1
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Nenclares P, Larkeryd A, Manodoro F, Lee JY, Lalondrelle S, Gilbert DC, Punta M, O’Leary B, Rullan A, Sadanandam A, Chain B, Melcher A, Harrington KJ, Bhide SA. T-cell receptor determinants of response to chemoradiation in locally-advanced HPV16-driven malignancies. Front Oncol 2024; 13:1296948. [PMID: 38234396 PMCID: PMC10791873 DOI: 10.3389/fonc.2023.1296948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/28/2023] [Indexed: 01/19/2024] Open
Abstract
Background The effect of chemoradiation on the anti-cancer immune response is being increasingly acknowledged; however, its clinical implications in treatment responses are yet to be fully understood. Human papillomavirus (HPV)-driven malignancies express viral oncogenic proteins which may serve as tumor-specific antigens and represent ideal candidates for monitoring the peripheral T-cell receptor (TCR) changes secondary to chemoradiotherapy (CRT). Methods We performed intra-tumoral and pre- and post-treatment peripheral TCR sequencing in a cohort of patients with locally-advanced HPV16-positive cancers treated with CRT. An in silico computational pipeline was used to cluster TCR repertoire based on epitope-specificity and to predict affinity between these clusters and HPV16-derived epitopes. Results Intra-tumoral repertoire diversity, intra-tumoral and post-treatment peripheral CDR3β similarity clustering were predictive of response. In responders, CRT triggered an increase peripheral TCR clonality and clonal relatedness. Post-treatment expansion of baseline peripheral dominant TCRs was associated with response. Responders showed more baseline clustered structures of TCRs maintained post-treatment and displayed significantly more maintained clustered structures. When applying clustering by TCR-specificity methods, responders displayed a higher proportion of intra-tumoral TCRs predicted to recognise HPV16 peptides. Conclusions Baseline TCR characteristics and changes in the peripheral T-cell clones triggered by CRT are associated with treatment outcome. Maintenance and boosting of pre-existing clonotypes are key elements of an effective anti-cancer immune response driven by CRT, supporting a paradigm in which the immune system plays a central role in the success of CRT in current standard-of-care protocols.
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Affiliation(s)
- Pablo Nenclares
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Adrian Larkeryd
- Bioinformatics Unit, The Centre for Translational Immunotherapy, The Institute of Cancer Research, London, United Kingdom
| | - Floriana Manodoro
- Genomics Facility, The Institute of Cancer Research, London, United Kingdom
| | - Jen Y. Lee
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
| | - Susan Lalondrelle
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
| | - Duncan C. Gilbert
- Sussex Cancer Centre, University Hospitals Sussex NHS Foundation Trust, Brighton, United Kingdom
| | - Marco Punta
- Unit of Immunogenetic, Leukemia Genomics and Immunobiology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Ben O’Leary
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Antonio Rullan
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Anguraj Sadanandam
- Systems and Precision Cancer Medicine Team, The Institute of Cancer Research, London, United Kingdom
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Alan Melcher
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
| | - Kevin J. Harrington
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Shreerang A. Bhide
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
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2
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Mota I, Patrucco E, Mastini C, Mahadevan NR, Thai TC, Bergaggio E, Cheong TC, Leonardi G, Karaca-Atabay E, Campisi M, Poggio T, Menotti M, Ambrogio C, Longo DL, Klaeger S, Keshishian H, Sztupinszki ZM, Szallasi Z, Keskin DB, Duke-Cohan JS, Reinhold B, Carr SA, Wu CJ, Moynihan KD, Irvine DJ, Barbie DA, Reinherz EL, Voena C, Awad MM, Blasco RB, Chiarle R. ALK peptide vaccination restores the immunogenicity of ALK-rearranged non-small cell lung cancer. NATURE CANCER 2023; 4:1016-1035. [PMID: 37430060 DOI: 10.1038/s43018-023-00591-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/07/2023] [Indexed: 07/12/2023]
Abstract
Anaplastic lymphoma kinase (ALK)-rearranged non-small cell lung cancer (NSCLC) is treated with ALK tyrosine kinase inhibitors (TKIs), but the lack of activity of immune checkpoint inhibitors (ICIs) is poorly understood. Here, we identified immunogenic ALK peptides to show that ICIs induced rejection of ALK+ tumors in the flank but not in the lung. A single-peptide vaccination restored priming of ALK-specific CD8+ T cells, eradicated lung tumors in combination with ALK TKIs and prevented metastatic dissemination of tumors to the brain. The poor response of ALK+ NSCLC to ICIs was due to ineffective CD8+ T cell priming against ALK antigens and is circumvented through specific vaccination. Finally, we identified human ALK peptides displayed by HLA-A*02:01 and HLA-B*07:02 molecules. These peptides were immunogenic in HLA-transgenic mice and were recognized by CD8+ T cells from individuals with NSCLC, paving the way for the development of a clinical vaccine to treat ALK+ NSCLC.
