Background: Large studies have identified immune checkpoint inhibitors (ICI) as an effective therapy for deficient mismatch repair/microsatellite instability high (dMMR/MSI-H) colorectal cancer (CRC). However, a subset of dMMR/MSI-H CRC patients exist that do not benefit from ICI and show rapid cancer progression within the first 6 months of therapy. Genetic alterations of the host immune system, including loss of β2M and single copy loss of HLA molecules, can contribute to innate resistance to ICI. In this study, we sought to analyze the role of expression of HLA genes and β2M as determinants of innate resistance to ICI by analyzing an extensive clinico-genomic database.
Methods: Next-generation sequencing (NGS) of DNA (592-gene or whole exome) and RNA (whole transcriptome) was performed on CRC patient samples (n = 24,394) submitted to a CLIA-certified laboratory (Caris Life Sciences, Phoenix, AZ). dMMR/MSI-H was assessed by IHC/NGS. PD-L1 expression was tested by IHC (SP142; positive (+): ≥2+, ≥%5). Real world overall survival and treatment data were obtained from insurance claims data. Time-To-Next-treatment (TTNT) was calculated from start of ICI monotherapy to the start of next therapy, or death. Kaplan-Meier estimates were used for comparison. A composite signature of MHC II gene expression was tested for molecular associations. Immune cell infiltration was estimated by RNA deconvolution using quanTIseq. Statistical significance was determined using Fisher’s Exact/Mann Whitney/X2 tests.
Results: We identified 1549 patients with dMMR/MSI-H CRC; 242 patients of these had received pembrolizumab or nivolumab. Using TTNT as a proxy for progression on treatment, we divided the patients into two cohorts: >180 days TTNT and <180 days TTNT. Following manual curation of the cases by two oncologists and limiting the patients to those who had received ≥ 2 doses of either ICI and at least 180 days of recorded follow up, we generated cohorts of 77 patients (>180 days TTNT; good responders) and 34 patients (<180 days TTNT; poor responders). High expression of HLA genes (HLA-DRB1, HLA-B, HLA-DQB1, HLA-DPB1, HLA-DPA1- p<0.02; fold change 2.1-3) was found in the good responder group. No β2M alterations were detected in either subgroup. After dividing the entire cohort into quartiles, patients in the highest quartile of expression for either CD74, HLA-DQA1, HLA-DQB1, HLA-DPB1 or HLA-DRB1 had improved survival when compared to lower expressors (p< 0.05). High MHC II signature expression was associated with an increased rate of PD-L1+ (34 vs 8%, p<0.0001) and infiltration of M1 macrophages (9.1 vs 4.9%, p<0.0001).
Conclusions: We identify elevated expression of HLA genes involved in formation of the MHC-II complex as a potential biomarker of improved response to immunotherapy that could, if further validated, optimize patient selection for ICI in CRC.