1
|
Aparicio B, Theunissen P, Hervas-Stubbs S, Fortes P, Sarobe P. Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies. Hum Vaccin Immunother 2024; 20:2303799. [PMID: 38346926 PMCID: PMC10863374 DOI: 10.1080/21645515.2024.2303799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/06/2024] [Indexed: 02/15/2024] Open
Abstract
Efficacy of cancer immunotherapies relies on correct recognition of tumor antigens by lymphocytes, eliciting thus functional responses capable of eliminating tumor cells. Therefore, important efforts have been carried out in antigen identification, with the aim of understanding mechanisms of response to immunotherapy and to design safer and more efficient strategies. In addition to classical tumor-associated antigens identified during the last decades, implementation of next-generation sequencing methodologies is enabling the identification of neoantigens (neoAgs) arising from mutations, leading to the development of new neoAg-directed therapies. Moreover, there are numerous non-classical tumor antigens originated from other sources and identified by new methodologies. Here, we review the relevance of neoAgs in different immunotherapies and the results obtained by applying neoAg-based strategies. In addition, the different types of non-classical tumor antigens and the best approaches for their identification are described. This will help to increase the spectrum of targetable molecules useful in cancer immunotherapies.
Collapse
Affiliation(s)
- Belen Aparicio
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Patrick Theunissen
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Sandra Hervas-Stubbs
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Puri Fortes
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Spain
| | - Pablo Sarobe
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| |
Collapse
|
2
|
Hofman DA, Prensner JR, van Heesch S. Microproteins in cancer: identification, biological functions, and clinical implications. Trends Genet 2024:S0168-9525(24)00211-7. [PMID: 39379206 DOI: 10.1016/j.tig.2024.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 08/19/2024] [Accepted: 09/17/2024] [Indexed: 10/10/2024]
Abstract
Cancer continues to be a major global health challenge, accounting for 10 million deaths annually worldwide. Since the inception of genome-wide cancer sequencing studies 20 years ago, a core set of ~700 oncogenes and tumor suppressor genes has become the basis for cancer research. However, this research has been based largely on an understanding that the human genome encodes ~19 500 protein-coding genes. Complementing this genomic landscape, recent advances have described numerous microproteins which are now poised to redefine our understanding of oncogenic processes and open new avenues for therapeutic intervention. This review explores the emerging evidence for microprotein involvement in cancer mechanisms and discusses potential therapeutic applications, with an emphasis on highlighting recent advances in the field.
Collapse
Affiliation(s)
- Damon A Hofman
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584, CS, Utrecht, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - John R Prensner
- Department of Pediatrics, Division of Pediatric Hematology/Oncology and Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584, CS, Utrecht, The Netherlands; Oncode Institute, Utrecht, The Netherlands.
| |
Collapse
|
3
|
Wohlfarth J, Kosnopfel C, Faber D, Berthold M, Siedel C, Bernhardt M, Schlosser A, Aprati T, Liu D, Schrama D, Houben R, Schadendorf D, Goebeler M, Meierjohann S, Schilling B. Loss of p14 diminishes immunogenicity in melanoma via non-canonical Wnt signaling by reducing the peptide surface density. Mol Oncol 2024; 18:2449-2470. [PMID: 38807304 PMCID: PMC11459041 DOI: 10.1002/1878-0261.13660] [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: 01/03/2024] [Revised: 03/04/2024] [Accepted: 04/26/2024] [Indexed: 05/30/2024] Open
Abstract
Immunotherapy has achieved tremendous success in melanoma. However, only around 50% of advanced melanoma patients benefit from immunotherapy. Cyclin-dependent kinase inhibitor 2A (CDKN2A), encoding the two tumor-suppressor proteins p14ARF and p16INK4a, belongs to the most frequently inactivated gene loci in melanoma and leads to decreased T cell infiltration. While the role of p16INK4a has been extensively investigated, knowledge about p14ARF in melanoma is scarce. In this study, we elucidate the impact of reduced p14ARF expression on melanoma immunogenicity. Knockdown of p14ARF in melanoma cell lines diminished their recognition and killing by melanoma differentiation antigen (MDA)-specific T cells. Resistance was caused by a reduction of the peptide surface density of presented MDAs. Immunopeptidomic analyses revealed that antigen presentation via human leukocyte antigen class I (HLA-I) molecules was enhanced upon p14ARF downregulation in general, but absolute and relative expression of cognate peptides was decreased. However, this phenotype is associated with a favorable outcome for melanoma patients. Limiting Wnt5a signaling reverted this phenotype, suggesting an involvement of non-canonical Wnt signaling. Taken together, our data indicate a new mechanism limiting MDA-specific T cell responses by decreasing both absolute and relative MDA-peptide presentation in melanoma.
Collapse
Affiliation(s)
- Jonas Wohlfarth
- Department of Dermatology, Venereology and AllergologyUniversity Hospital WürzburgGermany
| | - Corinna Kosnopfel
- Department of Dermatology, Venereology and AllergologyUniversity Hospital WürzburgGermany
| | - Dominic Faber
- Department of Dermatology, Venereology and AllergologyUniversity Hospital WürzburgGermany
| | - Marion Berthold
- Department of Dermatology, Venereology and AllergologyUniversity Hospital WürzburgGermany
| | - Claudia Siedel
- Department of Dermatology, Venereology and AllergologyUniversity Hospital WürzburgGermany
| | - Melissa Bernhardt
- Rudolf‐Virchow‐Centre for Integrative and Translational BioimagingUniversity of WürzburgGermany
| | - Andreas Schlosser
- Rudolf‐Virchow‐Centre for Integrative and Translational BioimagingUniversity of WürzburgGermany
| | - Tyler Aprati
- Dana‐Farber Cancer InstituteBostonMAUSA
- Harvard Medical SchoolCambridgeMAUSA
- Broad Institute of Harvard and MITCambridgeMAUSA
| | - David Liu
- Dana‐Farber Cancer InstituteBostonMAUSA
- Harvard Medical SchoolCambridgeMAUSA
- Broad Institute of Harvard and MITCambridgeMAUSA
| | - David Schrama
- Department of Dermatology, Venereology and AllergologyUniversity Hospital WürzburgGermany
| | - Roland Houben
- Department of Dermatology, Venereology and AllergologyUniversity Hospital WürzburgGermany
| | - Dirk Schadendorf
- Department of Dermatology, Comprehensive Cancer Center (Westdeutsches Tumorzentrum)German Cancer Consortium (DKTK, partner site Essen) and University Hospital EssenGermany
| | - Matthias Goebeler
- Department of Dermatology, Venereology and AllergologyUniversity Hospital WürzburgGermany
| | | | - Bastian Schilling
- Department of Dermatology, Venereology and AllergologyUniversity Hospital WürzburgGermany
| |
Collapse
|
4
|
Deutsch EW, Kok LW, Mudge JM, Ruiz-Orera J, Fierro-Monti I, Sun Z, Abelin JG, Alba MM, Aspden JL, Bazzini AA, Bruford EA, Brunet MA, Calviello L, Carr SA, Carvunis AR, Chothani S, Clauwaert J, Dean K, Faridi P, Frankish A, Hubner N, Ingolia NT, Magrane M, Martin MJ, Martinez TF, Menschaert G, Ohler U, Orchard S, Rackham O, Roucou X, Slavoff SA, Valen E, Wacholder A, Weissman JS, Wu W, Xie Z, Choudhary J, Bassani-Sternberg M, Vizcaíno JA, Ternette N, Moritz RL, Prensner JR, van Heesch S. High-quality peptide evidence for annotating non-canonical open reading frames as human proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.612016. [PMID: 39314370 PMCID: PMC11419116 DOI: 10.1101/2024.09.09.612016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
A major scientific drive is to characterize the protein-coding genome as it provides the primary basis for the study of human health. But the fundamental question remains: what has been missed in prior genomic analyses? Over the past decade, the translation of non-canonical open reading frames (ncORFs) has been observed across human cell types and disease states, with major implications for proteomics, genomics, and clinical science. However, the impact of ncORFs has been limited by the absence of a large-scale understanding of their contribution to the human proteome. Here, we report the collaborative efforts of stakeholders in proteomics, immunopeptidomics, Ribo-seq ORF discovery, and gene annotation, to produce a consensus landscape of protein-level evidence for ncORFs. We show that at least 25% of a set of 7,264 ncORFs give rise to translated gene products, yielding over 3,000 peptides in a pan-proteome analysis encompassing 3.8 billion mass spectra from 95,520 experiments. With these data, we developed an annotation framework for ncORFs and created public tools for researchers through GENCODE and PeptideAtlas. This work will provide a platform to advance ncORF-derived proteins in biomedical discovery and, beyond humans, diverse animals and plants where ncORFs are similarly observed.
Collapse
Affiliation(s)
- Eric W Deutsch
- Institute for Systems Biology (ISB), Seattle, WA, 98109, USA
| | - Leron W Kok
- Princess Máxima Center for Pediatric Oncology, Utrecht, 3584 CS, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, 13125, Germany
| | - Ivo Fierro-Monti
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Zhi Sun
- Institute for Systems Biology (ISB), Seattle, WA, 98109, USA
| | | | - M Mar Alba
- Hospital del Mar Research Institute, Barcelona, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Julie L Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Elspeth A Bruford
- HUGO Gene Nomenclature Committee (HGNC), Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Marie A Brunet
- Pediatrics Department, University of Sherbrooke, Sherbrooke, Québec, Canada
- Centre de Recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, Québec, Canada
| | | | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Sonia Chothani
- Centre for Computational Biology and Program in Cardiovascular and Metabolic Disorders, Duke-NUS (National University of Singapore) Medical School, Singapore
| | - Jim Clauwaert
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kellie Dean
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pouya Faridi
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Monash Proteomics & Metabolomics Platform, Department of Medicine, School of Clinical Sciences, Monash University, Clayton, VIC, Australia
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, 13125, Germany
- Charité-Universitätsmedizin Berlin, Berlin, 10117, Germany
- Helmholtz-Institute for Translational AngioCardioScience (HI-TAC) of the Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) at Heidelberg University, Heidelberg, 69117, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Berlin, Berlin, 13347, Germany
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, Center for Computational Biology, University of California, Berkeley, Berkeley, CA, 94720-3202, USA
| | - Michele Magrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Maria Jesus Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Thomas F Martinez
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92617, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92617, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92617, USA
| | - Gerben Menschaert
- Biobix, Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Uwe Ohler
- Department of Biology, Humboldt University Berlin, Berlin, 10117, Germany
- Berlin Institute of Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, 10115, Germany
| | - Sandra Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | | | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Sarah A Slavoff
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, 06516, USA
| | - Eivind Valen
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Aaron Wacholder
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02138, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Wei Wu
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Pharmacy & Pharmaceutical sciences, National University of Singapore (NUS), Singapore
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jyoti Choudhary
- Functional Proteomics Group, Institute of Cancer Research, Chester Betty Labs, London, SW3 6JB, UK
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, 1005, Switzerland
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Lausanne, 1005, Switzerland
- Agora Cancer Research Centre, Lausanne, 1011, Switzerland
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Nicola Ternette
- School of Life Sciences, Division Cell Signalling and Immunology, University of Dundee, Dundee, DD1 5EH, UK
- Centre for Immuno-Oncology, University of Oxford, Oxford, OX37DQ, UK
| | - Robert L Moritz
- Institute for Systems Biology (ISB), Seattle, WA, 98109, USA
| | - John R Prensner
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Utrecht, 3584 CS, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| |
Collapse
|
5
|
Nichols C, Do-Thi VA, Peltier DC. Noncanonical microprotein regulation of immunity. Mol Ther 2024; 32:2905-2929. [PMID: 38734902 PMCID: PMC11403233 DOI: 10.1016/j.ymthe.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/19/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024] Open
Abstract
The immune system is highly regulated but, when dysregulated, suboptimal protective or overly robust immune responses can lead to immune-mediated disorders. The genetic and molecular mechanisms of immune regulation are incompletely understood, impeding the development of more precise diagnostics and therapeutics for immune-mediated disorders. Recently, thousands of previously unrecognized noncanonical microprotein genes encoded by small open reading frames have been identified. Many of these microproteins perform critical functions, often in a cell- and context-specific manner. Several microproteins are now known to regulate immunity; however, the vast majority are uncharacterized. Therefore, illuminating what is often referred to as the "dark proteome," may present opportunities to tune immune responses more precisely. Here, we review noncanonical microprotein biology, highlight recently discovered examples regulating immunity, and discuss the potential and challenges of modulating dysregulated immune responses by targeting microproteins.
