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Abelin JG, Cox AL. Innovations towards immunopeptidomics. Mol Cell Proteomics 2024:100823. [PMID: 39095021 DOI: 10.1016/j.mcpro.2024.100823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
Over the past 30 years, immunopeptidomics has grown alongside improvements in mass spectrometry technology, genomics, transcriptomics, T cell receptor sequencing, and immunological assays to identify and characterize the targets of activated T cells. Together, multiple research groups with expertise in immunology, biochemistry, chemistry, and peptide mass spectrometry have come together to enable the isolation and sequence identification of endogenous MHC bound peptides. The idea to apply highly sensitive mass spectrometry techniques to study the landscape of peptide antigens presented by cell surface major histocompatibility complexes was innovative and continues to be successfully used and improved upon to deepen our understanding of how peptide antigens are processed and presented to T cells. Multiple research groups were involved in this bringing immunopeptidomics to the forefront of translational research, and we will highlight the contributions of one of the earliest developers, Professor Donald F. Hunt, and his research group at the University of Virginia. The Hunt laboratory applied cutting edge mass spectroscopy based immunopeptidomics to study cancer, autoimmunity, transplant rejection, and infectious diseases. Across these diverse research areas, the Hunt laboratory and collaborators would characterize previously unknown MHC peptide binding motifs and identify immunologically active antigens using ultra sensitive mass spectrometry techniques. Amazingly, many of the MHC bound peptide antigens discovered in collaborations with the Hunt laboratory were sequenced by mass spectrometry before the completion of the human genome using manual de novo sequencing. In this perspective article, we will chronicle the work of the Hunt laboratory and their many collaborators that would be a major part of the foundation for mass spectrometry-based immunopeptidomics and its application to immunology research.
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Affiliation(s)
| | - Andrea L Cox
- Johns Hopkins Bloomberg School of Public Health, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Baltimore, Maryland, USA; Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Diseases, Baltimore, Maryland, USA
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Naskar S, Sriraman N, Sarkar A, Mahajan N, Sarkar K. Tumor antigen presentation and the associated signal transduction during carcinogenesis. Pathol Res Pract 2024; 261:155485. [PMID: 39088877 DOI: 10.1016/j.prp.2024.155485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 08/03/2024]
Abstract
Numerous developments have been achieved in the study and treatment of cancer throughout the decades that it has been common. After decades of research, about 100 different kinds of cancer have been found, each with unique subgroups within certain organs. This has significantly expanded our understanding of the illness. A mix of genetic, environmental, and behavioral variables contribute to the complicated and diverse process of cancer formation. Mutations, or changes in the DNA sequence, are crucial to the development of cancer. These mutations have the ability to downregulate the expression and function of Major Histocompatibility Complex class I (MHC I) and MHCII receptors, as well as activate oncogenes and inactivate tumor suppressor genes. Cancer cells use this tactic to avoid being recognized by cytotoxic CD8+T lymphocytes, which causes issues with antigen presentation and processing. This review goes into great length into the PI3K pathway, changes to MHC I, and positive impacts of tsMHC-II on disease-free survival and overall survival and the involvement of dendritic cells (DCs) in different tumor microenvironments. The vital functions that the PI3K pathway and its link to the mTOR pathway are highlighted and difficulties in developing effective cancer targeted therapies and feedback systems has also been mentioned, where resistance mechanisms include RAS-mediated oncogenic changes and active PI3K signalling.
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Affiliation(s)
- Sohom Naskar
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
| | - Nawaneetan Sriraman
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
| | - Ankita Sarkar
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
| | - Nitika Mahajan
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
| | - Koustav Sarkar
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India.
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Levi R, Levi L, Louzoun Y. Bw4 ligand and direct T-cell receptor binding induced selection on HLA A and B alleles. Front Immunol 2023; 14:1236080. [PMID: 38077375 PMCID: PMC10703150 DOI: 10.3389/fimmu.2023.1236080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction The HLA region is the hallmark of balancing selection, argued to be driven by the pressure to present a wide variety of viral epitopes. As such selection on the peptide-binding positions has been proposed to drive HLA population genetics. MHC molecules also directly binds to the T-Cell Receptor and killer cell immunoglobulin-like receptors (KIR). Methods We here combine the HLA allele frequencies in over six-million Hematopoietic Stem Cells (HSC) donors with a novel machine-learning-based method to predict allele frequency. Results We show for the first time that allele frequency can be predicted from their sequences. This prediction yields a natural measure for selection. The strongest selection is affecting KIR binding regions, followed by the peptide-binding cleft. The selection from the direct interaction with the KIR and TCR is centered on positively charged residues (mainly Arginine), and some positions in the peptide-binding cleft are not associated with the allele frequency, especially Tyrosine residues. Discussion These results suggest that the balancing selection for peptide presentation is combined with a positive selection for KIR and TCR binding.
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Affiliation(s)
| | | | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
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Molvi Z, Klatt MG, Dao T, Urraca J, Scheinberg DA, O'Reilly RJ. The landscape of MHC-presented phosphopeptides yields actionable shared tumor antigens for cancer immunotherapy across multiple HLA alleles. J Immunother Cancer 2023; 11:e006889. [PMID: 37775115 PMCID: PMC10546156 DOI: 10.1136/jitc-2023-006889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Certain phosphorylated peptides are differentially presented by major histocompatibility complex (MHC) molecules on cancer cells characterized by aberrant phosphorylation. Phosphopeptides presented in complex with the human leukocyte antigen HLA-A*02:01 provide a stability advantage over their non-phosphorylated counterparts. This stability is thought to contribute to enhanced immunogenicity. Whether tumor-associated phosphopeptides presented by other common alleles exhibit immunogenicity and structural characteristics similar to those presented by A*02:01 is unclear. Therefore, we determined the identity, structural features, and immunogenicity of phosphopeptides presented by the prevalent alleles HLA-A*03:01, HLA-A*11:01, HLA-C*07:01, and HLA-C*07:02. METHODS We isolated peptide-MHC complexes by immunoprecipitation from 11 healthy and neoplastic tissue samples using mass spectrometry, and then combined the resulting data with public immunopeptidomics data sets to assemble a curated set of phosphopeptides presented by 96 samples spanning 20 distinct healthy and neoplastic tissue types. We determined the biochemical features of selected phosphopeptides by in vitro binding assays and in silico docking, and their immunogenicity by analyzing healthy donor T cells for phosphopeptide-specific multimer binding and cytokine production. RESULTS We identified a subset of phosphopeptides presented by HLA-A*03:01, A*11:01, C*07:01 and C*07:02 on multiple tumor types, particularly lymphomas and leukemias, but not healthy tissues. These phosphopeptides are products of genes essential to lymphoma and leukemia survival. The presented phosphopeptides generally exhibited similar or worse binding to A*03:01 than their non-phosphorylated counterparts. HLA-C*07:01 generally presented phosphopeptides but not their unmodified counterparts. Phosphopeptide binding to HLA-C*07:01 was dependent on B-pocket interactions that were absent in HLA-C*07:02. While HLA-A*02:01 and HLA-A*11:01 phosphopeptide-specific T cells could be readily detected in an autologous setting even when the non-phosphorylated peptide was co-presented, HLA-A*03:01 or HLA-C*07:01 phosphopeptides were repeatedly non-immunogenic, requiring use of allogeneic T cells to induce phosphopeptide-specific T cells. CONCLUSIONS Phosphopeptides presented by multiple alleles that are differentially expressed on tumors constitute tumor-specific antigens that could be targeted for cancer immunotherapy, but the immunogenicity of such phosphopeptides is not a general feature. In particular, phosphopeptides presented by HLA-A*02:01 and A*11:01 exhibit consistent immunogenicity, while phosphopeptides presented by HLA-A*03:01 and C*07:01, although appropriately presented, are not immunogenic. Thus, to address an expanded patient population, phosphopeptide-targeted immunotherapies should be wary of allele-specific differences.
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Affiliation(s)
- Zaki Molvi
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Martin G Klatt
- Department of Hematology, Oncology and Tumor Immunology, Charite Universitatsmedizin Berlin, Berlin, Germany
- German Cancer Research Center, Heidelberg, Baden-Württemberg, Germany
- Berlin Institute of Health at Charité -Universitätsmedizin Berlin, BIH Biomedical 13 Innovation Academy, BIH Charité Clinician Scientist Program, Berlin, Germany
| | - Tao Dao
- Department of Pediatrics, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jessica Urraca
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David A Scheinberg
- Department of Pediatrics, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medicine, New York, New York, USA
| | - Richard J O'Reilly
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Patskovsky Y, Natarajan A, Patskovska L, Nyovanie S, Joshi B, Morin B, Brittsan C, Huber O, Gordon S, Michelet X, Schmitzberger F, Stein RB, Findeis MA, Hurwitz A, Van Dijk M, Chantzoura E, Yague AS, Pollack Smith D, Buell JS, Underwood D, Krogsgaard M. Molecular mechanism of phosphopeptide neoantigen immunogenicity. Nat Commun 2023; 14:3763. [PMID: 37353482 PMCID: PMC10290117 DOI: 10.1038/s41467-023-39425-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/12/2023] [Indexed: 06/25/2023] Open
Abstract
Altered protein phosphorylation in cancer cells often leads to surface presentation of phosphopeptide neoantigens. However, their role in cancer immunogenicity remains unclear. Here we describe a mechanism by which an HLA-B*0702-specific acute myeloid leukemia phosphoneoantigen, pMLL747-755 (EPR(pS)PSHSM), is recognized by a cognate T cell receptor named TCR27, a candidate for cancer immunotherapy. We show that the replacement of phosphoserine P4 with serine or phosphomimetics does not affect pMHC conformation or peptide-MHC affinity but abrogates TCR27-dependent T cell activation and weakens binding between TCR27 and pMHC. Here we describe the crystal structures for TCR27 and cognate pMHC, map of the interface produced by nuclear magnetic resonance, and a ternary complex generated using information-driven protein docking. Our data show that non-covalent interactions between the epitope phosphate group and TCR27 are crucial for TCR specificity. This study supports development of new treatment options for cancer patients through target expansion and TCR optimization.