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Affiliation(s)
- Ines Mota
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Enrico Patrucco
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Cristina Mastini
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Navin R Mahadevan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Tran C Thai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Elisa Bergaggio
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Taek-Chin Cheong
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Giulia Leonardi
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | | | - Marco Campisi
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Teresa Poggio
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Matteo Menotti
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Chiara Ambrogio
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Dario L Longo
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
- Molecular Imaging Center, University of Torino, Torino, Italy
- Institute of Biostructures and Bioimaging (IBB), National Research Council of Italy (CNR), Torino, Italy
| | - Susan Klaeger
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Zsófia M Sztupinszki
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| | - Derin B Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Jonathan S Duke-Cohan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bruce Reinhold
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kelly D Moynihan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Darrell J Irvine
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ellis L Reinherz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Claudia Voena
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Mark M Awad
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Rafael B Blasco
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA.
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.
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3
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Peng X, Woodhouse I, Hancock G, Parker R, Marx K, Müller J, Salatino S, Partridge T, Nicastri A, Liao H, Kruppa G, Hellner K, Dorrell L, Ternette N. Novel canonical and non-canonical viral antigens extend current targets for immunotherapy of HPV-driven cervical cancer. iScience 2023; 26:106101. [PMID: 36876126 PMCID: PMC9978627 DOI: 10.1016/j.isci.2023.106101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/30/2022] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
Current immunotherapeutic approaches for human papillomavirus (HPV)-driven cervical cancer target the viral oncogenes E6 and E7. We report viral canonical and alternative reading frame (ARF)-derived sequences presented on cervical tumor cells, including antigens encoded by the conserved viral gene E1. We confirm immunogenicity of the identified viral peptides in HPV-positive women, and women with cervical intraepithelial neoplasia. We observe consistent transcription of the E1, E6, and E7 genes in 10 primary cervical tumor resections from the four most common high-risk HPV subtypes (HPV16, 18, 31, and 45), suggesting the suitability of E1 as therapeutic target. We finally confirm HLA presentation of canonical peptides derived from E6 and E7, and ARF-derived viral peptides from a reverse-strand transcript spanning the HPV E1 and E2 genes in primary human cervical tumor tissue. Our results extend currently known viral immunotherapeutic targets in cervical cancer and highlight E1 as an important cervical cancer antigen.
