Integrated transcriptomics identifies ITGB5 as a hub linking coding and non-coding RNAs to signaling regulation in hepatocellular carcinoma

Abstract

Aim: To elucidate integrin β5 (ITGB5)-associated transcriptomic alterations in hepatocellular carcinoma cells and identify key coding and non-coding RNA regulators and their associated signaling pathways.

Methods: Whole-transcriptome sequencing was conducted on HepG2 (human hepatocellular carcinoma cell line) cells overexpressing ITGB5. Differential expression analysis was performed, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses for messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). Candidate transcripts were validated using real-time quantitative polymerase chain reaction (RT-qPCR).

Results: ITGB5 overexpression induced extensive transcriptomic alterations. KEGG enrichment highlighted the phospholipase D, vascular endothelial growth factor (VEGF), and ErbB signaling pathways, with significant involvement of the phosphoinositide 3-kinase/protein kinase B (PI3K/Akt) and mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK) cascades. Pathway-level analyses suggested a relative attenuation of PI3K/Akt signaling alongside the preferential engagement of MAPK/ERK-related programs. GO analysis indicated shifts in biological processes, notably the negative regulation of peptidase activity and cell-matrix adhesion. Furthermore, ITGB5 was associated with widespread lncRNA and circRNA regulation; predicted target genes of these non-coding RNAs were enriched in PI3K/Akt signaling, protein processing in the endoplasmic reticulum, and cell cycle regulation. RT-qPCR confirmed the upregulation of key transcripts, including dystroglycan 1 (DAG1; mRNA), small nucleolar RNA host gene 1 (SNHG1; lncRNA), and circFN1 (circRNA), in ITGB5-overexpressing cells.

Conclusion: Our findings identify ITGB5 as a regulatory hub in hepatocellular carcinoma (HCC) associated with coding and non-coding RNA regulatory networks, offering insights into potential therapeutic targets.

Keywords

ITGB5 / hepatocellular carcinoma / transcriptome profiling / PI3K/Akt pathway / MAPK/ERK pathway

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