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Grants
- P30 GM133893 NIGMS NIH HHS
- P30 CA016087 NCI NIH HHS
- U01 CA214354 NCI NIH HHS
- P50 CA225450 NCI NIH HHS
- R01 GM085586 NIGMS NIH HHS
- R01 GM124489 NIGMS NIH HHS
- R01 CA243486 NCI NIH HHS
- S10 OD016343 NIH HHS
- P41 GM118302 NIGMS NIH HHS
- U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
- This work was supported by the NIH grant NIGMS R01 GM124489 (to M.K.), NCI R01 CA243486 (to M.K) and a Sponsored Research Agreement from Agenus to M.K. Results shown in this report are partially derived from work performed at Argonne National Laboratory, Structural Biology Center at the Advanced Photon Source. SBC is operated by UChicago Argonne, LLC, for the U.S. Department of Energy, Office of Biological and Environmental Research under contract DE-AC02-06CH11357. Results in this report are partially derived from work performed at The Center for BioMolecular Structure (CBMS) primarily supported by the National Institutes of Health, National Institute of General Medical Sciences (NIGMS) through a Center Core P30 Grant (P30GM133893), and by the DOE Office of Biological and Environmental Research (KP1607011). As part of NSLS-II, a national user facility at Brookhaven National Laboratory, work performed at the CBMS is supported in part by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences Program under contract number and DE-SC0012704. The NMR spectrometers at the NYU Chemistry Shared Instrumentation Facility were supported by NYU and the NIH Grant 1S10-OD016343. The facilities at the NYSBC were supported by the NIH Grant P41GM118302.
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Affiliation(s)
- Yury Patskovsky
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center at NYU Langone Health, New York, NY, USA
| | - Aswin Natarajan
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center at NYU Langone Health, New York, NY, USA
| | - Larysa Patskovska
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center at NYU Langone Health, New York, NY, USA
| | - Samantha Nyovanie
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center at NYU Langone Health, New York, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Michelle Krogsgaard
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA.
- Laura and Isaac Perlmutter Cancer Center at NYU Langone Health, New York, NY, USA.
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Molvi Z, Klatt MG, Dao T, Urraca J, Scheinberg DA, O’Reilly RJ. The landscape of MHC-presented phosphopeptides yields actionable shared tumor antigens for cancer immunotherapy across multiple HLA alleles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.527552. [PMID: 36798179 PMCID: PMC9934604 DOI: 10.1101/2023.02.08.527552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Background Certain phosphorylated peptides are differentially presented by MHC molecules on cancer cells characterized by aberrant phosphorylation. Phosphopeptides presented in complex with the human leukocyte antigen HLA-A*02:01 provide a stability advantage over their nonphosphorylated counterparts. This stability is thought to contribute to enhanced immunogenicity. Whether tumor-associated phosphopeptides presented by other common alleles exhibit immunogenicity and structural characteristics similar to those presented by A*02:01 is unclear. Therefore, we determined the identity, structural features, and immunogenicity of phosphopeptides presented by the prevalent alleles HLA-A*03:01, -A*11:01, -C*07:01, and - C*07:02. Methods We isolated peptide-MHC complexes by immunoprecipitation from 10 healthy and neoplastic tissue samples using mass spectrometry, and then combined the resulting data with public immunopeptidomics datasets to assemble a curated set of phosphopeptides presented by 20 distinct healthy and neoplastic tissue types. We determined the biochemical features of selected phosphopeptides by in vitro binding assays and in silico docking, and their immunogenicity by analyzing healthy donor T cells for phosphopeptide-specific multimer binding and cytokine production. Results We identified a subset of phosphopeptides presented by HLA-A*03:01, A*11:01, C*07:01 and C*07:02 on multiple tumor types, particularly lymphomas and leukemias, but not healthy tissues. These phosphopeptides are products of genes essential to lymphoma and leukemia survival. The presented phosphopeptides generally exhibited similar or worse binding to A*03:01 than their nonphosphorylated counterparts. HLA-C*07:01 generally presented phosphopeptides but not their unmodified counterparts. Phosphopeptide binding to HLA-C*07:01 was dependent on B- pocket interactions that were absent in HLA-C*07:02. While HLA-A*02:01 and -A*11:01 phosphopeptide-specific T cells could be readily detected in an autologous setting even when the nonphosphorylated peptide was co-presented, HLA-A*03:01 or -C*07:01 phosphopeptides were repeatedly nonimmunogenic, requiring use of allogeneic T cells to induce phosphopeptide- specific T cells. Conclusions Phosphopeptides presented by multiple alleles that are differentially expressed on tumors constitute tumor-specific antigens that could be targeted for cancer immunotherapy, but the immunogenicity of such phosphopeptides is not a general feature. In particular, phosphopeptides presented by HLA-A*02:01 and A*11:01 exhibit consistent immunogenicity, while phosphopeptides presented by HLA-A*03:01 and C*07:01, although appropriately presented, are not immunogenic. Thus, to address an expanded patient population, phosphopeptide-targeted immunotherapies should be wary of allele-specific differences. What is already known on this topic - Phosphorylated peptides presented by the common HLA alleles A*02:01 and B*07:02 are differentially expressed by multiple tumor types, exhibit structural fitness due to phosphorylation, and are targets of healthy donor T cell surveillance, but it is not clear, however, whether such features apply to phosphopeptides presented by other common HLA alleles. What this study adds - We investigated the tumor presentation, binding, structural features, and immunogenicity of phosphopeptides to the prevalent alleles A*03:01, A*11:01, C*07:01, and C*07:02, selected on the basis of their presentation by malignant cells but not normal cells. We found tumor antigens derived from genetic dependencies in lymphomas and leukemias that bind HLA-A3, -A11, -C7 molecules. While we could detect circulating T cell responses in healthy individuals to A*02:01 and A*11:01 phosphopeptides, we did not find such responses to A*03:01 or C*07:01 phosphopeptides, except when utilizing allogeneic donor T cells, indicating that these phosphopeptides may not be immunogenic in an autologous setting but can still be targeted by other means. How this study might affect research, practice or policy - An expanded patient population expressing alleles other than A*02:01 can be addressed through the development of immunotherapies specific for phosphopeptides profiled in the present work, provided the nuances we describe between alleles are taken into consideration.
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Affiliation(s)
- Zaki Molvi
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Martin G. Klatt
- Department of Hematology, Oncology and Tumor Immunology, Campus Benjamin Franklin, Charité- University Medicine Berlin, Berlin, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Berlin Institute of Health at Charité –Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Berlin, Germany
| | - Tao Dao
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Jessica Urraca
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - David A. Scheinberg
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Weill Cornell Medicine, NY, NY, USA
| | - Richard J. O’Reilly
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Weill Cornell Medicine, NY, NY, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
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Kacen A, Javitt A, Kramer MP, Morgenstern D, Tsaban T, Shmueli MD, Teo GC, da Veiga Leprevost F, Barnea E, Yu F, Admon A, Eisenbach L, Samuels Y, Schueler-Furman O, Levin Y, Nesvizhskii AI, Merbl Y. Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors. Nat Biotechnol 2023; 41:239-251. [PMID: 36203013 PMCID: PMC11197725 DOI: 10.1038/s41587-022-01464-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 08/09/2022] [Indexed: 11/08/2022]
Abstract
Post-translational modification (PTM) of antigens provides an additional source of specificities targeted by immune responses to tumors or pathogens, but identifying antigen PTMs and assessing their role in shaping the immunopeptidome is challenging. Here we describe the Protein Modification Integrated Search Engine (PROMISE), an antigen discovery pipeline that enables the analysis of 29 different PTM combinations from multiple clinical cohorts and cell lines. We expanded the antigen landscape, uncovering human leukocyte antigen class I binding motifs defined by specific PTMs with haplotype-specific binding preferences and revealing disease-specific modified targets, including thousands of new cancer-specific antigens that can be shared between patients and across cancer types. Furthermore, we uncovered a subset of modified peptides that are specific to cancer tissue and driven by post-translational changes that occurred in the tumor proteome. Our findings highlight principles of PTM-driven antigenicity, which may have broad implications for T cell-mediated therapies in cancer and beyond.