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Affiliation(s)
- Xu Peng
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
| | - Isaac Woodhouse
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
| | - Gemma Hancock
- Nuffield Department of Medicine, University of Oxford, OX3 7FZ Oxford, UK
| | - Robert Parker
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
| | - Kristina Marx
- Bruker Daltonics, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Julius Müller
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
| | - Silvia Salatino
- Wellcome Centre Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Thomas Partridge
- Nuffield Department of Medicine, University of Oxford, OX3 7FZ Oxford, UK
| | - Annalisa Nicastri
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
| | - Hanqing Liao
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
| | - Gary Kruppa
- Bruker Daltonics, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Karin Hellner
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, John Radcliffe Hospital, OX3 9DU Oxford, UK
| | - Lucy Dorrell
- Nuffield Department of Medicine, University of Oxford, OX3 7FZ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
- Immunocore Ltd., OX14 4RY Abingdon, UK
| | - Nicola Ternette
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
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4
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Weingarten-Gabbay S, Pearlman LR, Chen DY, Klaeger S, Taylor HB, Welch NL, Keskin DB, Carr SA, Abelin JG, Saeed M, Sabeti PC. HLA-I immunopeptidome profiling of human cells infected with high-containment enveloped viruses. STAR Protoc 2022; 3:101910. [PMID: 36595954 PMCID: PMC9731565 DOI: 10.1016/j.xpro.2022.101910] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/10/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022] Open
Abstract
Immunopeptidome profiling of infected cells is a powerful technique for detecting viral peptides that are naturally processed and loaded onto class I human leukocyte antigens (HLAs-I). Here, we provide a protocol for preparing samples for immunopeptidome profiling that can inactivate enveloped viruses while still preserving the integrity of the HLA-I complex. We detail steps for lysate preparation of infected cells followed by HLA-I immunoprecipitation and virus inactivation. We further describe peptide purification for mass spectrometry outside a high-containment facility. For complete details on the use and execution of this protocol, please refer to Weingarten-Gabbay et al. (2021).1.
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Affiliation(s)
- Shira Weingarten-Gabbay
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA,Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA,Corresponding author
| | | | - Da-Yuan Chen
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Susan Klaeger
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nicole L. Welch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Derin B. Keskin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA,Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA,Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA,Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Howard Hughes Medical Institute, Chevy Chase, MD, USA
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5
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Blagovic K, Smith CK, Ramakrishnan A, Moore L, Soto DR, Thompson Z, Stockmann AP, Kruszelnicki S, Thakkar A, Murray J, Torres S, Wondimagegnhu B, Yi R, Dadgar M, Paracha AM, Page C, Clear L, Chaudhry OA, Myint M, Bridgen DT, Gilbert JB, Seidl KJ, Sharei A, Loughhead S, Bernstein H, Yarar D. Engineered red blood cells (activating antigen carriers) drive potent T cell responses and tumor regression in mice. Front Immunol 2022; 13:1015585. [PMID: 36263022 PMCID: PMC9573954 DOI: 10.3389/fimmu.2022.1015585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/14/2022] [Indexed: 11/22/2022] Open
Abstract
Activation of T cell responses is essential for effective tumor clearance; however, inducing targeted, potent antigen presentation to stimulate T cell responses remains challenging. We generated Activating Antigen Carriers (AACs) by engineering red blood cells (RBCs) to encapsulate relevant tumor antigens and the adjuvant polyinosinic-polycytidylic acid (poly I:C), for use as a tumor-specific cancer vaccine. The processing method and conditions used to create the AACs promote phosphatidylserine exposure on RBCs and thus harness the natural process of aged RBC clearance to enable targeting of the AACs to endogenous professional antigen presenting cells (APCs) without the use of chemicals or viral vectors. AAC uptake, antigen processing, and presentation by APCs drive antigen-specific activation of T cells, both in mouse in vivo and human in vitro systems, promoting polyfunctionality of CD8+ T cells and, in a tumor model, driving high levels of antigen-specific CD8+ T cell infiltration and tumor killing. The efficacy of AAC therapy was further enhanced by combination with the chemotherapeutic agent Cisplatin. In summary, these findings support AACs as a potential vector-free immunotherapy strategy to enable potent antigen presentation and T cell stimulation by endogenous APCs with broad therapeutic potential.
