1
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Christophersen A. Peptide-MHC class I and class II tetramers: From flow to mass cytometry. HLA 2020; 95:169-178. [PMID: 31891448 DOI: 10.1111/tan.13789] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 11/26/2019] [Accepted: 12/30/2019] [Indexed: 12/31/2022]
Abstract
To develop better vaccines and more targeted treatments for cancer and autoimmune disorders, the disease-specific T cells and their cognate antigens need to be better characterized. For more than two decades, peptide-major histocompatibility complex (pMHC) tetramers and flow cytometry have been the gold standard for detection of CD8+ and CD4+ T cells specific to antigens in the context of MHC class I and class II, respectively. Nonetheless, more recent studies combining such reagents with mass cytometry, that is, cytometry by time of flight (CyTOF), have offered far more comprehensive profiling of antigen-specific T-cell responses. In addition, mass cytometry has enabled ex vivo screening of CD8+ T-cell reactivities against hundreds of MHC class I restricted candidate epitopes. MHC class II molecules, on the other hand, have been challenging to combine with mass cytometry as they are more complex and bind with lower affinities to cognate T-cell receptors than MHC class I molecules. In this review, I discuss how techniques originally developed to improve the staining capacity of pMHC tetramers in flow cytometry led to the successful combination of such reagents with mass cytometry. Especially, I will highlight very recent advances facilitating the combination with pMHC class II tetramers. Together, these mass cytometry-based studies can help develop more targeted treatments for cancer and autoimmune disorders.
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Affiliation(s)
- Asbjørn Christophersen
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Norway.,Department of Immunology, University of Oslo, Oslo, Norway
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2
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Lim SY, Rizos H. Immune cell profiling in the age of immune checkpoint inhibitors: implications for biomarker discovery and understanding of resistance mechanisms. Mamm Genome 2018; 29:866-878. [PMID: 29968076 PMCID: PMC6267680 DOI: 10.1007/s00335-018-9757-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/28/2018] [Indexed: 12/27/2022]
Abstract
Immunotherapy has changed the landscape of cancer treatment. The introduction of immune checkpoint inhibitors has seen tremendous success in improving overall survival of patients with advanced metastatic cancers and has now become the standard of care for multiple tumor types. However, efficacy of immune checkpoint blockade appears to be limited to immunogenic cancers, and even amongst immune-reactive cancers, response rates are low and variable between patients. Recent data have also demonstrated the rapid emergence of resistance to immune checkpoint inhibitors, with some patients progressing on treatment within one year. Significant research efforts are now directed at identifying predictive biomarkers and mechanisms of resistance to immune checkpoint blockade. These studies are underpinned by comprehensive and detailed profiling of the immune milieu. In this review, we discuss the utility and efficacy of immune cell profiling to uncover biomarkers of response and mechanisms of resistance to immune checkpoint inhibitors.
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Affiliation(s)
- Su Yin Lim
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia. .,Melanoma Institute Australia, Sydney, NSW, Australia.
| | - Helen Rizos
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, Sydney, NSW, Australia
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3
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Simoni Y, Chng MHY, Li S, Fehlings M, Newell EW. Mass cytometry: a powerful tool for dissecting the immune landscape. Curr Opin Immunol 2018; 51:187-196. [PMID: 29655022 DOI: 10.1016/j.coi.2018.03.023] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 03/25/2018] [Accepted: 03/26/2018] [Indexed: 10/17/2022]
Abstract
Advancement in methodologies for single cell analysis has historically been a major driver of progress in immunology. Currently, high dimensional flow cytometry, mass cytometry and various forms of single cell sequencing-based analysis methods are being widely adopted to expose the staggering heterogeneity of immune cells in many contexts. Here, we focus on mass cytometry, a form of flow cytometry that allows for simultaneous interrogation of more than 40 different marker molecules, including cytokines and transcription factors, without the need for spectral compensation. We argue that mass cytometry occupies an important niche within the landscape of single-cell analysis platforms that enables the efficient and in-depth study of diverse immune cell subsets with an ability to zoom-in on myeloid and lymphoid compartments in various tissues in health and disease. We further discuss the unique features of mass cytometry that are favorable for combining multiplex peptide-MHC multimer technology and phenotypic characterization of antigen specific T cells. By referring to recent studies revealing the complexities of tumor immune infiltrates, we highlight the particular importance of this technology for studying cancer in the context of cancer immunotherapy. Finally, we provide thoughts on current technical limitations and how we imagine these being overcome.
