A comprehensive bioinformatic analysis of the role of TGF-β1-stimulated activating transcription factor 3 by non-coding RNAs during breast cancer progression

A potent growth inhibitor for normal mammary epithelial cells is transforming growth factor beta 1 (TGF-β1). When breast tissues lose the anti-proliferative activity of this factor, invasion and bone metastases increase. Human breast cancer (hBC) cells express more activating transcription factor 3 (ATF3) when exposed to TGF-β1, and this transcription factor is essential for BC development and bone metastases. Non-coding RNAs (ncRNAs), including circular RNAs (circRNAs) and microRNAs (miRNAs), have emerged as key regulators controlling several cellular processes. In hBC cells, TGF-β1 stimulated the expression of hsa-miR-4653–5p that putatively targets ATF3. Bioinformatics analysis predicted that hsa-miR-4653–5p targets several key signaling components and transcription factors, including NFKB1, STAT1, STAT3, NOTCH1, JUN, TCF3, p300, NRF2, SUMO2, and NANOG, suggesting the diversified role of hsa-miR-4653–5p under physiological and pathological conditions. Despite the high abundance of hsa-miR-4653–5p in hBC cells, the ATF3 level remained elevated, indicating other ncRNAs could inhibit hsa-miR-4653–5p’s activity. In silico analysis identified several circRNAs having the binding sites for hsa-miR-4653–5p, indicating the sponging activity of circRNAs towards hsa-miR-4653–5p. The study's findings suggest that TGF-β1 regulates circRNAs and hsa-miR-4653–5p, which in turn affects ATF3 expression, thus influencing BC progression and bone metastasis. Therefore, focusing on the TGF-β1/circRNAs/hsa-miR-4653–5p/ATF3 network could lead to new ways of diagnosing and treating BC.