Collapse
Affiliation(s)
- Cydney Nichols
- Morris Green Scholars Program, Department of Pediatrics, Riley Hospital for Children, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Van Anh Do-Thi
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Daniel C Peltier
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| |
Collapse
|
6
|
Camarena ME, Theunissen P, Ruiz M, Ruiz-Orera J, Calvo-Serra B, Castelo R, Castro C, Sarobe P, Fortes P, Perera-Bel J, Albà MM. Microproteins encoded by noncanonical ORFs are a major source of tumor-specific antigens in a liver cancer patient meta-cohort. SCIENCE ADVANCES 2024; 10:eadn3628. [PMID: 38985879 PMCID: PMC11235171 DOI: 10.1126/sciadv.adn3628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
The expression of tumor-specific antigens during cancer progression can trigger an immune response against the tumor. Here, we investigate if microproteins encoded by noncanonical open reading frames (ncORFs) are a relevant source of tumor-specific antigens. We analyze RNA sequencing data from 117 hepatocellular carcinoma (HCC) tumors and matched healthy tissue together with ribosome profiling and immunopeptidomics data. Combining human leukocyte antigen-epitope binding predictions and experimental validation experiments, we conclude that around 40% of the tumor-specific antigens in HCC are likely to be derived from ncORFs, including two peptides that can trigger an immune response in humanized mice. We identify a subset of 33 tumor-specific long noncoding RNAs expressing novel cancer antigens shared by more than 10% of the HCC samples analyzed, which, when combined, cover a large proportion of the patients. The results of the study open avenues for extending the range of anticancer vaccines.
Collapse
Affiliation(s)
| | - Patrick Theunissen
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Marta Ruiz
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Jorge Ruiz-Orera
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Beatriz Calvo-Serra
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Robert Castelo
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carla Castro
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Pablo Sarobe
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
- Cancer Clinic University of Navarra (CCUN), Pamplona, Spain
| | - Puri Fortes
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
- Cancer Clinic University of Navarra (CCUN), Pamplona, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Madrid, Spain
| | | | - M Mar Albà
- Hospital del Mar Research Institute, Barcelona, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| |
Collapse
|
7
|
Gerke C, Bauersfeld L, Schirmeister I, Mireisz CNM, Oberhardt V, Mery L, Wu D, Jürges CS, Spaapen RM, Mussolino C, Le-Trilling VTK, Trilling M, Dölken L, Paster W, Erhard F, Hofmann M, Schlosser A, Hengel H, Momburg F, Halenius A. Multimodal HLA-I genotype regulation by human cytomegalovirus US10 and resulting surface patterning. eLife 2024; 13:e85560. [PMID: 38900146 PMCID: PMC11189632 DOI: 10.7554/elife.85560] [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: 12/13/2022] [Accepted: 05/14/2024] [Indexed: 06/21/2024] Open
Abstract
Human leucocyte antigen class I (HLA-I) molecules play a central role for both NK and T-cell responses that prevent serious human cytomegalovirus (HCMV) disease. To create opportunities for viral spread, several HCMV-encoded immunoevasins employ diverse strategies to target HLA-I. Among these, the glycoprotein US10 is so far insufficiently studied. While it was reported that US10 interferes with HLA-G expression, its ability to manipulate classical HLA-I antigen presentation remains unknown. In this study, we demonstrate that US10 recognizes and binds to all HLA-I (HLA-A, -B, -C, -E, -G) heavy chains. Additionally, impaired recruitment of HLA-I to the peptide loading complex was observed. Notably, the associated effects varied significantly dependending on HLA-I genotype and allotype: (i) HLA-A molecules evaded downregulation by US10, (ii) tapasin-dependent HLA-B molecules showed impaired maturation and cell surface expression, and (iii) β2m-assembled HLA-C, in particular HLA-C*05:01 and -C*12:03, and HLA-G were strongly retained in complex with US10 in the endoplasmic reticulum. These genotype-specific effects on HLA-I were confirmed through unbiased HLA-I ligandome analyses. Furthermore, in HCMV-infected fibroblasts inhibition of overlapping US10 and US11 transcription had little effect on HLA-A, but induced HLA-B antigen presentation. Thus, the US10-mediated impact on HLA-I results in multiple geno- and allotypic effects in a so far unparalleled and multimodal manner.
Collapse
Affiliation(s)
- Carolin Gerke
- Institute of Virology, Medical Center University of FreiburgFreiburgGermany
- Faculty of Medicine, University of FreiburgFreiburgGermany
- Spemann Graduate School of Biology and Medicine (SGBM), University of FreiburgFreiburgGermany
- Faculty of Biology, University of FreiburgFreiburgGermany
| | - Liane Bauersfeld
- Institute of Virology, Medical Center University of FreiburgFreiburgGermany
- Faculty of Medicine, University of FreiburgFreiburgGermany
| | - Ivo Schirmeister
- Institute of Virology, Medical Center University of FreiburgFreiburgGermany
- Faculty of Medicine, University of FreiburgFreiburgGermany
| | - Chiara Noemi-Marie Mireisz
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of WürzburgWürzburgGermany
| | - Valerie Oberhardt
- Faculty of Medicine, University of FreiburgFreiburgGermany
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Medical Center University of FreiburgFreiburgGermany
| | - Lea Mery
- Institute of Virology, Medical Center University of FreiburgFreiburgGermany
- Faculty of Medicine, University of FreiburgFreiburgGermany
| | - Di Wu
- Institute of Virology, Medical Center University of FreiburgFreiburgGermany
- Faculty of Medicine, University of FreiburgFreiburgGermany
| | | | - Robbert M Spaapen
- Department of Immunopathology, Sanquin ResearchAmsterdamNetherlands
- Landsteiner Laboratory, Amsterdam UMC, University of AmsterdamAmsterdamNetherlands
| | - Claudio Mussolino
- Faculty of Medicine, University of FreiburgFreiburgGermany
- Institute for Transfusion Medicine and Gene Therapy, Medical Center University of FreiburgFreiburgGermany
- Center for Chronic Immunodeficiency, Medical Center University of FreiburgFreiburgGermany
| | | | - Mirko Trilling
- Institute for Virology, University Hospital Essen, University of Duisburg-EssenEssenGermany
- Institute for the Research on HIV and AIDS-associated Diseases, University Hospital EssenEssenGermany
| | - Lars Dölken
- Institute for Virology and Immunobiology, University of WürzburgWürzburgGermany
- Institute of Virology, Hannover Medical SchoolHannoverGermany
| | - Wolfgang Paster
- St. Anna Children’s Cancer Research Institute (CCRI)ViennaAustria
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of WürzburgWürzburgGermany
| | - Maike Hofmann
- Faculty of Medicine, University of FreiburgFreiburgGermany
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Medical Center University of FreiburgFreiburgGermany
| | - Andreas Schlosser
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of WürzburgWürzburgGermany
| | - Hartmut Hengel
- Faculty of Medicine, University of FreiburgFreiburgGermany
| | - Frank Momburg
- Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center, National Center for Tumor Diseases (NCT), Heidelberg University HospitalHeidelbergGermany
| | - Anne Halenius
- Institute of Virology, Medical Center University of FreiburgFreiburgGermany
- Faculty of Medicine, University of FreiburgFreiburgGermany
| |
Collapse
|
8
|
Santamorena MM, Tischer-Zimmermann S, Bonifacius A, Mireisz CNM, Costa B, Khan F, Kulkarni U, Lauruschkat CD, Sampaio KL, Stripecke R, Blasczyk R, Maecker-Kolhoff B, Kraus S, Schlosser A, Cicin-Sain L, Kalinke U, Eiz-Vesper B. Engineered HCMV-infected APCs enable the identification of new immunodominant HLA-restricted epitopes of anti-HCMV T-cell immunity. HLA 2024; 103:e15541. [PMID: 38923358 DOI: 10.1111/tan.15541] [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: 10/27/2023] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 06/28/2024]
Abstract
Complications due to HCMV infection or reactivation remain a challenging clinical problem in immunocompromised patients, mainly due to insufficient or absent T-cell functionality. Knowledge of viral targets is crucial to improve monitoring of high-risk patients and optimise antiviral T-cell therapy. To expand the epitope spectrum, genetically-engineered dendritic cells (DCs) and fibroblasts were designed to secrete soluble (s)HLA-A*11:01 and infected with an HCMV mutant lacking immune evasion molecules (US2-6 + 11). More than 700 HLA-A*11:01-restricted epitopes, including more than 50 epitopes derived from a broad range of HCMV open-reading-frames (ORFs) were identified by mass spectrometry and screened for HLA-A*11:01-binding using established prediction tools. The immunogenicity of the 24 highest scoring new candidates was evaluated in vitro in healthy HLA-A*11:01+/HCMV+ donors. Thus, four subdominant epitopes and one immunodominant epitope, derived from the anti-apoptotic protein UL36 and ORFL101C (A11SAL), were identified. Their HLA-A*11:01 complex stability was verified in vitro. In depth analyses revealed highly proliferative and cytotoxic memory T-cell responses against A11SAL, with T-cell responses comparable to the immunodominant HLA-A*02:01-restricted HCMVpp65NLV epitope. A11SAL-specific T cells were also detectable in vivo in immunosuppressed transplant patients and shown to be effective in an in vitro HCMV-infection model, suggesting their crucial role in inhibiting viral replication and improvement of patient's outcome. The developed in vitro pipeline is the first to utilise genetically-engineered DCs to identify naturally presented immunodominant HCMV-derived epitopes. It therefore offers advantages over in silico predictions, is transferable to other HLA alleles, and will significantly expand the repertoire of viral targets to improve therapeutic options.
Collapse
Affiliation(s)
- Maria Michela Santamorena
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School (MHH), Hannover, Germany
| | - Sabine Tischer-Zimmermann
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School (MHH), Hannover, Germany
| | - Agnes Bonifacius
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School (MHH), Hannover, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
| | - Chiara Noemi-Marie Mireisz
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Wuerzburg, Wuerzburg, Germany
| | - Bibiana Costa
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Fawad Khan
- Immune Ageing and Chronic Infection, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Upasana Kulkarni
- Immune Ageing and Chronic Infection, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | | | - Renata Stripecke
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Center for Molecular Medicine Cologne (CMMC), Institute of Translational Immuno-oncology, Cologne, Germany
- German Center for Infections Research (DZIF) Bonn-Cologne, Cologne, Germany
| | - Rainer Blasczyk
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School (MHH), Hannover, Germany
| | - Britta Maecker-Kolhoff
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
- German Center for Infections Research (DZIF) Bonn-Cologne, Cologne, Germany
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Sabrina Kraus
- Department of Internal Medicine II, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Wuerzburg, Wuerzburg, Germany
| | - Luka Cicin-Sain
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
- Immune Ageing and Chronic Infection, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Cluster of Excellence - Resolving Infection Susceptibility (RESIST, EXC 2155), Hannover Medical School, Hannover, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Cluster of Excellence - Resolving Infection Susceptibility (RESIST, EXC 2155), Hannover Medical School, Hannover, Germany
| | - Britta Eiz-Vesper
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School (MHH), Hannover, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
| |
Collapse
|
9
|
Adams C, Gabriel W, Laukens K, Picciani M, Wilhelm M, Bittremieux W, Boonen K. Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF. Nat Commun 2024; 15:3956. [PMID: 38730277 PMCID: PMC11087512 DOI: 10.1038/s41467-024-48322-0] [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: 07/17/2023] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
Immunopeptidomics is crucial for immunotherapy and vaccine development. Because the generation of immunopeptides from their parent proteins does not adhere to clear-cut rules, rather than being able to use known digestion patterns, every possible protein subsequence within human leukocyte antigen (HLA) class-specific length restrictions needs to be considered during sequence database searching. This leads to an inflation of the search space and results in lower spectrum annotation rates. Peptide-spectrum match (PSM) rescoring is a powerful enhancement of standard searching that boosts the spectrum annotation performance. We analyze 302,105 unique synthesized non-tryptic peptides from the ProteomeTools project on a timsTOF-Pro to generate a ground-truth dataset containing 93,227 MS/MS spectra of 74,847 unique peptides, that is used to fine-tune the deep learning-based fragment ion intensity prediction model Prosit. We demonstrate up to 3-fold improvement in the identification of immunopeptides, as well as increased detection of immunopeptides from low input samples.
