156O - Pharmacologic inhibition of nonsense-mediated decay induces anti-tumour immunogenicity in ex vivo patient tumours

Background

Neoantigens derived from somatic tumor mutations are essential to initiate and sustain 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, leading to mRNA degradation by the nonsense-mediated mRNA decay (NMD) pathway. In cancer, NMD activity is increased in response to the heightened burden of somatic fs-indel mutations, preventing the generation of immunogenic neoantigens, thus promoting immune evasion.

Methods

We pharmacologically targeted SMG1, a core NMD pathway component, for the first-time in patient tumor samples and in human and mouse cancer cell lines, and patient-derived tumour organoids (PDTOs). We analyzed the changes in transcriptome, proteome and immunopeptidome following SMG1 inhibition (SMG1i) and peptide reactivity in in vitro priming experiments. 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 and in vivo immunological responses were assessed by high-dimensional flow cytometry, cytometric bead array and single-cell RNA- and TCR-sequencing.

Results

SMG1i induces activation and expansion of tumor-reactive intratumoural CD8⁺ lymphocytes in vivo and in ex vivo PTDFs but not in matched normal tissue and tumour control and synergy with immune checkpoint blockade (ICB) in in vivo syngeneic mouse models. Mechanistically, SMG1i increases the abundance and HLA presentation of a plethora of neoantigens able to elicit potent T cell activation in in vitro priming experiments, converting the neoepitope count from a low- to a high-TMB-like state without inducing mutations. Co-culture of tumor cells and PDTOs with CD8⁺ T cells upon SMG1i induced potent MHC class I antigen-dependent T cell activation and tumor cell killing.

Conclusions

Our findings highlight SMG1 inhibition as a promising strategy to exploit an untapped source of highly immunogenic peptides and to induce anti-tumor immunogenicity without introducing DNA mutations irrespective of the tumor type or TMB status and provide means to enhance response to ICB that is readily translatable.

Editorial acknowledgement

Clinical trial identification

Legal entity responsible for the study

The authors.

Funding

Cancer Research UK TDL-Ono-LifeArc, Genesis Therapeutics, Medical Research Council, Rosetrees Trust UK Charity, Cancer Research UK Lung Cancer Centre of Excellence, Cancer Research Horizons.

Disclosure

R. Vendramin: Financial Interests, Personal, Funding: CRUK TDL-Ono-LifeArc alliance, Genesis Therapeutics. S. Fernandez Patel: Financial Interests, Personal, Full or part-time Employment: Genesis Therapeutics. A. Castro: Financial Interests, Personal, Advisory Role: Tempus. J. Murai: Financial Interests, Personal, Full or part-time Employment: Ono Pharmaceutical. S. Quezada: Financial Interests, Personal, Advisory Board: DROIA Oncology; Financial Interests, Personal, Full or part-time Employment: Achilles Therapeutics; Financial Interests, Personal, Stocks/Shares: Achilles Therapeutics; Financial Interests, Personal, Royalties: Dartmouth College, MSKCC, UCL. J.L. Reading: Financial Interests, Personal, Advisory Role: Achilles Therapeutics. C. Swanton: Financial Interests, Personal, Invited Speaker, Activity took place in 2016: Pfizer, Celgene; Financial Interests, Personal, Invited Speaker, October 26th 2020: Novartis; Financial Interests, Personal, Invited Speaker: Roche/Ventana, BMS, AstraZeneca, MSD, Illumina, GSK; Financial Interests, Personal, Advisory Board, Ad Board - November 12th, 2020: Amgen; Financial Interests, Personal, Advisory Board, Current - since 2018: Genentech; Financial Interests, Personal, Advisory Board: Sarah Canon Research Institute; Financial Interests, Personal, Advisory Board, Joined October 2020. Also have stock options: Bicycle Therapeutics; Financial Interests, Personal, Other, Consultancy: Medicxi; Financial Interests, Personal, Advisory Board, Member of the Science Advisory Board. Also had stock options until June 2021: GRAIL; Financial Interests, Personal, Other, Consultancy agreement: Roche Innovation Centre Shanghai; Financial Interests, Personal, Advisory Board, 29 November - 1 December 2022: Novartis; Financial Interests, Personal, Invited Speaker, Oncology Collective - 2nd Nov - 4 Nov 2022 - Atlanta, USA: Roche; Financial Interests, Personal, Advisory Board, ctDNA advisory Board - 24th March 2023: AstraZeneca; Financial Interests, Personal, Invited Speaker, Pfizer Oncology 'Leading the revolution for the future: Pfizer; Financial Interests, Personal, Advisory Board, Scientific Advisory Board and Stock options from September 2023: Relay Therapeutics; Financial Interests, Personal, Advisory Board, Member of the Scientific Advisory Board: SAGA Diagnostics; Financial Interests, Personal, Full or part-time Employment, Chief Clinician since October 2017: Cancer Research UK; Financial Interests, Personal, Ownership Interest, Co-Founder of Achilles Therapeutics. Also, have stock options in this company: Achilles Therapeutics; Financial Interests, Personal, Stocks/Shares, Stocks owned until June 2021: GRAIL, Apogen Biotechnologies; Financial Interests, Personal, Stocks/Shares: Epic Biosciences, Bicycle Therapeutics; Financial Interests, Personal, Stocks/Shares, Stock options: Relay Therapeutics; Financial Interests, Institutional, Research Grant, Funded RUBICON grant - October 2018 - April 2021: Bristol Myers Squibb; Financial Interests, Institutional, Research Grant, Collaboration in minimal residual disease sequencing technologies: Archer Dx Inc; Financial Interests, Institutional, Research Grant: Pfizer, Boehringer Ingelheim; Financial Interests, Institutional, Invited Speaker, Chief Investigator for the MeRmaiD 1and 2 clinical trials and chair of the steering committee: AstraZeneca; Financial Interests, Institutional, Research Grant, Research grant from Oct 2019 - July 2023 - Genetics of CIN and SCNAs for Targeted Discovery (SCEPTRE): Ono Pharmaceutical; Financial Interests, Institutional, Research Grant, Research Grants from 2015: Roche; Financial Interests, Personal, Other, Co-chief investigator: NHS-Galleri Clinical Trial; Financial Interests, Institutional, Research Grant, from October 2022: Personalis; Non-Financial Interests, Personal, Principal Investigator, Chief Investigator for MeRmaiD 1and 2 clinical trials: AstraZeneca; Non-Financial Interests, Personal, Member of Board of Directors, From 2019-2022: AACR; Non-Financial Interests, Personal, Other, Board of Directors: AACR; Non-Financial Interests, Personal, Advisory Role, EACR Advisory Council member: EACR. K.R. Litchfield: Financial Interests, Personal, Invited Speaker: Roche tissue diagnostics; Financial Interests, Personal, Funding: CRUK TDL–Ono–LifeArc alliance, Genesis Therapeutics; Financial Interests, Personal, Advisory Role: Ellipses Pharma, Monopteros, Kynos Therapeutics. All other authors have declared no conflicts of interest.