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Freudenmann LK, Marcu A, Stevanović S. Mapping the tumour human leukocyte antigen (HLA) ligandome by mass spectrometry. Immunology 2018; 154:331-345. [PMID: 29658117 DOI: 10.1111/imm.12936] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 03/29/2018] [Accepted: 04/02/2018] [Indexed: 12/13/2022] Open
Abstract
The entirety of human leukocyte antigen (HLA)-presented peptides is referred to as the HLA ligandome of a cell or tissue, in tumours often termed immunopeptidome. Mapping the tumour immunopeptidome by mass spectrometry (MS) comprehensively views the pathophysiologically relevant antigenic signature of human malignancies. MS is an unbiased approach stringently filtering the candidates to be tested as opposed to epitope prediction algorithms. In the setting of peptide-specific immunotherapies, MS-based strategies significantly diminish the risk of lacking clinical benefit, as they yield highly enriched amounts of truly presented peptides. Early immunopeptidomic efforts were severely limited by technical sensitivity and manual spectra interpretation. The technological progress with development of orbitrap mass analysers and enhanced chromatographic performance led to vast improvements in mass accuracy, sensitivity, resolution, and speed. Concomitantly, bioinformatic tools were developed to process MS data, integrate sequencing results, and deconvolute multi-allelic datasets. This enabled the immense advancement of tumour immunopeptidomics. Studying the HLA-presented peptide repertoire bears high potential for both answering basic scientific questions and translational application. Mapping the tumour HLA ligandome has started to significantly contribute to target identification for the design of peptide-specific cancer immunotherapies in clinical trials and compassionate need treatments. In contrast to prediction algorithms, rare HLA allotypes and HLA class II can be adequately addressed when choosing MS-guided target identification platforms. Herein, we review the identification of tumour HLA ligands focusing on sources, methods, bioinformatic data analysis, translational application, and provide an outlook on future developments.
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Affiliation(s)
- Lena Katharina Freudenmann
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Ana Marcu
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
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A meta-analysis of HLA peptidome composition in different hematological entities: entity-specific dividing lines and "pan-leukemia" antigens. Oncotarget 2018; 8:43915-43924. [PMID: 28159928 PMCID: PMC5546449 DOI: 10.18632/oncotarget.14918] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/26/2016] [Indexed: 12/15/2022] Open
Abstract
Hematological malignancies (HM) are highly amenable targets for immunotherapeutic intervention and may be effectively treated by antigen-specific T-cell based treatment. Recent studies demonstrate that physiologically occurring anti-cancer T-cell responses in certain HM entities target broadly presented non-mutated epitopes. HLA ligands are thus implied as prime targets for broadly applicable and antigen-specific off-the-shelf compounds. With the aim of assessing the presence of common targets shared among different HM which may enable addressing a larger patient collective we conducted a meta-analysis of 83 mass spectrometry-based HLA peptidome datasets (comprising 40,361 unique peptide identifications) across four major HM (19 AML, 16 CML, 35 CLL, and 13 MM/MCL samples) and investigated similarities and differences within the HLA presented antigenic landscape. We found the cancer HLA peptidome datasets to cluster specifically along entity and lineage lines, suggesting that the immunopeptidome directly reflects the differences in the underlying (tumor-)biology. In line with these findings, we only detected a small set of entity-spanning antigens, which were predominantly characterized by low presentation frequencies within the different patient cohorts. These findings suggest that design of T-cell immunotherapies for the treatment of HM should ideally be conducted in an entity-specific fashion.
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Chong C, Marino F, Pak H, Racle J, Daniel RT, Müller M, Gfeller D, Coukos G, Bassani-Sternberg M. High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome. Mol Cell Proteomics 2018; 17:533-548. [PMID: 29242379 PMCID: PMC5836376 DOI: 10.1074/mcp.tir117.000383] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/12/2017] [Indexed: 12/11/2022] Open
Abstract
Comprehensive knowledge of the human leukocyte antigen (HLA) class-I and class-II peptides presented to T-cells is crucial for designing innovative therapeutics against cancer and other diseases. However methodologies for their purification for mass-spectrometry analysis have been a major limitation. We designed a novel high-throughput, reproducible and sensitive method for sequential immuno-affinity purification of HLA-I and -II peptides from up to 96 samples in a plate format, suitable for both cell lines and tissues. Our methodology drastically reduces sample-handling and can be completed within five hours. We challenged our methodology by extracting HLA peptides from multiple replicates of tissues (n = 7) and cell lines (n = 21, 108 cells per replicate), which resulted in unprecedented depth, sensitivity and high reproducibility (Pearson correlations up to 0.98 and 0.97 for HLA-I and HLA-II). Because of the method's achieved sensitivity, even single measurements of peptides purified from 107 B-cells resulted in the identification of more than 1700 HLA-I and 2200 HLA-II peptides. We demonstrate the feasibility of performing drug-screening by using ovarian cancer cells treated with interferon gamma (IFNγ). Our analysis revealed an augmented presentation of chymotryptic-like and longer ligands associated with IFNγ induced changes of the antigen processing and presentation machinery. This straightforward method is applicable for basic and clinical applications.
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Affiliation(s)
- Chloe Chong
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Fabio Marino
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - HuiSong Pak
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Julien Racle
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
- **Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Roy T Daniel
- ¶Service of Neurosurgery, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Markus Müller
- ‖Vital IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - David Gfeller
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
- **Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - George Coukos
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland;
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
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Abstract
Peptidomics is the comprehensive characterization of peptides from biological sources mainly by HPLC and mass spectrometry. Mass spectrometry allows the detection of a multitude of single peptides in complex mixtures. The term first appeared in full papers in the year 2001, after over 100 years of peptide research with a main focus on one or a few specific peptides. Within the last 15 years, this new field has grown to over 1200 publications. Mass spectrometry techniques, in combination with other analytical methods, were developed for the fast and comprehensive analysis of peptides in proteomics and specifically adjusted to implement peptidomics technologies. Although peptidomics is closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. The development of peptidomics is described, including the most important implementations for its technological basis. Different strategies are covered which are applied to several important applications, such as neuropeptidomics and discovery of bioactive peptides or biomarkers. This overview includes links to all other chapters in the book as well as recent developments of separation, mass spectrometric, and data processing technologies. Additionally, some new applications in food and plant peptidomics as well as immunopeptidomics are introduced.
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Mihailovic PM, Lio WM, Yano J, Zhao X, Zhou J, Chyu KY, Shah PK, Cercek B, Dimayuga PC. The cathelicidin protein CRAMP is a potential atherosclerosis self-antigen in ApoE(-/-) mice. PLoS One 2017; 12:e0187432. [PMID: 29091929 PMCID: PMC5665601 DOI: 10.1371/journal.pone.0187432] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/19/2017] [Indexed: 11/18/2022] Open
Abstract
Auto-immunity is believed to contribute to inflammation in atherosclerosis. The antimicrobial peptide LL-37, a fragment of the cathelicidin protein precursor hCAP18, was previously identified as an autoantigen in psoriasis. Given the reported link between psoriasis and coronary artery disease, the biological relevance of the autoantigen to atherosclerosis was tested in vitro using a truncated (t) form of the mouse homolog of hCAP18, CRAMP, on splenocytes from athero-prone ApoE(-/-) mice. Stimulation with tCRAMP resulted in increased CD8+ T cells with Central Memory and Effector Memory phenotypes in ApoE(-/-) mice, differentially activated by feeding with normal chow or high fat diet. Immunization of ApoE(-/-) with different doses of the shortened peptide (Cramp) resulted in differential outcomes with a lower dose reducing atherosclerosis whereas a higher dose exacerbating the disease with increased neutrophil infiltration of the atherosclerotic plaques. Low dose Cramp immunization also resulted in increased splenic CD8+ T cell degranulation and reduced CD11b+CD11c+ conventional dendritic cells (cDCs), whereas high dose increased CD11b+CD11c+ cDCs. Our results identified CRAMP, the mouse homolog of hCAP-18, as a potential self-antigen involved in the immune response to atherosclerosis in the ApoE(-/-) mouse model.
