Non-canonical antigens are the largest fraction of peptides presented by MHC class I in mismatch repair deficient murine colorectal cancer
Abstract Background Immunotherapy based on checkpoint inhibitors is highly effective in mismatch repair deficient (MMRd) colorectal cancer (CRC). These tumors carry a high number of mutations, which are predicted to translate into a wide array of neoepitopes; however, a systematic classification of...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2024-01-01
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| Series: | Genome Medicine |
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| Online Access: | https://doi.org/10.1186/s13073-023-01275-3 |
| _version_ | 1797349768989507584 |
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| author | Giuseppe Rospo Rosaria Chilà Vittoria Matafora Veronica Basso Simona Lamba Alice Bartolini Angela Bachi Federica Di Nicolantonio Anna Mondino Giovanni Germano Alberto Bardelli |
| author_facet | Giuseppe Rospo Rosaria Chilà Vittoria Matafora Veronica Basso Simona Lamba Alice Bartolini Angela Bachi Federica Di Nicolantonio Anna Mondino Giovanni Germano Alberto Bardelli |
| author_sort | Giuseppe Rospo |
| collection | DOAJ |
| description | Abstract Background Immunotherapy based on checkpoint inhibitors is highly effective in mismatch repair deficient (MMRd) colorectal cancer (CRC). These tumors carry a high number of mutations, which are predicted to translate into a wide array of neoepitopes; however, a systematic classification of the neoantigen repertoire in MMRd CRC is lacking. Mass spectrometry peptidomics has demonstrated the existence of MHC class I associated peptides (MAPs) originating from non-coding DNA regions. Based on these premises we investigated DNA genomic regions responsible for generating MMRd-induced peptides. Methods We exploited mouse CRC models in which the MMR gene Mlh1 was genetically inactivated. Isogenic cell lines CT26 Mlh1 +/+ and Mlh1 -/- were inoculated in immunocompromised and immunocompetent mice. Whole genome and RNA sequencing data were generated from samples obtained before and after injection in murine hosts. First, peptide databases were built from transcriptomes of isogenic cell lines. We then compiled a database of peptides lost after tumor cells injection in immunocompetent mice, likely due to immune editing. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) and matched next-generation sequencing databases were employed to identify the DNA regions from which the immune-targeted MAPs originated. Finally, we adopted in vitro T cell assays to verify whether MAP-specific T cells were part of the in vivo immune response against Mlh1 -/- cells. Results Whole genome sequencing analyses revealed an unbalanced distribution of immune edited alterations across the genome in Mlh1 -/- cells grown in immunocompetent mice. Specifically, untranslated (UTR) and coding regions exhibited the largest fraction of mutations leading to highly immunogenic peptides. Moreover, the integrated computational and LC-MS/MS analyses revealed that MAPs originate mainly from atypical translational events in both Mlh1 +/+ and Mlh1 -/- tumor cells. In addition, mutated MAPs—derived from UTRs and out-of-frame translation of coding regions—were highly enriched in Mlh1 -/- cells. The MAPs trigger T-cell activation in mice primed with Mlh1 -/- cells. Conclusions Our results suggest that—in comparison to MMR proficient CRC—MMRd tumors generate a significantly higher number of non-canonical mutated peptides able to elicit T cell responses. These results reveal the importance of evaluating the diversity of neoepitope repertoire in MMRd tumors. |
| first_indexed | 2024-03-08T12:35:13Z |
| format | Article |
| id | doaj.art-382e5842e7284601869b1fcf804efca3 |
| institution | Directory Open Access Journal |
| issn | 1756-994X |
| language | English |
| last_indexed | 2024-03-08T12:35:13Z |
| publishDate | 2024-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Medicine |