Collapse
Affiliation(s)
- Charlotte Adams
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Wassim Gabriel
- Computational Mass Spectrometry, Technical University of Munich, 85354, Freising, Germany
| | - Kris Laukens
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Mario Picciani
- Computational Mass Spectrometry, Technical University of Munich, 85354, Freising, Germany
| | - Mathias Wilhelm
- Computational Mass Spectrometry, Technical University of Munich, 85354, Freising, Germany
- Munich Data Science Institute, Technical University of Munich, 85748, Garching, Germany
| | - Wout Bittremieux
- Department of Computer Science, University of Antwerp, Antwerp, Belgium.
| | - Kurt Boonen
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
- Sustainable Health Department, Flemish Institute for Technological Research (VITO), Antwerp, Belgium.
| |
Collapse
|
10
|
Choi S, Paek E. pXg: Comprehensive Identification of Noncanonical MHC-I-Associated Peptides From De Novo Peptide Sequencing Using RNA-Seq Reads. Mol Cell Proteomics 2024; 23:100743. [PMID: 38403075 PMCID: PMC10979277 DOI: 10.1016/j.mcpro.2024.100743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 02/27/2024] Open
Abstract
Discovering noncanonical peptides has been a common application of proteogenomics. Recent studies suggest that certain noncanonical peptides, known as noncanonical major histocompatibility complex-I (MHC-I)-associated peptides (ncMAPs), that bind to MHC-I may make good immunotherapeutic targets. De novo peptide sequencing is a great way to find ncMAPs since it can detect peptide sequences from their tandem mass spectra without using any sequence databases. However, this strategy has not been widely applied for ncMAP identification because there is not a good way to estimate its false-positive rates. In order to completely and accurately identify immunopeptides using de novo peptide sequencing, we describe a unique pipeline called proteomics X genomics. In contrast to current pipelines, it makes use of genomic data, RNA-Seq abundance and sequencing quality, in addition to proteomic features to increase the sensitivity and specificity of peptide identification. We show that the peptide-spectrum match quality and genetic traits have a clear relationship, showing that they can be utilized to evaluate peptide-spectrum matches. From 10 samples, we found 24,449 canonical MHC-I-associated peptides and 956 ncMAPs by using a target-decoy competition. Three hundred eighty-seven ncMAPs and 1611 canonical MHC-I-associated peptides were new identifications that had not yet been published. We discovered 11 ncMAPs produced from a squirrel monkey retrovirus in human cell lines in addition to the two ncMAPs originating from a complementarity determining region 3 in an antibody thanks to the unrestricted search space assumed by de novo sequencing. These entirely new identifications show that proteomics X genomics can make the most of de novo peptide sequencing's advantages and its potential use in the search for new immunotherapeutic targets.
Collapse
Affiliation(s)
- Seunghyuk Choi
- Department of Computer Science, Hanyang University, Seoul, Republic of Korea
| | - Eunok Paek
- Department of Computer Science, Hanyang University, Seoul, Republic of Korea; Institute for Artificial Intelligence Research, Hanyang University, Seoul, Republic of Korea.
| |
Collapse
|
11
|
Minegishi Y, Haga Y, Ueda K. Emerging potential of immunopeptidomics by mass spectrometry in cancer immunotherapy. Cancer Sci 2024; 115:1048-1059. [PMID: 38382459 PMCID: PMC11007014 DOI: 10.1111/cas.16118] [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: 12/18/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
With significant advances in analytical technologies, research in the field of cancer immunotherapy, such as adoptive T cell therapy, cancer vaccine, and immune checkpoint blockade (ICB), is currently gaining tremendous momentum. Since the efficacy of cancer immunotherapy is recognized only by a minority of patients, more potent tumor-specific antigens (TSAs, also known as neoantigens) and predictive markers for treatment response are of great interest. In cancer immunity, immunopeptides, presented by human leukocyte antigen (HLA) class I, play a role as initiating mediators of immunogenicity. The latest advancement in the interdisciplinary multiomics approach has rapidly enlightened us about the identity of the "dark matter" of cancer and the associated immunopeptides. In this field, mass spectrometry (MS) is a viable option to select because of the naturally processed and actually presented TSA candidates in order to grasp the whole picture of the immunopeptidome. In the past few years the search space has been enlarged by the multiomics approach, the sensitivity of mass spectrometers has been improved, and deep/machine-learning-supported peptide search algorithms have taken immunopeptidomics to the next level. In this review, along with the introduction of key technical advancements in immunopeptidomics, the potential and further directions of immunopeptidomics will be reviewed from the perspective of cancer immunotherapy.
Collapse
Affiliation(s)
- Yuriko Minegishi
- Cancer Proteomics Group, Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Yoshimi Haga
- Cancer Proteomics Group, Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
| |
Collapse
|
12
|
Manoutcharian K, Gevorkian G. Are we getting closer to a successful neoantigen cancer vaccine? Mol Aspects Med 2024; 96:101254. [PMID: 38354548 DOI: 10.1016/j.mam.2024.101254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
Although significant advances in immunotherapy have revolutionized the treatment of many cancer types over the past decade, the field of vaccine therapy, an important component of cancer immunotherapy, despite decades-long intense efforts, is still transmitting signals of promises and awaiting strong data on efficacy to proceed with regulatory approval. The field of cancer vaccines faces standard challenges, such as tumor-induced immunosuppression, immune response in inhibitory tumor microenvironment (TME), intratumor heterogeneity (ITH), permanently evolving cancer mutational landscape leading to neoantigens, and less known obstacles: neoantigen gain/loss upon immunotherapy, the timing and speed of appearance of neoantigens and responding T cell clonotypes and possible involvement of immune interference/heterologous immunity, in the complex interplay between evolving tumor epitopes and the immune system. In this review, we discuss some key issues related to challenges hampering the development of cancer vaccines, along with the current approaches focusing on neoantigens. We summarize currently well-known ideas/rationales, thus revealing the need for alternative vaccine approaches. Such a discussion should stimulate vaccine researchers to apply out-of-box, unconventional thinking in search of new avenues to deal with critical, often yet unaddressed challenges on the road to a new generation of therapeutics and vaccines.
Collapse
Affiliation(s)
- Karen Manoutcharian
- Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico (UNAM), CDMX, Apartado Postal 70228, Cuidad Universitaria, Mexico DF, CP, 04510, Mexico.
| | - Goar Gevorkian
- Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico (UNAM), CDMX, Apartado Postal 70228, Cuidad Universitaria, Mexico DF, CP, 04510, Mexico.
| |
Collapse
|
13
|
Ilangumaran S, Gui Y, Shukla A, Ramanathan S. SOCS1 expression in cancer cells: potential roles in promoting antitumor immunity. Front Immunol 2024; 15:1362224. [PMID: 38415248 PMCID: PMC10897024 DOI: 10.3389/fimmu.2024.1362224] [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: 12/27/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024] Open
Abstract
Suppressor of cytokine signaling 1 (SOCS1) is a potent regulator immune cell responses and a proven tumor suppressor. Inhibition of SOCS1 in T cells can boost antitumor immunity, whereas its loss in tumor cells increases tumor aggressivity. Investigations into the tumor suppression mechanisms so far focused on tumor cell-intrinsic functions of SOCS1. However, it is possible that SOCS1 expression in tumor cells also regulate antitumor immune responses in a cell-extrinsic manner via direct and indirect mechanisms. Here, we discuss the evidence supporting the latter, and its implications for antitumor immunity.
Collapse
Affiliation(s)
- Subburaj Ilangumaran
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | | | | | | |
Collapse
|
14
|
Soh WT, Roetschke HP, Cormican JA, Teo BF, Chiam NC, Raabe M, Pflanz R, Henneberg F, Becker S, Chari A, Liu H, Urlaub H, Liepe J, Mishto M. Protein degradation by human 20S proteasomes elucidates the interplay between peptide hydrolysis and splicing. Nat Commun 2024; 15:1147. [PMID: 38326304 PMCID: PMC10850103 DOI: 10.1038/s41467-024-45339-3] [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: 01/17/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
If and how proteasomes catalyze not only peptide hydrolysis but also peptide splicing is an open question that has divided the scientific community. The debate has so far been based on immunopeptidomics, in vitro digestions of synthetic polypeptides as well as ex vivo and in vivo experiments, which could only indirectly describe proteasome-catalyzed peptide splicing of full-length proteins. Here we develop a workflow-and cognate software - to analyze proteasome-generated non-spliced and spliced peptides produced from entire proteins and apply it to in vitro digestions of 15 proteins, including well-known intrinsically disordered proteins such as human tau and α-Synuclein. The results confirm that 20S proteasomes produce a sizeable variety of cis-spliced peptides, whereas trans-spliced peptides are a minority. Both peptide hydrolysis and splicing produce peptides with well-defined characteristics, which hint toward an intricate regulation of both catalytic activities. At protein level, both non-spliced and spliced peptides are not randomly localized within protein sequences, but rather concentrated in hotspots of peptide products, in part driven by protein sequence motifs and proteasomal preferences. At sequence level, the different peptide sequence preference of peptide hydrolysis and peptide splicing suggests a competition between the two catalytic activities of 20S proteasomes during protein degradation.
Collapse
Affiliation(s)
- Wai Tuck Soh
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Hanna P Roetschke
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL, London, UK
- Research Group of Molecular Immunology, Francis Crick Institute, NW1 1AT, London, UK
| | - John A Cormican
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Bei Fang Teo
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL, London, UK
- Research Group of Molecular Immunology, Francis Crick Institute, NW1 1AT, London, UK
- Immunology Programme, Life Sciences Institute; Immunology Translational Research Program and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Nyet Cheng Chiam
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Monika Raabe
- Research Group of Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Ralf Pflanz
- Research Group of Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Fabian Henneberg
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Ashwin Chari
- Research Group of Structural Biochemistry and Mechanisms, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Haiyan Liu
- Immunology Programme, Life Sciences Institute; Immunology Translational Research Program and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Henning Urlaub
- Research Group of Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Juliane Liepe
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany.
| | - Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL, London, UK.
- Research Group of Molecular Immunology, Francis Crick Institute, NW1 1AT, London, UK.
| |
Collapse
|
15
|
Liao H, Barra C, Zhou Z, Peng X, Woodhouse I, Tailor A, Parker R, Carré A, Borrow P, Hogan MJ, Paes W, Eisenlohr LC, Mallone R, Nielsen M, Ternette N. MARS an improved de novo peptide candidate selection method for non-canonical antigen target discovery in cancer. Nat Commun 2024; 15:661. [PMID: 38253617 PMCID: PMC10803737 DOI: 10.1038/s41467-023-44460-z] [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: 07/24/2022] [Accepted: 12/14/2023] [Indexed: 01/24/2024] Open
Abstract
Understanding the nature and extent of non-canonical human leukocyte antigen (HLA) presentation in tumour cells is a priority for target antigen discovery for the development of next generation immunotherapies in cancer. We here employ a de novo mass spectrometric sequencing approach with a refined, MHC-centric analysis strategy to detect non-canonical MHC-associated peptides specific to cancer without any prior knowledge of the target sequence from genomic or RNA sequencing data. Our strategy integrates MHC binding rank, Average local confidence scores, and peptide Retention time prediction for improved de novo candidate Selection; culminating in the machine learning model MARS. We benchmark our model on a large synthetic peptide library dataset and reanalysis of a published dataset of high-quality non-canonical MHC-associated peptide identifications in human cancer. We achieve almost 2-fold improvement for high quality spectral assignments in comparison to de novo sequencing alone with an estimated accuracy of above 85.7% when integrated with a stepwise peptide sequence mapping strategy. Finally, we utilize MARS to detect and validate lncRNA-derived peptides in human cervical tumour resections, demonstrating its suitability to discover novel, immunogenic, non-canonical peptide sequences in primary tumour tissue.
Collapse
Affiliation(s)
- Hanqing Liao
- The Jenner Institute, University of Oxford, Oxford, OX3 7BN, UK
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | | | - Zhicheng Zhou
- Université Paris Cité, Institut Cochin, CNRS, INSERM, 75014, Paris, France
| | - Xu Peng
- The Jenner Institute, University of Oxford, Oxford, OX3 7BN, UK
| | - Isaac Woodhouse
- The Jenner Institute, University of Oxford, Oxford, OX3 7BN, UK
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Arun Tailor
- The Jenner Institute, University of Oxford, Oxford, OX3 7BN, UK
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Robert Parker
- The Jenner Institute, University of Oxford, Oxford, OX3 7BN, UK
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Alexia Carré
- Université Paris Cité, Institut Cochin, CNRS, INSERM, 75014, Paris, France
| | - Persephone Borrow
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Michael J Hogan
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Wayne Paes
- The Jenner Institute, University of Oxford, Oxford, OX3 7BN, UK
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Laurence C Eisenlohr
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Roberto Mallone
- Université Paris Cité, Institut Cochin, CNRS, INSERM, 75014, Paris, France
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, 75014, Paris, France
| | | | - Nicola Ternette
- The Jenner Institute, University of Oxford, Oxford, OX3 7BN, UK.
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK.
- University of Utrecht, Department of Pharmaceutical Sciences, 3584 CH, Utrecht, The Netherlands.
| |
Collapse
|
16
|
Gabriel W, Picciani M, The M, Wilhelm M. Deep Learning-Assisted Analysis of Immunopeptidomics Data. Methods Mol Biol 2024; 2758:457-483. [PMID: 38549030 DOI: 10.1007/978-1-0716-3646-6_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Liquid chromatography-coupled mass spectrometry (LC-MS/MS) is the primary method to obtain direct evidence for the presentation of disease- or patient-specific human leukocyte antigen (HLA). However, compared to the analysis of tryptic peptides in proteomics, the analysis of HLA peptides still poses computational and statistical challenges. Recently, fragment ion intensity-based matching scores assessing the similarity between predicted and observed spectra were shown to substantially increase the number of confidently identified peptides, particularly in use cases where non-tryptic peptides are analyzed. In this chapter, we describe in detail three procedures on how to benefit from state-of-the-art deep learning models to analyze and validate single spectra, single measurements, and multiple measurements in mass spectrometry-based immunopeptidomics. For this, we explain how to use the Universal Spectrum Explorer (USE), online Oktoberfest, and offline Oktoberfest. For intensity-based scoring, Oktoberfest uses fragment ion intensity and retention time predictions from the deep learning framework Prosit, a deep neural network trained on a very large number of synthetic peptides and tandem mass spectra generated within the ProteomeTools project. The examples shown highlight how deep learning-assisted analysis can increase the number of identified HLA peptides, facilitate the discovery of confidently identified neo-epitopes, or provide assistance in the assessment of the presence of cryptic peptides, such as spliced peptides.