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Affiliation(s)
- Peter M. Mihailovic
- Oppenheimer Atherosclerosis Research Center, Division of Cardiology, Cedars-Sinai Heart Institute, Los Angeles, California, United States of America
| | - Wai Man Lio
- Oppenheimer Atherosclerosis Research Center, Division of Cardiology, Cedars-Sinai Heart Institute, Los Angeles, California, United States of America
| | - Juliana Yano
- Oppenheimer Atherosclerosis Research Center, Division of Cardiology, Cedars-Sinai Heart Institute, Los Angeles, California, United States of America
| | - Xiaoning Zhao
- Oppenheimer Atherosclerosis Research Center, Division of Cardiology, Cedars-Sinai Heart Institute, Los Angeles, California, United States of America
| | - Jianchang Zhou
- Oppenheimer Atherosclerosis Research Center, Division of Cardiology, Cedars-Sinai Heart Institute, Los Angeles, California, United States of America
| | - Kuang-Yuh Chyu
- Oppenheimer Atherosclerosis Research Center, Division of Cardiology, Cedars-Sinai Heart Institute, Los Angeles, California, United States of America
| | - Prediman K. Shah
- Oppenheimer Atherosclerosis Research Center, Division of Cardiology, Cedars-Sinai Heart Institute, Los Angeles, California, United States of America
| | - Bojan Cercek
- Oppenheimer Atherosclerosis Research Center, Division of Cardiology, Cedars-Sinai Heart Institute, Los Angeles, California, United States of America
| | - Paul C. Dimayuga
- Oppenheimer Atherosclerosis Research Center, Division of Cardiology, Cedars-Sinai Heart Institute, Los Angeles, California, United States of America
- * E-mail:
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56
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Parker BL, Burchfield JG, Clayton D, Geddes TA, Payne RJ, Kiens B, Wojtaszewski JFP, Richter EA, James DE. Multiplexed Temporal Quantification of the Exercise-regulated Plasma Peptidome. Mol Cell Proteomics 2017; 16:2055-2068. [PMID: 28982716 DOI: 10.1074/mcp.ra117.000020] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Indexed: 01/06/2023] Open
Abstract
Exercise is extremely beneficial to whole body health reducing the risk of a number of chronic human diseases. Some of these physiological benefits appear to be mediated via the secretion of peptide/protein hormones into the blood stream. The plasma peptidome contains the entire complement of low molecular weight endogenous peptides derived from secretion, protease activity and PTMs, and is a rich source of hormones. In the current study we have quantified the effects of intense exercise on the plasma peptidome to identify novel exercise regulated secretory factors in humans. We developed an optimized 2D-LC-MS/MS method and used multiple fragmentation methods including HCD and EThcD to analyze endogenous peptides. This resulted in quantification of 5,548 unique peptides during a time course of exercise and recovery. The plasma peptidome underwent dynamic and large changes during exercise on a time-scale of minutes with many rapidly reversible following exercise cessation. Among acutely regulated peptides, many were known hormones including insulin, glucagon, ghrelin, bradykinin, cholecystokinin and secretogranins validating the method. Prediction of bioactive peptides regulated with exercise identified C-terminal peptides from Transgelins, which were increased in plasma during exercise. In vitro experiments using synthetic peptides identified a role for transgelin peptides on the regulation of cell-cycle, extracellular matrix remodeling and cell migration. We investigated the effects of exercise on the regulation of PTMs and proteolytic processing by building a site-specific network of protease/substrate activity. Collectively, our deep peptidomic analysis of plasma revealed that exercise rapidly modulates the circulation of hundreds of bioactive peptides through a network of proteases and PTMs. These findings illustrate that peptidomics is an ideal method for quantifying changes in circulating factors on a global scale in response to physiological perturbations such as exercise. This will likely be a key method for pinpointing exercise regulated factors that generate health benefits.
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Affiliation(s)
- Benjamin L Parker
- From the ‡Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - James G Burchfield
- From the ‡Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Daniel Clayton
- §School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Thomas A Geddes
- From the ‡Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Richard J Payne
- §School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Bente Kiens
- ¶Department of Nutrition, Exercise and Sports, August Krogh Centre, University of Copenhagen, Copenhagen 2100, Denmark
| | - Jørgen F P Wojtaszewski
- ¶Department of Nutrition, Exercise and Sports, August Krogh Centre, University of Copenhagen, Copenhagen 2100, Denmark
| | - Erik A Richter
- ¶Department of Nutrition, Exercise and Sports, August Krogh Centre, University of Copenhagen, Copenhagen 2100, Denmark
| | - David E James
- From the ‡Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia; .,‖School of Medicine, University of Sydney, Sydney, NSW 2006, Australia
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57
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Next-Generation Proteomics and Its Application to Clinical Breast Cancer Research. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 187:2175-2184. [DOI: 10.1016/j.ajpath.2017.07.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 07/05/2017] [Accepted: 07/06/2017] [Indexed: 12/17/2022]
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58
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Bräunlein E, Krackhardt AM. Tools to define the melanoma-associated immunopeptidome. Immunology 2017; 152:536-544. [PMID: 28755382 DOI: 10.1111/imm.12803] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 07/25/2017] [Accepted: 07/25/2017] [Indexed: 12/26/2022] Open
Abstract
Immunotherapies have been traditionally applied in malignant melanoma, which represent one of the most immunogenic tumours. Recently, immune checkpoint modulation has shown high therapeutic efficacy and may provide long-term survival in a significant proportion of affected patients. T cells are the major players in tumour rejection and recognize tumour cells predominantly in an MHC-dependent way. The immunopeptidome comprises the peptide repertoire presented by MHC class I and II molecules on the surface of the body's cells including tumour cells. To understand characteristics of suitable rejection antigens as well as respective effective T-cell responses, determination of the immunopeptidome is of utmost importance. Suitable rejection antigens need to be further characterized and validated not only to systematically improve current therapeutic approaches, but also to develop individualized treatment options. In this review, we report on current tools to explore the immunopeptidome in human melanoma and discuss current understanding and future developments to specifically detect and select those antigens that may be most relevant and promising for effective tumour rejection.
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Affiliation(s)
- Eva Bräunlein
- Medizinische Klinik III, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Angela M Krackhardt
- Medizinische Klinik III, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,German Cancer Consortium of Translational Cancer Research (DKTK) and German Cancer Research Centre (DKFZ), Heidelberg, Germany
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59
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Vaughan K, Xu X, Caron E, Peters B, Sette A. Deciphering the MHC-associated peptidome: a review of naturally processed ligand data. Expert Rev Proteomics 2017; 14:729-736. [PMID: 28756714 DOI: 10.1080/14789450.2017.1361825] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION The availability of big data sets ('OMICS') has greatly impacted fundamental and translational science. High-throughput analysis of HLA class I and II associated peptidomes by mass spectrometry (MS) has generated large datasets, with the last decade witnessing tremendous growth in the breadth and number of studies. Areas covered: For this, we first analyzed naturally processed peptide (NP) data captured within the IEDB to survey and characterize the current state of NP data. We next asked to what extent the NP data overlap with existing T cell epitope and MHC binding data. Expert commentary: The current collection of NP data represents a large and diverse set of class I/II peptides mostly derived from self-antigens. These data overlap only marginally with existing immunogenicity and binding data and it is thus difficult to ascertain the correspondence between the different assay methodologies. This highlights a need for unbiased studies benchmarking in model antigen systems how well MHC binding and NP data predicts immunogenicity. Going forward, efforts at generating an integrated process for capturing all NP, curating associated metadata and accessing NP data from an immunological viewpoint will be important for development of novel methods for identifying optimal target antigens and for class I and II epitope prediction.
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Affiliation(s)
- Kerrie Vaughan
- a Vaccine Discovery , La Jolla Institute for Allergy and Immunology , La Jolla , CA , USA
| | - Xiaojun Xu
- a Vaccine Discovery , La Jolla Institute for Allergy and Immunology , La Jolla , CA , USA
| | - Etienne Caron
- b Department of Biology , Institute of Molecular Systems Biology , Zurich , Switzerland
| | - Bjoern Peters
- a Vaccine Discovery , La Jolla Institute for Allergy and Immunology , La Jolla , CA , USA
| | - Alessandro Sette
- a Vaccine Discovery , La Jolla Institute for Allergy and Immunology , La Jolla , CA , USA
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60
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Ritz D, Gloger A, Weide B, Garbe C, Neri D, Fugmann T. High-sensitivity HLA class I peptidome analysis enables a precise definition of peptide motifs and the identification of peptides from cell lines and patients' sera. Proteomics 2017; 16:1570-80. [PMID: 26992070 DOI: 10.1002/pmic.201500445] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/09/2016] [Accepted: 02/23/2016] [Indexed: 11/09/2022]
Abstract
The characterization of peptides bound to human leukocyte antigen (HLA) class I is of fundamental importance for understanding CD8+ T cell-driven immunological processes and for the development of immunomodulatory therapeutic strategies. However, until now, the mass spectrometric analysis of HLA-bound peptides has typically required billions of cells, still resulting in relatively few high-confidence peptide identifications. Capitalizing on the recent developments in mass spectrometry and bioinformatics, we have implemented a methodology for the efficient recovery of acid-eluted HLA peptides after purification with the pan-reactive antibody W6/32 and have identified a total of 27 862 unique peptides with high confidence (1% false discovery rate) from five human cancer cell lines. More than 93% of the identified peptides were eight to 11 amino acids in length and contained signatures that were in excellent agreement with published HLA binding motifs. Furthermore, by purifying soluble HLA class I complexes (sHLA) from sera of melanoma patients, up to 972 high-confidence peptides could be identified, including melanoma-associated antigens already described in the literature. Knowledge of the HLA class I peptidome should facilitate multiplex tetramer technology-based characterization of T cells, and allow the development of patient selection, stratification and immunomodulatory therapeutic strategies.
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Affiliation(s)
| | - Andreas Gloger
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Benjamin Weide
- Department of Dermatology, Division of Dermatologic Oncology, Eberhard-Karls-University, Tuebingen, Germany.,Department of Immunology, Eberhard-Karls-University, Tuebingen, Germany
| | - Claus Garbe
- Department of Dermatology, Division of Dermatologic Oncology, Eberhard-Karls-University, Tuebingen, Germany
| | - Dario Neri
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
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61
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Barnea E, Melamed Kadosh D, Haimovich Y, Satumtira N, Dorris ML, Nguyen MT, Hammer RE, Tran TM, Colbert RA, Taurog JD, Admon A. The Human Leukocyte Antigen (HLA)-B27 Peptidome in Vivo, in Spondyloarthritis-susceptible HLA-B27 Transgenic Rats and the Effect of Erap1 Deletion. Mol Cell Proteomics 2017; 16:642-662. [PMID: 28188227 DOI: 10.1074/mcp.m116.066241] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/05/2017] [Indexed: 01/20/2023] Open
Abstract
HLA-B27 is a class I major histocompatibility (MHC-I) allele that confers susceptibility to the rheumatic disease ankylosing spondylitis (AS) by an unknown mechanism. ERAP1 is an aminopeptidase that trims peptides in the endoplasmic reticulum for binding to MHC-I molecules. ERAP1 shows genetic epistasis with HLA-B27 in conferring susceptibility to AS. Male HLA-B27 transgenic rats develop arthritis and serve as an animal model of AS, whereas female B27 transgenic rats remain healthy. We used large scale quantitative mass spectrometry to identify over 15,000 unique HLA-B27 peptide ligands, isolated after immunoaffinity purification of the B27 molecules from the spleens of HLA-B27 transgenic rats. Heterozygous deletion of Erap1, which reduced the Erap1 level to less than half, had no qualitative or quantitative effects on the B27 peptidome. Homozygous deletion of Erap1 affected approximately one-third of the B27 peptidome but left most of the B27 peptidome unchanged, suggesting the possibility that some of the HLA-B27 immunopeptidome is not processed in the presence of Erap1. Deletion of Erap1 was permissive for the AS-like phenotype, increased mean peptide length and increased the frequency of C-terminal hydrophobic residues and of N-terminal Ala, Ser, or Lys. The presence of Erap1 increased the frequency of C-terminal Lys and Arg, of Glu and Asp at intermediate residues, and of N-terminal Gly. Several peptides of potential interest in AS pathogenesis, previously identified in human cell lines, were isolated. However, rats susceptible to arthritis had B27 peptidomes similar to those of non-susceptible rats, and no peptides were found to be uniquely associated with arthritis. Whether specific B27-bound peptides are required for AS pathogenesis remains to be determined. Data are available via ProteomeXchange with identifier PXD005502.
