Article
Multidisciplinary Sciences
Georges Bedran, Daniel A. Polasky, Yi Hsiao, Fengchao Yu, Felipe da Veiga Leprevost, Javier A. Alfaro, Marcin Cieslik, Alexey I. Nesvizhskii
Summary: In this study, a fast computational workflow merging the MSFragger-Glyco search algorithm with a false discovery rate control is introduced for analyzing glycopeptides from mass spectrometry-based immunopeptidome data. The authors analyze eight large-scale publicly available studies and find that glycosylated MHC-associated peptides are predominantly presented by MHC class II. They present a comprehensive resource, HLA-Glyco, which contains over 3,400 human leukocyte antigen (HLA) class II N-glycopeptides from 1,049 distinct protein glycosylation sites. This resource provides valuable insights into glycosylation properties in antigen recognition and immune modulation.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Yue A. Qi, Tapan K. Maity, Constance M. Cultraro, Vikram Misra, Xu Zhang, Catherine Ade, Shaojian Gao, David Milewski, Khoa D. Nguyen, Mohammad H. Ebrahimabadi, Ken-ichi Hanada, Javed Khan, Cenk Sahinalp, James C. Yang, Udayan Guha
Summary: The study identified potential immunogenic human leukocyte antigen (HLA) class I-presented peptides in melanoma and EGFR-mutant lung adenocarcinoma using large-scale proteogenomic profiling. This discovery could be valuable for developing precision immunotherapies.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Oncology
Yue A. Qi, Tapan K. Maity, Shaojian Gao, Tao Gong, Meriam Bahta, Abhilash Venugopalan, Xu Zhang, Udayan Guha
Summary: By studying the proteomics of EGFR TKI-resistant lung adenocarcinoma cells, we have identified a reduction in the HLA class I-presented immunopeptidome, downregulation of antigen presentation core complex and immunoproteasome, as well as differential alterations in certain components of the autophagy pathway. These findings reveal potential immune evasion mechanisms in osimertinib-resistant lung adenocarcinoma.
Article
Biochemical Research Methods
Jonathan W. Yewdell
Summary: In the past 35 years, significant progress has been made in the study of immunopeptidome, revealing the importance of short peptides binding to major histocompatibility complex in T-cell recognition. This article discusses the contribution of proteasome-mediated splicing to immunopeptidome and the recent findings linking immunopeptidome to the translatome revealed by ribosome profiling. It also emphasizes the need to attract talented young scientists to further advance antigen-processing research, which has seen remarkable success in T-cell-based cancer immunotherapy.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Oncology
Catherine M. Ade, Matthew J. Sporn, Sudipto Das, Zhiya Yu, Ken-ichi Hanada, Yue A. Qi, Tapan Maity, Xu Zhang, Udayan Guha, Thorkell Andresson, James C. Yang
Summary: This article introduces a method of using mass spectrometry to identify common tumor-specific neoepitopes derived from mutated oncogenes, and develop TCRs based on these data. The results of the study show that this method successfully identified precise neoepitopes derived from KRAS, EGFR, BRAF, and PIK3CA presented by HLA-A*03:01 and/or HLA-A*11:01 across multiple biological replicates.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2023)
Review
Immunology
Laura Santambrogio
Summary: Advances in the analysis of the MHC class II ligandome have increased our understanding of the factors that regulate the range and selection of presented peptides, and the landscape is highly sensitive to changes in protein composition.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Se-Jin Kim, Elham Karamooz
Summary: This review discusses the current understanding of MR1 and HLA-E antigen presentation in the context of Mycobacterium tuberculosis infection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Mepur H. Ravindranath, Narendranath M. Ravindranath, Senthamil R. Selvan, Fatiha El Hilali, Carly J. Amato-Menker, Edward J. Filippone
Summary: HLA-I molecules have different forms, including Face-1, Face-2, Face-3, and Face-4. Face-2 is expressed at low levels on normal cell surfaces but is upregulated on immune cells upon activation. It is associated with human cancer development and spontaneous arthritis.