Collapse
Affiliation(s)
- Wassim Gabriel
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mario Picciani
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Matthew The
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mathias Wilhelm
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
| |
Collapse
|
17
|
Nelde A, Schuster H, Heitmann JS, Bauer J, Maringer Y, Zwick M, Volkmer JP, Chen JY, Stanger AMP, Lehmann A, Appiah B, Märklin M, Rücker-Braun E, Salih HR, Roerden M, Schroeder SM, Häring MF, Schlosser A, Schetelig J, Schmitz M, Boerries M, Köhler N, Lengerke C, Majeti R, Weissman IL, Rammensee HG, Walz JS. Immune Surveillance of Acute Myeloid Leukemia Is Mediated by HLA-Presented Antigens on Leukemia Progenitor Cells. Blood Cancer Discov 2023; 4:468-489. [PMID: 37847741 PMCID: PMC10618727 DOI: 10.1158/2643-3230.bcd-23-0020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/13/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023] Open
Abstract
Therapy-resistant leukemia stem and progenitor cells (LSC) are a main cause of acute myeloid leukemia (AML) relapse. LSC-targeting therapies may thus improve outcome of patients with AML. Here we demonstrate that LSCs present HLA-restricted antigens that induce T-cell responses allowing for immune surveillance of AML. Using a mass spectrometry-based immunopeptidomics approach, we characterized the antigenic landscape of patient LSCs and identified AML- and AML/LSC-associated HLA-presented antigens absent from normal tissues comprising nonmutated peptides, cryptic neoepitopes, and neoepitopes of common AML driver mutations of NPM1 and IDH2. Functional relevance of shared AML/LSC antigens is illustrated by presence of their cognizant memory T cells in patients. Antigen-specific T-cell recognition and HLA class II immunopeptidome diversity correlated with clinical outcome. Together, these antigens shared among AML and LSCs represent prime targets for T cell-based therapies with potential of eliminating residual LSCs in patients with AML. SIGNIFICANCE The elimination of therapy-resistant leukemia stem and progenitor cells (LSC) remains a major challenge in the treatment of AML. This study identifies and functionally validates LSC-associated HLA class I and HLA class II-presented antigens, paving the way to the development of LSC-directed T cell-based immunotherapeutic approaches for patients with AML. See related commentary by Ritz, p. 430 . This article is featured in Selected Articles from This Issue, p. 419.
Collapse
Affiliation(s)
- Annika Nelde
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Heiko Schuster
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Jonas S. Heitmann
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Jens Bauer
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Yacine Maringer
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Melissa Zwick
- Department of Medicine I, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jens-Peter Volkmer
- Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, California
| | - James Y. Chen
- Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, California
| | - Anna M. Paczulla Stanger
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Ariane Lehmann
- Faculty of Medicine, Medical Center, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Germany
| | - Bismark Appiah
- Faculty of Medicine, Medical Center, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Germany
| | - Melanie Märklin
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Elke Rücker-Braun
- Department of Medicine I, University Hospital of Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Helmut R. Salih
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Malte Roerden
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Sarah M. Schroeder
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Tübingen, Tübingen, Germany
| | - Max-Felix Häring
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | | | - Johannes Schetelig
- Department of Medicine I, University Hospital of Dresden, Dresden, Germany
- German Bone Marrow Donor Center (DKMS), Clinical Trials Unit, Dresden, Germany
| | - Marc Schmitz
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), partner site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Boerries
- Faculty of Medicine, Medical Center, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site, Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Natalie Köhler
- Department of Medicine I, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Claudia Lengerke
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
- Clinic for Hematology, University of Basel and University Hospital Basel, Basel, Switzerland
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Germany
| | - Ravindra Majeti
- Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, California
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, California
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Germany
| | - Juliane S. Walz
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| |
Collapse
|
18
|
Nicholas B, Skipp P. What do cancer-specific CD8+ T cells see? The contribution of immunopeptidomics. Essays Biochem 2023; 67:957-965. [PMID: 37503576 DOI: 10.1042/ebc20220246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 07/03/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023]
Abstract
Immunopeptidomics is the survey of all peptides displayed on a cell or tissue when bound to human leukocyte antigen (HLA) molecules using tandem mass spectrometry. When attempting to determine the targets of tumour-specific CD8+ T cells, a survey of the potential ligands in tumour tissues is invaluable, and, in comparison with in-silico predictions, provides greater certainty of the existence of individual epitopes, as immunopeptidomics-confirmed CD8+ T-cell epitopes are known to be immunogenic, and direct observation should avoid the risk of autoreactivity which could arise following immunisation with structural homologues. The canonical sources of CD8+ T-cell tumour specific epitopes, such as tumour associated antigens, may be well conserved between patients and tumour types, but are often only weakly immunogenic. Direct observation of tumour-specific neoantigens by immunopeptidomics is rare, although valuable. Thus, there has been increasing interest in the non-canonical origins of tumour-reactive CD8+ T-cell epitopes, such as those arising from proteasomal splicing events, translational/turnover defects and alternative open reading frame reads. Such epitopes can be identified in silico, although validation is more challenging. Non-self CD8+ T-cell epitopes such as viral epitopes may be useful in certain cancer types with known viral origins, however these have been relatively unexplored with immunopeptidomics to date, possibly due to the paucity of source viral proteins in tumour tissues. This review examines the latest evidence for canonical, non-canonical and non-human CD8+ T-cell epitopes identified by immunopeptidomics, and concludes that the relative contribution for each of these sources to anti-tumour CD8+ T-cell reactivity is currently uncertain.
Collapse
Affiliation(s)
- Ben Nicholas
- Centre for Proteomic Research, Biological Sciences and Institute for Life Sciences, Building 85, University of Southampton, SO17 1BJ, U.K
| | - Paul Skipp
- Centre for Proteomic Research, Biological Sciences and Institute for Life Sciences, Building 85, University of Southampton, SO17 1BJ, U.K
| |
Collapse
|
19
|
Prensner JR, Abelin JG, Kok LW, Clauser KR, Mudge JM, Ruiz-Orera J, Bassani-Sternberg M, Moritz RL, Deutsch EW, van Heesch S. What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome? Mol Cell Proteomics 2023; 22:100631. [PMID: 37572790 PMCID: PMC10506109 DOI: 10.1016/j.mcpro.2023.100631] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/21/2023] [Accepted: 08/08/2023] [Indexed: 08/14/2023] Open
Abstract
Ribosome profiling (Ribo-Seq) has proven transformative for our understanding of the human genome and proteome by illuminating thousands of noncanonical sites of ribosome translation outside the currently annotated coding sequences (CDSs). A conservative estimate suggests that at least 7000 noncanonical ORFs are translated, which, at first glance, has the potential to expand the number of human protein CDSs by 30%, from ∼19,500 annotated CDSs to over 26,000 annotated CDSs. Yet, additional scrutiny of these ORFs has raised numerous questions about what fraction of them truly produce a protein product and what fraction of those can be understood as proteins according to conventional understanding of the term. Adding further complication is the fact that published estimates of noncanonical ORFs vary widely by around 30-fold, from several thousand to several hundred thousand. The summation of this research has left the genomics and proteomics communities both excited by the prospect of new coding regions in the human genome but searching for guidance on how to proceed. Here, we discuss the current state of noncanonical ORF research, databases, and interpretation, focusing on how to assess whether a given ORF can be said to be "protein coding."
Collapse
Affiliation(s)
- John R Prensner
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA; Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA.
| | | | - Leron W Kok
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Karl R Clauser
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, Agora Center Bugnon 25A, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland; Agora Cancer Research Centre, Lausanne, Switzerland
| | - Robert L Moritz
- Institute for Systems Biology (ISB), Seattle, Washington, USA
| | - Eric W Deutsch
- Institute for Systems Biology (ISB), Seattle, Washington, USA
| | | |
Collapse
|
20
|
Yang K, Halima A, Chan TA. Antigen presentation in cancer - mechanisms and clinical implications for immunotherapy. Nat Rev Clin Oncol 2023; 20:604-623. [PMID: 37328642 DOI: 10.1038/s41571-023-00789-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2023] [Indexed: 06/18/2023]
Abstract
Over the past decade, the emergence of effective immunotherapies has revolutionized the clinical management of many types of cancers. However, long-term durable tumour control is only achieved in a fraction of patients who receive these therapies. Understanding the mechanisms underlying clinical response and resistance to treatment is therefore essential to expanding the level of clinical benefit obtained from immunotherapies. In this Review, we describe the molecular mechanisms of antigen processing and presentation in tumours and their clinical consequences. We examine how various aspects of the antigen-presentation machinery (APM) shape tumour immunity. In particular, we discuss genomic variants in HLA alleles and other APM components, highlighting their influence on the immunopeptidomes of both malignant cells and immune cells. Understanding the APM, how it is regulated and how it changes in tumour cells is crucial for determining which patients will respond to immunotherapy and why some patients develop resistance. We focus on recently discovered molecular and genomic alterations that drive the clinical outcomes of patients receiving immune-checkpoint inhibitors. An improved understanding of how these variables mediate tumour-immune interactions is expected to guide the more precise administration of immunotherapies and reveal potentially promising directions for the development of new immunotherapeutic approaches.
Collapse
Affiliation(s)
- Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA
| | - Ahmed Halima
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA
| | - Timothy A Chan
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA.
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA.
- National Center for Regenerative Medicine, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, Cleveland, OH, USA.
| |
Collapse
|
21
|
Buonaguro L, Tagliamonte M. Peptide-based vaccine for cancer therapies. Front Immunol 2023; 14:1210044. [PMID: 37654484 PMCID: PMC10467431 DOI: 10.3389/fimmu.2023.1210044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
Different strategies based on peptides are available for cancer treatment, in particular to counter-act the progression of tumor growth and disease relapse. In the last decade, in the context of therapeutic strategies against cancer, peptide-based vaccines have been evaluated in different tumor models. The peptides selected for cancer vaccine development can be classified in two main type: tumor-associated antigens (TAAs) and tumor-specific antigens (TSAs), which are captured, internalized, processed and presented by antigen-presenting cells (APCs) to cell-mediated immunity. Peptides loaded onto MHC class I are recognized by a specific TCR of CD8+ T cells, which are activated to exert their cytotoxic activity against tumor cells presenting the same peptide-MHC-I complex. This process is defined as active immunotherapy as the host's immune system is either de novo activated or restimulated to mount an effective, tumor-specific immune reaction that may ultimately lead to tu-mor regression. However, while the preclinical data have frequently shown encouraging results, therapeutic cancer vaccines clinical trials, including those based on peptides have not provided satisfactory data to date. The limited efficacy of peptide-based cancer vaccines is the consequence of several factors, including the identification of specific target tumor antigens, the limited immunogenicity of peptides and the highly immunosuppressive tumor microenvironment (TME). An effective cancer vaccine can be developed only by addressing all such different aspects. The present review describes the state of the art for each of such factors.
Collapse
Affiliation(s)
| | - Maria Tagliamonte
- Innovative Immunological Models Unit, Istituto Nazionale Tumori - IRCCS - “Fond G. Pascale”, Naples, Italy
| |
Collapse
|
22
|
Holly J, Yewdell JW. Game of Omes: ribosome profiling expands the MHC-I immunopeptidome. Curr Opin Immunol 2023; 83:102342. [PMID: 37247567 PMCID: PMC10524008 DOI: 10.1016/j.coi.2023.102342] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023]
Abstract
Peptide ligands presented by cell-surface MHC class-I molecules enable T cells to eradicate intracellular pathogens and cancers. The presented peptide repertoire, the class-I immunopeptidome, is generated from each cell's translatome in a highly biased manner to avoid overrepresenting highly abundant translation products. The immunopeptidome can only be defined by mass spectrometry (MS). Here, we review recent advances in immunopeptidomics, focusing on using ribosome profiling as the optimal MS database to optimize the false- and failed-discovery rates and relate these findings to the contribution of defective ribosomal products and cellular quality control mechanisms to MHC class-I antigen processing and presentation.
