Validating the Role of TRAF2 and Nck-Interacting Kinase as a Potential Target in Colorectal Cancer Progression: A Deeper Insight from Expression Profiling and Epigenetic Analysis.

INTRODUCTION Colorectal cancer (CRC) remains a significant global health burden; therefore, a better understanding of its molecular underpinnings is needed to develop more effective therapeutic methods. Traf2 and Nck-interacting kinase (TNIK) have emerged as key regulators in various malignancies, including CRC, but their exact roles and regulatory mechanisms remain only partially understood. The present study aimed to characterize TNIK expression in colorectal cancer through integrative analysis of two independent GEO microarray datasets (GSE9348 and GSE21510) comprising a total of 193 CRC and 37 normal tissue samples.

Methods

Differential gene expression (DEG) analysis was conducted using GEO2R with the limma package, and protein-protein interaction network analysis was performed using STRING v12.0 and visualized in Cytoscape v3.8.2 to identify TNIK's functional partners within the Wnt signaling pathway. This work highlights genes that are up- and downregulated in CRC using a significance threshold of p < 0.05 and log FC > 1. Additionally, to investigate the epigenetic regulation of TNIK, an exploratory differential methylation analysis was performed on a murine CRC RRBS dataset (PRJNA589067) that models Wnt hyperactivation in APC-mutant CRC organoids. The data were processed through Bismark v0.24.2 for alignment and the Bioconductor package edgeR for DMR identification in the CpG context. Therefore, an epigenetic analysis of colorectal cancer was conducted to identify differentially methylated regions, using the thresholds p < 0.05 and logFC > 1.

Results

DEG analysis reveals that TNIK is significantly upregulated in cancer samples. From DMR analysis, TNIK was observed to be relatively hypomethylated in the murine experimental model, while expression analysis of human CRC microarray data identified TNIK as an upregulated gene, an inverse relationship consistent with established epigenetic regulatory trends.

Discussion

The data analyses and interpretations in this work provide a molecular basis for future pharmacological studies targeting TNIK kinase activity and aberrant DNA methylation in CRC, with potential implications for drug discovery efforts to restore normal Wnt pathway regulation. The study links changes in DNA methylation patterns to gene expression and provides important mechanistic definitions of how epigenetic modifications affect gene regulation.

Conclusion

The overall contribution of TNIK overexpression to carcinogenesis and tumor progression through epigenetic modulation in CRC could be applied as a clinical biomarker or candidate for tumor suppressor genes in future studies.