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Affiliation(s)
- Yannick Simoni
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), Singapore
| | - Melissa Hui Yen Chng
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), Singapore
| | - Shamin Li
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), Singapore
| | | | - Evan W Newell
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), Singapore.
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4
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Guillonneau C, David L, Anegon I. Improved Analyses of CD8+ T Cell Specificities Using Multimers of Peptide MHC Complexes Coupled to DNA Barcodes. Transplantation 2018; 101:219-221. [PMID: 28118315 DOI: 10.1097/tp.0000000000001601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Carole Guillonneau
- 1 INSERM, UMR 1064-Center for Research in Transplantation and Immunology, Nantes, F44093 France; CHU de Nantes, ITUN, Nantes, F44093 France; Université de Nantes, Faculté de Médecine, Nantes, F44093 France
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5
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Lim SY, Lee JH, Diefenbach RJ, Kefford RF, Rizos H. Liquid biomarkers in melanoma: detection and discovery. Mol Cancer 2018; 17:8. [PMID: 29343260 PMCID: PMC5772714 DOI: 10.1186/s12943-018-0757-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/02/2018] [Indexed: 12/18/2022] Open
Abstract
A vast array of tumor-derived genetic, proteomic and cellular components are constantly released into the circulation of cancer patients. These molecules including circulating tumor DNA and RNA, proteins, tumor and immune cells are emerging as convenient and accurate liquid biomarkers of cancer. Circulating cancer biomarkers provide invaluable information on cancer detection and diagnosis, prognosticate patient outcomes, and predict treatment response. In this era of effective molecular targeted treatments and immunotherapies, there is now an urgent need to implement use of these circulating biomarkers in the clinic to facilitate personalized therapy. In this review, we present recent findings in circulating melanoma biomarkers, examine the challenges and promise of evolving technologies used for liquid biomarker discovery, and discuss future directions and perspectives in melanoma biomarker research.
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Affiliation(s)
- Su Yin Lim
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, Sydney, NSW, Australia
| | - Jenny H Lee
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, Sydney, NSW, Australia
| | - Russell J Diefenbach
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, Sydney, NSW, Australia
| | - Richard F Kefford
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, Sydney, NSW, Australia.,Department of Medical Oncology, Crown Princess Mary Cancer Centre, Westmead and Blacktown Hospitals, Sydney, NSW, Australia
| | - Helen Rizos
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia. .,Melanoma Institute Australia, Sydney, NSW, Australia. .,Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, Sydney, NSW, 2109, Australia.