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Affiliation(s)
- Assaf Kacen
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Aaron Javitt
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Matthias P Kramer
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - David Morgenstern
- De Botton Institute for Protein Profiling, Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Tomer Tsaban
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Merav D Shmueli
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Eilon Barnea
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Lea Eisenbach
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Yishai Levin
- De Botton Institute for Protein Profiling, Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yifat Merbl
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
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Bloodworth N, Barbaro NR, Moretti R, Harrison DG, Meiler J. Rosetta FlexPepDock to predict peptide-MHC binding: An approach for non-canonical amino acids. PLoS One 2022; 17:e0275759. [PMID: 36512534 PMCID: PMC9746977 DOI: 10.1371/journal.pone.0275759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/22/2022] [Indexed: 12/15/2022] Open
Abstract
Computation methods that predict the binding of peptides to MHC-I are important tools for screening and identifying immunogenic antigens and have the potential to accelerate vaccine and drug development. However, most available tools are sequence-based and optimized only for peptides containing the twenty canonical amino acids. This omits a large number of peptides containing non-canonical amino acids (NCAA), or residues that undergo varied post-translational modifications such as glycosylation or phosphorylation. These modifications fundamentally alter peptide immunogenicity. Similarly, existing structure-based methods are biased towards canonical peptide backbone structures, which may or may not be preserved when NCAAs are present. Rosetta FlexPepDock ab-initio is a structure-based computational protocol able to evaluate peptide-receptor interaction where no prior information of the peptide backbone is known. We benchmarked FlexPepDock ab-initio for docking canonical peptides to MHC-I, and illustrate for the first time the method's ability to accurately model MHC-I bound epitopes containing NCAAs. FlexPepDock ab-initio protocol was able to recapitulate near-native structures (≤1.5Å) in the top lowest-energy models for 20 out of 25 cases in our initial benchmark. Using known experimental binding affinities of twenty peptides derived from an influenza-derived peptide, we showed that FlexPepDock protocol is able to predict relative binding affinity as Rosetta energies correlate well with experimental values (r = 0.59, p = 0.006). ROC analysis revealed 80% true positive and a 40% false positive rate, with a prediction power of 93%. Finally, we demonstrate the protocol's ability to accurately recapitulate HLA-A*02:01 bound phosphopeptide backbone structures and relative binding affinity changes, the theoretical structure of the lymphocytic choriomeningitis derived glycosylated peptide GP392 bound to MHC-I H-2Db, and isolevuglandin-adducted peptides. The ability to use non-canonical amino acids in the Rosetta FlexPepDock protocol may provide useful insight into critical amino acid positions where the post-translational modification modulates immunologic responses.
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Affiliation(s)
- Nathaniel Bloodworth
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Natália Ruggeri Barbaro
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Rocco Moretti
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - David G. Harrison
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jens Meiler
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Drug Discovery, Leipzig University, Leipzig, Germany
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León-Letelier RA, Katayama H, Hanash S. Mining the Immunopeptidome for Antigenic Peptides in Cancer. Cancers (Basel) 2022; 14:cancers14204968. [PMID: 36291752 PMCID: PMC9599891 DOI: 10.3390/cancers14204968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/05/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The immunopeptidome of cancer cells is a treasure trove of neoantigens bound to MHC molecules, thus a great source for mining immunopeptides for immunotherapy applications, including cancer vaccines. Immunopeptides may encompass post-translational modifications that are overlooked by genomic and transcriptomic tools. We review post-translational modifications that have been uncovered, and how this information could be harnessed for cancer vaccines. Abstract Although harnessing the immune system for cancer therapy has shown success, response to immunotherapy has been limited. The immunopeptidome of cancer cells presents an opportunity to discover novel antigens for immunotherapy applications. These neoantigens bind to MHC class I and class II molecules. Remarkably, the immunopeptidome encompasses protein post-translation modifications (PTMs) that may not be evident from genome or transcriptome profiling. A case in point is citrullination, which has been demonstrated to induce a strong immune response. In this review, we cover how the immunopeptidome, with a special focus on PTMs, can be utilized to identify cancer-specific antigens for immunotherapeutic applications.
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Sandalova T, Sala BM, Achour A. Structural aspects of chemical modifications in the MHC-restricted immunopeptidome; Implications for immune recognition. Front Chem 2022; 10:861609. [PMID: 36017166 PMCID: PMC9395651 DOI: 10.3389/fchem.2022.861609] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 07/12/2022] [Indexed: 11/26/2022] Open
Abstract
Significant advances in mass-spectroscopy (MS) have made it possible to investigate the cellular immunopeptidome, a large collection of MHC-associated epitopes presented on the surface of healthy, stressed and infected cells. These approaches have hitherto allowed the unambiguous identification of large cohorts of epitope sequences that are restricted to specific MHC class I and II molecules, enhancing our understanding of the quantities, qualities and origins of these peptide populations. Most importantly these analyses provide essential information about the immunopeptidome in responses to pathogens, autoimmunity and cancer, and will hopefully allow for future tailored individual therapies. Protein post-translational modifications (PTM) play a key role in cellular functions, and are essential for both maintaining cellular homeostasis and increasing the diversity of the proteome. A significant proportion of proteins is post-translationally modified, and thus a deeper understanding of the importance of PTM epitopes in immunopeptidomes is essential for a thorough and stringent understanding of these peptide populations. The aim of the present review is to provide a structural insight into the impact of PTM peptides on stability of MHC/peptide complexes, and how these may alter/modulate immune responses.
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Affiliation(s)
- Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Section for Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Benedetta Maria Sala
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Section for Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Section for Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- *Correspondence: Adnane Achour,
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11
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Zeneyedpour L, Stingl C, Kros JM, Sillevis Smitt PAE, Luider TM. Novel Antibody-Peptide Binding Assay Indicates Presence of Immunoglobulins against EGFR Phospho-Site S1166 in High-Grade Glioma. Int J Mol Sci 2022; 23:5061. [PMID: 35563452 PMCID: PMC9100080 DOI: 10.3390/ijms23095061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
We investigated the feasibility of detecting the presence of specific autoantibodies against potential tumor-associated peptide antigens by enriching these antibody-peptide complexes using Melon Gel resin and mass spectrometry. Our goal was to find tumor-associated phospho-sites that trigger immunoreactions and raise autoantibodies that are detectable in plasma of glioma patients. Such immunoglobulins can potentially be used as targets in immunotherapy. To that aim, we describe a method to detect the presence of antibodies in biological samples that are specific to selected clinically relevant peptides. The method is based on the formation of antibody-peptide complexes by mixing patient plasma with a glioblastoma multiforme (GBM) derived peptide library, enrichment of antibodies and antibody-peptide complexes, the separation of peptides after they are released from immunoglobulins by molecular weight filtration and finally mass spectrometric quantification of these peptides. As proof of concept, we successfully applied the method to dinitrophenyl (DNP)-labeled α-casein peptides mixed with anti-DNP. Further, we incubated human plasma with a phospho-peptide library and conducted targeted analysis on EGFR and GFAP phospho-peptides. As a result, immunoaffinity against phospho-peptide GSHQIS[+80]LDNPDYQQDFFPK (EGFR phospho-site S1166) was detected in high-grade glioma (HGG) patient plasma but not in healthy donor plasma. For the GFAP phospho-sites selected, such immunoaffinity was not observed.
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Affiliation(s)
- Lona Zeneyedpour
- Department of Neurology, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (L.Z.); (C.S.); (P.A.E.S.S.)
| | - Christoph Stingl
- Department of Neurology, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (L.Z.); (C.S.); (P.A.E.S.S.)
| | - Johan M. Kros
- Department of Pathology, Erasmus MC, 3015 GD Rotterdam, The Netherlands;
| | | | - Theo M. Luider
- Department of Neurology, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (L.Z.); (C.S.); (P.A.E.S.S.)
