Abstract 6737: Pharmacologic modulation of nonsense-mediated decay induces anti-tumor immunogenicity in <i>ex vivo</i> patient tumors
Authors: Roberto Vendramin, Hongchang Fu, Yue Zhao, Shanila Fernandez-Patel, Danwen Qian, Lorena Ligammari, Gordon Beattie, Ronen Levy, Polina Greenberg, Osnat Bartok, Krupa Thakkar, Jun Murai, Despoina Karagianni, Chris Sng, Mansi Shah, Felipe Galvez-Cancino, Krijn Djikstra, Sergio Quezada, Yardena Samuels, James Reading, Charles Swanton, Kevin Litchfield
Journal: Cancer Research (2024)

Abstract Introduction: Immunogenic neoantigens derived from somatic tumor mutations are essential to initiate and sustain robust anti-tumor immune responses. Frameshift insertion/deletions (fs-indels) are a key source of immunogenic neoantigens. However, fs-indels often result in the introduction of premature termination codons (PTCs), leading to mRNA degradation by the nonsense-mediated mRNA decay (NMD) pathway. In human malignancies, NMD activity is increased in response to the heightened burden of somatic fs-indel mutations and effectively prevents the generation of highly immunogenic tumor-specific neoantigens, thereby promoting immune evasion. Approach: Here, we pharmacologically targeted SMG1, a core component of the NMD pathway, for the first time in patient tumor and normal samples as well as in a panel of human cancer cell lines and patient-derived organoids, to prevent the degradation of highly immunogenic frame-shifted transcripts. We analyzed the changes in transcriptome, proteome and immunopeptidome following SMG1 inhibition (SMG1i). We then made use of tumor-T cell co-cultures and Patient-Derived Tumor Fragments (PDTFs) to assess the effects of SMG1i on anti-tumor immunogenicity. Ex vivo immunological responses were measured by high-dimensional flow cytometry, cytometric bead array and single cell RNA and TCR sequencing. Results: Our data demonstrates a significant increase in T cell activation, expansion of tumor-reactive intratumoural CD8+ lymphocytes and cytokine secretion following SMG1 inhibition in ex vivo PTDFs (n=15) but not in matched normal-adjacent tissue (n=10). Mechanistically, SMG1 inhibition increased the abundance of frame-shifted mRNA transcripts, and aberrant HLA-presented peptides. Co-culture of tumor cells and patient-derived organoids with CD8+ T cells upon SMG1 inhibition induced potent MHC class I antigen-dependent T cell activation and tumor cell killing. Conclusion: Our findings, in a clinically relevant platform, highlight SMG1 inhibition as a novel cancer immunotherapy approach to promote neoantigen production and to induce anti-tumor immunogenicity irrespective of the tumor type or TMB status. Citation Format: Roberto Vendramin, Hongchang Fu, Yue Zhao, Shanila Fernandez-Patel, Danwen Qian, Lorena Ligammari, Gordon Beattie, Ronen Levy, Polina Greenberg, Osnat Bartok, Krupa Thakkar, Jun Murai, Despoina Karagianni, Chris Sng, Mansi Shah, Felipe Galvez-Cancino, Krijn Djikstra, Sergio Quezada, Yardena Samuels, TRACERx consortium, James Reading, Charles Swanton, Kevin Litchfield. Pharmacologic modulation of nonsense-mediated decay induces anti-tumor immunogenicity in ex vivo patient tumors [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 6737.