Review
Immunology
Luca Hensen, Patricia T. Illing, Louise C. Rowntree, Jane Davies, Adrian Miller, Steven Y. C. Tong, Jennifer R. Habel, Carolien E. van de Sandt, Katie L. Flanagan, Anthony W. Purcell, Katherine Kedzierska, E. Bridie Clemens
Summary: This article discusses the complexity of CD8(+) T cell immune response and the use of immunopeptidomics approach to identify CD8(+) T cell epitopes restricted by specific HLA allotypes. The focus is on the identification of influenza-specific CD8(+) T cell epitopes in Indigenous Australians to improve vaccine coverage and efficacy.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Oncology
Georges Bedran, Hans-Christof Gasser, Kenneth Weke, Tongjie Wang, Dominika Bedran, Alexander Laird, Christophe Battail, Fabio Massimo Zanzotto, Catia Pesquita, Hakan Axelson, Ajitha Rajan, David J. Harrison, Aleksander Palkowski, Maciej Pawlik, Maciej Parys, Robert O'Neill, Paul M. Brennan, Stefan N. Symeonides, David R. Goodlett, Kevin Litchfield, Robin Fahraeus, Ted R. Hupp, Sachin Kote, Javier A. Alfaro
Summary: Using deep learning mass spectrometry, we developed a proteogenomic pipeline to discover noncanonical MHC class I-associated peptides (ncMAP) from noncoding regions. Analyzing data from 26 MHC class I immunopeptidomic studies across 11 different cancer types, we identified an atlas of 8,601 ncMAPs and suggested 17 cancer-selective ncMAPs as attractive therapeutic targets.
CANCER IMMUNOLOGY RESEARCH
(2023)
Article
Biochemical Research Methods
Laura C. Demmers, Wei Wu, Albert J. R. Heck
Summary: HLA molecules play critical roles in the adaptive immune system by presenting small peptides to signal cell health status to the immune system. This study investigated the adaptive response of a B lymphoblastic cell line to high temperature treatment, revealing potential preparations for immune-like responses in the absence of invading pathogenic peptides. The findings suggest intriguing temperature-sensitive adaptations in this particular B cell line.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Immunology
Gabriel Goncalves, Kerry A. Mullan, Divya Duscharla, Rochelle Ayala, Nathan P. Croft, Pouya Faridi, Anthony W. Purcell
Summary: Peptide vaccination is a promising strategy to induce T-cell mediated tumor killing. In this study, the effect of IFN gamma on TNBC cells was analyzed, revealing a significant remodeling of the immunopeptidome with increased diversity and abundance of peptides. The results suggest that cytokine stimulation can unveil a wider range of potential HLA-I and HLA-II vaccine targets, which has important implications for personalized cancer vaccination strategies.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Immunology
Patricia T. Illing, Andy van Hateren, Rachel Darley, Nathan P. Croft, Nicole A. Mifsud, Samuel King, Lyudmila Kostenko, Mandvi Bharadwaj, James McCluskey, Tim Elliott, Anthony W. Purcell
Summary: Abacavir hypersensitivity syndrome occurs in individuals with a specific gene expression, altering immune responses. Research shows that abacavir affects the assembly of HLA-B*57:01 complexes.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemical Research Methods
Yue Shen, Jerry M. Parks, Jeremy C. Smith
Summary: The HLA-Clus package provides a clustering method for HLA Class I alleles based on their 3D structural similarity. It can be used in HLA functional studies and disease association studies.
BMC BIOINFORMATICS
(2023)
Article
Oncology
Sofia Khazan-Kost, Gal Cafri, Dganit Melamed Kadosh, Navit Mooshayef, Sumit Chatterji, Dan Dominissini, Sigal Manor, Bracha Zisser, Limor Broday, Efrosiniia Talalai, Anat Shemer, Oranit Zadok, Efrat Ofek, Amir Onn, Arie Admon, Michael Peled
Summary: sHLA-peptide complexes in pleural effusions can serve as a source of biomarkers for malignant tumors and potential candidates for personalized immunotherapy.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2022)
Article
Hematology
Martin G. Klatt, Tao Dao, Zhiyuan Yang, Jianying Liu, Sung Soo Mun, Megan M. Dacek, Hanzhi Luo, Thomas J. Gardner, Christopher Bourne, Leila Peraro, Zita E. H. Aretz, Tanya Korontsvit, Michael Lau, Michael G. Kharas, Cheng Liu, David A. Scheinberg
Summary: Mass spectrometry identified a non-immunogenic HLA ligand as a target for CAR T-cell therapy, which showed broad effectiveness against multiple cancer types, particularly hematologic cancers, and had no toxic effects on healthy cells.
Article
Biochemistry & Molecular Biology
Smita S. Chandran, Jiaqi Ma, Martin G. Klatt, Friederike Dundar, Chaitanya Bandlamudi, Pedram Razavi, Hannah Y. Wen, Britta Weigelt, Paul Zumbo, Si Ning Fu, Lauren B. Banks, Fei Yi, Enric Vercher, Inaki Etxeberria, Watchain D. Bestman, Arnaud Da Cruz Paula, Ilinca S. Aricescu, Alexander Drilon, Doron Betel, David A. Scheinberg, Brian M. Baker, Christopher A. Klebanoff
Summary: Using a high-throughput platform combining single-cell transcriptomic and T cell receptor sequencing, researchers identified an immunogenic public neoantigen derived from mutant PIK3CA. The study further demonstrated that this neoantigen has therapeutic potential and can induce tumor regression when TCR-engineered T cells are adoptively transferred.
