Comprehensive analysis of coexpressed long noncoding RNAs and genes in breast cancer

To identify the differentially expressed long noncoding RNAs (lncRNAs) in breast cancer and analyze the potential roles.

RNA-sequencing data (ID: GSE52194) of breast cancer and normal breast samples were downloaded from Gene Expression Omnibus. Clean reads were aligned against the human genome hg19 using TopHat2 and assembled into transcripts using cufflinks. Protein-coding potential of transcripts with length 200 bp or more were assessed using Coding Potential Calculator, followed by alignment against human lncRNAs using Blastn. Differentially expressed lncRNAs and genes were identified using NOISeq, followed by coexpression analysis with the criterion of Pearson correlation coefficient greater than 0.99. Enrichment analysis was performed using Database for Annotation, Visualization and Integrated Discovery.

Totally 181 differentially expressed lncRNAs and 3967 differentially expressed genes (DEG) were obtained. Besides, coexpression analysis revealed ST6GALNAC3, ST6GALNAC4, ST8SIA5 and DEDD were coexpressed with FAM9B, LINC00320, LOC100169752 and RFX5. H2AFY2 and NOL11 were coexpressed with LOC286002. ADORA2B was coexpressed with GRHPR, LOC100652909 and TEX26-AS1. CD226, FCER1A and ADORA3 were coexpressed with LINC00323 and LOC100505540. PVRL2 and CD300LB were coexpressed with C1QTNF1, CENPA, FAM22F and SNX2. The DEG were predominantly enriched in biological processes of regulation of transcription from RNA polymerase I (e.g. H2AFY2, NOL11 and DEDD) and regulation of mast cell activation (e.g. ADORA3, CD226, FCER1A, MS4A2, ADORA2B and PVRL2), as well as pathways of glycosphingolipid biosynthesis (e.g. ST6GALNAC3, ST6GALNAC4 and ST8SIA5) and peroxisome.

This study revealed the potential involvement of lncRNAs in the progression of breast cancer via participating in glycosphingolipid biosynthesis pathway and regulation of transcription and mast cell activation biological processes.