Identification of circRNA/lncRNA-miRNA-Transcription Factor-mRNA Networks to Identify Potential Biomarkers in...

Neoadjuvant therapy (NAT) is the standard treatment option for locally advanced breast cancer (BC). Noncoding RNAs are known to play a significant role in cancer development. However, the involvement of the circular RNA (circRNA)/long non-coding RNA (lncRNA)-(miRNA)-mRNA competitive endogenous RNA (ceRNA) network in the antitumor effects of NAT in BC remains unclear.

Ribosomal RNA (rRNA)-depleted RNA sequencing (RNA-seq) was performed to identify differentially expressed lncRNAs (DElncRNAs), circRNAs (DEcircRNAs), mRNAs (DEmRNAs) and transcription factors (DE-TFs) between pre-therapy tumor tissues and adjacent normal tissues, as well as between post-NAT tumor tissues and pre-therapy tumor tissues. The changes in gene expression in the ceRNA network were confirmed by RT-qPCR.

We identified dysregulated RNAs associated with NAT, including 2693 DEcircRNAs, 25 DElncRNAs, 58 DE-TFs, and 878 DEmRNAs. Three core ceRNA networks were constructed bioinformatically, centered on the key DE-TFs, including HOXC11, NKX2-2, and PRAME. RT-qPCR results confirmed a significant increase in the levels of circRNA_31003, circRNA_42276, MIAT, HOXC11, NKX2-2, PRAME, CCL5, NEK2, and RAD54L in tumor tissues before therapy when compared to normal tissues, but these levels decreased in post-NAT tumor group compared to pre-therapy tumor group. In contrast, the expression of miR-1225-3p, miR-661, and miR-143-5p showed a notable decline in pre-therapy tumors in comparison to normal tissues; however, these expressions elevated significantly in post-NAT tumor group compared to pre-therapy tumor group.

Associated regulatory networks were constructed to explore candidate biomarkers that may respond to NAT treatment in BC.