Molecular Profiling Provides Clinical Insights into Targeted and Immunotherapies as well as Prognosis for Colorectal Cancer

Background and aims Tumor genetic testing is indispensable in the management of primary and advanced colorectal cancer, with one-third of patients progressing despite standard care. We aimed to refine the indications for genomics-guided precision therapy. Methods We prospectively sequenced 869 tumors from Chinese patients with colorectal cancer and performed a comprehensive analysis of clinical and genomic profiles. The clinical significance of single mutation and co-occurring events was assessed in metastatic colorectal cancer (mCRC). The tumor immune microenvironment was evaluated by Immunoscore assay and single-cell sequencing. Results Single gene somatic mutations in BRAF and RBM10 were associated with shorter progression-free survival (PFS) in treatment-naive mCRC patients (BRAF: hazard ratio [HR] = 2.2 [95% CI, 1.1-4.4]; RBM10: HR= 6.8 [95% CI, 2.6-17.3]), and RBM10 remained a risk factor irrespective of the addition of bevacizumab to the chemotherapy regimens. KRAS mutations coexisting with those in AMER1 or APC were enriched in the metastatic cohort (26.23%), which had poor PFS and did not benefit from bevacizumab. 40 patients (4.6%) carried pathogenic or likely pathogenic germline alterations in the DNA damage repair pathway and 30% of them had double-hit events in the tumor with higher MSI scores. High tumor indel burden with MSI-high suggested a large number of tumor-infiltrating lymphocytes, whereas POLE-mutant with TMB-ultrahigh indicated a relatively quiescent immunophenotype. The heterogeneous genomic-immunological ecosystem was reflected in the divergent antigen presentation, immune checkpoint protein expression and responses of T cells to pembrolizumab treatment. Conclusion Integrated analysis of the clinical, genomic, and immunological profiles of colorectal cancer provides insights into prognostic stratification, drug response and potential clinical trials. mRNA sequencing was performed on 12 MSI-high/TIB-high and 6 POLE-mutant/TMB-UH individuals to elucidate the significance of genetic indicators on the immune contexture.