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6
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Kranz LM, Birtel M, Hilscher L, Grunwitz C, Petschenka J, Vascotto F, Vormehr M, Voss RH, Kreiter S, Diken M. CIMT 2016: Mechanisms of efficacy in cancer immunotherapy - Report on the 14th Annual Meeting of the Association for Cancer Immunotherapy May 10-12 2016, Mainz, Germany. Hum Vaccin Immunother 2016; 12:2805-2812. [PMID: 27435168 PMCID: PMC5137546 DOI: 10.1080/21645515.2016.1206677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Lena M Kranz
- a TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH , Mainz , Germany.,b Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University , Mainz , Germany
| | - Matthias Birtel
- a TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH , Mainz , Germany.,b Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University , Mainz , Germany
| | - Lina Hilscher
- a TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH , Mainz , Germany
| | - Christian Grunwitz
- a TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH , Mainz , Germany.,c BioNTech RNA Pharmaceuticals GmbH , Mainz , Germany
| | - Jutta Petschenka
- a TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH , Mainz , Germany
| | - Fulvia Vascotto
- a TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH , Mainz , Germany
| | - Mathias Vormehr
- a TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH , Mainz , Germany.,c BioNTech RNA Pharmaceuticals GmbH , Mainz , Germany
| | - Ralf-Holger Voss
- a TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH , Mainz , Germany
| | - Sebastian Kreiter
- a TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH , Mainz , Germany
| | - Mustafa Diken
- a TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH , Mainz , Germany
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7
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Lindestam Arlehamn CS, McKinney DM, Carpenter C, Paul S, Rozot V, Makgotlho E, Gregg Y, van Rooyen M, Ernst JD, Hatherill M, Hanekom WA, Peters B, Scriba TJ, Sette A. A Quantitative Analysis of Complexity of Human Pathogen-Specific CD4 T Cell Responses in Healthy M. tuberculosis Infected South Africans. PLoS Pathog 2016; 12:e1005760. [PMID: 27409590 PMCID: PMC4943605 DOI: 10.1371/journal.ppat.1005760] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/18/2016] [Indexed: 12/13/2022] Open
Abstract
We performed a quantitative analysis of the HLA restriction, antigen and epitope specificity of human pathogen specific responses in healthy individuals infected with M. tuberculosis (Mtb), in a South African cohort as a test case. The results estimate the breadth of T cell responses for the first time in the context of an infection and human population setting. We determined the epitope repertoire of eleven representative Mtb antigens and a large panel of previously defined Mtb epitopes. We estimated that our analytic methods detected 50-75% of the total response in a cohort of 63 individuals. As expected, responses were highly heterogeneous, with responses to a total of 125 epitopes detected. The 66 top epitopes provided 80% coverage of the responses identified in our study. Using a panel of 48 HLA class II-transfected antigen-presenting cells, we determined HLA class II restrictions for 278 epitope/donor recognition events (36% of the total). The majority of epitopes were restricted by multiple HLA alleles, and 380 different epitope/HLA combinations comprised less than 30% of the estimated Mtb-specific response. Our results underline the complexity of human T cell responses at a population level. Efforts to capture and characterize this broad and highly HLA promiscuous Mtb-specific T cell epitope repertoire will require significant peptide multiplexing efforts. We show that a comprehensive "megapool" of Mtb peptides captured a large fraction of the Mtb-specific T cells and can be used to characterize this response.
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Affiliation(s)
- Cecilia S. Lindestam Arlehamn
- La Jolla Institute for Allergy and Immunology, Department of Vaccine Discovery, La Jolla, California, United States of America
| | - Denise M. McKinney
- La Jolla Institute for Allergy and Immunology, Department of Vaccine Discovery, La Jolla, California, United States of America
| | - Chelsea Carpenter
- La Jolla Institute for Allergy and Immunology, Department of Vaccine Discovery, La Jolla, California, United States of America
| | - Sinu Paul
- La Jolla Institute for Allergy and Immunology, Department of Vaccine Discovery, La Jolla, California, United States of America
