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Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma
Immune checkpoint inhibitors and adoptive lymphocyte transfer–based therapies have shown great therapeutic potential in cancers with high tumor mutational burden (TMB), such as melanoma, but not in cancers with low TMB, such as mutant epidermal growth factor receptor (EGFR)–driven lung adenocarcinom...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Society for Biochemistry and Molecular Biology
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8724932/ https://www.ncbi.nlm.nih.gov/pubmed/34391887 http://dx.doi.org/10.1016/j.mcpro.2021.100136 |
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author | Qi, Yue A. Maity, Tapan K. Cultraro, Constance M. Misra, Vikram Zhang, Xu Ade, Catherine Gao, Shaojian Milewski, David Nguyen, Khoa D. Ebrahimabadi, Mohammad H. Hanada, Ken-ichi Khan, Javed Sahinalp, Cenk Yang, James C. Guha, Udayan |
author_facet | Qi, Yue A. Maity, Tapan K. Cultraro, Constance M. Misra, Vikram Zhang, Xu Ade, Catherine Gao, Shaojian Milewski, David Nguyen, Khoa D. Ebrahimabadi, Mohammad H. Hanada, Ken-ichi Khan, Javed Sahinalp, Cenk Yang, James C. Guha, Udayan |
author_sort | Qi, Yue A. |
collection | PubMed |
description | Immune checkpoint inhibitors and adoptive lymphocyte transfer–based therapies have shown great therapeutic potential in cancers with high tumor mutational burden (TMB), such as melanoma, but not in cancers with low TMB, such as mutant epidermal growth factor receptor (EGFR)–driven lung adenocarcinoma. Precision immunotherapy is an unmet need for most cancers, particularly for cancers that respond inadequately to immune checkpoint inhibitors. Here, we employed large-scale MS-based proteogenomic profiling to identify potential immunogenic human leukocyte antigen (HLA) class I-presented peptides in melanoma and EGFR-mutant lung adenocarcinoma. Similar numbers of peptides were identified from both tumor types. Cell line and patient-specific databases (DBs) were constructed using variants identified from whole-exome sequencing. A de novo search algorithm was used to interrogate the HLA class I immunopeptidome MS data. We identified 12 variant peptides and several classes of tumor-associated antigen-derived peptides. We constructed a cancer germ line (CG) antigen DB with 285 antigens. This allowed us to identify 40 class I-presented CG antigen–derived peptides. The class I immunopeptidome comprised more than 1000 post-translationally modified (PTM) peptides representing 58 different PTMs, underscoring the critical role PTMs may play in HLA binding. Finally, leveraging de novo search algorithm and an annotated long noncoding RNA (lncRNA) DB, we developed a novel lncRNA-encoded peptide discovery pipeline to identify 44 lncRNA-derived peptides that are presented by class I. We validated tandem MS spectra of select variant, CG antigen, and lncRNA-derived peptides using synthetic peptides and performed HLA class I-binding assays to demonstrate binding to class I proteins. In summary, we provide direct evidence of HLA class I presentation of a large number of variant and tumor-associated peptides in both low and high TMB cancer. These results can potentially be useful for precision immunotherapies, such as vaccine or adoptive cell therapies in melanoma and EGFR-mutant lung cancers. |
format | Online Article Text |
id | pubmed-8724932 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | American Society for Biochemistry and Molecular Biology |
record_format | MEDLINE/PubMed |
spelling | pubmed-87249322022-01-11 Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma Qi, Yue A. Maity, Tapan K. Cultraro, Constance M. Misra, Vikram Zhang, Xu Ade, Catherine Gao, Shaojian Milewski, David Nguyen, Khoa D. Ebrahimabadi, Mohammad H. Hanada, Ken-ichi Khan, Javed Sahinalp, Cenk Yang, James C. Guha, Udayan Mol Cell Proteomics Research Immune checkpoint inhibitors and adoptive lymphocyte transfer–based therapies have shown great therapeutic potential in cancers with high tumor mutational burden (TMB), such as melanoma, but not in cancers with low TMB, such as mutant epidermal growth factor receptor (EGFR)–driven lung adenocarcinoma. Precision immunotherapy is an unmet need for most cancers, particularly for cancers that respond inadequately to immune checkpoint inhibitors. Here, we employed large-scale MS-based proteogenomic profiling to identify potential immunogenic human leukocyte antigen (HLA) class I-presented peptides in melanoma and EGFR-mutant lung adenocarcinoma. Similar numbers of peptides were identified from both tumor types. Cell line and patient-specific databases (DBs) were constructed using variants identified from whole-exome sequencing. A de novo search algorithm was used to interrogate the HLA class I immunopeptidome MS data. We identified 12 variant peptides and several classes of tumor-associated antigen-derived peptides. We constructed a cancer germ line (CG) antigen DB with 285 antigens. This allowed us to identify 40 class I-presented CG antigen–derived peptides. The class I immunopeptidome comprised more than 1000 post-translationally modified (PTM) peptides representing 58 different PTMs, underscoring the critical role PTMs may play in HLA binding. Finally, leveraging de novo search algorithm and an annotated long noncoding RNA (lncRNA) DB, we developed a novel lncRNA-encoded peptide discovery pipeline to identify 44 lncRNA-derived peptides that are presented by class I. We validated tandem MS spectra of select variant, CG antigen, and lncRNA-derived peptides using synthetic peptides and performed HLA class I-binding assays to demonstrate binding to class I proteins. In summary, we provide direct evidence of HLA class I presentation of a large number of variant and tumor-associated peptides in both low and high TMB cancer. These results can potentially be useful for precision immunotherapies, such as vaccine or adoptive cell therapies in melanoma and EGFR-mutant lung cancers. American Society for Biochemistry and Molecular Biology 2021-08-13 /pmc/articles/PMC8724932/ /pubmed/34391887 http://dx.doi.org/10.1016/j.mcpro.2021.100136 Text en https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Research Qi, Yue A. Maity, Tapan K. Cultraro, Constance M. Misra, Vikram Zhang, Xu Ade, Catherine Gao, Shaojian Milewski, David Nguyen, Khoa D. Ebrahimabadi, Mohammad H. Hanada, Ken-ichi Khan, Javed Sahinalp, Cenk Yang, James C. Guha, Udayan Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma |
title | Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma |
title_full | Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma |
title_fullStr | Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma |
title_full_unstemmed | Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma |
title_short | Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma |
title_sort | proteogenomic analysis unveils the hla class i-presented immunopeptidome in melanoma and egfr-mutant lung adenocarcinoma |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8724932/ https://www.ncbi.nlm.nih.gov/pubmed/34391887 http://dx.doi.org/10.1016/j.mcpro.2021.100136 |
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