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6
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Jung K, Son MJ, Lee SY, Kim JA, Ko DH, Yoo S, Kim CH, Kim YS. Antibody-mediated delivery of a viral MHC-I epitope into the cytosol of target tumor cells repurposes virus-specific CD8 + T cells for cancer immunotherapy. Mol Cancer 2022; 21:102. [PMID: 35459256 PMCID: PMC9027861 DOI: 10.1186/s12943-022-01574-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 04/13/2022] [Indexed: 12/24/2022] Open
Abstract
Background Redirecting pre-existing virus-specific cytotoxic CD8+ T lymphocytes (CTLs) to tumors by simulating a viral infection of the tumor cells has great potential for cancer immunotherapy. However, this strategy is limited by lack of amenable method for viral antigen delivery into the cytosol of target tumors. Here, we addressed the limit by developing a CD8+T cell epitope-delivering antibody, termed a TEDbody, which was engineered to deliver a viral MHC-I epitope peptide into the cytosol of target tumor cells by fusion with a tumor-specific cytosol-penetrating antibody. Methods To direct human cytomegalovirus (CMV)-specific CTLs against tumors, we designed a series of TEDbodies carrying various CMV pp65 antigen-derived peptides. CMV-specific CTLs from blood of CMV-seropositive healthy donors were expanded for use in in vitro and in vivo experiments. Comprehensive cellular assays were performed to determine the presentation mechanism of TEDbody-mediated CMV peptide-MHC-I complex (CMV-pMHCI) on the surface of target tumor cells and the recognition and lysis by CMV-specific CTLs. In vivo CMV-pMHCI presentation and antitumor efficacy of TEDbody were evaluated in immunodeficient mice bearing human tumors. Results TEDbody delivered the fused epitope peptides into target tumor cells to be intracellularly processed and surface displayed in the form of CMV-pMHCI, leading to disguise target tumor cells as virally infected cells for recognition and lysis by CMV-specific CTLs. When systemically injected into tumor-bearing immunodeficient mice, TEDbody efficiently marked tumor cells with CMV-pMHCI to augment the proliferation and cytotoxic property of tumor-infiltrated CMV-specific CTLs, resulting in significant inhibition of the in vivo tumor growth by redirecting adoptively transferred CMV-specific CTLs. Further, combination of TEDbody with anti-OX40 agonistic antibody substantially enhanced the in vivo antitumor activity. Conclusion Our study offers an effective technology for MHC-I antigen cytosolic delivery. TEDbody may thus have utility as a therapeutic cancer vaccine to redirect pre-existing anti-viral CTLs arising from previously exposed viral infections to attack tumors. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-022-01574-0.
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Affiliation(s)
- Keunok Jung
- Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
| | - Min-Jeong Son
- Department of Molecular Science and Technology, Ajou University, 206 Worldcup-ro, Yeongtong-gu, Suwon, 16499, Republic of Korea
| | - Se-Young Lee
- Department of Molecular Science and Technology, Ajou University, 206 Worldcup-ro, Yeongtong-gu, Suwon, 16499, Republic of Korea
| | - Jeong-Ah Kim
- Department of Molecular Science and Technology, Ajou University, 206 Worldcup-ro, Yeongtong-gu, Suwon, 16499, Republic of Korea
| | - Deok-Han Ko
- Department of Molecular Science and Technology, Ajou University, 206 Worldcup-ro, Yeongtong-gu, Suwon, 16499, Republic of Korea
| | - Sojung Yoo
- Department of Molecular Science and Technology, Ajou University, 206 Worldcup-ro, Yeongtong-gu, Suwon, 16499, Republic of Korea
| | - Chul-Ho Kim
- Department of Molecular Science and Technology, Ajou University, 206 Worldcup-ro, Yeongtong-gu, Suwon, 16499, Republic of Korea.,Department of Otolaryngology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
| | - Yong-Sung Kim
- Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea. .,Department of Molecular Science and Technology, Ajou University, 206 Worldcup-ro, Yeongtong-gu, Suwon, 16499, Republic of Korea.