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Affiliation(s)
- Eilon Barnea
- From the ‡Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Dganit Melamed Kadosh
- From the ‡Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Yael Haimovich
- From the ‡Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Nimman Satumtira
- §Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8884
| | - Martha L Dorris
- §Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8884
| | - Mylinh T Nguyen
- ¶Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8816
| | - Robert E Hammer
- ¶Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8816
| | - Tri M Tran
- ‖NIAMS, National Institutes of Health, Bethesda, Maryland 20892-1560
| | - Robert A Colbert
- ‖NIAMS, National Institutes of Health, Bethesda, Maryland 20892-1560
| | - Joel D Taurog
- §Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8884;
| | - Arie Admon
- From the ‡Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel;
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62
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Use of HLA peptidomics and whole exome sequencing to identify human immunogenic neo-antigens. Oncotarget 2017; 7:5110-7. [PMID: 26819371 PMCID: PMC4868674 DOI: 10.18632/oncotarget.6960] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 12/30/2015] [Indexed: 01/08/2023] Open
Abstract
The antigenicity of cells is demarcated by the peptides bound by their Human Leucocyte Antigen (HLA) molecules. Through this antigen presentation, T cell specificity response is controlled. As a fraction of the expressed mutated peptides is presented on the HLA, these neo-epitopes could be immunogenic. Such neo-antigens have recently been identified through screening for predicted mutated peptides, using synthetic peptides or ones expressed from minigenes, combined with screening of patient tumor-infiltrating lymphocytes (TILs). Here we present a time and cost-effective method that combines whole-exome sequencing analysis with HLA peptidome mass spectrometry, to identify neo-antigens in a melanoma patient. Of the 1,019 amino acid changes identified through exome sequencing, two were confirmed by mass spectrometry to be presented by the cells. We then synthesized peptides and evaluated the two mutated neo-antigens for reactivity with autologous bulk TILs, and found that one yielded mutant-specific T-cell response. Our results demonstrate that this method can be used for immune response prediction and promise to provide an alternative approach for identifying immunogenic neo-epitopes in cancer.
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63
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Herrera FG, Bourhis J, Coukos G. Radiotherapy combination opportunities leveraging immunity for the next oncology practice. CA Cancer J Clin 2017; 67:65-85. [PMID: 27570942 DOI: 10.3322/caac.21358] [Citation(s) in RCA: 317] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Approximately one-half of patients with newly diagnosed cancer and many patients with persistent or recurrent tumors receive radiotherapy (RT), with the explicit goal of eliminating tumors through direct killing. The current RT dose and schedule regimens have been empirically developed. Although early clinical studies revealed that RT could provoke important responses not only at the site of treatment but also on remote, nonirradiated tumor deposits-the so-called "abscopal effect"- the underlying mechanisms were poorly understood and were not therapeutically exploited. Recent work has elucidated the immune mechanisms underlying these effects and has paved the way for developing combinations of RT with immune therapy. In the wake of recent therapeutic breakthroughs in the field of immunotherapy, rational combinations of immunotherapy with RT could profoundly change the standard of care for many tumor types in the next decade. Thus, a deep understanding of the immunologic effects of RT is urgently needed to design the next generation of therapeutic combinations. Here, the authors review the immune mechanisms of tumor radiation and summarize the preclinical and clinical evidence on immunotherapy-RT combinations. Furthermore, a framework is provided for the practicing clinician and the clinician investigator to guide the development of novel combinations to more rapidly advance this important field. CA Cancer J Clin 2017;67:65-85. © 2016 American Cancer Society.
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Affiliation(s)
- Fernanda G Herrera
- Radiation Oncologist, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
- Instructor, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Jean Bourhis
- Professor, Chief of Radiation Oncology Service, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - George Coukos
- Professor, Director, Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
- Director, Ludwig Institute for Cancer Research, University of Lausanne Branch, Lausanne, Switzerland
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64
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Abstract
The human plasma proteome represents an important secreted sub-proteome. Proteomic analysis of blood plasma with mass spectrometry is a challenging task. The high complexity and wide dynamic range of proteins as well as the presence of several proteins at very high concentrations complicate the profiling of the human plasma proteome. The peptidome (or low-molecular-weight fraction, LMF) of the human plasma proteome is an invaluable source of biological information, especially in the context of identifying plasma-based markers of disease. Peptides are generated by active synthesis and proteolytic processing, often yielding proteolytic fragments that mediate a variety of physiological and pathological functions. As such, degradomic studies, investigating cleavage products via peptidomics and top-down proteomics in particular, have warranted significant research interest. However, due to their molecular weight, abundance, and solubility, issues with identifying specific cleavage sites and coverage of peptide fragments remain challenging. Peptidomics is currently focused toward comprehensively studying peptides cleaved from precursor proteins by endogenous proteases. This protocol outlines a standardized rapid and reproducible procedure for peptidomic profiling of human plasma using centrifugal ultrafiltration and mass spectrometry. Ultrafiltration is a convective process that uses anisotropic semipermeable membranes to separate macromolecular species on the basis of size. We have optimized centrifugal ultrafiltration (cellulose triacetate membrane) for plasma fractionation with respect to buffer and solvent composition, centrifugal force, duration, and temperature to facilitate recovery >95% and enrichment of the human plasma peptidome. This method serves as a comprehensive and facile process to enrich and identify a key, underrepresented sub-proteome of human blood plasma.
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65
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Ritz D, Gloger A, Neri D, Fugmann T. Purification of soluble HLA class I complexes from human serum or plasma deliver high quality immuno peptidomes required for biomarker discovery. Proteomics 2016; 17. [PMID: 27862975 DOI: 10.1002/pmic.201600364] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/24/2016] [Accepted: 11/10/2016] [Indexed: 12/29/2022]
Abstract
Soluble human leukocyte antigen class I (sHLA)-peptide complexes have been suggested to play a role in the modulation of immune responses and in immune evasion of cancer cells. The set of peptides eluted from sHLA molecules could serve as biomarker for the monitoring of patients with cancer or other conditions. Here, we describe an improved sHLA peptidomics methodology resulting in the identification of 1816 to 2761 unique peptide sequences from triplicate analyses of serum or plasma taken from three healthy donors. More than 90% of the identified peptides were 8-11mers and 74% of these sequences were predicted to bind to cognate HLA alleles, confirming the quality of the resulting immunopeptidomes. In comparison to the HLA peptidome of cultured cells, the plasma-derived peptides were predicted to have a higher stability in complex with the cognate HLA molecules and mainly derived from proteins of the plasma membrane or from the extracellular space. The sHLA peptidomes can efficiently be characterized by using the new methodology, thus serving as potential source of biomarkers in various pathological conditions.
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Affiliation(s)
| | - Andreas Gloger
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Dario Neri
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
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66
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Wang Q, Drouin EE, Yao C, Zhang J, Huang Y, Leon DR, Steere AC, Costello CE. Immunogenic HLA-DR-Presented Self-Peptides Identified Directly from Clinical Samples of Synovial Tissue, Synovial Fluid, or Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis. J Proteome Res 2016; 16:122-136. [PMID: 27726376 DOI: 10.1021/acs.jproteome.6b00386] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Human leukocyte antigen-antigen D related (HLA-DR) molecules are highly expressed in synovial tissue (ST), the target of the immune response in chronic inflammatory forms of arthritis. Here, we used LC-MS/MS to identify HLA-DR-presented self-peptides in cells taken directly from clinical samples: ST, synovial fluid mononuclear cells (SFMC), or peripheral blood mononuclear cells (PBMC) from five patients with rheumatoid arthritis (RA) and eight with Lyme arthritis (LA). We identified 1593 non-redundant HLA-DR-presented peptides, derived from 870 source proteins. A total of 67% of the peptides identified in SFMC and 55% of those found in PBMC were found in ST, but analysis of SFMC/PBMC also revealed new antigen-presented peptides. Peptides were synthesized and examined for reactivity with the patients' PBMC. To date, three autoantigens in RA and four novel autoantigens in LA, presented in ST and/or PBMC, were shown to be targets of T- and B-cell responses in these diseases; ongoing analyses may add to this list. Thus, immunoprecipitation and LC-MS/MS can now identify hundreds of HLA-DR-presented self-peptides from individual patients' tissues or fluids with mixed cell populations. Importantly, identification of HLA-DR-presented peptides from SFMC or PBMC allows testing of more patients, including those early in the disease. Direct analysis of clinical samples facilitates identification of novel immunogenic T-cell epitopes.