| | - Virginie Rozot
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Edward Makgotlho
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Yolande Gregg
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Michele van Rooyen
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Joel D. Ernst
- Department of Medicine, Division of Infectious Diseases, New York University School of Medicine, New York, New York, United States of America
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Willem A. Hanekom
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, Department of Vaccine Discovery, La Jolla, California, United States of America
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, Department of Vaccine Discovery, La Jolla, California, United States of America
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8
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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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9
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Yuan J, Hegde PS, Clynes R, Foukas PG, Harari A, Kleen TO, Kvistborg P, Maccalli C, Maecker HT, Page DB, Robins H, Song W, Stack EC, Wang E, Whiteside TL, Zhao Y, Zwierzina H, Butterfield LH, Fox BA. Novel technologies and emerging biomarkers for personalized cancer immunotherapy. J Immunother Cancer 2016. [PMID: 26788324 DOI: 10.1186/s40425-016-0107-3.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The culmination of over a century's work to understand the role of the immune system in tumor control has led to the recent advances in cancer immunotherapies that have resulted in durable clinical responses in patients with a variety of malignancies. Cancer immunotherapies are rapidly changing traditional treatment paradigms and expanding the therapeutic landscape for cancer patients. However, despite the current success of these therapies, not all patients respond to immunotherapy and even those that do often experience toxicities. Thus, there is a growing need to identify predictive and prognostic biomarkers that enhance our understanding of the mechanisms underlying the complex interactions between the immune system and cancer. Therefore, the Society for Immunotherapy of Cancer (SITC) reconvened an Immune Biomarkers Task Force to review state of the art technologies, identify current hurdlers, and make recommendations for the field. As a product of this task force, Working Group 2 (WG2), consisting of international experts from academia and industry, assembled to identify and discuss promising technologies for biomarker discovery and validation. Thus, this WG2 consensus paper will focus on the current status of emerging biomarkers for immune checkpoint blockade therapy and discuss novel technologies as well as high dimensional data analysis platforms that will be pivotal for future biomarker research. In addition, this paper will include a brief overview of the current challenges with recommendations for future biomarker discovery.
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Affiliation(s)
- Jianda Yuan
- Memorial Sloan-Kettering Cancer Center, 1275 New York Ave Box 386, New York, NY 10065 USA
| | - Priti S Hegde
- Genentech, Inc., 1 DNA Way South, San Francisco, CA 94080 USA
| | - Raphael Clynes
- Bristol-Myers Squibb, 3551 Lawrenceville Road, Princeton, NJ 08648 USA
| | - Periklis G Foukas
- Center of Experimental Therapeutics and Ludwig Institute of Cancer Research, University Hospital of Lausanne, Rue du Bugnon 21, 1011 Lausanne, Switzerland ; Department of Pathology, University of Athens Medical School, "Attikon" University Hospital, 1st Rimini St, 12462 Haidari, Greece
| | - Alexandre Harari
- Center of Experimental Therapeutics and Ludwig Institute of Cancer Research, University Hospital of Lausanne, Rue du Bugnon 21, 1011 Lausanne, Switzerland
| | - Thomas O Kleen
- Epiontis GmbH, Rudower Chaussee 29, 12489 Berlin, Germany
| | - Pia Kvistborg
- Netherlands Cancer Institute, Postbus 90203, 1006 BE Amsterdam, Netherlands
| | - Cristina Maccalli
- Italian Network for Biotherapy of Tumors (NIBIT)-Laboratory, c/o Medical Oncology and Immunotherapy, University Hospital of Siena, V.le Bracci,16, Siena, 53100 Italy
| | - Holden T Maecker
- Stanford University Medical Center, 299 Campus Drive, Stanford, CA 94303 USA
| | - David B Page
- Earle A. Chiles Research Institute, Providence Cancer Center, 4805 NE Glisan Street, Portland, OR 97213 USA
| | - Harlan Robins
- Adaptive Technologies, Inc., 1551 Eastlake Avenue East Suite 200, Seattle, WA 98102 USA
| | - Wenru Song
