CRISPR-GEMM Pooled Mutagenic Screening Identifies KMT2D as a Major Modulator of Immune Checkpoint Blockade

Abstract

Immune checkpoint blockade (ICB) has shown remarkable clinical efficacy in several cancer types. However, only a fraction of patients will respond to ICB. Here, we performed pooled mutagenic screening with CRISPR-mediated genetically engineered mouse models (CRISPR-GEMM) in ICB settings, and identified KMT2D as a major modulator of ICB response across multiple cancer types. <i>KMT2D</i> encodes a histone H3K4 methyltransferase and is among the most frequently mutated genes in patients with cancer. <i>Kmt2d</i> loss led to increased DNA damage and mutation burden, chromatin remodeling, intron retention, and activation of transposable elements. In addition, <i>Kmt2d</i>-mutant cells exhibited increased protein turnover and IFNγ-stimulated antigen presentation. In turn, <i>Kmt2d</i>-mutant tumors in both mouse and human were characterized by increased immune infiltration. These data demonstrate that <i>Kmt2d</i> deficiency sensitizes tumors to ICB by augmenting tumor immunogenicity, and also highlight the power of CRISPR-GEMMs for interrogating complex molecular landscapes in immunotherapeutic contexts that preserve the native tumor microenvironment. SIGNIFICANCE: ICB is ineffective in the majority of patients. Through direct <i>in vivo</i> CRISPR mutagenesis screening in GEMMs of cancer, we find <i>Kmt2d</i> deficiency sensitizes tumors to ICB. Considering the prevalence of <i>KMT2D</i> mutations, this finding potentially has broad implications for patient stratification and clinical decision-making.<i>This article is highlighted in the In This Issue feature, p. 1775</i>.