Article
Multidisciplinary Sciences
Tao Dao, Sungsoo Mun, Tatyana Korontsvit, Abdul G. Khan, Mary Ann Pohl, Thomas White, Martin G. Klatt, David Andrew, Ivo C. Lorenz, David A. Scheinberg
Summary: Although HPV virus vaccination is available, more effective treatments are needed for HPV-induced cancers. This study discovered TCR mimic monoclonal antibodies that could potentially serve as a therapeutic strategy for HPV-induced human cancers.
Article
Medicine, Research & Experimental
Tao Dao, Sung Soo Mun, Zaki Molvi, Tatyana Korontsvit, Martin G. Klatt, Abdul G. Khan, Elisabeth K. Nyakatura, Mary Ann Pohl, Thomas E. White, Paul J. Balderes, Ivo C. Lorenz, Richard J. O'Reilly, David A. Scheinberg
Summary: Phosphopeptides derived from dysregulated protein phosphorylation in cancer cells can be processed and presented by MHC class I and class II molecules, making them a potential source of widely expressed tumor-specific antigens. In this study, a TCR mimic antibody specific for a phosphopeptide derived from insulin receptor substrate 2 (pIRS2) presented by HLA-A*02:01 was developed. This antibody successfully recognized the pIRS2/HLA-A2 complex on tumor cell lines and exhibited tumor cell killing ability in a restricted manner. This is the first TCR mimic antibody targeting a phosphopeptide/MHC class I complex, suggesting its potential for clinical applications.
Article
Hematology
Christopher M. Bourne, Sung Soo Mun, Tao Dao, Zita E. H. Aretz, Zaki Molvi, Ron S. Gejman, Andrew Daman, Katsuyoshi Takata, Christian Steidl, Martin G. Klatt, David A. Scheinberg
Summary: The downregulation of MHC expression in DLBCLs can be restored by epigenetic drug treatment and IFN-γ, and this treatment expands the repertoire of MHC ligands presented on DLBCLs, allowing the identification of new potential immunotherapy targets.
Editorial Material
Oncology
Christopher M. Bourne, Henry J. Henderson, Elshaddai White, Julia Morris, Mamadou A. Bah, Rhea Harewood, Stephanie Pierre, Tanimola Martins, Tumisang Ntereke, Briana White, Sigourney Bonner
Article
Oncology
Sung Soo Mun, Jeremy Meyerberg, Leila Peraro, Tatyana Korontsvit, Thomas Gardner, Manish Malviya, Chrisann Kyi, Roisin E. O'Cearbhaill, Cheng Liu, Tao Dao, David A. Scheinberg
Summary: This study describes an engineered cell with dual targeting and orthogonal cytotoxic modalities to overcome the limitations of CAR T cell therapy in epithelial ovarian cancer. The engineered cell showed enhanced anticancer activity against cancer cells with low Muc16 expression, presenting a promising strategy to overcome resistance to CAR T cell therapy.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2023)
Article
Oncology
Zaki Molvi, Martin G. Klatt, Tao Dao, Jessica Urraca, David A. Scheinberg, Richard J. O'Reilly
Summary: This study identified phosphopeptides presented by different alleles on tumors, which could be targeted for cancer immunotherapy, but the immunogenicity of these phosphopeptides is not consistent. While phosphopeptides presented by HLA-A*02:01 and A*11:01 were consistently immunogenic, those presented by HLA-A*03:01 and C*07:01, although properly presented, were not. This indicates the need to consider allele-specific differences in phosphopeptide-targeted immunotherapies to address a broader patient population.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2023)
Article
Medicine, Research & Experimental
Katsuyoshi Takata, Lauren C. Chong, Daisuke Ennishi, Tomohiro Aoki, Michael Yu Li, Avinash Thakur, Shannon Healy, Elena Vigano, Tao Dao, Daniel Kwon, Gerben Duns, Julie S. Nielsen, Susana Ben-Neriah, Ethan Tse, Stacy S. Hung, Merrill Boyle, Sung Soo Mun, Christopher M. Bourne, Bruce Woolcock, Adele Telenius, Makoto Kishida, Shinya Rai, Allen W. Zhang, Ali Bashashati, Saeed Saberi, Gianluca D'Antonio, Brad H. Nelson, Sohrab P. Shah, Pamela A. Hoodless, Ari M. Melnick, Randy D. Gascoyne, Joseph M. Connors, David A. Scheinberg, Wendy Beguelin, David W. Scott, Christian Steidl
Summary: PRAME is a key player in the cancer testis antigen family, with deletions in DLBCL being associated with poor outcome, immune escape, and cold tumor microenvironments. Additionally, PRAME downregulation is linked to EZH2 mutations, with PRAME directly interacting with EZH2 as a negative regulator.
JOURNAL OF CLINICAL INVESTIGATION
(2022)