Microsatellite-stable colorectal cancer with low chromosomal instability responds to immunotherapy and is sensitized by proteasome inhibition

Microsatellite-stable (MSS) colorectal cancer (CRC) is typically considered poorly responsive to immunotherapy. This study aims to identify characteristics of MSS CRC patients who are likely to benefit from immunotherapy and to investigate effective agents that could improve immunotherapy efficacy for this subgroup. We performed an integrated analysis combining single-cell RNA sequencing, bulk RNA sequencing, and whole-exome sequencing data from patient-derived organoids and tumor tissues to identify a specific MSS subtype that potentially benefits from immunotherapy. To validate our findings, we employed a humanized mouse model to assess the effects of anti-programmed cell death protein 1 (PD-1) therapy in different CRC subtypes. Subsequently, we conducted drug screening to identify compounds that could inhibit mismatch repair capacity. In vivo models were developed for further validation. Western blot and co-immunoprecipitation were employed to investigate the molecular mechanisms by which bortezomib enhances immunotherapy efficacy. Our analysis revealed that MSS CRC with low chromosomal instability (CIN), characterized by a low fraction of genome altered (FGA) level, displayed heightened immunogenicity and a gene expression profile similar to CRC with microsatellite instability (MSI), indicating potential responsiveness to immunotherapy. In the humanized mouse model, anti-PD-1 therapy significantly increased immune cell activation within the FGA low MSS CRC subtype. Analysis of clinical single-cell RNA sequencing samples from patients undergoing anti-PD-1 therapy further indicated that FGA low MSS CRC patients were more likely to respond to immunotherapy. Furthermore, we identified bortezomib, a proteasome inhibitor, as a promising agent to potentiate immunotherapy in FGA low MSS CRC by promoting anti-tumor immunity in humanized mouse models. Mechanistically, bortezomib was found to inhibit tumor cells’ DNA mismatch repair by inducing autophagic degradation of mismatch repair proteins and activate the cyclic GMP-AMP synthase–stimulator of interferon genes (cGAS-STING) pathway to evoke an endogenous anti-tumor immune response. Our study identified MSS CRC with low CIN as potential candidates for immunotherapy and highlighted the proteasome inhibitor bortezomib as a strategic addition to augment immunotherapy efficacy for this specific subset.