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Affiliation(s)
- Qi Wang
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
| | - Elise E Drouin
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School , Boston, Massachusetts 02114, United States
| | - Chunxiang Yao
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
| | - Jiyang Zhang
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States.,National University of Defense Technology , Changsha, 410000 Hunan Province, China
| | - Yu Huang
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
| | - Deborah R Leon
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
| | - Allen C Steere
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School , Boston, Massachusetts 02114, United States
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
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67
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Bailey P, Chang DK, Forget MA, Lucas FAS, Alvarez HA, Haymaker C, Chattopadhyay C, Kim SH, Ekmekcioglu S, Grimm EA, Biankin AV, Hwu P, Maitra A, Roszik J. Exploiting the neoantigen landscape for immunotherapy of pancreatic ductal adenocarcinoma. Sci Rep 2016; 6:35848. [PMID: 27762323 PMCID: PMC5071896 DOI: 10.1038/srep35848] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/06/2016] [Indexed: 02/06/2023] Open
Abstract
Immunotherapy approaches for pancreatic ductal adenocarcinoma (PDAC) have met with limited success. It has been postulated that a low mutation load may lead to a paucity of T cells within the tumor microenvironment (TME). However, it is also possible that while neoantigens are present, an effective immune response cannot be generated due to an immune suppressive TME. To discern whether targetable neoantigens exist in PDAC, we performed a comprehensive study using genomic profiles of 221 PDAC cases extracted from public databases. Our findings reveal that: (a) nearly all PDAC samples harbor potentially targetable neoantigens; (b) T cells are present but generally show a reduced activation signature; and (c) markers of efficient antigen presentation are associated with a reduced signature of markers characterizing cytotoxic T cells. These findings suggest that despite the presence of tumor specific neoepitopes, T cell activation is actively suppressed in PDAC. Further, we identify iNOS as a potential mediator of immune suppression that might be actionable using pharmacological avenues.
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Affiliation(s)
- Peter Bailey
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK
| | - David K. Chang
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, United Kingdom
- Department of Surgery, Bankstown Hospital, Eldridge Road, Bankstown, Sydney, New South Wales 2200, Australia
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, New South Wales 2170, Australia
| | - Marie-Andrée Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Francis A. San Lucas
- Departments of Pathology and Translational Molecular Pathology, Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Hector A. Alvarez
- Departments of Pathology and Translational Molecular Pathology, Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Cara Haymaker
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Chandrani Chattopadhyay
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Sun-Hee Kim
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Suhendan Ekmekcioglu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Elizabeth A. Grimm
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Andrew V. Biankin
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, United Kingdom
- Department of Surgery, Bankstown Hospital, Eldridge Road, Bankstown, Sydney, New South Wales 2200, Australia
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, New South Wales 2170, Australia
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Anirban Maitra
- Departments of Pathology and Translational Molecular Pathology, Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
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68
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Caron E, Kowalewski DJ, Chiek Koh C, Sturm T, Schuster H, Aebersold R. Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry. Mol Cell Proteomics 2016; 14:3105-17. [PMID: 26628741 DOI: 10.1074/mcp.o115.052431] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The myriad of peptides presented at the cell surface by class I and class II major histocompatibility complex (MHC) molecules are referred to as the immunopeptidome and are of great importance for basic and translational science. For basic science, the immunopeptidome is a critical component for understanding the immune system; for translational science, exact knowledge of the immunopeptidome can directly fuel and guide the development of next-generation vaccines and immunotherapies against autoimmunity, infectious diseases, and cancers. In this mini-review, we summarize established isolation techniques as well as emerging mass spectrometry-based platforms (i.e. SWATH-MS) to identify and quantify MHC-associated peptides. We also highlight selected biological applications and discuss important current technical limitations that need to be solved to accelerate the development of this field.
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Affiliation(s)
- Etienne Caron
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland;
| | - Daniel J Kowalewski
- §Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Ching Chiek Koh
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Theo Sturm
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Heiko Schuster
- §Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Ruedi Aebersold
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; ¶Faculty of Science, University of Zurich, Zurich, Switzerland
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69
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Bassani-Sternberg M, Coukos G. Mass spectrometry-based antigen discovery for cancer immunotherapy. Curr Opin Immunol 2016; 41:9-17. [PMID: 27155075 DOI: 10.1016/j.coi.2016.04.005] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/19/2016] [Indexed: 12/14/2022]
Abstract
The antigenic landscape of tumors is distinct from healthy cells and has been the rationale behind a variety of vaccination trials. Typically the target tumor-associated antigens have been of self origin and have rarely induced effective anti-tumor responses. Recent data show that activation of the immune system by immune checkpoint blocking therapies leads to tumor rejection and that recognition of mutated antigens, known as 'neo-antigens' plays a key role. Discovery of neo-antigens relies mainly on prediction-based interrogation of the 'mutanome' using genomic information as input, followed by T-cell screening. Recent breakthroughs in mass spectrometry (MS) based immunopeptidomics have allowed the discovery of very large pools of naturally presented peptides, among them neo-epitopes. This review highlights the current progress related to neo-antigens discovery with emphasis on prediction algorithms and MS as well as the synergy of the two methodologies and how they can be exploited to develop effective personalized immunotherapy.
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Affiliation(s)
- Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne Branch & Department of Oncology, CHUV, Lausanne, Switzerland.
| | - George Coukos
- Ludwig Institute for Cancer Research, University of Lausanne Branch & Department of Oncology, CHUV, Lausanne, Switzerland
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70
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Gfeller D, Bassani-Sternberg M, Schmidt J, Luescher IF. Current tools for predicting cancer-specific T cell immunity. Oncoimmunology 2016; 5:e1177691. [PMID: 27622028 DOI: 10.1080/2162402x.2016.1177691] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 04/06/2016] [Accepted: 04/06/2016] [Indexed: 12/20/2022] Open
Abstract
Tumor exome and RNA sequencing data provide a systematic and unbiased view on cancer-specific expression, over-expression, and mutations of genes, which can be mined for personalized cancer vaccines and other immunotherapies. Of key interest are tumor-specific mutations, because T cells recognizing neoepitopes have the potential to be highly tumoricidal. Here, we review recent developments and technical advances in identifying MHC class I and class II-restricted tumor antigens, especially neoantigen derived MHC ligands, including in silico predictions, immune-peptidome analysis by mass spectrometry, and MHC ligand validation by biochemical methods on T cells.
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Affiliation(s)
- David Gfeller
- Ludwig Center for Cancer Research, University of Lausanne, Epalinges, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Julien Schmidt
- Ludwig Center for Cancer Research, University of Lausanne , Epalinges, Switzerland
| | - Immanuel F Luescher
- Ludwig Center for Cancer Research, University of Lausanne , Epalinges, Switzerland
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71
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Richens JL, Spencer HL, Butler M, Cantlay F, Vere KA, Bajaj N, Morgan K, O'Shea P. Rationalising the role of Keratin 9 as a biomarker for Alzheimer's disease. Sci Rep 2016; 6:22962. [PMID: 26973255 PMCID: PMC4789650 DOI: 10.1038/srep22962] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/19/2016] [Indexed: 02/07/2023] Open
Abstract
Keratin 9 was recently identified as an important component of a biomarker panel which demonstrated a high diagnostic accuracy (87%) for Alzheimer's disease (AD). Understanding how a protein which is predominantly expressed in palmoplantar epidermis is implicated in AD may shed new light on the mechanisms underlying the disease. Here we use immunoassays to examine blood plasma expression patterns of Keratin 9 and its relationship to other AD-associated proteins. We correlate this with the use of an in silico analysis tool VisANT to elucidate possible pathways through which the involvement of Keratin 9 may take place. We identify possible links with Dickkopf-1, a negative regulator of the wnt pathway, and propose that the abnormal expression of Keratin 9 in AD blood and cerebrospinal fluid may be a result of blood brain barrier dysregulation and disruption of the ubiquitin proteasome system. Our findings suggest that dysregulated Keratin 9 expression is a consequence of AD pathology but, as it interacts with a broad range of proteins, it may have other, as yet uncharacterized, downstream effects which could contribute to AD onset and progression.
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Affiliation(s)
- Joanna L Richens
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Hannah L Spencer
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Molly Butler
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Fiona Cantlay
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Kelly-Ann Vere
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Nin Bajaj
- Department of Neurology, Nottingham University Hospitals NHS Trust, Queen's Medical Centre, Nottingham, United Kingdom
| | - Kevin Morgan
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Paul O'Shea
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
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72
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Kiefer JD, Neri D. Immunocytokines and bispecific antibodies: two complementary strategies for the selective activation of immune cells at the tumor site. Immunol Rev 2016; 270:178-92. [PMID: 26864112 PMCID: PMC5154379 DOI: 10.1111/imr.12391] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The activation of the immune system for a selective removal of tumor cells represents an attractive strategy for the treatment of metastatic malignancies, which cannot be cured by existing methodologies. In this review, we examine the design and therapeutic potential of immunocytokines and bispecific antibodies, two classes of bifunctional products which can selectively activate the immune system at the tumor site. Certain protein engineering aspects, such as the choice of the antibody format, are common to both classes of therapeutic agents and can have a profound impact on tumor homing performance in vivo of individual products. However, immunocytokines and bispecific antibodies display different mechanisms of action. Future research activities will reveal whether an additive of even synergistic benefit can be obtained from the judicious combination of these two types of biopharmaceutical agents.