- AstraZeneca, One MedImmune Way, Gaithersburg, MD 20878 USA
| | | | - Ena Wang
- Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
| | - Theresa L Whiteside
- University of Pittsburgh Cancer Institute, 5117 Centre Ave, Suite 1.27, Pittsburgh, PA 15213 USA
| | - Yingdong Zhao
- National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20850 USA
| | - Heinz Zwierzina
- Innsbruck Medical University, Medizinische Klinik, Anichstrasse 35, Innsbruck, A-6020 Austria
| | - Lisa H Butterfield
- Department of Medicine, Surgery and Immunology, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA 15213 USA
| | - Bernard A Fox
- Earle A. Chiles Research Institute, Providence Cancer Center, 4805 NE Glisan Street, Portland, OR 97213 USA
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10
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Yuan J, Hegde PS, Clynes R, Foukas PG, Harari A, Kleen TO, Kvistborg P, Maccalli C, Maecker HT, Page DB, Robins H, Song W, Stack EC, Wang E, Whiteside TL, Zhao Y, Zwierzina H, Butterfield LH, Fox BA. Novel technologies and emerging biomarkers for personalized cancer immunotherapy. J Immunother Cancer 2016; 4:3. [PMID: 26788324 PMCID: PMC4717548 DOI: 10.1186/s40425-016-0107-3] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 01/05/2016] [Indexed: 12/13/2022] Open
Abstract
The culmination of over a century’s work to understand the role of the immune system in tumor control has led to the recent advances in cancer immunotherapies that have resulted in durable clinical responses in patients with a variety of malignancies. Cancer immunotherapies are rapidly changing traditional treatment paradigms and expanding the therapeutic landscape for cancer patients. However, despite the current success of these therapies, not all patients respond to immunotherapy and even those that do often experience toxicities. Thus, there is a growing need to identify predictive and prognostic biomarkers that enhance our understanding of the mechanisms underlying the complex interactions between the immune system and cancer. Therefore, the Society for Immunotherapy of Cancer (SITC) reconvened an Immune Biomarkers Task Force to review state of the art technologies, identify current hurdlers, and make recommendations for the field. As a product of this task force, Working Group 2 (WG2), consisting of international experts from academia and industry, assembled to identify and discuss promising technologies for biomarker discovery and validation. Thus, this WG2 consensus paper will focus on the current status of emerging biomarkers for immune checkpoint blockade therapy and discuss novel technologies as well as high dimensional data analysis platforms that will be pivotal for future biomarker research. In addition, this paper will include a brief overview of the current challenges with recommendations for future biomarker discovery.
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Affiliation(s)
- Jianda Yuan
- Memorial Sloan-Kettering Cancer Center, 1275 New York Ave Box 386, New York, NY 10065 USA
| | - Priti S Hegde
- Genentech, Inc., 1 DNA Way South, San Francisco, CA 94080 USA
| | - Raphael Clynes
- Bristol-Myers Squibb, 3551 Lawrenceville Road, Princeton, NJ 08648 USA
| | - Periklis G Foukas
- Center of Experimental Therapeutics and Ludwig Institute of Cancer Research, University Hospital of Lausanne, Rue du Bugnon 21, 1011 Lausanne, Switzerland ; Department of Pathology, University of Athens Medical School, "Attikon" University Hospital, 1st Rimini St, 12462 Haidari, Greece
| | - Alexandre Harari
- Center of Experimental Therapeutics and Ludwig Institute of Cancer Research, University Hospital of Lausanne, Rue du Bugnon 21, 1011 Lausanne, Switzerland
| | - Thomas O Kleen
- Epiontis GmbH, Rudower Chaussee 29, 12489 Berlin, Germany
| | - Pia Kvistborg
- Netherlands Cancer Institute, Postbus 90203, 1006 BE Amsterdam, Netherlands
| | - Cristina Maccalli
- Italian Network for Biotherapy of Tumors (NIBIT)-Laboratory, c/o Medical Oncology and Immunotherapy, University Hospital of Siena, V.le Bracci,16, Siena, 53100 Italy
| | - Holden T Maecker
- Stanford University Medical Center, 299 Campus Drive, Stanford, CA 94303 USA
| | - David B Page
- Earle A. Chiles Research Institute, Providence Cancer Center, 4805 NE Glisan Street, Portland, OR 97213 USA
| | - Harlan Robins
- Adaptive Technologies, Inc., 1551 Eastlake Avenue East Suite 200, Seattle, WA 98102 USA
| | - Wenru Song
- AstraZeneca, One MedImmune Way, Gaithersburg, MD 20878 USA
| | | | - Ena Wang
- Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
| | - Theresa L Whiteside
