Transformative insights from transcriptome analysis of colorectal cancer patient tissues: identification of four key prognostic genes

Belder, Nevin, Charyyeva, Sulgun, Abaci Oruc, Edibe Ece, Kawalya, Hakiimu, Sahar, Namood-e, Omidvar, Nader, Savas, Berna, Ensari, Arzu and Ozdag, Hilal 2025. Transformative insights from transcriptome analysis of colorectal cancer patient tissues: identification of four key prognostic genes. PeerJ – the Journal of Life & Environmental Sciences 13 , e19852. 10.7717/peerj.19852

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Abstract

Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide, necessitating accurate and robust predictive approaches to assist oncologists with prognosis prediction and therapeutic decision-making in clinical practice. Here, we aimed to identify key genes involved in colorectal cancer pathology and develop a model for prognosis prediction and guide therapeutic decisions in CRC patients. We profiled 49 matched tumour and normal formalin-fixed paraffin-embedded (FFPE) samples using Affymetrix HGU133-X3P arrays and identified 845 differentially expressed genes (FDR ≤ 0.001, fold change ≥2), predominantly enriched in the extracellular matrix (ECM)-receptor interaction pathway. The integrative analysis of our data with publicly available mRNA and miRNA datasets, including their differentially expressed gene analyses, identified four overexpressed genes in the ECM-receptor interaction pathway as key regulators of human CRC development and progression. These four genes were independently validated for their differential expression and association with prognosis in a newly collected CRC cohort and publicly available datasets. A prognostic risk score was developed using these genes, with patient stages weighted by multivariate Cox regression coefficients to stratify patients into low-risk and high-risk groups, showing significantly poorer overall survival (OS) in the high-risk group. In conclusion, our risk assessment model exhibits strong potential for predicting poor survival and unfavorable clinicopathological features in CRC patients, offering valuable insights for personalised management strategies.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Schools > Medicine
Publisher:	PeerJ
ISSN:	2167-8359
Date of First Compliant Deposit:	1 September 2025
Date of Acceptance:	15 July 2025
Last Modified:	01 Sep 2025 12:00
URI:	https://orca.cardiff.ac.uk/id/eprint/180781

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