Multi-omic characterization of high tumor mutational burden in colorectal cancer.

Abstract

e15724 Background: High Tumor Mutational Burden (TMB-H) is a primary biomarker for immune checkpoint inhibitor response in colorectal cancer (CRC). While the correlation between TMB and microsatellite instability (MSI) is established, the specific co-occurring driver mutations and the downstream transcriptomic programs that define TMB-H tumors in clinical cohorts remain to be fully elucidated. This study integrates TMB, DNA mutations, and RNA expression to define the molecular architecture of TMB-H tumors in 192 CRC patients. Methods: We performed integrated genomic and transcriptomic profiling of 192 CRC samples. Patients were stratified by TMB values into TMB-H (n = 54) and Low-TMB (n = 138). Mutation enrichment analysis was performed using Fisher’s exact test, and differential expression analysis (DEA) was conducted to identify mRNA signatures associated with mutational load. Results: TMB-H tumors demonstrated a significantly higher prevalence of key oncogenic drivers compared to Low-TMB tumors: KRAS (66.7% vs 47.8%, p < 0.05), PIK3CA (24.1% vs 10.9%, p < 0.05), and FBXW7 (16.7% vs 2.2%, p < 0.01). This suggests that high mutational load is strongly linked to heightened activation of the MAPK and PI3K/AKT signaling axes. Integrated differential expression analysis identified a robust mRNA profile for TMB-H tumors, most notably characterized by the significant upregulation of RBP4 (retinol binding protein 4; p = 0.0003). Furthermore, the oncogenic growth factor MDK (midkine) was markedly elevated in the TMB-H subset (p = 0.02), suggesting that these tumors are associated with a distinct molecular program. TMB-H tumors exhibited a profound downregulation of stromal and myogenic markers, including CNN1 (calponin-1, p = 0.0006) and DES (desmin, p = 0.0014). This depletion of structural extracellular matrix components in TMB-H tumors suggests a more proliferative epithelial state with reduced stromal interference, potentially facilitating better immune cell infiltration. Conclusions: High-TMB CRC is characterized by a distinct molecular phenotype defined by KRAS/PIK3CA driver enrichment and a qualitative transcriptomic shift ( RBP4 / MDK high, CNN1 / DES low). The specific upregulation of RBP4 suggests an altered metabolic or retinoid signaling state, highlighting a potential novel therapeutic vulnerability and co-target for TMB-H patients.