein interaction network was constructed, and hub genes were screened out. A lncRNA-mRNA co-expression network was also constructed. Gene Ontology and Kyoto Encyclopedia of Genes, Genomes enrichment analyses and Cis-regulatory element analyses were conducted on the DEGs and the top 10 upregulated DEL-co-expressed DEGs. The expression of the key genes was further analyzed in the GSE149507 data set and validated in H69/H69AR and H446/H446DDP cells by quantitative polymerase chain reaction assays.

Results: The microarray results showed that a total of 609 mRNAs and 394 lncRNAs were differentially expressed in the chemoresistant SCLC cells. The mammalian target of rapamycin (mTOR) signaling pathway was enriched among the DEGs, the top 10 upregulated DEL-co-expressed DEGs, and the NCRNA00173-co-expressed DEGs, which included IGF1, INS, WNT6, WNT11, WNT2B, and SESN2. IGF1, WNT2B, and SESN2 were downregulated, and WNT11 was upregulated in the SCLC tumor tissues in the GSE149507 data set. Further, IGF1, WNT6, WNT11, and WNT2B were lowlier expressed and SESN2 and NCRNA00173 were more highly expressed in the chemoresistant cells than sensitive cells.

Conclusions: The top 10 upregulated DELs containing NCRNA00173 may be involved in the regulation of drug resistance in SCLC. These DELs may regulate the genes related to the mTOR signaling pathway. These genes may also be biomarkers and potential targets for the treatment of SCLC.

Keywords: Small cell lung cancer (SCLC); chemoresistance; long non-coding RNA (lncRNA); mTOR pathway; microarray analysis.