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12
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Zhao Y, Sun M, Zhang N, Liu X, Yue C, Feng L, Ji S, Liu X, Qi J, Wong CC, Gao GF, Liu WJ. Phosphosite-dependent presentation of dual phosphorylated peptides by MHC class I molecules. iScience 2022; 25:104013. [PMID: 35310951 PMCID: PMC8931367 DOI: 10.1016/j.isci.2022.104013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/14/2022] [Accepted: 02/25/2022] [Indexed: 11/30/2022] Open
Abstract
Phosphopeptides presented by major histocompatibility complex (MHC) class I have been regarded as a pivotal type of cancer neoantigens that are recognized by T cells. The structural basis of single-phosphorylated peptide presentation has been well studied. Diphosphorylation with one interval between two sites is one of the prevalent forms of multisite-phosphorylated peptides. Herein, we determined the molecular basis of presentation of two P4/P6 double pS-containing peptides by HLA-B27 and compared them with unmodified and single-phosphorylated peptide complexes. These data clarified not only the HLA allele-specific presentation of phosphopeptides by MHC class I molecules but also the cooperativity of peptide conformation within P4 and P6 phosphorylation sites. The phosphorylation of P6 site can influence the binding mode of P4 phosphorylated site to HLA-B27. And we found the diphospho-dependent attenuated effect of peptide binding affinity. This study provides insights into the MHC presentation features of diphosphopeptides, which is different from monophosphopeptides. Diphosphorylation with an interval is prevalent among multiphosphorylated peptides Diphosphopeptide presentation is HLA specific and different from monophosphopeptide The cooperativity of peptide conformation within P4 and P6 phosphorylation sites The diphosphorylation attenuates peptide binding affinity to HLA-B27
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Affiliation(s)
- Yingze Zhao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Mingwei Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Nan Zhang
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing 100191, China
| | - Xueyuan Liu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 100052, China
- School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Can Yue
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 100052, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Feng
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 100052, China
| | - Shushen Ji
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing 100191, China
| | - Xiao Liu
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing 100191, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Catherine C.L. Wong
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing 100191, China
- Corresponding author
| | - George F. Gao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing 102206, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Corresponding author
| | - William J. Liu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing 102206, China
- Corresponding author
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13
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Dao T, Mun SS, Molvi Z, Korontsvit T, Klatt MG, Khan AG, Nyakatura EK, Pohl MA, White TE, Balderes PJ, Lorenz IC, O'Reilly RJ, Scheinberg DA. A TCR mimic monoclonal antibody reactive with the "public" phospho-neoantigen pIRS2/HLA-A*02:01 complex. JCI Insight 2022; 7:151624. [PMID: 35260532 PMCID: PMC8983142 DOI: 10.1172/jci.insight.151624] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 01/26/2022] [Indexed: 02/06/2023] Open
Abstract
Phosphopeptides derived from dysregulated protein phosphorylation in cancer cells can be processed and presented by MHC class I and class II molecules and, therefore, represent an untapped class of tumor-specific antigens that could be used as widely expressed “public” cancer neoantigens (NeoAgs). We generated a TCR mimic (TCRm) mAb, 6B1, specific for a phosphopeptide derived from insulin receptor substrate 2 (pIRS2) presented by HLA-A*02:01. The pIRS2 epitope’s presentation by HLA-A*02:01 was confirmed by mass spectrometry. The TCRm 6B1 specifically bound to pIRS2/HLA-A2 complex on tumor cell lines that expressed pIRS2 in the context of HLA-A*02:01. Bispecific mAbs engaging CD3 of T cells were able to kill tumor cell lines in a pIRS2- and HLA-A*02:01–restricted manner. Structure modeling shows a prerequisite for an arginine or lysine at the first position to bind mAb. Therefore, 6B1 could recognize phosphopeptides derived from various phosphorylated proteins with similar amino acid compositions. This raised the possibility that a TCRm specific for the pIRS2/HLA-A2 complex could target a range of phosphopeptides presented by HLA-A*02:01 in various tumor cells. This is the first TCRm mAb to our knowledge targeting a phosphopeptide/MHC class I complex; the potential of this class of agents for clinical applications warrants further investigation.
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Affiliation(s)
- Tao Dao
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Sung Soo Mun
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Zaki Molvi
- Immunology Program, Weill Cornell Medicine, New York, New York, USA
| | - Tatyana Korontsvit
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Martin G Klatt
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Abdul G Khan
- Tri-Institutional Therapeutics Discovery Institute, New York, New York, USA
| | | | - Mary Ann Pohl
- Tri-Institutional Therapeutics Discovery Institute, New York, New York, USA
| | - Thomas E White
- Tri-Institutional Therapeutics Discovery Institute, New York, New York, USA
| | - Paul J Balderes
- Tri-Institutional Therapeutics Discovery Institute, New York, New York, USA
| | - Ivo C Lorenz
- Tri-Institutional Therapeutics Discovery Institute, New York, New York, USA
| | - Richard J O'Reilly
- Immunology Program, Weill Cornell Medicine, New York, New York, USA.,Weill Cornell Medicine, New York, New York, USA
| | - David A Scheinberg
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Weill Cornell Medicine, New York, New York, USA
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14
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Mitochondrial Proteins as Source of Cancer Neoantigens. Int J Mol Sci 2022; 23:ijms23052627. [PMID: 35269772 PMCID: PMC8909979 DOI: 10.3390/ijms23052627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 01/27/2023] Open
Abstract
In the past decade, anti-tumour immune responses have been successfully exploited to improve the outcome of patients with different cancers. Significant progress has been made in taking advantage of different types of T cell functions for therapeutic purposes. Despite these achievements, only a subset of patients respond favorably to immunotherapy. Therefore, there is a need of novel approaches to improve the effector functions of immune cells and to recognize the major targets of anti-tumour immunity. A major hallmark of cancer is metabolic rewiring associated with switch of mitochondrial functions. These changes are a consequence of high energy demand and increased macromolecular synthesis in cancer cells. Such adaptations in tumour cells might generate novel targets of tumour therapy, including the generation of neoantigens. Here, we review the most recent advances in research on the immune response to mitochondrial proteins in different cellular conditions.
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15
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Mukherjee S, Sanchez-Bernabeu A, Demmers LC, Wu W, Heck AJR. The HLA Ligandome Comprises a Limited Repertoire of O-GlcNAcylated Antigens Preferentially Associated With HLA-B*07:02. Front Immunol 2021; 12:796584. [PMID: 34925382 PMCID: PMC8671986 DOI: 10.3389/fimmu.2021.796584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 11/15/2021] [Indexed: 12/30/2022] Open
Abstract
Mass-spectrometry based immunopeptidomics has provided unprecedented insights into antigen presentation, not only charting an enormous ligandome of self-antigens, but also cancer neoantigens and peptide antigens harbouring post-translational modifications. Here we concentrate on the latter, focusing on the small subset of HLA Class I peptides (less than 1%) that has been observed to be post-translationally modified (PTM) by a O-linked N-acetylglucosamine (GlcNAc). Just like neoantigens these modified antigens may have specific immunomodulatory functions. Here we compiled from literature, and a new dataset originating from the JY B cell lymphoblastoid cell line, a concise albeit comprehensive list of O-GlcNAcylated HLA class I peptides. This cumulative list of O-GlcNAcylated HLA peptides were derived from normal and cancerous origin, as well as tissue specimen. Remarkably, the overlap in detected O-GlcNAcylated HLA peptides as well as their source proteins is strikingly high. Most of the O-GlcNAcylated HLA peptides originate from nuclear proteins, notably transcription factors. From this list, we extract that O-GlcNAcylated HLA Class I peptides are preferentially presented by the HLA-B*07:02 allele. This allele loads peptides with a Proline residue anchor at position 2, and features a binding groove that can accommodate well the recently proposed consensus sequence for O-GlcNAcylation, P(V/A/T/S)g(S/T), essentially explaining why HLA-B*07:02 is a favoured binding allele. The observations drawn from the compiled list, may assist in the prediction of novel O-GlcNAcylated HLA antigens, which will be best presented by patients harbouring HLA-B*07:02 or related alleles that use Proline as anchoring residue.
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Affiliation(s)
- Soumya Mukherjee
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Centre, Utrecht University, Utrecht, Netherlands
| | - Alvaro Sanchez-Bernabeu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Centre, Utrecht University, Utrecht, Netherlands
| | - Laura C Demmers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Centre, Utrecht University, Utrecht, Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Centre, Utrecht University, Utrecht, Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Centre, Utrecht University, Utrecht, Netherlands
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16
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Lulu AM, Cummings KL, Jeffery ED, Myers PT, Underwood D, Lacy RM, Chianese-Bullock KA, Slingluff CL, Modesitt SC, Engelhard VH. Characteristics of Immune Memory and Effector Activity to Cancer-Expressed MHC Class I Phosphopeptides Differ in Healthy Donors and Ovarian Cancer Patients. Cancer Immunol Res 2021; 9:1327-1341. [PMID: 34413086 PMCID: PMC8568670 DOI: 10.1158/2326-6066.cir-21-0111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/22/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022]
Abstract
Elevated immunity to cancer-expressed antigens can be detected in people with no history of cancer and may contribute to cancer prevention. We have previously reported that MHC-restricted phosphopeptides are cancer-expressed antigens and targets of immune recognition. However, the extent to which this immunity reflects prior or ongoing phosphopeptide exposures was not investigated. In this study, we found that preexisting immune memory to cancer-expressed phosphopeptides was evident in most healthy donors, but the breadth among donors was highly variable. Although three phosphopeptides were recognized by most donors, suggesting exposures to common microbial/infectious agents, most of the 205 tested phosphopeptides were not recognized by peripheral blood mononuclear cells (PBMC) from any donor and the remainder were recognized by only 1 to 3 donors. In longitudinal analyses of 2 donors, effector immune response profiles suggested active reexposures to a subset of phosphopeptides. These findings suggest that the immunogens generating most phosphopeptide-specific immune memory are rare infectious agents or incipient cancer cells with distinct phosphoproteome dysregulations, and that repetitive immunogenic exposures occur in individual donors. Phosphopeptide-specific immunity in PBMCs and tumor-infiltrating lymphocytes from ovarian cancer patients was limited, regardless of whether the phosphopeptide was expressed on the tumor. However, 4 of 10 patients responded to 1 to 2 immunodominant phosphopeptides, and 1 showed an elevated effector response to a tumor-expressed phosphopeptide. As the tumors from these patients displayed many phosphopeptides, these data are consistent with lack of prior exposure or impaired ability to respond to some phosphopeptides and suggest that enhancing phosphopeptide-specific T-cell responses could be a useful approach to improve tumor immunotherapy.