Collapse
Affiliation(s)
- Jaroslav Holly
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan W Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
23
|
Lozano-Rabella M, Garcia-Garijo A, Palomero J, Yuste-Estevanez A, Erhard F, Farriol-Duran R, Martín-Liberal J, Ochoa-de-Olza M, Matos I, Gartner JJ, Ghosh M, Canals F, Vidal A, Piulats JM, Matías-Guiu X, Brana I, Muñoz-Couselo E, Garralda E, Schlosser A, Gros A. Exploring the Immunogenicity of Noncanonical HLA-I Tumor Ligands Identified through Proteogenomics. Clin Cancer Res 2023; 29:2250-2265. [PMID: 36749875 PMCID: PMC10261919 DOI: 10.1158/1078-0432.ccr-22-3298] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/20/2022] [Accepted: 02/03/2023] [Indexed: 02/09/2023]
Abstract
PURPOSE Tumor antigens are central to antitumor immunity. Recent evidence suggests that peptides from noncanonical (nonC) aberrantly translated proteins can be presented on HLA-I by tumor cells. Here, we investigated the immunogenicity of nonC tumor HLA-I ligands (nonC-TL) to better understand their contribution to cancer immunosurveillance and their therapeutic applicability. EXPERIMENTAL DESIGN Peptides presented on HLA-I were identified in 9 patient-derived tumor cell lines from melanoma, gynecologic, and head and neck cancer through proteogenomics. A total of 507 candidate tumor antigens, including nonC-TL, neoantigens, cancer-germline, or melanocyte differentiation antigens, were tested for T-cell recognition of preexisting responses in patients with cancer. Donor peripheral blood lymphocytes (PBL) were in vitro sensitized against 170 selected nonC-TL to isolate antigen-specific T-cell receptors (TCR) and evaluate their therapeutic potential. RESULTS We found no recognition of the 507 nonC-TL tested by autologous ex vivo expanded tumor-reactive T-cell cultures while the same cultures demonstrated reactivity to mutated, cancer-germline, or melanocyte differentiation antigens. However, in vitro sensitization of donor PBL against 170 selected nonC-TL, led to the identification of TCRs specific to three nonC-TL, two of which mapped to the 5' UTR regions of HOXC13 and ZKSCAN1, and one mapping to a noncoding spliced variant of C5orf22C. T cells targeting these nonC-TL recognized cancer cell lines naturally presenting their corresponding antigens. Expression of the three immunogenic nonC-TL was shared across tumor types and barely or not detected in normal cells. CONCLUSIONS Our findings predict a limited contribution of nonC-TL to cancer immunosurveillance but demonstrate they may be attractive novel targets for widely applicable immunotherapies. See related commentary by Fox et al., p. 2173.
Collapse
Affiliation(s)
- Maria Lozano-Rabella
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Andrea Garcia-Garijo
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Jara Palomero
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Anna Yuste-Estevanez
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Roc Farriol-Duran
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Juan Martín-Liberal
- Early Drug Development Unit (UITM) Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital, Barcelona, Spain
| | - Maria Ochoa-de-Olza
- Early Drug Development Unit (UITM) Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital, Barcelona, Spain
| | - Ignacio Matos
- Early Drug Development Unit (UITM) Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital, Barcelona, Spain
| | - Jared J. Gartner
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, Maryland
| | - Michael Ghosh
- Institute for Cell Biology Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Francesc Canals
- Proteomics, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital, Barcelona, Spain
| | - August Vidal
- Department of Pathology. Hospital Universitari de Bellvitge-IDIBELL, CIBERONC, Barcelona, Spain
| | - Josep Maria Piulats
- Medical Oncology, Catalan Institute of Cancer (ICO), IDIBELL-Oncobell, Hospitalet de Llobregat, Spain
| | - Xavier Matías-Guiu
- Department of Pathology. Hospital Universitari de Bellvitge-IDIBELL, CIBERONC, Barcelona, Spain
| | - Irene Brana
- Early Drug Development Unit (UITM) Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital, Barcelona, Spain
| | - Eva Muñoz-Couselo
- Melanoma and other skin tumors unit, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital, Barcelona, Spain
| | - Elena Garralda
- Early Drug Development Unit (UITM) Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital, Barcelona, Spain
| | - Andreas Schlosser
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Alena Gros
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| |
Collapse
|
24
|
Bedran G, Gasser HC, Weke K, Wang T, Bedran D, Laird A, Battail C, Zanzotto FM, Pesquita C, Axelson H, Rajan A, Harrison DJ, Palkowski A, Pawlik M, Parys M, O'Neill JR, Brennan PM, Symeonides SN, Goodlett DR, Litchfield K, Fahraeus R, Hupp TR, Kote S, Alfaro JA. The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I-Associated Peptides. Cancer Immunol Res 2023; 11:747-762. [PMID: 36961404 PMCID: PMC10236148 DOI: 10.1158/2326-6066.cir-22-0621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/25/2022] [Accepted: 03/16/2023] [Indexed: 03/25/2023]
Abstract
Tumor antigens can emerge through multiple mechanisms, including translation of noncoding genomic regions. This noncanonical category of tumor antigens has recently gained attention; however, our understanding of how they recur within and between cancer types is still in its infancy. Therefore, we developed a proteogenomic pipeline based on deep learning de novo mass spectrometry (MS) to enable the discovery of noncanonical MHC class I-associated peptides (ncMAP) from noncoding regions. Considering that the emergence of tumor antigens can also involve posttranslational modifications (PTM), we included an open search component in our pipeline. Leveraging the wealth of MS-based immunopeptidomics, we analyzed data from 26 MHC class I immunopeptidomic studies across 11 different cancer types. We validated the de novo identified ncMAPs, along with the most abundant PTMs, using spectral matching and controlled their FDR to 1%. The noncanonical presentation appeared to be 5 times enriched for the A03 HLA supertype, with a projected population coverage of 55%. The data reveal an atlas of 8,601 ncMAPs with varying levels of cancer selectivity and suggest 17 cancer-selective ncMAPs as attractive therapeutic targets according to a stringent cutoff. In summary, the combination of the open-source pipeline and the atlas of ncMAPs reported herein could facilitate the identification and screening of ncMAPs as targets for T-cell therapies or vaccine development.
Collapse
Affiliation(s)
- Georges Bedran
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Kenneth Weke
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Tongjie Wang
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Dominika Bedran
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Alexander Laird
- Urology Department, Western General Hospital, NHS Lothian, Edinburgh, United Kingdom
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Christophe Battail
- CEA, Grenoble Alpes University, INSERM, IRIG, Biosciences and Bioengineering for Health Laboratory (BGE) - UA13 INSERM-CEA-UGA, Grenoble, France
| | | | - Catia Pesquita
- LASIGE, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Håkan Axelson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Ajitha Rajan
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - David J. Harrison
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Aleksander Palkowski
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Maciej Pawlik
- Academic Computer Centre CYFRONET, AGH University of Science and Technology, Cracow, Poland
| | - Maciej Parys
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - J. Robert O'Neill
- Cambridge Oesophagogastric Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Paul M. Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Stefan N. Symeonides
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - David R. Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
- University of Victoria Genome BC Proteome Centre, Victoria, Canada
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Paris, France
| | - Ted R. Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Javier A. Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| |
Collapse
|
25
|
Prensner JR, Abelin JG, Kok LW, Clauser KR, Mudge JM, Ruiz-Orera J, Bassani-Sternberg M, Deutsch EW, van Heesch S. What can Ribo-seq and proteomics tell us about the non-canonical proteome? BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541049. [PMID: 37292611 PMCID: PMC10245706 DOI: 10.1101/2023.05.16.541049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ribosome profiling (Ribo-seq) has proven transformative for our understanding of the human genome and proteome by illuminating thousands of non-canonical sites of ribosome translation outside of the currently annotated coding sequences (CDSs). A conservative estimate suggests that at least 7,000 non-canonical open reading frames (ORFs) are translated, which, at first glance, has the potential to expand the number of human protein-coding sequences by 30%, from ∼19,500 annotated CDSs to over 26,000. Yet, additional scrutiny of these ORFs has raised numerous questions about what fraction of them truly produce a protein product and what fraction of those can be understood as proteins according to conventional understanding of the term. Adding further complication is the fact that published estimates of non-canonical ORFs vary widely by around 30-fold, from several thousand to several hundred thousand. The summation of this research has left the genomics and proteomics communities both excited by the prospect of new coding regions in the human genome, but searching for guidance on how to proceed. Here, we discuss the current state of non-canonical ORF research, databases, and interpretation, focusing on how to assess whether a given ORF can be said to be "protein-coding". In brief The human genome encodes thousands of non-canonical open reading frames (ORFs) in addition to protein-coding genes. As a nascent field, many questions remain regarding non-canonical ORFs. How many exist? Do they encode proteins? What level of evidence is needed for their verification? Central to these debates has been the advent of ribosome profiling (Ribo-seq) as a method to discern genome-wide ribosome occupancy, and immunopeptidomics as a method to detect peptides that are processed and presented by MHC molecules and not observed in traditional proteomics experiments. This article provides a synthesis of the current state of non-canonical ORF research and proposes standards for their future investigation and reporting. Highlights Combined use of Ribo-seq and proteomics-based methods enables optimal confidence in detecting non-canonical ORFs and their protein products.Ribo-seq can provide more sensitive detection of non-canonical ORFs, but data quality and analytical pipelines will impact results.Non-canonical ORF catalogs are diverse and span both high-stringency and low-stringency ORF nominations.A framework for standardized non-canonical ORF evidence will advance the research field.
Collapse
Affiliation(s)
- John R. Prensner
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Leron W. Kok
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - Karl R. Clauser
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jonathan M. Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center Bugnon 25A, 1005 Lausanne, Switzerland
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1005 Lausanne, Switzerland
- Agora Cancer Research Centre, 1011 Lausanne, Switzerland
| | - Eric W. Deutsch
- Institute for Systems Biology (ISB), Seattle, Washington 98109, USA
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| |
Collapse
|
26
|
Admon A. The biogenesis of the immunopeptidome. Semin Immunol 2023; 67:101766. [PMID: 37141766 DOI: 10.1016/j.smim.2023.101766] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
The immunopeptidome is the repertoire of peptides bound and presented by the MHC class I, class II, and non-classical molecules. The peptides are produced by the degradation of most cellular proteins, and in some cases, peptides are produced from extracellular proteins taken up by the cells. This review attempts to first describe some of its known and well-accepted concepts, and next, raise some questions about a few of the established dogmas in this field: The production of novel peptides by splicing is questioned, suggesting here that spliced peptides are extremely rare, if existent at all. The degree of the contribution to the immunopeptidome by degradation of cellular protein by the proteasome is doubted, therefore this review attempts to explain why it is likely that this contribution to the immunopeptidome is possibly overstated. The contribution of defective ribosome products (DRiPs) and non-canonical peptides to the immunopeptidome is noted and methods are suggested to quantify them. In addition, the common misconception that the MHC class II peptidome is mostly derived from extracellular proteins is noted, and corrected. It is stressed that the confirmation of sequence assignments of non-canonical and spliced peptides should rely on targeted mass spectrometry using spiking-in of heavy isotope-labeled peptides. Finally, the new methodologies and modern instrumentation currently available for high throughput kinetics and quantitative immunopeptidomics are described. These advanced methods open up new possibilities for utilizing the big data generated and taking a fresh look at the established dogmas and reevaluating them critically.
Collapse
Affiliation(s)
- Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Israel.
| |
Collapse
|
27
|
Phulphagar KM, Ctortecka C, Jacome ASV, Klaeger S, Verzani EK, Hernandez GM, Udeshi ND, Clauser KR, Abelin JG, Carr SA. Sensitive, high-throughput HLA-I and HLA-II immunopeptidomics using parallel accumulation-serial fragmentation mass spectrometry. Mol Cell Proteomics 2023:100563. [PMID: 37142057 DOI: 10.1016/j.mcpro.2023.100563] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/06/2023] Open
Abstract
Comprehensive, in-depth identification of the human leukocyte antigen HLA-I and HLA-II tumor immunopeptidome can inform the development of cancer immunotherapies. Mass spectrometry (MS) is powerful technology for direct identification of HLA peptides from patient derived tumor samples or cell lines. However, achieving sufficient coverage to detect rare, clinically relevant antigens requires highly sensitive MS-based acquisition methods and large amounts of sample. While immunopeptidome depth can be increased by off-line fractionation prior to MS, its use is impractical when analyzing limited amounts of primary tissue biopsies. To address this challenge, we developed and applied a high throughput, sensitive, single-shot MS-based immunopeptidomics workflow that leverages trapped ion mobility time-of-flight mass spectrometry on the Bruker timsTOF SCP. We demonstrate >2-fold improved coverage of HLA immunopeptidomes relative to prior methods with up to 15,000 distinct HLA-I and HLA-II peptides from 4e7 cells. Our optimized single-shot MS acquisition method on the timsTOF SCP maintains high coverage, eliminates the need for off-line fractionation and reduces input requirements to as few as 1e6 A375 cells for > 800 distinct HLA-I peptides. This depth is sufficient to identify HLA-I peptides derived from cancer-testis antigen, and non-canonical proteins. We also apply our optimized single-shot SCP acquisition methods to tumor derived samples, enabling sensitive, high throughput and reproducible immunopeptidome profiling with detection of clinically relevant peptides from less than 4e7 cells or 15 mg wet weight tissue.
