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Integrated bioinformatics analysis of microarray data from non-small cell lung cancer
Lulu Feng1, Wenping Cai2, Shan Jin3
1Treatment of Central Asia High Incidence Diseases (First Affiliated Hospital, School of Medicine, Shihezi University). fenglulu1996@163.com.
Abstract:
Non-small cell lung cancer (NSCLC), with its high mortality rate, lack of early diagnostic markers and prevention of distant metastases are the main challenges in treatment. To identify potential miRNAs and key genes in NSCLC to find new biomarkers and target gene therapies. The GSE102286, GSE56036, GSE25508, GSE53882, GSE29248 and GSE101929 datasets were obtained from the Gene Expression Omnibus (GEO) database and screened for differentially co-expressed miRNAs (DE-miRNAs) and lncRNAs (DElncRs) by GEO2R and R software package. Pathway enrichment analysis of DE-miRNAs-target genes was performed by String and Funrich database to construct protein-protein interaction (PPI) and competing endogenous RNA (ceRNA) network and visualized with Cytoscape software. Nineteen co-expressed DE-miRNAs were screened from five datasets. The 7683 predicted up- and down-regulated DE-miRNAs-target genes were significantly concentrated in cancer-related pathways. The top 10 hub nodes in the PPI were identified as hub genes, such as MYC, EGFR, HSP90AA1 and TP53, MYC, and ACTB. By constructing miRNA-hub gene networks, hsa-miR-21, hsa-miR-141, hsa-miR-200b and hsa-miR-30a, hsa-miR-30d, hsa-miR-145 may regulate most hub genes and hsa-miR-141, hsa-miR-200, hsa-miR-145 had higher levels in the miRNA and ceRNA regulatory networks, respectively. In conclusion, the identification of hsa-miR-21, hsa-miR-141, hsa-miR-200b hsa-miR-30a, hsa-miR-30d and hsa-miR-145 provides a new theoretical basis for understanding the development of NSCLC.
Insights
This study identifies key microRNAs (miRNAs) and genes involved in non-small cell lung cancer (NSCLC) development. These findings offer potential new biomarkers and therapeutic targets for NSCLC treatment.
Area of Science:
- Oncology
- Molecular Biology
- Bioinformatics
Background:
- Non-small cell lung cancer (NSCLC) presents significant challenges due to high mortality, lack of early diagnostic markers, and metastasis.
- Effective treatment strategies for NSCLC are limited, necessitating the identification of novel biomarkers and therapeutic targets.
Purpose of the Study:
- To identify potential microRNAs (miRNAs) and key genes in NSCLC for novel biomarker discovery and targeted gene therapies.
- To elucidate the regulatory networks underlying NSCLC pathogenesis.
Main Methods:
- Utilized Gene Expression Omnibus (GEO) datasets (GSE102286, GSE56036, etc.) to screen differentially expressed miRNAs (DE-miRNAs) and lncRNAs (DElncRs) using GEO2R and R.
- Performed pathway enrichment analysis, constructed protein-protein interaction (PPI) and competing endogenous RNA (ceRNA) networks using String, Funrich, and Cytoscape.
- Identified hub genes and miRNA-hub gene interactions.
Main Results:
- Screened nineteen co-expressed DE-miRNAs from five NSCLC datasets.
- Identified 7683 predicted DE-miRNA target genes significantly enriched in cancer-related pathways.
- Highlighted MYC, EGFR, HSP90AA1, TP53, and ACTB as top hub genes in the PPI network.
- Identified hsa-miR-21, hsa-miR-141, hsa-miR-200b, hsa-miR-30a, hsa-miR-30d, and hsa-miR-145 as key regulators of hub genes, with hsa-miR-141 and hsa-miR-145 prominent in regulatory networks.
Conclusions:
- The identified miRNAs, including hsa-miR-21, hsa-miR-141, hsa-miR-200b, hsa-miR-30a, hsa-miR-30d, and hsa-miR-145, provide a theoretical basis for understanding NSCLC development.
- These findings suggest potential novel biomarkers and therapeutic targets for NSCLC treatment.
