COPS4 is a novel prognostic biomarker and potential therapeutic target involved in regulation of immune microenvironment in numerous cancers

Abstract

CHOL, HNSC, ESCA, and LIHC are among the most aggressive and fatal malignancies worldwide. Despite their clinical burden, these cancers still lack dependable biomarkers for early detection, prognosis, and therapeutic targeting. The COP9 signalosome (COPS), a key regulator of the ubiquitin proteasome pathway, has been shown to be aberrantly expressed in various cancer types and is thought to contribute to tumor development and progression. Among its subunits, COPS4 plays an essential role in maintaining the functional integrity of the complex. However, its prognostic significance and clinicopathological relevance in cancer remain poorly understood.

This study adopted a comprehensive, integrative bioinformatics framework grounded in TCGA-derived datasets, incorporating analytical platforms encompassing UALCAN, GEPIA, MEXPRESS, OncoDB, UCSC Xena, ENCORI, TIMER, GeneMANIA, TNMplot, and TISIDB. Through this strategy, the investigation delineated the transcriptional landscape, genomic aberrations, immunological associations, and putative functional roles of COPS4 across CHOL, HNSC, ESCA, and LIHC. Virtual screening and molecular dynamics simulations were performed to explore its druggable potential. COPS4 expression was significantly upregulated in tumor tissues and exhibited strong associations with key clinical parameters, including pathological stage, histological grade, nodal involvement, and metastatic status. IHC analysis further validated elevated protein levels in tumor specimens compared to adjacent non-neoplastic tissues. Genomic alterations were frequent, with predominant mutations in LIHC, amplifications in CHOL, and both amplifications and deletions in HNSC and ESCA. COPS4 expression showed positive associations with subset of oncogenes and inverse correlations with tumor suppressors. Notably, NUP54 and HELQ emerged as consistent co-targets. Immune analysis revealed strong positive correlations between COPS4 and infiltrating immune cells, including CD8⁺ and CD4⁺ T cells, B cells, macrophages, neutrophils, and dendritic cells. Somatic copy number variations of COPS4 also influenced immune cell infiltration and patient survival outcomes. Promoter hypomethylation and gene amplification were identified as mechanisms driving its overexpression. Finally, virtual screening and molecular dynamics simulations identified FDA-approved drugs interacting with COPS4, emphasizing its oncogenic role and therapeutic potential.