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Affiliation(s)
- Amanda M Lulu
- Beirne B. Carter Center for Immunology Research, University of Virginia School of Medicine, Charlottesville, Virginia
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Kara L Cummings
- Beirne B. Carter Center for Immunology Research, University of Virginia School of Medicine, Charlottesville, Virginia
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia
| | | | | | | | - Rachel M Lacy
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Kimberly A Chianese-Bullock
- Division of Surgical Oncology, Department of Surgery, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Craig L Slingluff
- Beirne B. Carter Center for Immunology Research, University of Virginia School of Medicine, Charlottesville, Virginia
- Division of Surgical Oncology, Department of Surgery, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Susan C Modesitt
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Victor H Engelhard
- Beirne B. Carter Center for Immunology Research, University of Virginia School of Medicine, Charlottesville, Virginia.
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia
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17
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Penny SA, Abelin JG, Malaker SA, Myers PT, Saeed AZ, Steadman LG, Bai DL, Ward ST, Shabanowitz J, Hunt DF, Cobbold M. Tumor Infiltrating Lymphocytes Target HLA-I Phosphopeptides Derived From Cancer Signaling in Colorectal Cancer. Front Immunol 2021; 12:723566. [PMID: 34504498 PMCID: PMC8421858 DOI: 10.3389/fimmu.2021.723566] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/27/2021] [Indexed: 12/21/2022] Open
Abstract
There is a pressing need for novel immunotherapeutic targets in colorectal cancer (CRC). Cytotoxic T cell infiltration is well established as a key prognostic indicator in CRC, and it is known that these tumor infiltrating lymphocytes (TILs) target and kill tumor cells. However, the specific antigens that drive these CD8+ T cell responses have not been well characterized. Recently, phosphopeptides have emerged as strong candidates for tumor-specific antigens, as dysregulated signaling in cancer leads to increased and aberrant protein phosphorylation. Here, we identify 120 HLA-I phosphopeptides from primary CRC tumors, CRC liver metastases and CRC cell lines using mass spectrometry and assess the tumor-resident immunity against these posttranslationally modified tumor antigens. Several CRC tumor-specific phosphopeptides were presented by multiple patients’ tumors in our cohort (21% to 40%), and many have previously been identified on other malignancies (58% of HLA-A*02 CRC phosphopeptides). These shared antigens derived from mitogenic signaling pathways, including p53, Wnt and MAPK, and are therefore markers of malignancy. The identification of public tumor antigens will allow for the development of broadly applicable targeted therapeutics. Through analysis of TIL cytokine responses to these phosphopeptides, we have established that they are already playing a key role in tumor-resident immunity. Multifunctional CD8+ TILs from primary and metastatic tumors recognized the HLA-I phosphopeptides presented by their originating tumor. Furthermore, TILs taken from other CRC patients’ tumors targeted two of these phosphopeptides. In another cohort of CRC patients, the same HLA-I phosphopeptides induced higher peripheral T cell responses than they did in healthy donors, suggesting that these immune responses are specifically activated in CRC patients. Collectively, these results establish HLA-I phosphopeptides as targets of the tumor-resident immunity in CRC, and highlight their potential as candidates for future immunotherapeutic strategies.
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Affiliation(s)
- Sarah A Penny
- School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Jennifer G Abelin
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States
| | - Stacy A Malaker
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States
| | - Paisley T Myers
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States
| | - Abu Z Saeed
- School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Lora G Steadman
- School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Dina L Bai
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States
| | - Stephen T Ward
- School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.,Department of Colorectal Surgery, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States.,Department of Pathology, University of Virginia, Charlottesville, VA, United States
| | - Mark Cobbold
- School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.,Center for Cancer Immunology, Massachusetts General Hospital, Charlestown, MA, United States
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18
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Mahoney KE, Shabanowitz J, Hunt DF. MHC Phosphopeptides: Promising Targets for Immunotherapy of Cancer and Other Chronic Diseases. Mol Cell Proteomics 2021; 20:100112. [PMID: 34129940 PMCID: PMC8724925 DOI: 10.1016/j.mcpro.2021.100112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 05/11/2021] [Accepted: 06/02/2021] [Indexed: 12/27/2022] Open
Abstract
Major histocompatibility complex-associated peptides have been considered as potential immunotherapeutic targets for many years. MHC class I phosphopeptides result from dysregulated cell signaling pathways that are common across cancers and both viral and bacterial infections. These antigens are recognized by central memory T cells from healthy donors, indicating that they are considered antigenic by the immune system and that they are presented across different individuals and diseases. Based on these responses and the similar dysregulation, phosphorylated antigens are promising candidates for prevention or treatment of different cancers as well as a number of other chronic diseases.
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Affiliation(s)
- Keira E Mahoney
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA.
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA; Department of Pathology, University of Virginia, Charlottesville, Virginia, USA.
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19
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Engelhard VH, Obeng RC, Cummings KL, Petroni GR, Ambakhutwala AL, Chianese-Bullock KA, Smith KT, Lulu A, Varhegyi N, Smolkin ME, Myers P, Mahoney KE, Shabanowitz J, Buettner N, Hall EH, Haden K, Cobbold M, Hunt DF, Weiss G, Gaughan E, Slingluff CL. MHC-restricted phosphopeptide antigens: preclinical validation and first-in-humans clinical trial in participants with high-risk melanoma. J Immunother Cancer 2021; 8:jitc-2019-000262. [PMID: 32385144 PMCID: PMC7228659 DOI: 10.1136/jitc-2019-000262] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Phosphorylated peptides presented by MHC molecules represent a new class of neoantigens expressed on cancer cells and recognized by CD8 T-cells. These peptides are promising targets for cancer immunotherapy. Previous work identified an HLA-A*0201-restricted phosphopeptide from insulin receptor substrate 2 (pIRS2) as one such target. The purpose of this study was to characterize a second phosphopeptide, from breast cancer antiestrogen resistance 3 (BCAR3), and to evaluate safety and immunogenicity of a novel immunotherapic vaccine comprising either or both of these phosphorylated peptides. METHODS Phosphorylated BCAR3 protein was evaluated in melanoma and breast cancer cell lines by Western blot, and recognition by T-cells specific for HLA-A*0201-restricted phosphorylated BCAR3 peptide (pBCAR3126-134) was determined by 51Cr release assay and intracellular cytokine staining. Human tumor explants were also evaluated by mass spectrometry for presentation of pIRS2 and pBCAR3 peptides. For the clinical trial, participants with resected stage IIA-IV melanoma were vaccinated 6 times over 12 weeks with one or both peptides in incomplete Freund's adjuvant and Hiltonol (poly-ICLC). Adverse events (AEs) were coded based on National Cancer Institute (NCI) Common Terminology Criteria for Adverse Events (CTCAE) V.4.03, with provision for early study termination if dose-limiting toxicity (DLT) rates exceeded 33%. The enrollment target was 12 participants evaluable for immune response to each peptide. T-cell responses were assessed by interferon-γ ELISpot assay. RESULTS pBCAR3 peptides were immunogenic in vivo in mice, and in vitro in normal human donors, and T-cells specific for pBCAR3126-134 controlled outgrowth of a tumor xenograft. The pIRS21097-1105 peptide was identified by mass spectrometry from human hepatocellular carcinoma tumors. In the clinical trial, 15 participants were enrolled. All had grade 1 or 2 treatment-related AEs, but there were no grade 3-4 AEs, DLTs or deaths on study. T-cell responses were induced to the pIRS21097-1105 peptide in 5/12 patients (42%, 90% CI 18% to 68%) and to the pBCAR3126-134 peptide in 2/12 patients (17%, 90% CI 3% to 44%). CONCLUSION This study supports the safety and immunogenicity of vaccines containing the cancer-associated phosphopeptides pBCAR3126-134 and pIRS21097-1105, and the data support continued development of immune therapy targeting phosphopeptides. Future studies will define ways to further enhance the magnitude and durability of phosphopeptide-specific immune responses. TRIAL REGISTRATION NUMBER NCT01846143.