Collapse
|
28
|
Oreper D, Klaeger S, Jhunjhunwala S, Delamarre L. The peptide woods are lovely, dark and deep: Hunting for novel cancer antigens. Semin Immunol 2023; 67:101758. [PMID: 37027981 DOI: 10.1016/j.smim.2023.101758] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 04/08/2023]
Abstract
Harnessing the patient's immune system to control a tumor is a proven avenue for cancer therapy. T cell therapies as well as therapeutic vaccines, which target specific antigens of interest, are being explored as treatments in conjunction with immune checkpoint blockade. For these therapies, selecting the best suited antigens is crucial. Most of the focus has thus far been on neoantigens that arise from tumor-specific somatic mutations. Although there is clear evidence that T-cell responses against mutated neoantigens are protective, the large majority of these mutations are not immunogenic. In addition, most somatic mutations are unique to each individual patient and their targeting requires the development of individualized approaches. Therefore, novel antigen types are needed to broaden the scope of such treatments. We review high throughput approaches for discovering novel tumor antigens and some of the key challenges associated with their detection, and discuss considerations when selecting tumor antigens to target in the clinic.
Collapse
Affiliation(s)
- Daniel Oreper
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
| | - Susan Klaeger
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
| | | | | |
Collapse
|
29
|
Abstract
Our defenses against infection rely on the ability of the immune system to distinguish invading pathogens from self. This task is exceptionally challenging, if not seemingly impossible, in the case of retroviruses that have integrated almost seamlessly into the host. This review examines the limits of innate and adaptive immune responses elicited by endogenous retroviruses and other retroelements, the targets of immune recognition, and the consequences for host health and disease. Contrary to theoretical expectation, endogenous retroelements retain substantial immunogenicity, which manifests most profoundly when their epigenetic repression is compromised, contributing to autoinflammatory and autoimmune disease and age-related inflammation. Nevertheless, recent evidence suggests that regulated immune reactivity to endogenous retroelements is integral to immune system development and function, underpinning cancer immunosurveillance, resistance to infection, and responses to the microbiota. Elucidation of the interaction points with endogenous retroelements will therefore deepen our understanding of immune system function and contribution to disease.
Collapse
Affiliation(s)
- George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, United Kingdom;
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| |
Collapse
|
30
|
Lichti CF, Wan X. Using mass spectrometry to identify neoantigens in autoimmune diseases: The type 1 diabetes example. Semin Immunol 2023; 66:101730. [PMID: 36827760 PMCID: PMC10324092 DOI: 10.1016/j.smim.2023.101730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/24/2023]
Abstract
In autoimmune diseases, recognition of self-antigens presented by major histocompatibility complex (MHC) molecules elicits unexpected attack of tissue by autoantibodies and/or autoreactive T cells. Post-translational modification (PTM) may alter the MHC-binding motif or TCR contact residues in a peptide antigen, transforming the tolerance to self to autoreactivity. Mass spectrometry-based immunopeptidomics provides a valuable mechanism for identifying MHC ligands that contain PTMs and can thus provide valuable insights into pathogenesis and therapeutics of autoimmune diseases. A plethora of PTMs have been implicated in this process, and this review highlights their formation and identification.
Collapse
Affiliation(s)
- Cheryl F Lichti
- Department of Pathology and Immunology, Division of Immunobiology, The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, 660 S. Euclid Ave, Campus Box 8118, St. Louis, MO 63110, USA.
| | - Xiaoxiao Wan
- Department of Pathology and Immunology, Division of Immunobiology, The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, 660 S. Euclid Ave, Campus Box 8118, St. Louis, MO 63110, USA.
| |
Collapse
|
31
|
Ahn R, Cui Y, White FM. Antigen discovery for the development of cancer immunotherapy. Semin Immunol 2023; 66:101733. [PMID: 36841147 DOI: 10.1016/j.smim.2023.101733] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023]
Abstract
Central to successful cancer immunotherapy is effective T cell antitumor immunity. Multiple targeted immunotherapies engineered to invigorate T cell-driven antitumor immunity rely on identifying the repertoire of T cell antigens expressed on the tumor cell surface. Mass spectrometry-based survey of such antigens ("immunopeptidomics") combined with other omics platforms and computational algorithms has been instrumental in identifying and quantifying tumor-derived T cell antigens. In this review, we discuss the types of tumor antigens that have emerged for targeted cancer immunotherapy and the immunopeptidomics methods that are central in MHC peptide identification and quantification. We provide an overview of the strength and limitations of mass spectrometry-driven approaches and how they have been integrated with other technologies to discover targetable T cell antigens for cancer immunotherapy. We highlight some of the emerging cancer immunotherapies that successfully capitalized on immunopeptidomics, their challenges, and mass spectrometry-based strategies that can support their development.
Collapse
Affiliation(s)
- Ryuhjin Ahn
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yufei Cui
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Forest M White
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
32
|
Shapiro IE, Bassani-Sternberg M. The impact of immunopeptidomics: From basic research to clinical implementation. Semin Immunol 2023; 66:101727. [PMID: 36764021 DOI: 10.1016/j.smim.2023.101727] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/10/2023]
Abstract
The immunopeptidome is the set of peptides presented by the major histocompatibility complex (MHC) molecules, in humans also known as the human leukocyte antigen (HLA), on the surface of cells that mediate T-cell immunosurveillance. The immunopeptidome is a sampling of the cellular proteome and hence it contains information about the health state of cells. The peptide repertoire is influenced by intra- and extra-cellular perturbations - such as in the case of drug exposure, infection, or oncogenic transformation. Immunopeptidomics is the bioanalytical method by which the presented peptides are extracted from biological samples and analyzed by high-performance liquid chromatography coupled to tandem mass spectrometry (MS), resulting in a deep qualitative and quantitative snapshot of the immunopeptidome. In this review, we discuss published immunopeptidomics studies from recent years, grouped into three main domains: i) basic, ii) pre-clinical and iii) clinical research and applications. We review selected fundamental immunopeptidomics studies on the antigen processing and presentation machinery, on HLA restriction and studies that advanced our understanding of various diseases, and how exploration of the antigenic landscape allowed immune targeting at the pre-clinical stage, paving the way to pioneering exploratory clinical trials where immunopeptidomics is directly implemented in the conception of innovative treatments for cancer patients.
Collapse
Affiliation(s)
- Ilja E Shapiro
- Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), 1005 Lausanne, Switzerland; Agora Cancer Research Centre, 1011 Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), 1005 Lausanne, Switzerland; Agora Cancer Research Centre, 1011 Lausanne, Switzerland; Center of Experimental Therapeutics, Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), 1005 Lausanne, Switzerland.
| |
Collapse
|
33
|
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: 34] [Impact Index Per Article: 34.0] [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.
Collapse
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.
| |
Collapse
|
34
|
Neoantigens: promising targets for cancer therapy. Signal Transduct Target Ther 2023; 8:9. [PMID: 36604431 PMCID: PMC9816309 DOI: 10.1038/s41392-022-01270-x] [Citation(s) in RCA: 205] [Impact Index Per Article: 205.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/14/2022] [Accepted: 11/27/2022] [Indexed: 01/07/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development and regulatory approval of tumor immunotherapies, including cancer vaccines, adoptive cell therapy and antibody-based therapies, especially for solid tumors. Neoantigens are newly formed antigens generated by tumor cells as a result of various tumor-specific alterations, such as genomic mutation, dysregulated RNA splicing, disordered post-translational modification, and integrated viral open reading frames. Neoantigens are recognized as non-self and trigger an immune response that is not subject to central and peripheral tolerance. The quick identification and prediction of tumor-specific neoantigens have been made possible by the advanced development of next-generation sequencing and bioinformatic technologies. Compared to tumor-associated antigens, the highly immunogenic and tumor-specific neoantigens provide emerging targets for personalized cancer immunotherapies, and serve as prospective predictors for tumor survival prognosis and immune checkpoint blockade responses. The development of cancer therapies will be aided by understanding the mechanism underlying neoantigen-induced anti-tumor immune response and by streamlining the process of neoantigen-based immunotherapies. This review provides an overview on the identification and characterization of neoantigens and outlines the clinical applications of prospective immunotherapeutic strategies based on neoantigens. We also explore their current status, inherent challenges, and clinical translation potential.
Collapse
|
35
|
McDonnell K, Abram F, Howley E. Application of a Novel Hybrid CNN-GNN for Peptide Ion Encoding. J Proteome Res 2022; 22:323-333. [PMID: 36534699 PMCID: PMC9903319 DOI: 10.1021/acs.jproteome.2c00234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Almost all state-of-the-art de novo peptide sequencing algorithms now use machine learning models to encode fragment peaks and hence identify amino acids in mass spectrometry (MS) spectra. Previous work has highlighted how the inherent MS challenges of noise and missing peptide peaks detrimentally affect the performance of these models. In the present research we extracted and evaluated the encoding modules from 3 state-of-the-art de novo peptide sequencing algorithms. We also propose a convolutional neural network-graph neural network machine learning model for encoding peptide ions in tandem MS spectra. We compared the proposed encoding module to those used in the state-of-the-art de novo peptide sequencing algorithms by assessing their ability to identify b-ions and y-ions in MS spectra. This included a comprehensive evaluation in both real and artificial data across various levels of noise and missing peptide peaks. The proposed model performed best across all data sets using two different metrics (area under the receiver operating characteristic curve (AUC) and average precision). The work also highlighted the effect of including additional features such as intensity rank in these encoding modules as well as issues with using the AUC as a metric. This work is of significance to those designing future de novo peptide identification algorithms as it is the first step toward a new approach.
Collapse
Affiliation(s)
- Kevin McDonnell
- Department
of Information Technology, School of Computer Science, University of Galway, GalwayH91 TK33, Ireland,Functional
Environmental Microbiology, School of Natural Sciences, Ryan Institute, University of Galway, GalwayH91 TK33, Ireland,E-mail:
| | - Florence Abram
- Functional
Environmental Microbiology, School of Natural Sciences, Ryan Institute, University of Galway, GalwayH91 TK33, Ireland
| | - Enda Howley
- Department
of Information Technology, School of Computer Science, University of Galway, GalwayH91 TK33, Ireland
| |
Collapse
|
36
|
Jürgens L, Wethmar K. The Emerging Role of uORF-Encoded uPeptides and HLA uLigands in Cellular and Tumor Biology. Cancers (Basel) 2022; 14:6031. [PMID: 36551517 PMCID: PMC9776223 DOI: 10.3390/cancers14246031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
Recent technological advances have facilitated the detection of numerous non-canonical human peptides derived from regulatory regions of mRNAs, long non-coding RNAs, and other cryptic transcripts. In this review, we first give an overview of the classification of these novel peptides and summarize recent improvements in their annotation and detection by ribosome profiling, mass spectrometry, and individual experimental analysis. A large fraction of the novel peptides originates from translation at upstream open reading frames (uORFs) that are located within the transcript leader sequence of regular mRNA. In humans, uORF-encoded peptides (uPeptides) have been detected in both healthy and malignantly transformed cells and emerge as important regulators in cellular and immunological pathways. In the second part of the review, we focus on various functional implications of uPeptides. As uPeptides frequently act at the transition of translational regulation and individual peptide function, we describe the mechanistic modes of translational regulation through ribosome stalling, the involvement in cellular programs through protein interaction and complex formation, and their role within the human leukocyte antigen (HLA)-associated immunopeptidome as HLA uLigands. We delineate how malignant transformation may lead to the formation of novel uORFs, uPeptides, or HLA uLigands and explain their potential implication in tumor biology. Ultimately, we speculate on a potential use of uPeptides as peptide drugs and discuss how uPeptides and HLA uLigands may facilitate translational inhibition of oncogenic protein messages and immunotherapeutic approaches in cancer therapy.
