Pan-cancer landscape of AID-related mutations, composite mutations, and their potential role in the ICI response
Abstract Activation-induced cytidine deaminase, AICDA or AID, is a driver of somatic hypermutation and class-switch recombination in immunoglobulins. In addition, this deaminase belonging to the APOBEC family may have off-target effects genome-wide, but its effects at pan-cancer level are not well e...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-12-01
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| Series: | npj Precision Oncology |
| Online Access: | https://doi.org/10.1038/s41698-022-00331-2 |
| _version_ | 1797642073239715840 |
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| author | Isaias Hernández-Verdin Kadir C. Akdemir Daniele Ramazzotti Giulio Caravagna Karim Labreche Karima Mokhtari Khê Hoang-Xuan Matthieu Peyre Franck Bielle Mehdi Touat Ahmed Idbaih Alex Duval Marc Sanson Agustí Alentorn |
| author_facet | Isaias Hernández-Verdin Kadir C. Akdemir Daniele Ramazzotti Giulio Caravagna Karim Labreche Karima Mokhtari Khê Hoang-Xuan Matthieu Peyre Franck Bielle Mehdi Touat Ahmed Idbaih Alex Duval Marc Sanson Agustí Alentorn |
| author_sort | Isaias Hernández-Verdin |
| collection | DOAJ |
| description | Abstract Activation-induced cytidine deaminase, AICDA or AID, is a driver of somatic hypermutation and class-switch recombination in immunoglobulins. In addition, this deaminase belonging to the APOBEC family may have off-target effects genome-wide, but its effects at pan-cancer level are not well elucidated. Here, we used different pan-cancer datasets, totaling more than 50,000 samples analyzed by whole-genome, whole-exome, or targeted sequencing. AID mutations are present at pan-cancer level with higher frequency in hematological cancers and higher presence at transcriptionally active TAD domains. AID synergizes initial hotspot mutations by a second composite mutation. AID mutational load was found to be independently associated with a favorable outcome in immune-checkpoint inhibitors (ICI) treated patients across cancers after analyzing 2000 samples. Finally, we found that AID-related neoepitopes, resulting from mutations at more frequent hotspots if compared to other mutational signatures, enhance CXCL13/CCR5 expression, immunogenicity, and T-cell exhaustion, which may increase ICI sensitivity. |
| first_indexed | 2024-03-11T13:55:51Z |
| format | Article |
| id | doaj.art-10e4ff93711e45efae0a1c2b4a7ff33b |
| institution | Directory Open Access Journal |
| issn | 2397-768X |
| language | English |
| last_indexed | 2024-03-11T13:55:51Z |
| publishDate | 2022-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Precision Oncology |
| spelling | doaj.art-10e4ff93711e45efae0a1c2b4a7ff33b2023-11-02T07:00:15ZengNature Portfolionpj Precision Oncology2397-768X2022-12-016111410.1038/s41698-022-00331-2Pan-cancer landscape of AID-related mutations, composite mutations, and their potential role in the ICI responseIsaias Hernández-Verdin0Kadir C. Akdemir1Daniele Ramazzotti2Giulio Caravagna3Karim Labreche4Karima Mokhtari5Khê Hoang-Xuan6Matthieu Peyre7Franck Bielle8Mehdi Touat9Ahmed Idbaih10Alex Duval11Marc Sanson12Agustí Alentorn13Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICMDepartments of Genomic Medicine and Neurosurgery, University of Texas MD Anderson Cancer CenterDepartment of Medicine and Surgery, University of Milano-BicoccaCancer Data Science Laboratory, Dipartimento di Matematica e Geoscienze, Università degli Studi di TriesteSorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICMSorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICMSorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICMSorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICMSorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICMSorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICMSorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICMSorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité des Microsatellites et Cancer, Equipe labellisée par la Ligue Nationale contre le CancerSorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICMSorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICMAbstract Activation-induced cytidine deaminase, AICDA or AID, is a driver of somatic hypermutation and class-switch recombination in immunoglobulins. In addition, this deaminase belonging to the APOBEC family may have off-target effects genome-wide, but its effects at pan-cancer level are not well elucidated. Here, we used different pan-cancer datasets, totaling more than 50,000 samples analyzed by whole-genome, whole-exome, or targeted sequencing. AID mutations are present at pan-cancer level with higher frequency in hematological cancers and higher presence at transcriptionally active TAD domains. AID synergizes initial hotspot mutations by a second composite mutation. AID mutational load was found to be independently associated with a favorable outcome in immune-checkpoint inhibitors (ICI) treated patients across cancers after analyzing 2000 samples. Finally, we found that AID-related neoepitopes, resulting from mutations at more frequent hotspots if compared to other mutational signatures, enhance CXCL13/CCR5 expression, immunogenicity, and T-cell exhaustion, which may increase ICI sensitivity.https://doi.org/10.1038/s41698-022-00331-2 |
| spellingShingle | Isaias Hernández-Verdin Kadir C. Akdemir Daniele Ramazzotti Giulio Caravagna Karim Labreche Karima Mokhtari Khê Hoang-Xuan Matthieu Peyre Franck Bielle Mehdi Touat Ahmed Idbaih Alex Duval Marc Sanson Agustí Alentorn Pan-cancer landscape of AID-related mutations, composite mutations, and their potential role in the ICI response npj Precision Oncology |
| title | Pan-cancer landscape of AID-related mutations, composite mutations, and their potential role in the ICI response |
| title_full | Pan-cancer landscape of AID-related mutations, composite mutations, and their potential role in the ICI response |
| title_fullStr | Pan-cancer landscape of AID-related mutations, composite mutations, and their potential role in the ICI response |
| title_full_unstemmed | Pan-cancer landscape of AID-related mutations, composite mutations, and their potential role in the ICI response |
| title_short | Pan-cancer landscape of AID-related mutations, composite mutations, and their potential role in the ICI response |
| title_sort | pan cancer landscape of aid related mutations composite mutations and their potential role in the ici response |
| url | https://doi.org/10.1038/s41698-022-00331-2 |
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