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Affiliation(s)
- Jonathan D Kiefer
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland
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73
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Abstract
The past several years can be considered a renaissance era in the treatment of metastatic melanoma. Following a 30-year stretch in which oncologists barely put a dent in a very grim overall survival (OS) rate for these patients, things have rapidly changed course with the recent approval of three new melanoma drugs by the FDA. Both oncogene-targeted therapy and immune checkpoint blockade approaches have shown remarkable efficacy in a subset of melanoma patients and have clearly been game-changers in terms of clinical impact. However, most patients still succumb to their disease, and thus, there remains an urgent need to improve upon current therapies. Fortunately, innovations in molecular medicine have led to many silent gains that have greatly increased our understanding of the nature of cancer biology as well as the complex interactions between tumors and the immune system. They have also allowed for the first time a detailed understanding of an individual patient's cancer at the genomic and proteomic level. This information is now starting to be employed at all stages of cancer treatment, including diagnosis, choice of drug therapy, treatment monitoring, and analysis of resistance mechanisms upon recurrence. This new era of personalized medicine will foreseeably lead to paradigm shifts in immunotherapeutic treatment approaches such as individualized cancer vaccines and adoptive transfer of genetically modified T cells. Advances in xenograft technology will also allow for the testing of drug combinations using in vivo models, a truly necessary development as the number of new drugs needing to be tested is predicted to skyrocket in the coming years. This chapter will provide an overview of recent technological developments in cancer research, and how they are expected to impact future diagnosis, monitoring, and development of novel treatments for metastatic melanoma.
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Affiliation(s)
| | | | | | - Patrick Hwu
- University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Gregory Lizée
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
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74
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Gu H, Ren JM, Jia X, Levy T, Rikova K, Yang V, Lee KA, Stokes MP, Silva JC. Quantitative Profiling of Post-translational Modifications by Immunoaffinity Enrichment and LC-MS/MS in Cancer Serum without Immunodepletion. Mol Cell Proteomics 2015; 15:692-702. [PMID: 26635363 DOI: 10.1074/mcp.o115.052266] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Indexed: 12/24/2022] Open
Abstract
A robust method was developed and optimized for enrichment and quantitative analysis of posttranslational modifications (PTMs) in serum/plasma samples by combining immunoaffinity purification and LC-MS/MS without depletion of abundant proteins. The method was used to survey serum samples of patients with acute myeloid leukemia (AML), breast cancer (BC), and nonsmall cell lung cancer (NSCLC). Peptides were identified from serum samples containing phosphorylation, acetylation, lysine methylation, and arginine methylation. Of the PTMs identified, lysine acetylation (AcK) and arginine mono-methylation (Rme) were more prevalent than other PTMs. Label-free quantitative analysis of AcK and Rme peptides was performed for sera from AML, BC, and NSCLC patients. Several AcK and Rme sites showed distinct abundance distribution patterns across the three cancer types. The identification and quantification of posttranslationally modified peptides in serum samples reported here can be used for patient profiling and biomarker discovery research.
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Affiliation(s)
- Hongbo Gu
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Jian Min Ren
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Xiaoying Jia
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Tyler Levy
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Klarisa Rikova
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Vicky Yang
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Kimberly A Lee
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Matthew P Stokes
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Jeffrey C Silva
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
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75
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Sofron A, Ritz D, Neri D, Fugmann T. High-resolution analysis of the murine MHC class II immunopeptidome. Eur J Immunol 2015; 46:319-28. [PMID: 26495903 DOI: 10.1002/eji.201545930] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/09/2015] [Accepted: 10/19/2015] [Indexed: 02/06/2023]
Abstract
The reliable identification of peptides bound to major histocompatibility complex (MHC) class II is fundamental for the study of the host immune response against pathogens and the pathogenesis of autoimmune conditions. Here, we describe an improved methodology combining immuno-affinity enrichment of MHC class II complexes, optimized elution conditions and quadrupole Orbitrap mass spectrometry-based characterization of the immunopeptidome. The methodology allowed the identification of over 1000 peptides with 1% false discovery rate from 10(8) murine A20 lymphoma cells. The study revealed the I-A(d) -specific motif in high resolution after multisequence alignment. The methodology was generally applied to the purification of MHC class II from cell lines and murine spleens. We identified 2963 peptides from BALB/c and 2712 from C57BL/6 mouse spleens. The identification of peptides bound to MHC class II in vitro and in vivo will facilitate the characterization of T-cell specificities, as well as the development of biotherapeutics and vaccines.
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Affiliation(s)
- Adriana Sofron
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | | | - Dario Neri
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
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76
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Wang Y, Gu LQ. Biomedical diagnosis perspective of epigenetic detections using alpha-hemolysin nanopore. AIMS MATERIALS SCIENCE 2015; 2:448-472. [PMID: 30931380 PMCID: PMC6436813 DOI: 10.3934/matersci.2015.4.448] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The α-hemolysin nanopore has been studied for applications in DNA sequencing, various single-molecule detections, biomolecular interactions, and biochips. The detection of single molecules in a clinical setting could dramatically improve cancer detection and diagnosis as well as develop personalized medicine practices for patients. This brief review shortly presents the current solid state and protein nanopore platforms and their applications like biosensing and sequencing. We then elaborate on various epigenetic detections (like microRNA, G-quadruplex, DNA damages, DNA modifications) with the most widely used alpha-hemolysin pore from a biomedical diagnosis perspective. In these detections, a nanopore electrical current signature was generated by the interaction of a target with the pore. The signature often was evidenced by the difference in the event duration, current level, or both of them. An ideal signature would provide obvious differences in the nanopore signals between the target and the background molecules. The development of cancer biomarker detection techniques and nanopore devices have the potential to advance clinical research and resolve health problems. However, several challenges arise in applying nanopore devices to clinical studies, including super low physiological concentrations of biomarkers resulting in low sensitivity, complex biological sample contents resulting in false signals, and fast translocating speed through the pore resulting in poor detections. These issues and possible solutions are discussed.
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Affiliation(s)
- Yong Wang
- Department of Biological Engineering, Dalton Cardiovascular Research Center, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Li-qun Gu
- Department of Biological Engineering, Dalton Cardiovascular Research Center, University of Missouri-Columbia, Columbia, MO 65211, USA
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77
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Zhang J, Tan K, Meng X, Yang W, Wei H, Sun R, Yin L, Pu Y. Overexpression of G6PD and HSP90 Beta in Mice with Benzene Exposure Revealed by Serum Peptidome Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2015; 12:11241-53. [PMID: 26378550 PMCID: PMC4586672 DOI: 10.3390/ijerph120911241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/15/2015] [Accepted: 09/01/2015] [Indexed: 12/04/2022]
Abstract
The small peptides representation of the original proteins are a valuable source of information that can be used as biomarkers involved in toxicity mechanism for chemical exposure. The aim of this study is to investigate serum peptide biomarkers of benzene exposure. C57BL/6 mice were enrolled into control group and benzene groups of 150 and 300 mg/kg/d Serum peptides were identified by mass spectrometry using an assisted laser desorption ionization/time of flight mass spectrometry (MS). Differential peptide spectra were obtained by tandem mass spectrometry and analyzed by searching the International Protein Index using the Sequest program. Forty-one peptide peaks were found in the range of 1000-10,000 Da molecular weight. Among them, seven peaks showed significantly different expression between exposure groups and control group. Two peptide peaks (1231.2 and 1241.8), which showed a two-fold increase in expression, were sequenced and confirmed as glucose 6-phosphate dehydrogenase (G6PD) and heat shock protein 90 Beta (HSP90 Beta), respectively. Furthermore, the expression of the two proteins in liver cells showed the same trend as in serum. In conclusion, G6PD and HSP90 beta might be the candidate serum biomarkers of benzene exposure. It also provided possible clues for the molecular mechanism of benzene-induced oxidative stress.
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Affiliation(s)
- Juan Zhang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Kehong Tan
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Xing Meng
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Wenwen Yang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Haiyan Wei
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Rongli Sun
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
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78
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Simhadri VL, Banerjee AS, Simon J, Kimchi-Sarfaty C, Sauna ZE. Personalized approaches to the treatment of hemophilia A and B. Per Med 2015; 12:403-415. [PMID: 29771661 DOI: 10.2217/pme.15.6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The recognition that individuals respond differently to the same medication is not new and dates almost to the founding of western medicine. In the last century it came to be recognized that genetic factors influence the heterogeneity of individual responses to medications with respect to both toxicity and effectiveness. Nonetheless, it has been challenging to integrate pharmacogenetic approaches in the routine practice of medicine as the identification of biomarkers is difficult due to the inherent complexity of biological systems. Here, we present potential applications of pharmacogenetics in managing hemophilia A and B. We discuss how predicting and circumventing immunogenicity, an important impediment to treating hemophilia patients, particularly lends itself to a pharmacogenetic approach. In addition, we discuss new trends toward personalizing the management of hemophilia in clinical settings.
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Affiliation(s)
- Vijaya L Simhadri
- Laboratory of Hemostasis, Division of Hematology Research & Review, Center for Biologics Evaluation & Research, Food & Drug Administration, New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Aditi Sengupta Banerjee
- Laboratory of Hemostasis, Division of Hematology Research & Review, Center for Biologics Evaluation & Research, Food & Drug Administration, New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Jonathan Simon
- Laboratory of Hemostasis, Division of Hematology Research & Review, Center for Biologics Evaluation & Research, Food & Drug Administration, New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Chava Kimchi-Sarfaty
- Laboratory of Hemostasis, Division of Hematology Research & Review, Center for Biologics Evaluation & Research, Food & Drug Administration, New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Zuben E Sauna
- Laboratory of Hemostasis, Division of Hematology Research & Review, Center for Biologics Evaluation & Research, Food & Drug Administration, New Hampshire Ave, Silver Spring, MD 20993, USA
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79
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Efficient peptide recovery from secreted recombinant MHC-I molecules expressed via mRNA transfection. Immunol Lett 2015; 165:32-8. [DOI: 10.1016/j.imlet.2015.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 03/24/2015] [Indexed: 12/24/2022]
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80
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Whole Tumor Antigen Vaccines: Where Are We? Vaccines (Basel) 2015; 3:344-72. [PMID: 26343191 PMCID: PMC4494356 DOI: 10.3390/vaccines3020344] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/13/2015] [Accepted: 04/16/2015] [Indexed: 12/19/2022] Open
Abstract
With its vast amount of uncharacterized and characterized T cell epitopes available for activating CD4+ T helper and CD8+ cytotoxic lymphocytes simultaneously, whole tumor antigen represents an attractive alternative source of antigens as compared to tumor-derived peptides and full-length recombinant tumor proteins for dendritic cell (DC)-based immunotherapy. Unlike defined tumor-derived peptides and proteins, whole tumor lysate therapy is applicable to all patients regardless of their HLA type. DCs are essentially the master regulators of immune response, and are the most potent antigen-presenting cell population for priming and activating naïve T cells to target tumors. Because of these unique properties, numerous DC-based immunotherapies have been initiated in the clinics. In this review, we describe the different types of whole tumor antigens that we could use to pulse DCs ex vivo and in vivo. We also discuss the different routes of delivering whole tumor antigens to DCs in vivo and activating them with toll-like receptor agonists.
