Abstract 1040: Development of a novel RNA-based microsatellite stable predictive response signature (MSS-PRS) to identify MSS colorectal cancer (CRC) patients with a microsatellite instability-high (MSI-H) molecular phenotype
Authors: Pappan Kirk , Mayhew Gregory , Shepherd Jonathan , Guo Yuelong , Beebe Kirk , Eisner Joel , Milburn Michael 
Published: March 2024

Introduction: MSI-H and mismatch repair deficient (dMMR) tumors are associated with favorable immune checkpoint inhibitor (ICI) responses (PMID: 3326454). However, up to 95% of CRC tumors are MSS/proficient MMR (pMMR) leading to poorer prognosis and treatment outcomes than MSI-H/dMMR patients (PMID: 12867608, 26028255). In MSS/pMMR metastatic CRC, multiple combination therapies are being investigated despite a lack of biomarkers to guide therapy. Therefore, we developed an RNA-based MSS-PRS with a primary objective to identify MSS tumors that have MSI-H/dMMR molecular features indicative of ICI response.

Experimental Procedures: The MSS-PRS was developed using the TCGA CRC cohort (COAD; n=268). Training labels were assigned using the MSI Mantis score and mutation status from 8 genes with reported MSI association. Samples called “activated” had both a gene mutation and an MSI Mantis score &gt; 0.4 (i.e., MSI-H), and samples called “non-activated” were wild type for all genes and had MSI Mantis score &lt; 0.4. All other samples were designated “ambiguous” and excluded from training. Two thirds of the non-ambiguous samples were assigned to the classifier training set and all remaining samples were assigned to the test set. Using ClaNC software (PMID: 16269418) and cross-validation in the training set, a nearest centroid classifier was developed from a set of high mean, high variance candidate genes to select an optimal gene set to separate activated and non-activated groups. The classifier performance was evaluated in the test set.

Results: The MSS-PRS contained 112-genes enriched for mismatched DNA binding, DNA damage repair, PD-L1, innate and adaptive immune response, cellular immunity, and cytokines. In the test set, the classifier called 44 of 46 MSI-H samples activated; of the remaining 77 samples that were MSS tumors, 38 were called activated and 39 were called not activated. Visual inspection of heat maps of tumor by MSI/MSS-PRS status and their association with TMB and CRC-related mutations suggest greater differences between MSS tumors called activated and MSI-H tumors than between MSS tumors called activated and MSS tumors called not activated. In contrast, immune marker expression profiles in MSS tumors called activated were markedly more similar to MSI-H tumors compared to MSS tumors called non-activated.

Summary and Conclusions: Herein we described the development of a novel MSS-PRS that captures an MSI-H/dMMR-like molecular phenotype in a subset of patients with MSS tumors despite their lack of high TMB or overt MSI defects. Based upon these initial findings, further development of the MSS-PRS and its clinical validation as a tool to select patients with MSS tumors who may benefit from ICI-containing treatment regimens is warranted.

Citation Format: Kirk Pappan, Gregory Mayhew, Jonathan Shepherd, Yuelong Guo, Kirk Beebe, Joel Eisner, Michael Milburn. Development of a novel RNA-based microsatellite stable predictive response signature (MSS-PRS) to identify MSS colorectal cancer (CRC) patients with a microsatellite instability-high (MSI-H) molecular phenotype [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1040.