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7
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Zhang X, Luo M, Dastagir SR, Nixon M, Khamhoung A, Schmidt A, Lee A, Subbiah N, McLaughlin DC, Moore CL, Gribble M, Bayhi N, Amin V, Pepi R, Pawar S, Lyford TJ, Soman V, Mellen J, Carpenter CL, Turka LA, Wickham TJ, Chen TF. Engineered red blood cells as an off-the-shelf allogeneic anti-tumor therapeutic. Nat Commun 2021; 12:2637. [PMID: 33976146 PMCID: PMC8113241 DOI: 10.1038/s41467-021-22898-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/31/2021] [Indexed: 02/03/2023] Open
Abstract
Checkpoint inhibitors and T-cell therapies have highlighted the critical role of T cells in anti-cancer immunity. However, limitations associated with these treatments drive the need for alternative approaches. Here, we engineer red blood cells into artificial antigen-presenting cells (aAPCs) presenting a peptide bound to the major histocompatibility complex I, the costimulatory ligand 4-1BBL, and interleukin (IL)-12. This leads to robust, antigen-specific T-cell expansion, memory formation, additional immune activation, tumor control, and antigen spreading in tumor models in vivo. The presence of 4-1BBL and IL-12 induces minimal toxicities due to restriction to the vasculature and spleen. The allogeneic aAPC, RTX-321, comprised of human leukocyte antigen-A*02:01 presenting the human papilloma virus (HPV) peptide HPV16 E711-19, 4-1BBL, and IL-12 on the surface, activates HPV-specific T cells and promotes effector function in vitro. Thus, RTX-321 is a potential 'off-the-shelf' in vivo cellular immunotherapy for treating HPV + cancers, including cervical and head/neck cancers.
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Affiliation(s)
- Xuqing Zhang
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Mengyao Luo
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Shamael R. Dastagir
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Mellissa Nixon
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Annie Khamhoung
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Andrea Schmidt
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Albert Lee
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Naren Subbiah
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | | | | | - Mary Gribble
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Nicholas Bayhi
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Viral Amin
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Ryan Pepi
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Sneha Pawar
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Timothy J. Lyford
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Vikram Soman
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Jennifer Mellen
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | | | - Laurence A. Turka
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Thomas J. Wickham
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Tiffany F. Chen
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
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8
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Aaes TL, Vandenabeele P. The intrinsic immunogenic properties of cancer cell lines, immunogenic cell death, and how these influence host antitumor immune responses. Cell Death Differ 2021; 28:843-860. [PMID: 33214663 PMCID: PMC7937679 DOI: 10.1038/s41418-020-00658-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 01/30/2023] Open
Abstract
Modern cancer therapies often involve the combination of tumor-directed cytotoxic strategies and generation of a host antitumor immune response. The latter is unleashed by immunotherapies that activate the immune system generating a more immunostimulatory tumor microenvironment and a stronger tumor antigen-specific immune response. Studying the interaction between antitumor cytotoxic therapies, dying cancer cells, and the innate and adaptive immune system requires appropriate experimental tumor models in mice. In this review, we discuss the immunostimulatory and immunosuppressive properties of cancer cell lines commonly used in immunogenic cell death (ICD) studies being apoptosis or necroptosis. We will especially focus on the antigenic component of immunogenicity. While in several cancer cell lines the epitopes of endogenously expressed tumor antigens are known, these intrinsic epitopes are rarely determined in experimental apoptotic or necroptotic ICD settings. Instead by far the most ICD research studies investigate the antigenic response against exogenously expressed model antigens such as ovalbumin or retroviral epitopes (e.g., AH1). In this review, we will argue that the immune response against endogenous tumor antigens and the immunopeptidome profile of cancer cell lines affect the eventual biological readouts in the typical prophylactic tumor vaccination type of experiments used in ICD research, and we will propose additional methods involving immunopeptidome profiling, major histocompatibility complex molecule expression, and identification of tumor-infiltrating immune cells to document intrinsic immunogenicity following different cell death modalities.