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81
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Weidanz JA, Doll KL, Mohana-Sundaram S, Wichner T, Lowe DB, Gimlin S, Wawro Weidanz D, Magnusson R, Hawkins OE. Detection of human leukocyte antigen biomarkers in breast cancer utilizing label-free biosensor technology. J Vis Exp 2015:52159. [PMID: 25867039 PMCID: PMC4401383 DOI: 10.3791/52159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
According to the American Cancer Society, more than 200,000 women will be diagnosed with invasive breast cancer each year and approximately 40,000 will die from the disease. The human leukocyte antigen (HLA) class I samples peptides derived from proteasomal degradation of cellular proteins and presents these fragments on the cell surface for interrogation by circulating cytotoxic T lymphocytes (CTL). Generation of T-cell receptor mimic (TCRm) monoclonal antibodies (mAbs) which recognize breast cancer specific peptide/HLA-A*02:01 complexes such as those derived from macrophage migration inhibitory factor (MIF19-27) and NY-ESO-1157-165 enable detection and destruction of breast cancer cells in the absence of an effective anti-tumor CTL response. Intact class I HLA/peptide complexes are shed by breast cancer cells and represent potentially relevant cancer biomarkers. In this work, a breakthrough biomarker screening system for cancer diagnostics incorporating T-cell receptor mimic monoclonal antibodies combined with a novel, label-free biosensor utilizing guided-mode resonance (GMR) sensor technology is presented. Detection of shed MIF/HLA-A*02:01 complexes in MDA-MB-231 cell supernatants, spiked human serum, and patient plasma is demonstrated. The impact of this work could revolutionize personalized medicine through development of companion disease diagnostics for targeted immunotherapies.
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Affiliation(s)
- Jon A Weidanz
- Experimmune, A Center for Immunotherapeutic Development, Department of Immunotherapeutics and Biotechnology, Texas Tech University Health Sciences Center
| | - Krysten L Doll
- Experimmune, A Center for Immunotherapeutic Development, Department of Immunotherapeutics and Biotechnology, Texas Tech University Health Sciences Center
| | - Soumya Mohana-Sundaram
- Experimmune, A Center for Immunotherapeutic Development, Department of Immunotherapeutics and Biotechnology, Texas Tech University Health Sciences Center
| | - Timea Wichner
- Experimmune, A Center for Immunotherapeutic Development, Department of Immunotherapeutics and Biotechnology, Texas Tech University Health Sciences Center
| | - Devin B Lowe
- Experimmune, A Center for Immunotherapeutic Development, Department of Immunotherapeutics and Biotechnology, Texas Tech University Health Sciences Center
| | | | | | | | - Oriana E Hawkins
- Experimmune, A Center for Immunotherapeutic Development, Department of Immunotherapeutics and Biotechnology, Texas Tech University Health Sciences Center;
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82
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Bassani-Sternberg M, Pletscher-Frankild S, Jensen LJ, Mann M. Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation. Mol Cell Proteomics 2015; 14:658-73. [PMID: 25576301 PMCID: PMC4349985 DOI: 10.1074/mcp.m114.042812] [Citation(s) in RCA: 325] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
HLA class I molecules reflect the health state of cells to cytotoxic T cells by presenting a repertoire of endogenously derived peptides. However, the extent to which the proteome shapes the peptidome is still largely unknown. Here we present a high-throughput mass-spectrometry-based workflow that allows stringent and accurate identification of thousands of such peptides and direct determination of binding motifs. Applying the workflow to seven cancer cell lines and primary cells, yielded more than 22,000 unique HLA peptides across different allelic binding specificities. By computing a score representing the HLA-I sampling density, we show a strong link between protein abundance and HLA-presentation (p < 0.0001). When analyzing overpresented proteins - those with at least fivefold higher density score than expected for their abundance - we noticed that they are degraded almost 3 h faster than similar but nonpresented proteins (top 20% abundance class; median half-life 20.8h versus 23.6h, p < 0.0001). This validates protein degradation as an important factor for HLA presentation. Ribosomal, mitochondrial respiratory chain, and nucleosomal proteins are particularly well presented. Taking a set of proteins associated with cancer, we compared the predicted immunogenicity of previously validated T-cell epitopes with other peptides from these proteins in our data set. The validated epitopes indeed tend to have higher immunogenic scores than the other detected HLA peptides. Remarkably, we identified five mutated peptides from a human colon cancer cell line, which have very recently been predicted to be HLA-I binders. Altogether, we demonstrate the usefulness of combining MS-analysis with immunogenesis prediction for identifying, ranking, and selecting peptides for therapeutic use.
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Affiliation(s)
- Michal Bassani-Sternberg
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Sune Pletscher-Frankild
- §Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Lars Juhl Jensen
- §Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Matthias Mann
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany; §Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
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83
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Pandey GS, Sauna ZE. Pharmacogenetics and the Immunogenicity of Protein Therapeutics. J Interferon Cytokine Res 2014; 34:931-937. [DOI: 10.1089/jir.2012.0136] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Gouri S. Pandey
- Laboratory of Hemostasis, Division of Hematology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland
| | - Zuben E. Sauna
- Laboratory of Hemostasis, Division of Hematology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland
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84
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Stratikos E. Regulating adaptive immune responses using small molecule modulators of aminopeptidases that process antigenic peptides. Curr Opin Chem Biol 2014; 23:1-7. [PMID: 25173825 DOI: 10.1016/j.cbpa.2014.08.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/10/2014] [Accepted: 08/12/2014] [Indexed: 01/19/2023]
Abstract
Antigenic peptide processing by intracellular aminopeptidases has emerged recently as an important pathway that regulates adaptive immune responses. Pathogens and cancer can manipulate the activity of key enzymes of this pathway to promote immune evasion. Furthermore, the activity of these enzymes is naturally variable due to polymorphic variation, contributing to predisposition to disease, most notably autoimmunity. Here, we review recent findings that suggest that the pharmacological regulation of the activity of these aminopeptidases constitutes a valid approach for regulating human immune responses. We furthermore review the state of the art in chemical tools for inhibiting these enzymes and how these tools can be useful for the development of innovative therapeutic approaches for a variety of diseases including cancer, viral infections and autoimmunity.
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Affiliation(s)
- Efstratios Stratikos
- National Center for Scientific Research Demokritos, Agia Paraskevi, Athens, Greece.
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85
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Therapeutic targeting of naturally presented myeloperoxidase-derived HLA peptide ligands on myeloid leukemia cells by TCR-transgenic T cells. Leukemia 2014; 28:2355-66. [PMID: 24736212 DOI: 10.1038/leu.2014.131] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 04/01/2014] [Accepted: 04/03/2014] [Indexed: 12/26/2022]
Abstract
T cells have been proven to be therapeutically effective in patients with relapsed leukemias, although target antigens on leukemic cells as well as T-cell receptors (TCRs), potentially recognizing those antigens, are mostly unknown. We have applied an immunopeptidomic approach and isolated human leukocyte antigen (HLA) ligands from primary leukemia cells. We identified a number of ligands derived from different genes that are restrictedly expressed in the hematopoietic system. We exemplarily selected myeloperoxidase (MPO) as a potential target and isolated a high-avidity TCR with specificity for a HLA-B*07:02-(HLA-B7)-restricted epitope of MPO in the single HLA-mismatched setting. T cells transgenic for this TCR demonstrated high peptide and antigen specificity as well as leukemia reactivity in vitro and in vivo. In contrast, no significant on- and off-target toxicity could be observed. In conclusion, we here demonstrate, exemplarily for MPO, that leukemia-derived HLA ligands can be selected for specific effector tool development to redirect T cells to be used for graft manipulation or adoptive T-cell therapies in diverse transplant settings. This approach can be extended to other HLA ligands and HLA molecules in order to provide better treatment options for this life-threatening disease.
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86
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The nature and extent of contributions by defective ribosome products to the HLA peptidome. Proc Natl Acad Sci U S A 2014; 111:E1591-9. [PMID: 24715725 DOI: 10.1073/pnas.1321902111] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
MHC class I peptides are products of endogenous cellular protein degradation. Their prompt presentation, after rapid degradation of their newly synthesized source proteins, is needed to alert the immune system during pathogen infection. A possible source for such rapidly degrading proteins can be defective ribosome products (DRiPs), which include polypeptides produced as part of the pioneer round of translation, premature translation termination, and proteins failing to fold properly or to assemble into their multisubunit protein complexes. However, the identities and relative contribution to the MHC peptidome of these mature or newly synthesized and rapidly degraded cellular proteins is not well understood. To clarify these issues, we used dynamic stable isotope labeling by amino acids in cell culture to define the relative rates of synthesis of the HLA class I peptidomes and the source proteomes of three cultured human hematopoietic cell lines. Large numbers of HLA class I peptides were observed to be derived from DRiPs, defined here as HLA peptides that shift from their light to heavy isotope forms faster than their source proteins. Specific groups of proteins, such as ribosomal and T-complex protein 1 (TCP-1), contributed a disproportionately large number of DRiPs to the HLA peptidomes. Furthermore, no significant preference was observed for HLA peptides derived from the amino terminal regions of the proteins, suggesting that the contribution of products of premature translation termination was minimal. Thus, the most likely sources of DRiPs-derived HLA peptides are full-sized, misassembled, and surplus subunits of large protein complexes.