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Affiliation(s)
- Victor H Engelhard
- Beirne Carter Center for Immunology Research and Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Rebecca C Obeng
- Beirne Carter Center for Immunology Research and Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Kara L Cummings
- Beirne Carter Center for Immunology Research and Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Gina R Petroni
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Angela L Ambakhutwala
- Beirne Carter Center for Immunology Research and Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Kimberly A Chianese-Bullock
- Department of Surgery/Division of Surgical Oncology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Kelly T Smith
- Department of Surgery/Division of Surgical Oncology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Amanda Lulu
- Beirne Carter Center for Immunology Research and Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Nikole Varhegyi
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Mark E Smolkin
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Paisley Myers
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Keira E Mahoney
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Nico Buettner
- 7Medical Research Council Centre for Immune Regulation and Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
| | - Emily H Hall
- Office of Clinical Research, University Virginia Cancer Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Kathleen Haden
- Department of Surgery/Division of Surgical Oncology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Mark Cobbold
- 7Medical Research Council Centre for Immune Regulation and Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Geoffrey Weiss
- Medicine/Division of Hematology-Oncology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Elizabeth Gaughan
- Medicine/Division of Hematology-Oncology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Craig L Slingluff
- Department of Surgery/Division of Surgical Oncology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
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Generation of Phosphopeptide-Specific T Cell Lines as Tools for Melanoma Immunotherapy. Methods Mol Biol 2021. [PMID: 33704746 DOI: 10.1007/978-1-0716-1205-7_45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The importance of tumor-associated antigen-specific T cells in the effective control of cancer has been highlighted by recent advances in cancer immunotherapies that target the programmed cell death-1 (PD-1) pathway or that utilize modified T cell receptors. Phosphopeptide-specific T cells are of interest because they recognize a new class of tumor antigens that are derived from proteins relevant for cancer development and growth. These T cell lines or their antigen receptors can be used in combination with other forms of therapy to improve the immune response and survival of cancer patients. We describe here a protocol for the generation of human and transgenic murine phosphopeptide-specific T cells lines as tools for investigating T cell reactivity against melanoma phosphoantigens displayed by HLA-A*0201.
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Abstract
The assessment of immunogenicity of biopharmaceuticals is a crucial step in the process of their development. Immunogenicity is related to the activation of adaptive immunity. The complexity of the immune system manifests through numerous different mechanisms, which allows the use of different approaches for predicting the immunogenicity of biopharmaceuticals. The direct experimental approaches are sometimes expensive and time consuming, or their results need to be confirmed. In this case, computational methods for immunogenicity prediction appear as an appropriate complement in the process of drug design. In this review, we analyze the use of various In silico methods and approaches for immunogenicity prediction of biomolecules: sequence alignment algorithms, predicting subcellular localization, searching for major histocompatibility complex (MHC) binding motifs, predicting T and B cell epitopes based on machine learning algorithms, molecular docking, and molecular dynamics simulations. Computational tools for antigenicity and allergenicity prediction also are considered.
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22
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Jones HF, Molvi Z, Klatt MG, Dao T, Scheinberg DA. Empirical and Rational Design of T Cell Receptor-Based Immunotherapies. Front Immunol 2021; 11:585385. [PMID: 33569049 PMCID: PMC7868419 DOI: 10.3389/fimmu.2020.585385] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/04/2020] [Indexed: 01/04/2023] Open
Abstract
The use of T cells reactive with intracellular tumor-associated or tumor-specific antigens has been a promising strategy for cancer immunotherapies in the past three decades, but the approach has been constrained by a limited understanding of the T cell receptor's (TCR) complex functions and specificities. Newer TCR and T cell-based approaches are in development, including engineered adoptive T cells with enhanced TCR affinities, TCR mimic antibodies, and T cell-redirecting bispecific agents. These new therapeutic modalities are exciting opportunities by which TCR recognition can be further exploited for therapeutic benefit. In this review we summarize the development of TCR-based therapeutic strategies and focus on balancing efficacy and potency versus specificity, and hence, possible toxicity, of these powerful therapeutic modalities.
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Affiliation(s)
- Heather F. Jones
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Weill Cornell Medicine, New York, NY, United States
| | - Zaki Molvi
- Weill Cornell Medicine, New York, NY, United States
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Martin G. Klatt
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Tao Dao
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - David A. Scheinberg
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Weill Cornell Medicine, New York, NY, United States
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23
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Minati R, Perreault C, Thibault P. A Roadmap Toward the Definition of Actionable Tumor-Specific Antigens. Front Immunol 2020; 11:583287. [PMID: 33424836 PMCID: PMC7793940 DOI: 10.3389/fimmu.2020.583287] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/30/2020] [Indexed: 12/15/2022] Open
Abstract
The search for tumor-specific antigens (TSAs) has considerably accelerated during the past decade due to the improvement of proteogenomic detection methods. This provides new opportunities for the development of novel antitumoral immunotherapies to mount an efficient T cell response against one or multiple types of tumors. While the identification of mutated antigens originating from coding exons has provided relatively few TSA candidates, the possibility of enlarging the repertoire of targetable TSAs by looking at antigens arising from non-canonical open reading frames opens up interesting avenues for cancer immunotherapy. In this review, we outline the potential sources of TSAs and the mechanisms responsible for their expression strictly in cancer cells. In line with the heterogeneity of cancer, we propose that discrete families of TSAs may be enriched in specific cancer types.
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Affiliation(s)
- Robin Minati
- École Normale Supérieure de Lyon, Université Claude Bernard Lyon I, Université de Lyon, Lyon, France
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Department of Chemistry, Université de Montréal, Montréal, QC, Canada
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Zeneyedpour L, Sten-van `t Hoff J, Luider T. Using phosphoproteomics and next generation sequencing to discover novel therapeutic targets in patient antibodies. Expert Rev Proteomics 2020; 17:675-684. [DOI: 10.1080/14789450.2020.1845147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Lona Zeneyedpour
- Department of Neurology, Erasmus MC, Laboratory of Neuro-Oncology/Clinical & Cancer Proteomics, Rotterdam, The Netherlands
| | - Jenny Sten-van `t Hoff
- Department of Neurology, Erasmus MC, Laboratory of Neuro-Oncology/Clinical & Cancer Proteomics, Rotterdam, The Netherlands
| | - Theo Luider
- Department of Neurology, Erasmus MC, Laboratory of Neuro-Oncology/Clinical & Cancer Proteomics, Rotterdam, The Netherlands
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25
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Gopanenko AV, Kosobokova EN, Kosorukov VS. Main Strategies for the Identification of Neoantigens. Cancers (Basel) 2020; 12:E2879. [PMID: 33036391 PMCID: PMC7600129 DOI: 10.3390/cancers12102879] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/24/2022] Open
Abstract
Genetic instability of tumors leads to the appearance of numerous tumor-specific somatic mutations that could potentially result in the production of mutated peptides that are presented on the cell surface by the MHC molecules. Peptides of this kind are commonly called neoantigens. Their presence on the cell surface specifically distinguishes tumors from healthy tissues. This feature makes neoantigens a promising target for immunotherapy. The rapid evolution of high-throughput genomics and proteomics makes it possible to implement these techniques in clinical practice. In particular, they provide useful tools for the investigation of neoantigens. The most valuable genomic approach to this problem is whole-exome sequencing coupled with RNA-seq. High-throughput mass-spectrometry is another option for direct identification of MHC-bound peptides, which is capable of revealing the entire MHC-bound peptidome. Finally, structure-based predictions could significantly improve the understanding of physicochemical and structural features that affect the immunogenicity of peptides. The development of pipelines combining such tools could improve the accuracy of the peptide selection process and decrease the required time. Here we present a review of the main existing approaches to investigating the neoantigens and suggest a possible ideal pipeline that takes into account all modern trends in the context of neoantigen discovery.
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Affiliation(s)
| | | | - Vyacheslav S. Kosorukov
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, 115478 Moscow, Russia; (A.V.G.); (E.N.K.)
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26
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Kote S, Pirog A, Bedran G, Alfaro J, Dapic I. Mass Spectrometry-Based Identification of MHC-Associated Peptides. Cancers (Basel) 2020; 12:cancers12030535. [PMID: 32110973 PMCID: PMC7139412 DOI: 10.3390/cancers12030535] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/15/2020] [Accepted: 02/20/2020] [Indexed: 02/06/2023] Open
Abstract
Neoantigen-based immunotherapies promise to improve patient outcomes over the current standard of care. However, detecting these cancer-specific antigens is one of the significant challenges in the field of mass spectrometry. Even though the first sequencing of the immunopeptides was done decades ago, today there is still a diversity of the protocols used for neoantigen isolation from the cell surface. This heterogeneity makes it difficult to compare results between the laboratories and the studies. Isolation of the neoantigens from the cell surface is usually done by mild acid elution (MAE) or immunoprecipitation (IP) protocol. However, limited amounts of the neoantigens present on the cell surface impose a challenge and require instrumentation with enough sensitivity and accuracy for their detection. Detecting these neopeptides from small amounts of available patient tissue limits the scope of most of the studies to cell cultures. Here, we summarize protocols for the extraction and identification of the major histocompatibility complex (MHC) class I and II peptides. We aimed to evaluate existing methods in terms of the appropriateness of the isolation procedure, as well as instrumental parameters used for neoantigen detection. We also focus on the amount of the material used in the protocols as the critical factor to consider when analyzing neoantigens. Beyond experimental aspects, there are numerous readily available proteomics suits/tools applicable for neoantigen discovery; however, experimental validation is still necessary for neoantigen characterization.