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Affiliation(s)
- Tania Løve Aaes
- grid.11486.3a0000000104788040Unit for Cell Clearance in Health and Disease, VIB Center for Inflammation Research, Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium ,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Peter Vandenabeele
- grid.5342.00000 0001 2069 7798Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium ,Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.11486.3a0000000104788040Unit of Molecular Signaling and Cell Death, VIB Center for Inflammation Research, Ghent, Belgium
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9
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Haibe Y, El Husseini Z, El Sayed R, Shamseddine A. Resisting Resistance to Immune Checkpoint Therapy: A Systematic Review. Int J Mol Sci 2020; 21:E6176. [PMID: 32867025 PMCID: PMC7504220 DOI: 10.3390/ijms21176176] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/11/2020] [Accepted: 07/12/2020] [Indexed: 12/14/2022] Open
Abstract
The treatment landscape in oncology has witnessed a major revolution with the introduction of checkpoint inhibitors: anti-PD1, anti-PDL1 and anti-CTLA-4. These agents enhance the immune response towards cancer cells instead of targeting the tumor itself, contrary to standard chemotherapy. Although long-lasting durable responses have been observed with immune checkpoints inhibitors, the response rate remains relatively low in many cases. Some patients respond in the beginning but then eventually develop acquired resistance to treatment and progress. Other patients having primary resistance never respond. Multiple studies have been conducted to further elucidate these variations in response in different tumor types and different individuals. This paper provides an overview of the mechanisms of resistance to immune checkpoint inhibitors and highlights the possible therapeutic approaches under investigation aiming to overcome such resistance in order to improve the clinical outcomes of cancer patients.
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Affiliation(s)
| | | | | | - Ali Shamseddine
- Division of Hematology/Oncology, Department of Internal Medicine, American University of Beirut-Medical Center, Beirut 11-0236, Lebanon; (Y.H.); (Z.E.H.); (R.E.S.)
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10
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Wickström SL, Lövgren T, Volkmar M, Reinhold B, Duke-Cohan JS, Hartmann L, Rebmann J, Mueller A, Melief J, Maas R, Ligtenberg M, Hansson J, Offringa R, Seliger B, Poschke I, Reinherz EL, Kiessling R. Cancer Neoepitopes for Immunotherapy: Discordance Between Tumor-Infiltrating T Cell Reactivity and Tumor MHC Peptidome Display. Front Immunol 2019; 10:2766. [PMID: 31921104 PMCID: PMC6918724 DOI: 10.3389/fimmu.2019.02766] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/12/2019] [Indexed: 12/22/2022] Open
Abstract
Tumor-infiltrating lymphocytes (TIL) are considered enriched for T cells recognizing shared tumor antigens or mutation-derived neoepitopes. We performed exome sequencing and HLA-A*02:01 epitope prediction from tumor cell lines from two HLA-A2-positive melanoma patients whose TIL displayed strong tumor reactivity. The potential neoepitopes were screened for recognition using autologous TIL by immunological assays and presentation on tumor major histocompatibility complex class I (MHC-I) molecules by Poisson detection mass spectrometry (MS). TIL from the patients recognized 5/181 and 3/49 of the predicted neoepitopes, respectively. MS screening detected 3/181 neoepitopes on tumor MHC-I from the first patient but only one was also among those recognized by TIL. Consequently, TIL enriched for neoepitope specificity failed to recognize tumor cells, despite being activated by peptides. For the second patient, only after IFN-γ treatment of the tumor cells was one of 49 predicted neoepitopes detected by MS, and this coincided with recognition by TIL sorted for the same specificity. Importantly, specific T cells could be expanded from patient and donor peripheral blood mononuclear cells (PBMC) for all neoepitopes recognized by TIL and/or detected on tumor MHC-I. In summary, stimulating the appropriate inflammatory environment within tumors may promote neoepitope MHC presentation while expanding T cells in blood may circumvent lack of specific TIL. The discordance in detection between physical and functional methods revealed here can be rationalized and used to improve neoantigen-targeted T cell immunotherapy.
