Co-occurrence of gene fusions and microsatellite instability (MSI) defines a clinically distinct subtype of colorectal cancer

Background : Microsatellite instability (MSI) is a well-established biomarker in colorectal cancer. Gene fusions may also influence prognosis, but the clinical significance of their co-occurrence with MSI remains poorly understood. Methods : We analyzed a cohort of colorectal (N = 29,099) cancer patients, all profiled with Tempus AIs xT platform. Fishers tests assessed the enrichment of pathogenic and likely pathogenic gene fusions within microsatellite stability groups. Cox models evaluated the independent and interaction effects of MSI status and gene fusions on real-world overall survival from at biopsy collection, adjusting for age, stage, line of therapy, tumor purity, tumor mutation burden, and PD-L1 combined positive score. We tested for enrichment of all fusions, kinase fusions ( NTRK1 , NTRK3 , RET , ALK , FGFR2 , BRAF ), and NTRK fusions ( NTRK1 , NTRK3 ). Results : The proportion of clinically relevant gene fusions was higher in MSI versus MSS colorectal cancer tumors (5.9% vs 1.8%): NTRK1 (2.2% vs. 0.048%), NTRK3 (1.2% vs. 0.14%), RET (0.87% vs. 0.096%), and TPM3 (1.0% vs. 0.0074%). Survival analyses revealed that all fusions and kinase fusions were both associated with significantly worse overall survival (Table 1). These trends persisted in sub-cohorts. MSI was associated with increased overall survival in models including all fusions, kinase fusions, and NTRK fusions. We did not detect a significant interaction between MSI and gene fusions across any of the models, likely due to smaller sample sizes. However, we confirmed fusions remained associated with poor overall survival when restricting to MSS tumors for all gene fusions and kinase fusions. Additional models fit to patients treated with specific therapies, such as immunotherapy, did not converge. Conclusion : Gene fusion rates differ between MSI and MSS colorectal tumors. While most fusions are generally associated with worse survival, this effect may be reversed in MSI cases. Table 1: Overall Survival Association Results with fusions and MSI in Colorectal Cancer. Restricted To Fusion Class Fusion MSI N Hazard Ratio P N Hazard Ratio P All All 274 1.261 0.015 575 0.643 3.51E-05 Stage 3/4 All 234 1.253 0.025 426 0.677 0.002 Pre-Treatment All 201 1.297 0.019 417 0.631 5.30E-04 MSS All 226 1.260 0.015 MSI All 48 0.927 0.763 All NTRK 52 0.564 0.13 575 0.652 4.53E-05 Stage 3/4 NTRK 40 0.692 0.368 426 0.693 0.003 Pre-Treatment NTRK 42 0.630 0.223 417 0.633 4.67E-04 MSS NTRK 22 0.564 0.130 MSI NTRK 30 0.684 0.297 All Kinase 136 1.427 0.010 575 0.648 4.65E-05 Stage 3/4 Kinase 117 1.518 0.004 426 0.685 0.003 Pre-Treatment Kinase 99 1.545 0.005 417 0.640 7.74E-04 MSI Kinase 89 1.426 0.010 MSS Kinase 47 0.860 0.593