| spelling | doaj.art-382e5842e7284601869b1fcf804efca32024-01-21T12:29:14ZengBMCGenome Medicine1756-994X2024-01-0116111710.1186/s13073-023-01275-3Non-canonical antigens are the largest fraction of peptides presented by MHC class I in mismatch repair deficient murine colorectal cancerGiuseppe Rospo0Rosaria Chilà1Vittoria Matafora2Veronica Basso3Simona Lamba4Alice Bartolini5Angela Bachi6Federica Di Nicolantonio7Anna Mondino8Giovanni Germano9Alberto Bardelli10Department of Oncology, Molecular Biotechnology Center, University of TorinoIFOM ETS - The AIRC Institute of Molecular OncologyIFOM ETS - The AIRC Institute of Molecular OncologyLymphocyte Activation Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute Via OlgettinaDepartment of Oncology, Molecular Biotechnology Center, University of TorinoCandiolo Cancer Institute, FPO-IRCCSIFOM ETS - The AIRC Institute of Molecular OncologyDepartment of Oncology, Molecular Biotechnology Center, University of TorinoLymphocyte Activation Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute Via OlgettinaDepartment of Oncology, Molecular Biotechnology Center, University of TorinoDepartment of Oncology, Molecular Biotechnology Center, University of TorinoAbstract Background Immunotherapy based on checkpoint inhibitors is highly effective in mismatch repair deficient (MMRd) colorectal cancer (CRC). These tumors carry a high number of mutations, which are predicted to translate into a wide array of neoepitopes; however, a systematic classification of the neoantigen repertoire in MMRd CRC is lacking. Mass spectrometry peptidomics has demonstrated the existence of MHC class I associated peptides (MAPs) originating from non-coding DNA regions. Based on these premises we investigated DNA genomic regions responsible for generating MMRd-induced peptides. Methods We exploited mouse CRC models in which the MMR gene Mlh1 was genetically inactivated. Isogenic cell lines CT26 Mlh1 +/+ and Mlh1 -/- were inoculated in immunocompromised and immunocompetent mice. Whole genome and RNA sequencing data were generated from samples obtained before and after injection in murine hosts. First, peptide databases were built from transcriptomes of isogenic cell lines. We then compiled a database of peptides lost after tumor cells injection in immunocompetent mice, likely due to immune editing. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) and matched next-generation sequencing databases were employed to identify the DNA regions from which the immune-targeted MAPs originated. Finally, we adopted in vitro T cell assays to verify whether MAP-specific T cells were part of the in vivo immune response against Mlh1 -/- cells. Results Whole genome sequencing analyses revealed an unbalanced distribution of immune edited alterations across the genome in Mlh1 -/- cells grown in immunocompetent mice. Specifically, untranslated (UTR) and coding regions exhibited the largest fraction of mutations leading to highly immunogenic peptides. Moreover, the integrated computational and LC-MS/MS analyses revealed that MAPs originate mainly from atypical translational events in both Mlh1 +/+ and Mlh1 -/- tumor cells. In addition, mutated MAPs—derived from UTRs and out-of-frame translation of coding regions—were highly enriched in Mlh1 -/- cells. The MAPs trigger T-cell activation in mice primed with Mlh1 -/- cells. Conclusions Our results suggest that—in comparison to MMR proficient CRC—MMRd tumors generate a significantly higher number of non-canonical mutated peptides able to elicit T cell responses. These results reveal the importance of evaluating the diversity of neoepitope repertoire in MMRd tumors.https://doi.org/10.1186/s13073-023-01275-3Colorectal cancerMismatch repairNeoantigensNon-coding DNANon-canonical antigensImmune surveillance |
| spellingShingle | Giuseppe Rospo Rosaria Chilà Vittoria Matafora Veronica Basso Simona Lamba Alice Bartolini Angela Bachi Federica Di Nicolantonio Anna Mondino Giovanni Germano Alberto Bardelli Non-canonical antigens are the largest fraction of peptides presented by MHC class I in mismatch repair deficient murine colorectal cancer Genome Medicine Colorectal cancer Mismatch repair Neoantigens Non-coding DNA Non-canonical antigens Immune surveillance |
| title | Non-canonical antigens are the largest fraction of peptides presented by MHC class I in mismatch repair deficient murine colorectal cancer |
| title_full | Non-canonical antigens are the largest fraction of peptides presented by MHC class I in mismatch repair deficient murine colorectal cancer |
| title_fullStr | Non-canonical antigens are the largest fraction of peptides presented by MHC class I in mismatch repair deficient murine colorectal cancer |
| title_full_unstemmed | Non-canonical antigens are the largest fraction of peptides presented by MHC class I in mismatch repair deficient murine colorectal cancer |
| title_short | Non-canonical antigens are the largest fraction of peptides presented by MHC class I in mismatch repair deficient murine colorectal cancer |
| title_sort | non canonical antigens are the largest fraction of peptides presented by mhc class i in mismatch repair deficient murine colorectal cancer |
| topic | Colorectal cancer Mismatch repair Neoantigens Non-coding DNA Non-canonical antigens Immune surveillance |
| url | https://doi.org/10.1186/s13073-023-01275-3 |
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