Journal Article

A Robust Immunohistochemistry‐Based Classification for BRAF V600E‐Mutant Colorectal Cancer With Clinical Implications

Ma, Yue, Meng, Hongxue, Liu, Chao, Ruan, Yuli, Luan, Xindi, Dang, Tianjiao, Zhang, Chunhui, Wang, Hong, Wu, Tong, Ou, Yiwen, Zhang, Yanqiao, Wang, Bojun

2026

Overview

BRAF V600E‐mutant colorectal cancer (CRC) represents a distinct molecular subtype with considerable heterogeneity in tumor biology and therapeutic response. Although gene expression‐based classifications (BM1/BM2 subtypes) provide valuable insights into underlying molecular and immune features, their clinical application is limited by the need for high‐throughput sequencing. This study aims to establish an immunohistochemistry (IHC)‐based classification system to enable practical subtype stratification and aid prognostic and therapeutic evaluation. Using two independent cohorts (public dataset, n = 218; institutional cohort, n = 122), we performed differential expression analysis, machine learning modeling, and clinical feasibility evaluation. Fourteen candidate markers were identified, and a decision tree algorithm selected CD8 and ARHGEF17 as optimal classifiers. Based on these markers, two IHC‐based subtypes were established: iBM1 (CD8+/ARHGEF17−) and iBM2 (CD8− with any ARHGEF17 expression or CD8+/ARHGEF17+). The IHC‐based subtypes showed concordance with transcriptomic BM subtypes (training: 82.69%, κ = 0.55; validation: 72.22%, κ = 0.44; prospective: 83.33%, κ = 0.57). Transcriptomic profiling revealed enrichment of immune activation and epithelial–mesenchymal transition in iBM1, and cell cycle‐related pathways in iBM2. In clinical validation, iBM1 was associated with poorer survival but greater sensitivity to immune checkpoint inhibitors. This IHC‐based classification provides a practical and accessible approach for BM subtype stratification, reflecting underlying molecular and immune characteristics, and may support prognostic assessment and therapeutic decision‐making in BRAF V600E‐mutant CRC. This study develops an immunohistochemistry (IHC)‐based classification system for BRAF V600E‐mutant colorectal cancer, enabling practical stratification into iBM1 and iBM2 subtypes using CD8 and ARHGEF17 markers. The IHC‐defined subtypes demonstrated concordance with transcriptomic BM1/BM2 classifications and reflected distinct molecular and immune features, with iBM1 associated with poorer prognosis but enhanced responsiveness to immune checkpoint blockade.

• Publisher: John Wiley & Sons, Inc,Wiley
• Subject: Aged / Algorithms / Antibodies / Biomarkers, Tumor - genetics / Biomarkers, Tumor - metabolism / BM subtypes / BRAF V600E‐mutant colorectal cancer / Cancer therapies / CD8 antigen / Cell cycle / Classification / Clinical medicine / Colorectal cancer / Colorectal Neoplasms - classification / Colorectal Neoplasms - genetics / Colorectal Neoplasms - metabolism / Colorectal Neoplasms - pathology / Decision making / Female / Gene expression / Gene Expression Profiling / Genomes / Humans / ICIs therapy / Immune checkpoint inhibitors / Immune response / Immunohistochemistry / Immunohistochemistry - methods / Kinases / Machine Learning / Male / Medical prognosis / Medical research / Middle Aged / Mutants / Mutation / Original / Prognosis / prognostic / Proto-Oncogene Proteins B-raf - genetics / Support vector machines / Transcriptome / Transcriptomics / Tumor necrosis factor-TNF