{
  "abstract": "Background Mismatch repair deficiency (MMRd) predicts response to immune checkpoint blockade (ICB), but not all patients respond equally. The mechanism of MMR loss, genetic mutation or epigenetic silencing, may explain this variability in response.Methods Patients with MMRd tumors were identified by IHC (MLH1/PMS2, MSH2/MSH6) across two pan-cancer cohorts: MSKCC (n=2,001; 779 ICB-treated) and Caris (n=13,421; 4,007 ICB-treated; 6,047 with RNA-seq). Any line of ICB was considered. MLH1 loss was classified as epigenetic or mutational and inferred from sequencing results, with lack of an observed pathogenic MLH1 mutation defining epigenetic loss. Overall Survival (OS) from time of ICB initiation and immune features derived from RNA-seq were analyzed by MMR subtype.Results MLH1/PMS2 loss was most frequent (63–75%), with >80% due to epigenetic silencing of MLH1, followed by MSH2 loss (13%-21%). In both cohorts, epigenetic loss of MLH1 was associated with worse OS post-ICB versus MLH1-mutated tumors (MSKCC: HR=2.0 [1.2–3.4], p=0.04; Caris: HR=1.2 [1.1-1.4], P=0.02). No survival difference was observed between patients with MLH1 epigenetic/mutation loss versus those with MSH2 loss after ICB. Tumor mutational burden was lower in tumors with epigenetic loss of MLH1 (25 mutations/Mb) versus MLH1-mutated or MSH2-deficient tumors (both 31 mutations/Mb, p<0.0001) while microsatellite instability scores were similar.In colorectal cancers (CRC), a clinical situation for which both dual (PD-1 + CTLA-4) and single (PD-1) ICB are used, patients with tumors with epigenetic loss of MLH1 had superior OS with dual ICB compared to PD-1 monotherapy (64.5 vs 40.4 months; HR=0.60 [0.36–0.99], p=0.05), while no statistical difference was observed when comparing dual blockade vs monotherapy in MLH1-mutated or MSH2-deficient subgroups.We next compared immune-related expression profiles in the overall Caris cohort to understand the differences between epigenetic and mutational inactivation of MLH1. Epigenetic loss of MLH1 was associated with lower IFNγ scores (-0.26 vs -0.17, p<0.0001) and less CD8+ T cell infiltration (0.44% vs 0.67%, p<0.0001) than MLH1-mutated tumors. In CRC specifically, PD-L1, PD-L2, and LAG-3 expression were significantly higher in tumors with MLH1 epigenetic loss compared to tumors with MLH1 loss from mutation or MSH2-loss.Conclusions MLH1 epigenetic silencing is associated with an immune-suppressive phenotype in MMRd cancers overall, differential sensitivity to ICB, and enhanced benefit from dual blockade in CRC. These results provide evidence for stratification of subclasses of MMRd tumors for refining decision-making and selection of ICB therapy.Acknowledgements Caris Life scienceEthics Approval Patients consented for sequencing and clinical data collection for this retrospective study. IRB approval was obtained for this study.",
  "authors": [
    {
      "affiliations": [
        "Memorial Sloan Kettering Cancer Center, New York, NY, USA"
      ],
      "name": "Benoit Rousseau"
    },
    {
      "affiliations": [
        "Poitiers University, Poitiers, NA, France"
      ],
      "name": "Violaine Randrian"
    },
    {
      "affiliations": [
        "Caris Life Science, Phoenix, AZ, USA"
      ],
      "name": "Kieran Sweeney"
    },
    {
      "affiliations": [
        "Washington University in St. Louis, St. Louis, MO, USA"
      ],
      "name": "Moh’d Khushman"
    },
    {
      "affiliations": [
        "Memorial Sloan Kettering Cancer Center, New York, NY, USA"
      ],
      "name": "Emily Alouani"
    },
    {
      "affiliations": [
        "Memorial Sloan Kettering Cancer Center, New York, NY, USA"
      ],
      "name": "Paul Johannet"
    },
    {
      "affiliations": [
        "Memorial Sloan Kettering Cancer Center, New York, NY, USA"
      ],
      "name": "Oliver Artz"
    },
    {
      "affiliations": [
        "Memorial Sloan Kettering Cancer Center, New York, NY, USA"
      ],
      "name": "Mike B Foote"
    },
    {
      "affiliations": [
        "Memorial Sloan Kettering Cancer Center, New York, NY, USA"
      ],
      "name": "Mohammad A Abbass"
    },
    {
      "affiliations": [
        "Memorial Sloan Kettering Cancer Center, New York, NY, USA"
      ],
      "name": "Somer Abdelfattah"
    },
    {
      "affiliations": [
        "Memorial Sloan Kettering Cancer Center, New York, NY, USA"
      ],
      "name": "David Mieles"
    },
    {
      "affiliations": [
        "Columbia University Irving Medical Center, New York, NY, USA"
      ],
      "name": "Ryan H Moy"
    },
    {
      "affiliations": [
        "Memorial Sloan Kettering Cancer Center, New York, NY, USA"
      ],
      "name": "Steve Maron"
    },
    {
      "affiliations": [
        "Memorial Sloan Kettering Cancer Center, New York, NY, USA"
      ],
      "name": "James J Harding"
    },
    {
      "affiliations": [
        "Memorial Sloan Kettering Cancer Center, New York, NY, USA"
      ],
      "name": "Eileen M O’Reilly"
    },
    {
      "affiliations": [
        "Memorial Sloan Kettering Cancer Center, New York, NY, USA"
      ],
      "name": "Wungki Park"
    },
    {
      "affiliations": [
        "Memorial Sloan Kettering Cancer Center, New York, NY, USA"
      ],
      "name": "Catherine O’Connor"
    },
    {
      "affiliations": [
        "Dana-Farber Cancer Institute, Boston, MA, USA"
      ],
      "name": "Harshabad Singh"
    },
    {
      "affiliations": [
        "Memorial Sloan Kettering Cancer Center, New York, NY, USA"
      ],
      "name": "Andrea Cercek"
    },
    {
      "affiliations": [
        "Memorial Sloan Kettering Cancer Center, New York, NY, USA"
      ],
      "name": "Zsofia Stadler"
    },
    {
      "affiliations": [
        "Caris Life Science, Phoenix, AZ, USA"
      ],
      "name": "Andrew Elliott"
    },
    {
      "affiliations": [
        "University of Minnesota, Minneapolis, MN, USA"
      ],
      "name": "Emil Lou"
    },
    {
      "affiliations": [
        "Memorial Sloan Kettering Cancer Center, New York, NY, USA"
      ],
      "name": "Luis A Diaz"
    }
  ],
  "title": "707 Mechanism of MLH1 inactivation predicts benefit to dual immune checkpoint blockade in mismatch repair deficient tumors",
  "uid": "41069617-42b8-5044-9b4c-b4c4a9a66add"
}