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87
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Borchers CH, Kast J, Foster LJ, Siu KWM, Overall CM, Binkowski TA, Hildebrand WH, Scherer A, Mansoor M, Keown PA. The Human Proteome Organization Chromosome 6 Consortium: integrating chromosome-centric and biology/disease driven strategies. J Proteomics 2014; 100:60-7. [PMID: 23933161 PMCID: PMC4096956 DOI: 10.1016/j.jprot.2013.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/01/2013] [Indexed: 11/20/2022]
Abstract
The Human Proteome Project (HPP) is designed to generate a comprehensive map of the protein-based molecular architecture of the human body, to provide a resource to help elucidate biological and molecular function, and to advance diagnosis and treatment of diseases. Within this framework, the chromosome-based HPP (C-HPP) has allocated responsibility for mapping individual chromosomes by country or region, while the biology/disease HPP (B/D-HPP) coordinates these teams in cross-functional disease-based groups. Chromosome 6 (Ch6) provides an excellent model for integration of these two tasks. This metacentric chromosome has a complement of 1002-1034 genes that code for known, novel or putative proteins. Ch6 is functionally associated with more than 120 major human diseases, many with high population prevalence, devastating clinical impact and profound societal consequences. The unique combination of genomic, proteomic, metabolomic, phenomic and health services data being drawn together within the Ch6 program has enormous potential to advance personalized medicine by promoting robust biomarkers, subunit vaccines and new drug targets. The strong liaison between the clinical and laboratory teams, and the structured framework for technology transfer and health policy decisions within Canada will increase the speed and efficacy of this transition, and the value of this translational research. BIOLOGICAL SIGNIFICANCE Canada has been selected to play a leading role in the international Human Proteome Project, the global counterpart of the Human Genome Project designed to understand the structure and function of the human proteome in health and disease. Canada will lead an international team focusing on chromosome 6, which is functionally associated with more than 120 major human diseases, including immune and inflammatory disorders affecting the brain, skeletal system, heart and blood vessels, lungs, kidney, liver, gastrointestinal tract and endocrine system. Many of these chronic and persistent diseases have a high population prevalence, devastating clinical impact and profound societal consequences. As a result, they impose a multi-billion dollar economic burden on Canada and on all advanced societies through direct costs of patient care, the loss of health and productivity, and extensive caregiver burden. There is no definitive treatment at the present time for any of these disorders. The manuscript outlines the research which will involve a systematic assessment of all chromosome 6 genes, development of a knowledge base, and development of assays and reagents for all chromosome 6 proteins. We feel that the informatic infrastructure and MRM assays developed will place the chromosome 6 consortium in an excellent position to be a leading player in this major international research initiative. This article is part of a Special Issue: Can Proteomics Fill the Gap Between Genomics and Phenotypes?
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Affiliation(s)
- C H Borchers
- University of Victoria/Genome BC Proteomics Centre, Victoria, BC, Canada
| | - J Kast
- Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - L J Foster
- Centre for High Throughput Biology, University of British Columbia, BC, Canada
| | - K W M Siu
- Centre for Research in Mass Spectrometry, York University, Ontario, Canada
| | - C M Overall
- Centre for Blood Research, Faculty of Dentistry, University of British Columbia, Canada
| | - T A Binkowski
- Midwest Centre for Structural Genomics, Argonne National Laboratory and Computation Institute, University of Chicago, USA
| | - W H Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma, OK, USA
| | - A Scherer
- Australian Genome Research Facility, Walter and Eliza Hall Institute, Parkville, Australia
| | - M Mansoor
- Department Medicine, University of British Columbia, Vancouver, BC, Canada
| | - P A Keown
- Department Medicine, University of British Columbia, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
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88
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Antón LC, Yewdell JW. Translating DRiPs: MHC class I immunosurveillance of pathogens and tumors. J Leukoc Biol 2014; 95:551-62. [PMID: 24532645 PMCID: PMC3958739 DOI: 10.1189/jlb.1113599] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 01/15/2014] [Accepted: 01/19/2014] [Indexed: 11/24/2022] Open
Abstract
MHC class I molecules display oligopeptides on the cell surface to enable T cell immunosurveillance of intracellular pathogens and tumors. Speed is of the essence in detecting viruses, which can complete a full replication cycle in just hours, whereas tumor detection is typically a finding-the-needle-in-the-haystack exercise. We review current evidence supporting a nonrandom, compartmentalized selection of peptidogenic substrates that focuses on rapidly degraded translation products as a main source of peptide precursors to optimize immunosurveillance of pathogens and tumors.
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Affiliation(s)
- Luis C Antón
- 1.NIAID, NIH, Bldg. 33, Bethesda, MD 20892, USA.
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89
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Cancer proteomics. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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90
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Overwijk WW, Wang E, Marincola FM, Rammensee HG, Restifo NP. Mining the mutanome: developing highly personalized Immunotherapies based on mutational analysis of tumors. J Immunother Cancer 2013; 1:11. [PMID: 24829748 PMCID: PMC4019909 DOI: 10.1186/2051-1426-1-11] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 07/22/2013] [Indexed: 11/10/2022] Open
Abstract
T cells can mediate remarkable tumor regressions including complete cure in patients with metastatic cancer. Genetic alterations in an individual's cancer cells (the mutanome) encode unique peptides (m-peptides) that can be targets for T cells. The recent advances in next-generation sequencing and computation prediction allows, for the first time, the rapid and affordable identification of m-peptides in individual patients. Despite excitement about the extended spectrum of potential targets in personalized immunotherapy, there is no experience or consensus on the path to their successful clinical application. Major questions remain, such as whether clinical responses to cytokine therapy, T cell transfer, and checkpoint blockade are primarily mediated by m-peptide-specific reactivity, whether m-peptides can be effectively used as vaccines, and which m-peptides are most potently recognized. These and other technological, immunological and translational questions will be explored during a 1-day Workshop on Personalized Cancer Immunotherapy by the Society for Immunotherapy of Cancer, directly before the Annual Meeting, on November 7, 2013 at the National Harbor, MD near Washington, DC.
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Affiliation(s)
- Willem W Overwijk
- Department of Melanoma Medical Oncology, The University of Texas M.D, Anderson Cancer Center, Houston, TX, USA
| | - Ena Wang
- Infectious Disease and Immunogenetics Section, Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Francesco M Marincola
- Infectious Disease and Immunogenetics Section, Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA ; Sidra Medical and Research Centre, Doha, Qatar
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Nicholas P Restifo
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA ; NIH Center for Regenerative Medicine, National Institutes of Health, Bethesda, MD, USA
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91
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Hemmerle T, Probst P, Giovannoni L, Green AJ, Meyer T, Neri D. The antibody-based targeted delivery of TNF in combination with doxorubicin eradicates sarcomas in mice and confers protective immunity. Br J Cancer 2013; 109:1206-13. [PMID: 23887603 PMCID: PMC3778281 DOI: 10.1038/bjc.2013.421] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 06/26/2013] [Accepted: 07/02/2013] [Indexed: 01/05/2023] Open
Abstract
Background: Soft-tissue sarcomas are a group of malignancies of mesenchymal origin, which typically have a dismal prognosis if they reach the metastatic stage. The observation of rare spontaneous remissions in patients suffering from concomitant bacterial infections had triggered the clinical investigation of the use of heat-killed bacteria as therapeutic agents (Coley's toxin), which induced complete responses in patients in the pre-chemotherapy era and is now known to mediate substantial elevations in serum TNF levels. Methods: We designed and developed a novel immunocytokine based on murine TNF sequentially fused to the antibody fragment F8 (specific to extra-domain A of fibronectin). The antitumor activity was studied in two syngeneic murine sarcoma models. Results: The L19 antibody (specific to extra-domain B of fibronectin) has shown by SPECT imaging procedures to selectively localise on sarcoma in a patient with a peripheral nerve sheath tumour, and immunohistochemical analysis of human soft-tissue sarcoma samples showed comparable antigen expression of EDA and EDB. The antibody-based pharmacodelivery of TNF by the fusion protein ‘F8–TNF' to oncofetal fibronectin in sarcoma-bearing mice leads to complete and long-lasting tumour eradications when administered in combination with doxorubicin, the first-line drug for the treatment of sarcomas in humans. Doxorubicin alone did not display any therapeutic effect in both tested models of this study. The cured mice had acquired protective immunity against the tumour, as they rejected subsequent challenges with sarcoma cells. Conclusion: The findings of this study provide a rationale for the clinical study of the fully human immunocytokine L19-TNF in combination with doxorubicin in patients with soft-tissue sarcoma.
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Affiliation(s)
- T Hemmerle
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
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92
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Milner E, Gutter-Kapon L, Bassani-Strenberg M, Barnea E, Beer I, Admon A. The effect of proteasome inhibition on the generation of the human leukocyte antigen (HLA) peptidome. Mol Cell Proteomics 2013; 12:1853-64. [PMID: 23538226 DOI: 10.1074/mcp.m112.026013] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Major histocompatibility complex (MHC) class I peptidome is thought to be generated mostly through proteasomal degradation of cellular proteins, a notion that is based on the alterations in presentation of selected peptides following proteasome inhibition. We evaluated the effects of proteasome inhibitors, epoxomicin and bortezomib, on human cultured cancer cells. Because the inhibitors did not reduce the level of presentation of the cell surface human leukocyte antigen (HLA) molecules, we followed their effects on the rates of synthesis of both HLA peptidome and proteome of the cells, using dynamic stable isotope labeling in tissue culture (dynamic-SILAC). The inhibitors reduced the rates of synthesis of most cellular proteins and HLA peptides, yet the synthesis rates of some of the proteins and HLA peptides was not decreased by the inhibitors and of some even increased. Therefore, we concluded that the inhibitors affected the production of the HLA peptidome in a complex manner, including modulation of the synthesis rates of the source proteins of the HLA peptides, in addition to their effect on their degradation. The collected data may suggest that the current reliance on proteasome inhibition may overestimate the centrality of the proteasome in the generation of the MHC peptidome. It is therefore suggested that the relative contribution of the proteasomal and nonproteasomal pathways to the production of the MHC peptidome should be revaluated in accordance with the inhibitors effects on the synthesis rates of the source proteins of the MHC peptides.
