ATOH1 and NPAS1 are immune related prognostic biomarkers in colorectal cancer

Basic helix-loop-helix (bHLH) transcription factors are implicated in tumorigenesis, but their comprehensive role in colorectal cancer (CRC) remains unclear. This study aims to systematically characterize the bHLH family in CRC.

Transcriptomic and clinical data from TCGA COAD/READ cohorts were analyzed as a discovery set and validated with GEO datasets (GSE39582, GSE17538). Differential expression, Kaplan-Meier survival, and Cox regression analyses identified prognostic bHLH genes. A prognostic risk model was constructed, and immune infiltration was assessed via TIMER2.0. Protein-protein interaction (PPI) networks and methylation associations were explored using STRING and MEXPRESS.

We identified 36 and 32 differentially expressed bHLH genes in colon and rectal adenocarcinoma, respectively. ATOH1 was an independent protective factor (HR = 0.467, P = 0.005), while NPAS1 was an independent risk factor (HR = 2.327, P = 0.001) for overall survival. ATOH1 expression positively correlated with CD8 + T-cell infiltration, whereas NPAS1 showed a negative correlation. A prognostic model constructed using ATOH1 and NPAS1, which remained significant in the multivariate regression analysis, together with T stage, N/M stage, and MSI status demonstrated moderate predictive efficacy (AUC = 0.796). PPI network analysis suggested ATOH1 involvement in WNT/β-catenin signaling and NPAS1 in hypoxia-response pathways.

The first systematic analysis of the expression, prognosis and immune correlation of bHLH family in CRC. bHLH family members, particularly ATOH1 and NPAS1, represent potential biomarkers for prognosis and immune microenvironment evaluation in CRC. This integrated analysis provides a foundation for developing bHLH-targeted therapies and informs future immunotherapy strategies.