Remodeling of the Immune and Stromal Cell Compartment by PD-1 Blockade in Mismatch Repair-Deficient Colorectal Cancer

Immune checkpoint inhibitor (ICI) therapy can induce complete responses in mismatch repair-deficient and microsatellite instability-high (d-MMR/MSI-H) colorectal cancers (CRCs). However, the mechanism responsible for pathological complete response (pCR) to immunotherapy has not been completely understood. We utilize single-cell RNA sequencing to examine the immune and stromal cell dynamics in 19 patients with d-MMR/MSI-H CRC treated with the neoadjuvant PD-1 blockade. In tumors with a pCR, the proportions of CD8+ Trm-mitotic, CD4+ Tregs, proinflammatory IL1B monocyte and CCL2+Fibroblast concertedly decrease following treatment, while those of CD8+ Tem, CD4+ Th, CD20+ B and HLA-DRA+ Endothelial cells increase. Proinflammatory features in tumor microenvironment mediate the persistence of residual tumors by modulating CD8+ T cells and other response-associated immune cell populations. Our study provides rich resources and biological insights into the mechanism of successful ICI therapy and potential targets to improve treatment efficacy. Illumina BCL files were converted to fastq files by using 10X Genomics Cell Ranger pipeline mkfastq function ( https://support.10xgenomics.com/). Next, cellranger count function was used to generate Gene-Barcode matrices from the fastq files, which uses the STAR algorithm to map high-quality reads to the human reference genome (GRCh38), followed by UMI counting. The raw FASTQ files in this study will be provided for scientific research upon request complying with the law due to human patient privacy concerns.