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27
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Solleder M, Guillaume P, Racle J, Michaux J, Pak HS, Müller M, Coukos G, Bassani-Sternberg M, Gfeller D. Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands. Mol Cell Proteomics 2020; 19:390-404. [PMID: 31848261 PMCID: PMC7000122 DOI: 10.1074/mcp.tir119.001641] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 12/06/2019] [Indexed: 12/19/2022] Open
Abstract
The presentation of peptides on class I human leukocyte antigen (HLA-I) molecules plays a central role in immune recognition of infected or malignant cells. In cancer, non-self HLA-I ligands can arise from many different alterations, including non-synonymous mutations, gene fusion, cancer-specific alternative mRNA splicing or aberrant post-translational modifications. Identifying HLA-I ligands remains a challenging task that requires either heavy experimental work for in vivo identification or optimized bioinformatics tools for accurate predictions. To date, no HLA-I ligand predictor includes post-translational modifications. To fill this gap, we curated phosphorylated HLA-I ligands from several immunopeptidomics studies (including six newly measured samples) covering 72 HLA-I alleles and retrieved a total of 2,066 unique phosphorylated peptides. We then expanded our motif deconvolution tool to identify precise binding motifs of phosphorylated HLA-I ligands. Our results reveal a clear enrichment of phosphorylated peptides among HLA-C ligands and demonstrate a prevalent role of both HLA-I motifs and kinase motifs on the presentation of phosphorylated peptides. These data further enabled us to develop and validate the first predictor of interactions between HLA-I molecules and phosphorylated peptides.
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Affiliation(s)
- Marthe Solleder
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Philippe Guillaume
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Julien Racle
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Justine Michaux
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - Hui-Song Pak
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - Markus Müller
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - George Coukos
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland.
| | - David Gfeller
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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28
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Croft NP. Peptide Presentation to T Cells: Solving the Immunogenic Puzzle: Systems Immunology Profiling of Antigen Presentation for Prediction of CD8 + T Cell Immunogenicity. Bioessays 2020; 42:e1900200. [PMID: 31958157 DOI: 10.1002/bies.201900200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/18/2019] [Indexed: 02/02/2023]
Abstract
The vertebrate immune system uses an impressive arsenal of mechanisms to combat harmful cellular states such as infection. One way is via cells delivering real-time snapshots of their protein content to the cell surface in the form of short peptides. Specialized immune cells (T cells) sample these peptides and assess whether they are foreign, warranting an action such as destruction of the infected cell. The delivery of peptides to the cell surface is termed antigen processing and presentation, and decades of research have provided unprecedented understanding of this process. However, predicting the capacity for a given peptide to be immunogenic-to elicit a T cell response-has remained both enigmatic and a long sought-after goal. In the era of big data, a point is being approached where the steps of antigen processing and presentation can be quantified and assessed against peptide immunogenicity in order to build predictive models. This review presents new findings in this area and contemplates challenges ahead.
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Affiliation(s)
- Nathan P Croft
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
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29
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Wang Y, Wang P, Xu J. Phosphorylation: A Fast Switch For Checkpoint Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1248:347-398. [PMID: 32185718 DOI: 10.1007/978-981-15-3266-5_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Checkpoint signaling involves a variety of upstream and downstream factors that participate in the regulation of checkpoint expression, activation, and degradation. During the process, phosphorylation plays a critical role. Phosphorylation is one of the most well-documented post-translational modifications of proteins. Of note, the importance of phosphorylation has been emphasized in aspects of cell activities, including proliferation, metabolism, and differentiation. Here we summarize how phosphorylation of specific molecules affects the immune activities with preference in tumor immunity. Of course, immune checkpoints are given extra attention in this book. There are many common pathways that are involved in signaling of different checkpoints. Some of them are integrated and presented as common activities in the early part of this chapter, especially those associated with PD-1/PD-L1 and CTLA-4, because investigations concerning them are particularly abundant and variant. Their distinct regulation is supplementarily discussed in their respective section. As for checkpoints that are so far not well explored, their related phosphorylation modulations are listed separately in the later part. We hope to provide a clear and systematic view of the phosphorylation-modulated immune signaling.
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Affiliation(s)
- Yiting Wang
- School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Wang
- Shanghai Tenth People's Hospital of Tongji University, School of Medicine, School of Life Sciences and Technology, Tongji University Cancer Center, Tongji University, Shanghai, 200092, China
| | - Jie Xu
- Institutes of Biomedical Sciences, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, 200032, China.
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30
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Heather JM, Myers PT, Shi F, Aziz-Zanjani MO, Mahoney KE, Perez M, Morin B, Brittsan C, Shabanowitz J, Hunt DF, Cobbold M. Murine xenograft bioreactors for human immunopeptidome discovery. Sci Rep 2019; 9:18558. [PMID: 31811195 PMCID: PMC6898210 DOI: 10.1038/s41598-019-54700-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/05/2019] [Indexed: 11/17/2022] Open
Abstract
The study of peptides presented by MHC class I and class II molecules is limited by the need for relatively large cell numbers, especially when studying post-translationally modified or otherwise rare peptide species. To overcome this problem, we pose the hypothesis that human cells grown as xenografts in immunodeficient mice should produce equivalent immunopeptidomes as cultured cells. Comparing human cell lines grown either in vitro or as murine xenografts, we show that the immunopeptidome is substantially preserved. Numerous features are shared across both sample types, including peptides and proteins featured, length distributions, and HLA-binding motifs. Peptides well-represented in both groups were from more abundant proteins, or those with stronger predicted HLA binding affinities. Samples grown in vivo also recapitulated a similar phospho-immunopeptidome, with common sequences being those found at high copy number on the cell surface. These data indicate that xenografts are indeed a viable methodology for the production of cells for immunopeptidomic discovery.
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Affiliation(s)
- James M Heather
- Center for Cancer Immunology, Massachusetts General Hospital, Boston, Massachusetts, USA.
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.
| | | | - Feng Shi
- Center for Cancer Immunology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Keira E Mahoney
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | | | | | | | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
- Department of Pathology, University of Virginia, Charlottesville, Virginia, USA
| | - Mark Cobbold
- Center for Cancer Immunology, Massachusetts General Hospital, Boston, Massachusetts, USA.
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.
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Structures of the four Ig-like domain LILRB2 and the four-domain LILRB1 and HLA-G1 complex. Cell Mol Immunol 2019; 17:966-975. [PMID: 31273318 PMCID: PMC7609294 DOI: 10.1038/s41423-019-0258-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/14/2019] [Indexed: 11/29/2022] Open
Abstract
Leukocyte immunoglobulin (Ig)-like receptors (LILRs), also known as CD85 and immunoglobulin-like transcripts (ILTs), play pivotal roles in regulating immune responses. These receptors define an immune checkpoint that immune therapy can target. Through cis or trans interactions with human leukocyte antigen (HLA)-G, the two most abundantly expressed inhibitory LILRs, LILRB1, and LILRB2 (LILRB1/2, also known as CD85j/d and ILT2/4), are involved in immunotolerance in pregnancy and transplantation, autoimmune diseases, and immune evasion by tumors. Although the discrete domains of LILRB1/2 are clear, the assembly mode of the four extracellular Ig-like domains (D1, D2, D3, and D4) remains unknown. Previous data indicate that D1D2 is responsible for binding to HLA class I (HLA-I), but the roles of D3D4 are still unclear. Here, we determined the crystal structure of the four Ig-like domain LILRB2 and four-domain LILRB1 in complex with HLA-G1. The angles between adjacent domains and the staggered assembly of the four domains suggest limited flexibility and limited plasticity of the receptors during ligand binding. The complex structure of four-domain LILRB1 and HLA-G1 supports the model that D1D2 is responsible for HLA-I binding, while D3D4 acts as a scaffold. Accordingly, cis and trans binding models for HLA-I binding to LILRB1/2 are proposed. The geometries of LILRB1/2 in complex with dimeric and monomeric HLA-G1 suggest the accessibility of the dimeric receptor, which in turn, transduces more inhibitory signals. The assembly of LILRB1/2 and its binding to HLA-G1 could aid in the design of immune regulators and benefit immune interference.
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Abstract
The incidence of melanoma continues to increase even as advances in immunotherapy have led to survival benefits in advanced stages. Vaccines are capable of inducing strong, antitumor immune responses with limited toxicity. Some vaccines have demonstrated clinical benefit in clinical trials alone; however, others have not despite inducing strong immune responses. Recent advancements have improved vaccine design, and combining vaccines with other immunotherapies offers promise. This review highlights the underlying principles of vaccine development, common components of vaccines, and the remaining challenges and future directions of vaccine therapy in melanoma.