- University of Pittsburgh Cancer Institute, 5117 Centre Ave, Suite 1.27, Pittsburgh, PA 15213 USA
| | - Yingdong Zhao
- National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20850 USA
| | - Heinz Zwierzina
- Innsbruck Medical University, Medizinische Klinik, Anichstrasse 35, Innsbruck, A-6020 Austria
| | - Lisa H Butterfield
- Department of Medicine, Surgery and Immunology, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA 15213 USA
| | - Bernard A Fox
- Earle A. Chiles Research Institute, Providence Cancer Center, 4805 NE Glisan Street, Portland, OR 97213 USA
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11
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Cohen CJ, Gartner JJ, Horovitz-Fried M, Shamalov K, Trebska-McGowan K, Bliskovsky VV, Parkhurst MR, Ankri C, Prickett TD, Crystal JS, Li YF, El-Gamil M, Rosenberg SA, Robbins PF. Isolation of neoantigen-specific T cells from tumor and peripheral lymphocytes. J Clin Invest 2015; 125:3981-91. [PMID: 26389673 DOI: 10.1172/jci82416] [Citation(s) in RCA: 290] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/13/2015] [Indexed: 12/19/2022] Open
Abstract
Adoptively transferred tumor-infiltrating T lymphocytes (TILs) that mediate complete regression of metastatic melanoma have been shown to recognize mutated epitopes expressed by autologous tumors. Here, in an attempt to develop a strategy for facilitating the isolation, expansion, and study of mutated antigen-specific T cells, we performed whole-exome sequencing on matched tumor and normal DNA isolated from 8 patients with metastatic melanoma. Candidate mutated epitopes were identified using a peptide-MHC-binding algorithm, and these epitopes were synthesized and used to generate panels of MHC tetramers that were evaluated for binding to tumor digests and cultured TILs used for the treatment of patients. This strategy resulted in the identification of 9 mutated epitopes from 5 of the 8 patients tested. Cells reactive with 8 of the 9 epitopes could be isolated from autologous peripheral blood, where they were detected at frequencies that were estimated to range between 0.4% and 0.002%. To the best of our knowledge, this represents the first demonstration of the successful isolation of mutation-reactive T cells from patients' peripheral blood prior to immune therapy, potentially providing the basis for designing personalized immunotherapies to treat patients with advanced cancer.
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12
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New technologies for monitoring human antigen-specific T cells and regulatory T cells by flow-cytometry. Curr Opin Pharmacol 2015; 23:17-24. [DOI: 10.1016/j.coph.2015.04.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 04/24/2015] [Indexed: 11/24/2022]
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13
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Tang Q, Nie F, Kang J, Ding H, Zhou P, Huang J. NIEluter: Predicting peptides eluted from HLA class I molecules. J Immunol Methods 2015; 422:22-7. [PMID: 25862605 DOI: 10.1016/j.jim.2015.03.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 02/18/2015] [Accepted: 03/31/2015] [Indexed: 11/30/2022]
Abstract
The immune system has evolved to make a diverse repertoire of peptides processed from self and foreign proteomes, which are displayed in antigen-binding grooves of major histocompatibility complex (MHC) proteins at cell surface for surveillance by T cells. These antigenic peptides are termed Naturally Processed Peptides or Naturally Presented Peptides (NPPs), which play a major role in cell-mediated immunity and rational vaccine design. Therefore, it is intensely desirable to predict NPPs from a given protein antigen, or to foretell if an MHC-binding peptide can be eluted from a given MHC protein. In this paper, we describe NIEluter, an ensemble predictor based on support vector machine (SVM). It consists of a combination of five SVM models trained with position-specific amino acid composition, position-specific dipeptide composition, Hidden Markov Model, binary encoding, and BLOSUM62 feature. NIEluter can predict NPPs of length 8-11 from six HLA alleles (A0201, B0702, B3501, B4403, B5301, and B5701) at present. Evaluated with five-fold cross-validation and independent datasets if available, NIEluter shows good performance. It outperforms MHC-NP in 7 out of 24 types of situation and precedes NetMHC3.2 in most cases, indicating that it is a helpful complement to available tools. NIEluter has been implemented as a free web service, which can be accessed at http://immunet.cn/nie/cgi-bin/nieluter.pl.
