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Identification of Potential Long Non-Coding RNA Candidates that Contribute to Triple-Negative Breast Cancer in Humans
Md Motiar Rahman1,2, Md Tofazzal Hossain3,4,5, Md Selim Reza3,4
1Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi 6205, Bangladesh.
Abstract:
Breast cancer (BC) is the most frequent malignancy identified in adult females, resulting in enormous financial losses worldwide. Owing to the heterogeneity as well as various molecular subtypes, the molecular pathways underlying carcinogenesis in various forms of BC are distinct. Therefore, the advancement of alternative therapy is required to combat the ailment. Recent analyses propose that long non-coding RNAs (lncRNAs) perform an essential function in controlling immune response, and therefore, may provide essential information about the disorder. However, their function in patients with triple-negative BC (TNBC) has not been explored in detail. Here, we analyzed the changes in the genomic expression of messenger RNA (mRNA) and lncRNA in standard control in response to cancer metastasis using publicly available single-cell RNA-Seq data. We identified a total of 197 potentially novel lncRNAs in TNBC patients of which 86 were differentially upregulated and 111 were differentially downregulated. In addition, among the 909 candidate lncRNA transcripts, 19 were significantly differentially expressed (DE) of which three were upregulated and 16 were downregulated. On the other hand, 1901 mRNA transcripts were significantly DE of which 1110 were upregulated and 791 were downregulated by TNBCs subtypes. The Gene Ontology (GO) analyses showed that some of the host genes were enriched in various biological, molecular, and cellular functions. The Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed that some of the genes were involved in only one pathway of prostate cancer. The lncRNA-miRNA-gene network analysis showed that the lncRNAs TCONS_00076394 and TCONS_00051377 interacted with breast cancer-related micro RNAs (miRNAs) and the host genes of these lncRNAs were also functionally related to breast cancer. Thus, this study provides novel lncRNAs as potential biomarkers for the therapeutic intervention of this cancer subtype.
Insights
Researchers identified novel long non-coding RNAs (lncRNAs) in triple-negative breast cancer (TNBC). These lncRNAs may serve as potential biomarkers for developing new therapies against this aggressive breast cancer subtype.
Area of Science:
- * Molecular biology
- * Genomics
- * Cancer research
Background:
- * Breast cancer (BC) is a prevalent malignancy in women, characterized by molecular heterogeneity.
- * Distinct molecular pathways drive carcinogenesis in different BC subtypes, necessitating alternative therapeutic strategies.
- * Long non-coding RNAs (lncRNAs) are implicated in immune response regulation, but their role in triple-negative breast cancer (TNBC) remains underexplored.
Purpose of the Study:
- * To analyze messenger RNA (mRNA) and lncRNA genomic expression changes in TNBC.
- * To identify novel lncRNAs and their potential roles in TNBC development and progression.
- * To explore the therapeutic potential of identified lncRNAs in TNBC.
Main Methods:
- * Utilized publicly available single-cell RNA-Seq data for analysis.
- * Performed genomic expression analysis of mRNA and lncRNA in TNBC patients.
- * Conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses.
- * Constructed lncRNA-microRNA (miRNA)-gene networks.
Main Results:
- * Identified 197 potentially novel lncRNAs in TNBC, with 86 upregulated and 111 downregulated.
- * Found 19 significantly differentially expressed lncRNA transcripts (3 upregulated, 16 downregulated).
- * Detected 1901 significantly differentially expressed mRNA transcripts (1110 upregulated, 791 downregulated).
- * GO and KEGG analyses revealed enrichment in biological functions and pathways.
- * Identified specific lncRNAs (TCONS_00076394, TCONS_00051377) interacting with BC-related miRNAs.
Conclusions:
- * This study identified novel lncRNAs with significant differential expression in TNBC.
- * The findings suggest these lncRNAs play a role in TNBC pathogenesis.
- * The identified lncRNAs represent potential novel biomarkers for therapeutic intervention in TNBC.