Collapse
Affiliation(s)
| | - Klaus Wethmar
- University Hospital Münster, Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, 48149 Münster, Germany
| |
Collapse
|
37
|
Schwarz S, Schmitz J, Löffler MW, Ghosh M, Rammensee HG, Olshvang E, Markel M, Mockel-Tenbrinck N, Dzionek A, Krake S, Arslan B, Kampe KD, Wendt A, Bauer P, Mullins CS, Schlosser A, Linnebacher M. T cells of colorectal cancer patients' stimulated by neoantigenic and cryptic peptides better recognize autologous tumor cells. J Immunother Cancer 2022; 10:jitc-2022-005651. [PMID: 36460334 PMCID: PMC9723954 DOI: 10.1136/jitc-2022-005651] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Patients with cancers that exhibit extraordinarily high somatic mutation numbers are ideal candidates for immunotherapy and enable identifying tumor-specific peptides through stimulation of tumor-reactive T cells (Tc). METHODS Colorectal cancers (CRC) HROC113 and HROC285 were selected based on high TMB, microsatellite instability and HLA class I expression. Their HLA ligandome was characterized using mass spectrometry, compared with the HLA ligand atlas and HLA class I-binding affinity was predicted. Cryptic peptides were identified using Peptide-PRISM. Patients' Tc were isolated from either peripheral blood (pTc) or tumor material (tumor-infiltrating Tc, TiTc) and expanded. In addition, B-lymphoblastoid cells (B-LCL) were generated and used as antigen-presenting cells. pTc and TiTc were stimulated twice for 7 days using peptide pool-loaded B-LCL. Subsequently, interferon gamma (IFNγ) release was quantified by ELISpot. Finally, cytotoxicity against autologous tumor cells was assessed in a degranulation assay. RESULTS 100 tumor-specific candidate peptides-97 cryptic peptides and 3 classically mutated neoantigens-were selected. The neoantigens originated from single nucleotide substitutions in the genes IQGAP1, CTNNB1, and TRIT1. Cryptic and neoantigenic peptides inducing IFNγ secretion of Tc were further investigated. Stimulation of pTc and TiTc with neoantigens and selected cryptic peptides resulted in increased release of cytotoxic granules in the presence of autologous tumor cells, substantiating their improved tumor cell recognition. Tetramer staining showed an enhanced number of pTc and TiTc specific for the IQGAP1 neoantigen. Subpopulation analysis prior to peptide stimulation revealed that pTc mainly consisted of memory Tc, whereas TiTc constituted primarily of effector and effector memory Tc. This allows to infer that TiTc reacting to neoantigens and cryptic peptides must be present within the tumor microenvironment. CONCLUSION These results prove that the analyzed CRC present both mutated neoantigenic and cryptic peptides on their HLA class I molecules. Moreover, stimulation with these peptides significantly strengthened tumor cell recognition by Tc. Since the overall number of neoantigenic peptides identifiable by HLA ligandome analysis hitherto is small, our data emphasize the relevance of increasing the target scope for cancer vaccines by the cryptic peptide category.
Collapse
Affiliation(s)
- Sandra Schwarz
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock University Medical Center, Rostock, Germany
| | - Johanna Schmitz
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock University Medical Center, Rostock, Germany
| | - Markus W Löffler
- Department of General, Visceral and Transplant Surgery, Universitätsklinikum Tübingen, Tubingen, Germany,Department of Immunology, University of Tübingen, Tubingen, Germany,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, University of Tübingen, Tübingen, Germany,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany,Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany
| | - Michael Ghosh
- Department of Immunology, University of Tübingen, Tubingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, University of Tübingen, Tubingen, Germany,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, University of Tübingen, Tübingen, Germany
| | | | - Marvin Markel
- Miltenyi Biotec BV & Co KG, Bergisch Gladbach, Germany
| | | | | | | | | | | | | | | | - Christina S Mullins
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock University Medical Center, Rostock, Germany
| | - Andreas Schlosser
- Center for Integrative and Translational Bioimaging, Rudolf-Virchow Center, University of Würzburg, Würzburg, Germany
| | - Michael Linnebacher
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock University Medical Center, Rostock, Germany
| |
Collapse
|
38
|
Manske F, Ogoniak L, Jürgens L, Grundmann N, Makałowski W, Wethmar K. The new uORFdb: integrating literature, sequence, and variation data in a central hub for uORF research. Nucleic Acids Res 2022; 51:D328-D336. [PMID: 36305828 PMCID: PMC9825577 DOI: 10.1093/nar/gkac899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 02/07/2023] Open
Abstract
Upstream open reading frames (uORFs) are initiated by AUG or near-cognate start codons and have been identified in the transcript leader sequences of the majority of eukaryotic transcripts. Functionally, uORFs are implicated in downstream translational regulation of the main protein coding sequence and may serve as a source of non-canonical peptides. Genetic defects in uORF sequences have been linked to the development of various diseases, including cancer. To simplify uORF-related research, the initial release of uORFdb in 2014 provided a comprehensive and manually curated collection of uORF-related literature. Here, we present an updated sequence-based version of uORFdb, accessible at https://www.bioinformatics.uni-muenster.de/tools/uorfdb. The new uORFdb enables users to directly access sequence information, graphical displays, and genetic variation data for over 2.4 million human uORFs. It also includes sequence data of >4.2 million uORFs in 12 additional species. Multiple uORFs can be displayed in transcript- and reading-frame-specific models to visualize the translational context. A variety of filters, sequence-related information, and links to external resources (UCSC Genome Browser, dbSNP, ClinVar) facilitate immediate in-depth analysis of individual uORFs. The database also contains uORF-related somatic variation data obtained from whole-genome sequencing (WGS) analyses of 677 cancer samples collected by the TCGA consortium.
Collapse
Affiliation(s)
- Felix Manske
- Institute of Bioinformatics, University of Münster, Münster 48149, Germany
| | - Lynn Ogoniak
- Institute of Bioinformatics, University of Münster, Münster 48149, Germany
| | - Lara Jürgens
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, Münster 48149, Germany
| | - Norbert Grundmann
- Institute of Bioinformatics, University of Münster, Münster 48149, Germany
| | - Wojciech Makałowski
- Correspondence may also be addressed to Wojciech Makałowski. Tel: +49 2518353006;
| | - Klaus Wethmar
- To whom correspondence should be addressed. Tel: +49 2518347587; Fax: +49 2518347588;
| |
Collapse
|
39
|
Nagel R, Pataskar A, Champagne J, Agami R. Boosting Antitumor Immunity with an Expanded Neoepitope Landscape. Cancer Res 2022; 82:3637-3649. [PMID: 35904353 PMCID: PMC9574376 DOI: 10.1158/0008-5472.can-22-1525] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/07/2022] [Accepted: 07/21/2022] [Indexed: 01/07/2023]
Abstract
Immune-checkpoint blockade therapy has been successfully applied to many cancers, particularly tumors that harbor a high mutational burden and consequently express a high abundance of neoantigens. However, novel approaches are needed to improve the efficacy of immunotherapy for treating tumors that lack a high load of classic genetically derived neoantigens. Recent discoveries of broad classes of nongenetically encoded and inducible neoepitopes open up new avenues for therapeutic development to enhance sensitivity to immunotherapies. In this review, we discuss recent work on neoantigen discovery, with an emphasis on novel classes of noncanonical neoepitopes.
Collapse
Affiliation(s)
- Remco Nagel
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Abhijeet Pataskar
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Julien Champagne
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Erasmus MC, Rotterdam University, Rotterdam, the Netherlands
| |
Collapse
|
40
|
Bernhardt M, Cruz-Garcia Y, Rech A, Meierjohann S, Erhard F, Schilling B, Schlosser A. Extending the Mass Spectrometry-Detectable Landscape of MHC Peptides by Use of Restricted Access Material. Anal Chem 2022; 94:14214-14222. [PMID: 36194871 DOI: 10.1021/acs.analchem.2c02198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass spectrometry-based immunopeptidomics enables the comprehensive identification of major histocompatibility complex (MHC) peptides from a cell culture as well as from tissue or tumor samples and is applied for the identification of tumor-specific and viral T-cell epitopes. Although mass spectrometry is generally considered an "unbiased" method for MHC peptide identification, the physicochemical properties of MHC peptides can greatly influence their detectability. Here, we demonstrate that highly hydrophobic peptides are lost during sample preparation when C18 solid-phase extraction (SPE) is used for separating MHC peptides from proteins. To overcome this limitation, we established an optimized protocol involving restricted access material (RAM). Compared to C18-SPE, RAM-SPE improved the overall MHC peptide recovery and extended the landscape of mass spectrometry-detectable MHC peptides toward more hydrophobic peptides.
Collapse
Affiliation(s)
- Melissa Bernhardt
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, Julius Maximilians University Würzburg, 97080 Würzburg, Germany
| | - Yiliam Cruz-Garcia
- Department of Biochemistry and Molecular Biology, Julius Maximilians University Würzburg, 97080 Würzburg, Germany
| | - Anne Rech
- Department of Dermatology, Venereology, and Allergology, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Svenja Meierjohann
- Institute of Pathology, Julius Maximilians University Würzburg, 97080 Würzburg, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius Maximilians University Würzburg, 97080 Würzburg, Germany
| | - Bastian Schilling
- Department of Dermatology, Venereology, and Allergology, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, Julius Maximilians University Würzburg, 97080 Würzburg, Germany
| |
Collapse
|
41
|
Sources of Cancer Neoantigens beyond Single-Nucleotide Variants. Int J Mol Sci 2022; 23:ijms231710131. [PMID: 36077528 PMCID: PMC9455963 DOI: 10.3390/ijms231710131] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
The success of checkpoint blockade therapy against cancer has unequivocally shown that cancer cells can be effectively recognized by the immune system and eliminated. However, the identity of the cancer antigens that elicit protective immunity remains to be fully explored. Over the last decade, most of the focus has been on somatic mutations derived from non-synonymous single-nucleotide variants (SNVs) and small insertion/deletion mutations (indels) that accumulate during cancer progression. Mutated peptides can be presented on MHC molecules and give rise to novel antigens or neoantigens, which have been shown to induce potent anti-tumor immune responses. A limitation with SNV-neoantigens is that they are patient-specific and their accurate prediction is critical for the development of effective immunotherapies. In addition, cancer types with low mutation burden may not display sufficient high-quality [SNV/small indels] neoantigens to alone stimulate effective T cell responses. Accumulating evidence suggests the existence of alternative sources of cancer neoantigens, such as gene fusions, alternative splicing variants, post-translational modifications, and transposable elements, which may be attractive novel targets for immunotherapy. In this review, we describe the recent technological advances in the identification of these novel sources of neoantigens, the experimental evidence for their presentation on MHC molecules and their immunogenicity, as well as the current clinical development stage of immunotherapy targeting these neoantigens.
Collapse
|
42
|
Apavaloaei A, Hesnard L, Hardy MP, Benabdallah B, Ehx G, Thériault C, Laverdure JP, Durette C, Lanoix J, Courcelles M, Noronha N, Chauhan KD, Lemieux S, Beauséjour C, Bhatia M, Thibault P, Perreault C. Induced pluripotent stem cells display a distinct set of MHC I-associated peptides shared by human cancers. Cell Rep 2022; 40:111241. [PMID: 35977509 DOI: 10.1016/j.celrep.2022.111241] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 06/20/2022] [Accepted: 07/27/2022] [Indexed: 11/03/2022] Open
Abstract
Previous reports showed that mouse vaccination with pluripotent stem cells (PSCs) induces durable anti-tumor immune responses via T cell recognition of some elusive oncofetal epitopes. We characterize the MHC I-associated peptide (MAP) repertoire of human induced PSCs (iPSCs) using proteogenomics. Our analyses reveal a set of 46 pluripotency-associated MAPs (paMAPs) absent from the transcriptome of normal tissues and adult stem cells but expressed in PSCs and multiple adult cancers. These paMAPs derive from coding and allegedly non-coding (48%) transcripts involved in pluripotency maintenance, and their expression in The Cancer Genome Atlas samples correlates with source gene hypomethylation and genomic aberrations common across cancer types. We find that several of these paMAPs were immunogenic. However, paMAP expression in tumors coincides with activation of pathways instrumental in immune evasion (WNT, TGF-β, and CDK4/6). We propose that currently available inhibitors of these pathways could synergize with immune targeting of paMAPs for the treatment of poorly differentiated cancers.
Collapse
Affiliation(s)
- Anca Apavaloaei
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada; Department of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Leslie Hesnard
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Marie-Pierre Hardy
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | | | - Gregory Ehx
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Catherine Thériault
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Jean-Philippe Laverdure
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Joël Lanoix
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Mathieu Courcelles
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Nandita Noronha
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada; Department of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Kapil Dev Chauhan
- Faculty of Health Sciences, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada; Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Christian Beauséjour
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; Department of Pharmacology and Physiology, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Mick Bhatia
- Faculty of Health Sciences, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada; Department of Chemistry, University of Montreal, Montreal, QC H3T 1J4, Canada.
| | - Claude Perreault
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada; Department of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada.
| |
Collapse
|
43
|
D’Amico S, Tempora P, Melaiu O, Lucarini V, Cifaldi L, Locatelli F, Fruci D. Targeting the antigen processing and presentation pathway to overcome resistance to immune checkpoint therapy. Front Immunol 2022; 13:948297. [PMID: 35936007 PMCID: PMC9352877 DOI: 10.3389/fimmu.2022.948297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/29/2022] [Indexed: 11/17/2022] Open
Abstract
Despite the significant clinical advances with the use of immune checkpoint inhibitors (ICIs) in a wide range of cancer patients, response rates to the therapy are variable and do not always result in long-term tumor regression. The development of ICI-resistant disease is one of the pressing issue in clinical oncology, and the identification of new targets and combination therapies is a crucial point to improve response rates and duration. Antigen processing and presentation (APP) pathway is a key element for an efficient response to ICI therapy. Indeed, malignancies that do not express tumor antigens are typically poor infiltrated by T cells and unresponsive to ICIs. Therefore, improving tumor immunogenicity potentially increases the success rate of ICI therapy. In this review, we provide an overview of the key elements of the APP machinery that can be exploited to enhance tumor immunogenicity and increase the efficacy of ICI-based immunotherapy.