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Affiliation(s)
- Qiang Tang
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Fulei Nie
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Juanjuan Kang
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hui Ding
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China; Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Peng Zhou
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China; Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Jian Huang
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China; Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
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14
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Alexander T, Bondanza A, Muraro PA, Greco R, Saccardi R, Daikeler T, Kazmi M, Hawkey C, Simoes BP, Leblanc K, Fibbe WE, Moore J, Snarski E, Martin T, Hiepe F, Velardi A, Toubert A, Snowden JA, Farge D. SCT for severe autoimmune diseases: consensus guidelines of the European Society for Blood and Marrow Transplantation for immune monitoring and biobanking. Bone Marrow Transplant 2014; 50:173-80. [PMID: 25387090 PMCID: PMC4317973 DOI: 10.1038/bmt.2014.251] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/01/2014] [Indexed: 12/19/2022]
Abstract
Over the past 15 years, SCT has emerged as a promising treatment option for patients with severe autoimmune diseases (ADs). Mechanistic studies recently provided the proof-of-concept that restoration of immunological tolerance can be achieved by haematopoietic SCT in chronic autoimmunity through eradication of the pathologic, immunologic memory and profound reconfiguration of the immune system, that is, immune ‘resetting'. Nevertheless, a number of areas remain unresolved and warrant further investigation to refine our understanding of the underlying mechanisms of action and to optimize clinical SCT protocols. Due to the low number of patients transplanted in each centre, it is essential to adequately collect and analyse biological samples in a larger cohort of patients under standardized conditions. The European society for blood and marrow transplantation Autoimmune Diseases and Immunobiology Working Parties have, therefore, undertaken a joint initiative to develop and implement guidelines for ‘good laboratory practice' in relation to procurement, processing, storage and analysis of biological specimens for immune reconstitution studies in AD patients before, during and after SCT. The aim of this document is to provide practical recommendations for biobanking of samples and laboratory immune monitoring in patients with ADs undergoing SCT, both for routine supportive care purposes and investigational studies.
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Affiliation(s)
- T Alexander
- Department of Rheumatology and Clinical Immunology, Charité-University Medicine Berlin, Berlin, Germany
| | - A Bondanza
- Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milano, Italy
| | - P A Muraro
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK
| | - R Greco
- Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milano, Italy
| | - R Saccardi
- Cord Blood Bank, Haematology department, Careggi University Hospital, Florence, Italy
| | - T Daikeler
- Department of Rheumatology, University Hospital Basel, Basel, Switzerland
| | - M Kazmi
- Department of Haematology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - C Hawkey
- Nottingham Digestive Diseases Centre, Nottingham, UK
| | - B P Simoes
- Department of Clinical Medicine, School of Medicine, University of Sao Paulo, Ribeirao Preto, Brazil
| | - K Leblanc
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - W E Fibbe
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, Leiden, The Netherlands
| | - J Moore
- Department of Haematology, St Vincent's Hospital, Darlinghurst, Sydney, Australia
| | - E Snarski
- Department of Hematology, Oncology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - T Martin
- Strasbourg University Hospital, Strasbourg, France
| | - F Hiepe
- Department of Rheumatology and Clinical Immunology, Charité-University Medicine Berlin, Berlin, Germany
| | - A Velardi
- Department of Medicine, Division of Haematology, University of Perugia, Perugia, Italy
| | - A Toubert
- Inserm U1160, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Hôpital Saint-Louis, Laboratoire d'Immunologie, Paris, France
| | - J A Snowden
- Department of Haematology, Sheffield Teaching Hospitals NHS Foundation Trust & University of Sheffield, Sheffield, UK
| | - D Farge
- Saint Louis Hospital, Unité de Médecine interne et Pathologie Vasculaire, Assistance Publique des Hôpitaux de Paris, Paris 7 University, INSERM U1160, Paris, France
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