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Affiliation(s)
- Elena Milner
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
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93
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Abstract
In this issue of Blood, Granados et al explore the relationship between the cellular transcriptome and immunopeptidome,1,2 the repertoire of peptides presented by MHC class I molecules for immunosurveillance.
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94
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Potier DN, Griffiths JR, Unwin RD, Walker MJ, Carrick E, Willamson AJK, Whetton AD. An assessment of peptide enrichment methods employing mTRAQ quantification approaches. Anal Chem 2012; 84:5604-10. [PMID: 22762262 DOI: 10.1021/ac300584y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The human plasma peptidome has potential in biomarker discovery not least because the plasma proteome is a challenging matrix due to its complexity and dynamic range. However, methods to significantly reduce the amount of protein present in plasma while retaining the less abundant peptides present in plasma samples has been a major issue. Here, we present a novel strategy which has been employed to assess the effectiveness of removing interfering proteins while retaining peptides of interest. To monitor peptide retention, a spiked in digested protein, in this case a synthetic QconCAT protein, was employed. This enabled a variety of target analytes (peptides) to be monitored for their retention in liquid phase, providing a broader picture of peptide loss from each method assessed. The incorporation of mTRAQ labeling allowed the presence of each peptide to be monitored, and accurate peptide losses to be determined in a Selected Reaction Monitoring (SRM) assay, thus, enabling an objective semiquantitative conclusion to be drawn regarding the suitability of each method for protein removal and peptide retention. We also assessed a range of methods for retaining nontryptic peptides in a plasma peptidomics workflow. From these data, we determined an optimal workflow for removing intact protein, while retaining peptides for MS-based analyses.
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Affiliation(s)
- David N Potier
- School of Cancer & Enabling Sciences, Wolfson Molecular Imaging Centre, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
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95
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Abstract
Strategies to achieve personalized medicine and improve public health encompass assessment of an individual's risk for disease, early detection, and molecular classification of disease resulting in an informed choice of the most appropriate treatment instituted at an early stage of disease development. An unmet need in this field for which proteomics is well suited to make a major contribution is the development of blood-based tests for early cancer detection. This is illustrated in proteomic studies of epithelial cancer that encompass analysis of specimens collected both at the time of diagnosis and specimens collected before onset of symptoms that are particularly suited for the identification of early detection markers. This overarching effort benefits from the availability of plasmas from subject cohorts and of engineered mouse models that are sampled at early stages of tumor development. Integration of findings from plasma with tumor tissue and cancer cell proteomic and genomic data allows elucidation of signatures in plasma for altered signaling pathways. The discovery and further development of early detection markers take advantage of the availability of in-depth quantitative proteomics methods and bioinformatics resources for data mining.
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96
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97
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Shetty V, Nickens Z, Testa J, Hafner J, Sinnathamby G, Philip R. Quantitative immunoproteomics analysis reveals novel MHC class I presented peptides in cisplatin-resistant ovarian cancer cells. J Proteomics 2012; 75:3270-90. [PMID: 22504797 DOI: 10.1016/j.jprot.2012.03.044] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 03/01/2012] [Accepted: 03/25/2012] [Indexed: 10/28/2022]
Abstract
Platinum-based chemotherapy is widely used to treat various cancers including ovarian cancer. However, the mortality rate for patients with ovarian cancer is extremely high, largely due to chemo-resistant progression in patients who respond initially to platinum based chemotherapy. Immunotherapy strategies, including antigen specific vaccines, are being tested to treat drug resistant ovarian cancer with variable results. The identification of drug resistant specific tumor antigens would potentially provide significant improvement in effectiveness when combined with current and emerging therapies. In this study, using an immunoproteomics method based on iTRAQ technology and an LC-MS platform, we identified 952 MHC class I presented peptides. Quantitative analysis of the iTRAQ labeled MHC peptides revealed that cisplatin-resistant ovarian cancer cells display increased levels of MHC peptides derived from proteins that are implicated in many important cancer pathways. In addition, selected differentially presented epitope specific CTL recognize cisplatin-resistant ovarian cancer cells significantly better than the sensitive cells. These over-presented, drug resistance specific MHC class I associated peptide antigens could be potential targets for the development of immunotherapeutic strategies for the treatment of ovarian cancer including the drug resistant phenotype.
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Affiliation(s)
- Vivekananda Shetty
- Immunotope, Inc., 3805 Old Easton Road, Doylestown, PA 18902, United States.
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98
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Scull KE, Dudek NL, Corbett AJ, Ramarathinam SH, Gorasia DG, Williamson NA, Purcell AW. Secreted HLA recapitulates the immunopeptidome and allows in-depth coverage of HLA A*02:01 ligands. Mol Immunol 2012; 51:136-42. [PMID: 22424782 DOI: 10.1016/j.molimm.2012.02.117] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 02/15/2012] [Accepted: 02/20/2012] [Indexed: 10/28/2022]
Abstract
HLA molecules are cell-surface glycoproteins that present peptides, derived from intracellular protein antigens, for surveillance by T lymphocytes. Secreted HLA (sHLA) technology is a powerful approach for studying these peptides, since it facilitates large-scale production of HLA-bound peptides. We compared secreted and membrane-bound forms of HLA A2 in terms of intracellular trafficking and their bound peptide repertoire (termed the immunopeptidome). We demonstrate that sHLA and membrane bound HLA (mHLA) negotiate intracellular compartments with similar maturation kinetics. Moreover, mass spectrometry revealed a substantial overlap in the immunopeptidome was observed when HLA A2-bound peptides were purified from various sources of sHLA and mHLA. By combining machine based algorithms with manual validation, we identified 1266 non-redundant peptides. Analysis of these peptides revealed a number bearing post-translational modifications, although some of these may arise spontaneously others represent modifications performed within the cell that survive antigen processing. Peptides bearing some of these modifications have not previously been described for HLA ligands, therefore, this compendium of 1266 non-redundant peptide sequences adds greatly to the existing database of HLA A2 ligands. Peptides from all sources displayed comparable HLA A2 consensus binding motifs, peptide lengths, predicted HLA A2 binding affinities and putative source antigens. We conclude that sHLA is a valid and useful technique for studying the immunopeptidome.
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Affiliation(s)
- Katherine E Scull
- Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC, Australia
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99
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Immunocytokines: a novel class of potent armed antibodies. Drug Discov Today 2012; 17:583-90. [PMID: 22289353 DOI: 10.1016/j.drudis.2012.01.007] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 12/14/2011] [Accepted: 01/16/2012] [Indexed: 11/20/2022]
Abstract
Several cytokines have been investigated in clinical trials, based on their potent therapeutic activity observed in animal models of cancer and other diseases. However, substantial toxicities are often reported at low doses, thus preventing escalation to therapeutically active regimens. The use of recombinant antibodies or antibody fragments as delivery vehicles promises to enhance greatly the therapeutic index of pro-inflammatory and anti-inflammatory cytokines. This review surveys preclinical and clinical data published in the field of antibody-cytokine fusions (immunocytokines). Molecular determinants (such as molecular format, valence, target antigen), which crucially contribute to immunocytokine performance in vivo, are discussed in the article, as well as recent trends for the combined use of this novel class of biopharmaceuticals with other therapeutic agents.
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100
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SZABADOS TAMÁS, BAKÁCS TIBOR. SUFFICIENT TO RECOGNIZE SELF TO ATTACK NON-SELF: BLUEPRINT FOR A ONE-SIGNAL T CELL MODEL. J BIOL SYST 2011. [DOI: 10.1142/s0218339011003919] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Current consensus postulates that the class I-antigen processing system is evolved to present microbial antigens to specific T cells. Since such cells are rare and short-lived, they require three to five days to attain fighting strength. During this critical period he innate immune system holds back the briskly multiplying pathogens. Nevertheless, a T cell response is measurable in the lymph nodes draining the infection site within 12 to 18 h. In order to explain this paradox here we suggest a new T cell model. This is based on the observation that T cells require continuous contact of the T cell receptor (TCR) with selecting self-peptide–major histocompatibility complex (MHC) molecules in the periphery for their survival. We postulate that a dynamic steady state, a so-called coupled system is formed through low affinity complementary TCR–MHC interactions between T cells and host cells. Under such condition it is sufficient to recognize what is self in order to attack what is not self. A coupled system is regulated via soluble forms of peptide–MHC and TCR molecules by the law of mass action. In a coupled system one signal is sufficient for T cell activation. The new model implies that a significant fraction of the naive polyclonal T cells are recruited into the first line of defense from the very outset of an infection, so the number of activated T cells is increased by several orders of magnitude compared to conventional models. The one-signal model also predicts that therapeutic administration of soluble agonist or antagonist T cell receptor ligands may be able to fine tune the homeostatic physiological regulatory mechanism and thus improve the treatment of some chronic diseases such as metastatic cancer, HIV/AIDS, and transplantation.
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Affiliation(s)
- TAMÁS SZABADOS
- Department of Mathematics, Budapest University of Technology and Economics, Műegyetem rkp 3, Budapest, 1521, Hungary
| | - TIBOR BAKÁCS
- Alfréd Rényi Institute of Mathematics, Hungarian Academy of Sciences, Reáltanoda u 13-15, Budapest, 1053, Hungary
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