Genome instability-related long non-coding RNA in clear renal cell carcinoma determined using computational biology

Background There is evidence that long non-coding RNA (lncRNA) is related to genetic stability. However, the complex biological functions of these lncRNAs are unclear. Method TCGA - KIRC lncRNAs expression matrix and somatic mutation information data were obtained from TCGA database. "GSVA"...

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Bibliographic Details
Published in:BMC cancer 2021-06, Vol.21 (1), p.1-727, Article 727
Main Authors: Wang, Yutao, Yan, Kexin, Wang, Linhui, Bi, Jianbin
Format: Article
Language:English
Subjects:
Base excision repair
Cancer
Cancer therapies
Carcinoma, Renal cell
Cell cycle
Clear cell-type renal cell carcinoma
Computational biology
Computer applications
Correlation analysis
DNA biosynthesis
DNA repair
Gene mutations
Gene set variation analysis
Genes
Genetic aspects
Genetic engineering
Genome instability
Genomes
Genomic instability
Genomics
Health aspects
Homologous recombination
Kidney cancer
Long non-coding RNA
Methods
Mismatch repair
Mutation
Non-coding RNA
Oncology, Experimental
p53 Protein
Prognosis
Proteins
Radiation
Regression analysis
Risk groups
Risk signature
RNA
Signal transduction
Software
Tumors
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Summary:Background There is evidence that long non-coding RNA (lncRNA) is related to genetic stability. However, the complex biological functions of these lncRNAs are unclear. Method TCGA - KIRC lncRNAs expression matrix and somatic mutation information data were obtained from TCGA database. "GSVA" package was applied to evaluate the genomic related pathway in each samples. GO and KEGG analysis were performed to show the biological function of lncRNAs-mRNAs. "Survival" package was applied to determine the prognostic significance of lncRNAs. Multivariate Cox proportional hazard regression analysis was applied to conduct lncRNA prognosis model. Results In the present study, we applied computational biology to identify genome-related long noncoding RNA and identified 26 novel genomic instability-associated lncRNAs in clear cell renal cell carcinoma. We identified a genome instability-derived six lncRNA-based gene signature that significantly divided clear renal cell samples into high- and low-risk groups. We validated it in test cohorts. To further elucidate the role of the six lncRNAs in the model's genome stability, we performed a gene set variation analysis (GSVA) on the matrix. We performed Pearson correlation analysis between the GSVA scores of genomic stability-related pathways and lncRNA. It was determined that LINC00460 and LINC01234 could be used as critical factors in this study. They may influence the genome stability of clear cell carcinoma by participating in mediating critical targets in the base excision repair pathway, the DNA replication pathway, homologous recombination, mismatch repair pathway, and the P53 signaling pathway. Conclusion subsections These data suggest that LINC00460 and LINC01234 are crucial for the stability of the clear cell renal cell carcinoma genome. Keywords: Genome instability, Long non-coding RNA, Computational biology, Gene set variation analysis, Risk signature
ISSN:1471-2407
1471-2407
DOI:10.1186/s12885-021-08356-9