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Affiliation(s)
- Minyoung Kwak
- Division of Surgical Oncology, Department of Surgery, University of Virginia, PO Box 800709, Charlottesville, VA 22908-0709, USA; Department of Surgery, SUNY Downstate, Brooklyn, NY, USA; Carter Immunology Center, University of Virginia, Charlottesville, VA, USA
| | - Katie M Leick
- Division of Surgical Oncology, Department of Surgery, University of Virginia, PO Box 800709, Charlottesville, VA 22908-0709, USA; Carter Immunology Center, University of Virginia, Charlottesville, VA, USA; Department of Surgery, University of Iowa, Iowa City, IA, USA
| | - Marit M Melssen
- Division of Surgical Oncology, Department of Surgery, University of Virginia, PO Box 800709, Charlottesville, VA 22908-0709, USA; Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA; Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Craig L Slingluff
- Division of Surgical Oncology, Department of Surgery, University of Virginia, PO Box 800709, Charlottesville, VA 22908-0709, USA; Carter Immunology Center, University of Virginia, Charlottesville, VA, USA.
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Deuss FA, Watson GM, Goodall KJ, Leece I, Chatterjee S, Fu Z, Thaysen-Andersen M, Andrews DM, Rossjohn J, Berry R. Structural basis for the recognition of nectin-like protein-5 by the human-activating immune receptor, DNAM-1. J Biol Chem 2019; 294:12534-12546. [PMID: 31253644 DOI: 10.1074/jbc.ra119.009261] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/27/2019] [Indexed: 11/06/2022] Open
Abstract
Nectin and nectin-like (Necl) adhesion molecules are broadly overexpressed in a wide range of cancers. By binding to these adhesion molecules, the immunoreceptors DNAX accessory molecule-1 (DNAM-1), CD96 molecule (CD96), and T-cell immunoreceptor with Ig and ITIM domains (TIGIT) play a crucial role in regulating the anticancer activities of immune effector cells. However, within this axis, it remains unclear how DNAM-1 recognizes its cognate ligands. Here, we determined the structure of human DNAM-1 in complex with nectin-like protein-5 (Necl-5) at 2.8 Å resolution. Unexpectedly, we found that the two extracellular domains (D1-D2) of DNAM-1 adopt an unconventional "collapsed" arrangement that is markedly distinct from those in other immunoglobulin-based immunoreceptors. The DNAM-1/Necl-5 interaction was underpinned by conserved lock-and-key motifs located within their respective D1 domains, but also included a distinct interface derived from DNAM-1 D2. Mutation of the signature DNAM-1 "key" motif within the D1 domain attenuated Necl-5 binding and natural killer cell-mediated cytotoxicity. Altogether, our results have implications for understanding the binding mode of an immune receptor family that is emerging as a viable candidate for cancer immunotherapy.
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Affiliation(s)
- Felix A Deuss
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Gabrielle M Watson
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Katharine J Goodall
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria 3800, Australia
| | - Isobel Leece
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria 3800, Australia
| | - Sayantani Chatterjee
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, New South Wales 2109, Australia
| | - Zhihui Fu
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, New South Wales 2109, Australia
| | - Daniel M Andrews
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria 3800, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia; Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom.
| | - Richard Berry
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.
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Abstract
The varied landscape of the adaptive immune response is determined by the peptides presented by immune cells, derived from viral or microbial pathogens or cancerous cells. The study of immune biomarkers or antigens is not new, and classical methods such as agglutination, enzyme-linked immunosorbent assay, or Western blotting have been used for many years to study the immune response to vaccination or disease. However, in many of these traditional techniques, protein or peptide identification has often been the bottleneck. Recent progress in genomics and mass spectrometry have led to many of the rapid advances in proteomics approaches. Immunoproteomics describes a rapidly growing collection of approaches that have the common goal of identifying and measuring antigenic peptides or proteins. This includes gel-based, array-based, mass spectrometry-based, DNA-based, or in silico approaches. Immunoproteomics is yielding an understanding of disease and disease progression, vaccine candidates, and biomarkers. This review gives an overview of immunoproteomics and closely related technologies that are used to define the full set of protein antigens targeted by the immune system during disease.
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Affiliation(s)
- Kelly M Fulton
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, ON, Canada
| | - Isabel Baltat
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, ON, Canada
| | - Susan M Twine
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, ON, Canada.
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Riley TP, Baker BM. The intersection of affinity and specificity in the development and optimization of T cell receptor based therapeutics. Semin Cell Dev Biol 2018; 84:30-41. [DOI: 10.1016/j.semcdb.2017.10.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 10/07/2017] [Accepted: 10/17/2017] [Indexed: 12/29/2022]
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Application of the immunoregulatory receptor LILRB1 as a crystallisation chaperone for human class I MHC complexes. J Immunol Methods 2018; 464:47-56. [PMID: 30365927 DOI: 10.1016/j.jim.2018.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 10/02/2018] [Accepted: 10/22/2018] [Indexed: 12/24/2022]
Abstract
X-ray crystallographic studies of class I peptide-MHC molecules (pMHC) continue to provide important insights into immune recognition, however their success depends on generation of diffraction-quality crystals, which remains a significant challenge. While protein engineering techniques such as surface-entropy reduction and lysine methylation have proven utility in facilitating and/or improving protein crystallisation, they risk affecting the conformation and biochemistry of the class I MHC antigen binding groove. An attractive alternative is the use of noncovalent crystallisation chaperones, however these have not been developed for pMHC. Here we describe a method for promoting class I pMHC crystallisation, by exploiting its natural ligand interaction with the immunoregulatory receptor LILRB1 as a novel crystallisation chaperone. First, focussing on a model HIV-1-derived HLA-A2-restricted peptide, we determined a 2.4 Å HLA-A2/LILRB1 structure, which validated that co-crystallisation with LILRB1 does not alter conformation of the antigenic peptide. We then demonstrated that addition of LILRB1 enhanced the crystallisation of multiple peptide-HLA-A2 complexes, and identified a generic condition for initial co-crystallisation. LILRB1 chaperone-based crystallisation enabled structure determination for HLA-A2 complexes previously intransigent to crystallisation, including both conventional and post-translationally-modified peptides, of diverse lengths. Since both the LILRB1 recognition interface on the HLA-A2 α3 domain molecule and HLA-A2-mediated crystal contacts are predominantly conserved across class I MHC molecules, the approach we outline could prove applicable to a diverse range of class I pMHC. LILRB1 chaperone-mediated crystallisation should expedite molecular insights into the immunobiology of diverse immune-related diseases and immunotherapeutic strategies, particularly involving class I pMHC complexes that are challenging to crystallise.
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Marino F. Gaining Insight Into Posttranslationally Modified HIV Antigens and Their Underlying Characteristics. Proteomics 2018. [PMID: 29513933 DOI: 10.1002/pmic.201800041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Mass spectrometry (MS)-based immunopeptidomics has developed as one of the leading methodologies for comprehensive characterization of in vivo presented human leukocyte antigen (HLA)-bound peptides. Unveiling the identity of HLA-bound peptides derived from diseased cells is crucial to gain knowledge on the constitution of efficient disease-specific T cell responses. The HLA-presented peptidome reflects the status of the cellular proteome, hence disease-related aberrations of posttranslational modifications (PTMs) might lead to presentation of peptides harboring PTMs. Therefore, characterization of HLA-bound PTM peptides could shed light on their relevance in immune and disease processes. In this issue, Ramarathinam et al. investigate the presentation of HIV envelope (HIVenv) peptides bound to the HLA-B*57:01 allele. Among these peptides, the authors specifically focused on a kynurenine-modified peptide. To this end, they characterize the possible origin of the kynurenine modification, its effect on HLA binding affinity, stability, conformation within the complex, and its immunogenicity compared to the native counterpart.
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Affiliation(s)
- Fabio Marino
- Departement de Medecine-Oncology, Centre Hospitalier Universitaire Vaudois, Switzerland
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Antunes DA, Abella JR, Devaurs D, Rigo MM, Kavraki LE. Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes. Curr Top Med Chem 2018; 18:2239-2255. [PMID: 30582480 PMCID: PMC6361695 DOI: 10.2174/1568026619666181224101744] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 11/29/2018] [Accepted: 12/08/2018] [Indexed: 12/26/2022]
Abstract
Understanding the mechanisms involved in the activation of an immune response is essential to many fields in human health, including vaccine development and personalized cancer immunotherapy. A central step in the activation of the adaptive immune response is the recognition, by T-cell lymphocytes, of peptides displayed by a special type of receptor known as Major Histocompatibility Complex (MHC). Considering the key role of MHC receptors in T-cell activation, the computational prediction of peptide binding to MHC has been an important goal for many immunological applications. Sequence- based methods have become the gold standard for peptide-MHC binding affinity prediction, but structure-based methods are expected to provide more general predictions (i.e., predictions applicable to all types of MHC receptors). In addition, structural modeling of peptide-MHC complexes has the potential to uncover yet unknown drivers of T-cell activation, thus allowing for the development of better and safer therapies. In this review, we discuss the use of computational methods for the structural modeling of peptide-MHC complexes (i.e., binding mode prediction) and for the structure-based prediction of binding affinity.
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Affiliation(s)
| | - Jayvee R. Abella
- Computer Science Department, Rice University, Houston, Texas, USA
| | - Didier Devaurs
- Computer Science Department, Rice University, Houston, Texas, USA
| | - Maurício M. Rigo
- School of Medicine, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Lydia E. Kavraki
- Computer Science Department, Rice University, Houston, Texas, USA
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