Transcriptomic Signatures of MSI-high Metastatic Colorectal Cancer Predict Efficacy of Immune Checkpoint Inhibitors.

Abstract

Microsatellite instability (MSI) is currently the only predictive biomarker of efficacy of immune checkpoint inhibitors (ICI) in metastatic colorectal cancers (mCRC). However, 10-40% of patients with MSI mCRC will experience a primary resistance to ICI. In 2 cohorts of patients with MSI mCRC treated with ICI (exploratory: N=103, validation: N=35), 3'RNAseq was performed from primary tumors. Previously described single-cell transcriptomic signatures of tumor microenvironment (TME) were analysed. In the exploratory cohort, the unsupervised clustering allowed the identification of three clusters of tumors with distinct transcriptional profiles: cluster A ("stromalHIGH-proliferationLOW"), cluster B ("stromalHIGH-proliferationMED"), and cluster C ("stromalLOW-proliferationHIGH"), with an enrichment of patients progressing at first disease assessment under ICI in the cluster A (30% vs 12% in cluster B and 8.1% in cluster C, p=0.074). Progression-free survival (PFS) was also significantly shorter in patients belonging to cluster A, compared to clusters B or C (p<0.001) with 2-year PFS rates of 33.5%, 80.5% and 78.3%, respectively. In multivariate analysis, PFS was still significantly longer in patients belonging to cluster B (HR: 0.19 95%CI 0.08-0.45, p<0.001) and cluster C (HR: 0.25 95%CI 0.10-0.59, p=0.02), compared to patients belonging to cluster A. The association of this clustering with PFS under ICI was confirmed in the validation cohort. PFS related to non-ICI-based regimens was not significantly different according to cluster. This unsupervised transcriptomic classification identified three groups of MSI mCRCs with different compositions of TME cells and proliferative capacities of TME/tumor cells. The "stromalHIGH-proliferationLOW" cluster is associated with a poorer prognosis with ICI treatment.