Identification of lncRNAs in Breast Cancer Through Bioinformatics Analysis: Implications for Pathogenesis and...

Breast cancer (BC) is a disease with a subtle onset, often diagnosed late, and has a high mortality rate. This study aimed to identify long non-coding RNAs (lncRNAs) linked to BC as prognostic markers using bioinformatics and initial experiments, explore their regulatory pathways, and assess their expression and prognostic significance.

Transcriptome data and clinical details of a BC cohort were obtained from The Cancer Genome Atlas and Gene Expression Omnibus. Bioinformatics methods, including Weighted Gene Co-expression Network Analysis (WGCNA), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA), and survival analysis, were used to evaluate lncRNAs, related microRNAs (miRNAs), and target genes. The competing endogenous RNA (ceRNA)-based regulatory axis of lncRNA-miRNA-messenger RNA (mRNA) was identified, and gene expression on this axis in normal human mammary epithelial and BC cell lines was analyzed using quantitative reverse transcription polymerase chain reaction (qRT-PCR).

We screened the lncRNA modules most associated with BC traits through bioinformatics analysis and analyzed the immune cell infiltration level of BC samples. Active cluster of differentiation 4+ (CD4+) memory T cells were more infiltrated in BC, whereas resting mast cells were less infiltrated in controls. WGCNA revealed 14 lncRNA modules linked to immune cells and 277 modules associated with BC and immune traits. Univariate Cox analysis identified 12 survival-related target mRNAs mainly involved in immune processes and cell proliferation. We constructed a putative BC-related ceRNA network, specifically the long intergenic non-protein coding RNA 200 (LINC00200)-microRNA 20b (miR-20b-5p)-high mobility group box 3 (HMGB3) axis, through the identification of survival-associated lncRNAs and their target mRNAs to identify key regulatory pathways in BC. qRT-PCR revealed elevated LINC00200 and HMGB3 levels in BC cells, with minor differences in LINC00200 across cell lines. The expression of miR-20b-5p decreased in MCF-7 cells but increased in BT549 and MDA-MB-231.

The study is the first to identify LINC00200 as a potential prognostic lncRNA predictive of survival outcomes in BC and to systematically delineate a novel ceRNA regulatory axis comprising LINC00200, miR-20b-5p, and HMGB3. Although this axis holds promise as a novel prognostic marker, further functional studies and assessment of diagnostic utility are warranted.