Collapse
Affiliation(s)
- Silvia D’Amico
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Patrizia Tempora
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Ombretta Melaiu
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Clinical Sciences and Translational Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Valeria Lucarini
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Loredana Cifaldi
- Department of Clinical Sciences and Translational Medicine, University of Rome “Tor Vergata”, Rome, Italy
- Academic Department of Pediatrics (DPUO), Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Franco Locatelli
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Catholic University of the Sacred Heart, Rome, Italy
| | - Doriana Fruci
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- *Correspondence: Doriana Fruci,
| |
Collapse
|
44
|
An unexplored angle: T cell antigen discoveries reveal a marginal contribution of proteasome splicing to the immunogenic MHC class I antigen pool. Proc Natl Acad Sci U S A 2022; 119:e2119736119. [PMID: 35858315 PMCID: PMC9303865 DOI: 10.1073/pnas.2119736119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the current era of T cell–based immunotherapies, it is crucial to understand which types of MHC-presented T cell antigens are produced by tumor cells. In addition to linear peptide antigens, chimeric peptides are generated through proteasome-catalyzed peptide splicing (PCPS). Whether such spliced peptides are abundantly presented by MHC is highly disputed because of disagreement in computational analyses of mass spectrometry data of MHC-eluted peptides. Moreover, such mass spectrometric analyses cannot elucidate how much spliced peptides contribute to the pool of immunogenic antigens. In this Perspective, we explain the significance of knowing the contribution of spliced peptides for accurate analyses of peptidomes on one hand, and to serve as a potential source of targetable tumor antigens on the other hand. Toward a strategy for mass spectrometry independent estimation of the contribution of PCPS to the immunopeptidome, we first reviewed methodologies to identify MHC-presented spliced peptide antigens expressed by tumors. Data from these identifications allowed us to compile three independent datasets containing 103, 74, and 83 confirmed T cell antigens from cancer patients. Only 3.9%, 1.4%, and between 0% and 7.2% of these truly immunogenic antigens are produced by PCPS, therefore providing a marginal contribution to the pool of immunogenic tumor antigens. We conclude that spliced peptides will not serve as a comprehensive source to expand the number of targetable antigens for immunotherapies.
Collapse
|
45
|
Ferrari V, Stroobant V, Abi Habib J, Naulaerts S, Van den Eynde BJ, Vigneron N. New Insights into the Mechanisms of Proteasome-Mediated Peptide Splicing Learned from Comparing Splicing Efficiency by Different Proteasome Subtypes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:2817-2828. [PMID: 35688464 DOI: 10.4049/jimmunol.2101198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/03/2022] [Indexed: 06/15/2023]
Abstract
By tying peptide fragments originally distant in parental proteins, the proteasome can generate spliced peptides that are recognized by CTL. This occurs by transpeptidation involving a peptide-acyl-enzyme intermediate and another peptide fragment present in the catalytic chamber. Four main subtypes of proteasomes exist: the standard proteasome (SP), the immunoproteasome, and intermediate proteasomes β1-β2-β5i (single intermediate proteasome) and β1i-β2-β5i (double intermediate proteasome). In this study, we use a tandem mass tag-quantification approach to study the production of six spliced human antigenic peptides by the four proteasome subtypes. Peptides fibroblast growth factor-5172-176/217-220, tyrosinase368-373/336-340, and gp10040-42/47-52 are better produced by the SP than the other proteasome subtypes. The peptides SP110296-301/286-289, gp100195-202/191or192, and gp10047-52/40-42 are better produced by the immunoproteasome and double intermediate proteasome. The current model of proteasome-catalyzed peptide splicing suggests that the production of a spliced peptide depends on the abundance of the peptide splicing partners. Surprisingly, we found that despite the fact that reciprocal peptides RTK_QLYPEW (gp10040-42/47-52) and QLYPEW_RTK (gp10047-52/40-42) are composed of identical splicing partners, their production varies differently according to the proteasome subtype. These differences were maintained after in vitro digestions involving identical amounts of the splicing fragments. Our results indicate that the amount of splicing partner is not the only factor driving peptide splicing and suggest that peptide splicing efficiency also relies on other factors, such as the affinity of the C-terminal splice reactant for the primed binding site of the catalytic subunit.
Collapse
Affiliation(s)
- Violette Ferrari
- Ludwig Institute for Cancer Research, Brussels, Belgium
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Lifesciences and Biotechnology, Brussels, Belgium; and
| | - Vincent Stroobant
- Ludwig Institute for Cancer Research, Brussels, Belgium
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Lifesciences and Biotechnology, Brussels, Belgium; and
| | - Joanna Abi Habib
- Ludwig Institute for Cancer Research, Brussels, Belgium
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Lifesciences and Biotechnology, Brussels, Belgium; and
| | - Stefan Naulaerts
- Ludwig Institute for Cancer Research, Brussels, Belgium
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Lifesciences and Biotechnology, Brussels, Belgium; and
| | - Benoit J Van den Eynde
- Ludwig Institute for Cancer Research, Brussels, Belgium;
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Lifesciences and Biotechnology, Brussels, Belgium; and
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Nathalie Vigneron
- Ludwig Institute for Cancer Research, Brussels, Belgium;
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Lifesciences and Biotechnology, Brussels, Belgium; and
| |
Collapse
|
46
|
Kloetzel PM. Neo-Splicetopes in Tumor Therapy: A Lost Case? Front Immunol 2022; 13:849863. [PMID: 35265089 PMCID: PMC8898901 DOI: 10.3389/fimmu.2022.849863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Proteasome generates spliced peptides by ligating two distant cleavage products in a reverse proteolysis reaction. The observation that CD8+ T cells recognizing a spliced peptide induced T cell rejection in a melanoma patient following adoptive T cell transfer (ATT), raised some hopes with regard to the general therapeutic and immune relevance of spliced peptides. Concomitantly, the identification of spliced peptides was also the start of a controversy with respect to their frequency, abundancy and their therapeutic applicability. Here I review some of the recent evidence favoring or disfavoring an immune relevance of splicetopes and discuss from a theoretical point of view the potential usefulness of tumor specific splicetopes and why against all odds it still may seem worth trying to identify such tumor and patient-specific neosplicetopes for application in ATT.
Collapse
Affiliation(s)
- Peter M Kloetzel
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Biochemistry, Berlin, Germany
| |
Collapse
|
47
|
Mishto M, Horokhovskyi Y, Cormican JA, Yang X, Lynham S, Urlaub H, Liepe J. Database search engines and target database features impinge upon the identification of post-translationally cis-spliced peptides in HLA class I immunopeptidomes. Proteomics 2022; 22:e2100226. [PMID: 35184383 PMCID: PMC9286349 DOI: 10.1002/pmic.202100226] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/19/2022] [Accepted: 02/10/2022] [Indexed: 11/08/2022]
Abstract
Unconventional epitopes presented by HLA class I complexes are emerging targets for T cell targeted immunotherapies. Their identification by mass spectrometry (MS) required development of novel methods to cope with the large number of theoretical candidates. Methods to identify post-translationally spliced peptides led to a broad range of outcomes. We here investigated the impact of three common database search engines - that is, Mascot, Mascot+Percolator, and PEAKS DB - as final identification step, as well as the features of target database on the ability to correctly identify non-spliced and cis-spliced peptides. We used ground truth datasets measured by MS to benchmark methods' performance and extended the analysis to HLA class I immunopeptidomes. PEAKS DB showed better precision and recall of cis-spliced peptides and larger number of identified peptides in HLA class I immunopeptidomes than the other search engine strategies. The better performance of PEAKS DB appears to result from better discrimination between target and decoy hits and hence a more robust FDR estimation, and seems independent to peptide and spectrum features here investigated.
Collapse
Affiliation(s)
- Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of ImmunobiologyKing's College LondonLondonUK
- Francis Crick InstituteLondonUK
| | | | - John A. Cormican
- Max‐Planck‐Institute for Multidisciplinary SciencesGöttingenGermany
| | - Xiaoping Yang
- Proteomics Core Facility, James Black CentreKing's CollegeLondonUK
| | - Steven Lynham
- Proteomics Core Facility, James Black CentreKing's CollegeLondonUK
| | - Henning Urlaub
- Max‐Planck‐Institute for Multidisciplinary SciencesGöttingenGermany
- Institute of Clinical ChemistryUniversity Medical Center GöttingenGöttingenGermany
| | - Juliane Liepe
- Max‐Planck‐Institute for Multidisciplinary SciencesGöttingenGermany
| |
Collapse
|
48
|
Nielsen M, Ternette N, Barra C. The interdependence of machine learning and LC-MS approaches for an unbiased understanding of the cellular immunopeptidome. Expert Rev Proteomics 2022; 19:77-88. [PMID: 35390265 DOI: 10.1080/14789450.2022.2064278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The comprehensive collection of peptides presented by Major Histocompatibility Complex (MHC) molecules on the cell surface is collectively known as the immunopeptidome. The analysis and interpretation of such data sets holds great promise for furthering our understanding of basic immunology and adaptive immune activation and regulation, and for direct rational discovery of T cell antigens and the design of T-cell based therapeutics and vaccines. These applications are however challenged by the complex nature of immunopeptidome data. AREAS COVERED Here, we describe the benefits and shortcomings of applying liquid chromatography-tandem mass spectrometry (MS) to obtain large scale immunopeptidome data sets and illustrate how the accurate analysis and optimal interpretation of such data is reliant on the availability of refined and highly optimized machine learning approaches. EXPERT OPINION Further we demonstrate how the accuracy of immunoinformatics prediction methods within the field of MHC antigen presentation has benefited greatly from the availability of MS-immunopeptidomics data, and exemplify how optimal antigen discovery is best performed in a synergistic combination of MS experiments and such in silico models trained on large scale immunopeptidomics data.
Collapse
Affiliation(s)
- Morten Nielsen
- Department of Health technology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Nicola Ternette
- Centre for Cellular and Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Carolina Barra
- Department of Health technology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| |
Collapse
|
49
|
Becker JP, Riemer AB. The Importance of Being Presented: Target Validation by Immunopeptidomics for Epitope-Specific Immunotherapies. Front Immunol 2022; 13:883989. [PMID: 35464395 PMCID: PMC9018990 DOI: 10.3389/fimmu.2022.883989] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/16/2022] [Indexed: 11/26/2022] Open
Abstract
Presentation of tumor-specific or tumor-associated peptides by HLA class I molecules to CD8+ T cells is the foundation of epitope-centric cancer immunotherapies. While often in silico HLA binding predictions or in vitro immunogenicity assays are utilized to select candidates, mass spectrometry-based immunopeptidomics is currently the only method providing a direct proof of actual cell surface presentation. Despite much progress in the last decade, identification of such HLA-presented peptides remains challenging. Here we review typical workflows and current developments in the field of immunopeptidomics, highlight the challenges which remain to be solved and emphasize the importance of direct target validation for clinical immunotherapy development.
Collapse
Affiliation(s)
- Jonas P. Becker
- Immunotherapy and Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelika B. Riemer
- Immunotherapy and Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Vaccine Design, German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| |
Collapse
|
50
|
Yewdell JW. MHC Class I Immunopeptidome: Past, Present, and Future. Mol Cell Proteomics 2022; 21:100230. [PMID: 35395404 PMCID: PMC9243166 DOI: 10.1016/j.mcpro.2022.100230] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 12/14/2022] Open
Abstract
In the 35 years since the revelation that short peptides bound to major histocompatibility complex class I and II molecules are the secret of the major histocompatibility complex–restricted nature of T-cell recognition, there has been enormous progress in characterizing the immunopeptidome, the repertoire of peptide presented for immunosurveillance. Here, the major milestones in the journey are marked, the contribution of proteasome-mediated splicing to the immunopeptidome is discussed, and exciting recent findings relating the immunopeptidome to the translatome revealed by ribosome profiling (RiboSeq) is detailed. Finally, what is needed for continued progress is opined about, which includes the infusion of talented young scientists into the antigen-processing field, currently undergoing a renaissance; thanks in part to the astounding success of T-cell–based cancer immunotherapy. Concise history of the discoveries leading to the molecular explanation for the phenomenon of the MHC class I–restricted nature of T-cell recognition. Historical review of how MS became a critical technique for defining MHC class I–associated peptides and understanding how peptides are generated from proteins biosynthesized by the antigen-presenting cell. Critical review of recent findings linking the translatome to the MHC class I immunopeptidome and the controversy regarding contribution of proteasome-mediated peptide splicing to the immunopeptidome. Speculative discussion of the future contributions of MS to understanding the generation of the MHC class I immunopeptidome.
Collapse
Affiliation(s)
- Jonathan W Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA.
| |
Collapse
|