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Affiliation(s)
- Stina L Wickström
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Tanja Lövgren
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Michael Volkmar
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bruce Reinhold
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Jonathan S Duke-Cohan
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Laura Hartmann
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Janina Rebmann
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anja Mueller
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Jeroen Melief
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Roeltje Maas
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Maarten Ligtenberg
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Johan Hansson
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Rienk Offringa
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Isabel Poschke
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany.,DKTK Immune Monitoring Unit, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Ellis L Reinherz
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Rolf Kiessling
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
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11
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Dadar M, Chakraborty S, Dhama K, Prasad M, Khandia R, Hassan S, Munjal A, Tiwari R, Karthik K, Kumar D, Iqbal HMN, Chaicumpa W. Advances in Designing and Developing Vaccines, Drugs and Therapeutic Approaches to Counter Human Papilloma Virus. Front Immunol 2018; 9:2478. [PMID: 30483247 PMCID: PMC6240620 DOI: 10.3389/fimmu.2018.02478] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 10/08/2018] [Indexed: 02/05/2023] Open
Abstract
Human papillomavirus (HPV) is a viral infection with skin-to-skin based transmission mode. HPV annually caused over 500,000 cancer cases including cervical, anogenital and oropharyngeal cancer among others. HPV vaccination has become a public-health concern, worldwide, to prevent the cases of HPV infections including precancerous lesions, cervical cancers, and genital warts especially in adolescent female and male population by launching national programs with international alliances. Currently, available prophylactic and therapeutic vaccines are expensive to be used in developing countries for vaccination programs. The recent progress in immunotherapy, biotechnology, recombinant DNA technology and molecular biology along with alternative and complementary medicinal systems have paved novel ways and valuable opportunities to design and develop effective prophylactic and therapeutic vaccines, drugs and treatment approach to counter HPV effectively. Exploration and more researches on such advances could result in the gradual reduction in the incidences of HPV cases across the world. The present review presents a current global scenario and futuristic prospects of the advanced prophylactic and therapeutic approaches against HPV along with recent patents coverage of the progress and advances in drugs, vaccines and therapeutic regimens to effectively combat HPV infections and its cancerous conditions.
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Affiliation(s)
- Maryam Dadar
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Sandip Chakraborty
- Department of Veterinary Microbiology, College of Veterinary Sciences and Animal Husbandry, West Tripura, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Minakshi Prasad
- Department of Animal Biotechnology, LLR University of Veterinary and Animal Sciences, Hisar, India
| | - Rekha Khandia
- Department of Genetics, Barkatullah University, Bhopal, India
| | - Sameer Hassan
- Department of Biomedical Informatics, National Institute for Research in Tuberculosis, Indian Council of Medical Research, Chennai, India
| | - Ashok Munjal
- Department of Genetics, Barkatullah University, Bhopal, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, U P Pt. Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan, Mathura, India
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Deepak Kumar
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Hafiz M. N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Wanpen Chaicumpa
- Department of Parasitology, Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Faculty of Medicine SIriraj Hospital, Mahidol University, Bangkok, Thailand
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12
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Blatnik R, Mohan N, Bonsack M, Falkenby LG, Hoppe S, Josef K, Steinbach A, Becker S, Nadler WM, Rucevic M, Larsen MR, Salek M, Riemer AB. A Targeted LC-MS Strategy for Low-Abundant HLA Class-I-Presented Peptide Detection Identifies Novel Human Papillomavirus T-Cell Epitopes. Proteomics 2018; 18:e1700390. [PMID: 29603667 PMCID: PMC6033010 DOI: 10.1002/pmic.201700390] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 03/16/2018] [Indexed: 12/12/2022]
Abstract
For rational design of therapeutic vaccines, detailed knowledge about target epitopes that are endogenously processed and truly presented on infected or transformed cells is essential. Many potential target epitopes (viral or mutation-derived), are presented at low abundance. Therefore, direct detection of these peptides remains a challenge. This study presents a method for the isolation and LC-MS3 -based targeted detection of low-abundant human leukocyte antigen (HLA) class-I-presented peptides from transformed cells. Human papillomavirus (HPV) was used as a model system, as the HPV oncoproteins E6 and E7 are attractive therapeutic vaccination targets and expressed in all transformed cells, but present at low abundance due to viral immune evasion mechanisms. The presented approach included preselection of target antigen-derived peptides by in silico predictions and in vitro binding assays. The peptide purification process was tailored to minimize contaminants after immunoprecipitation of HLA-peptide complexes, while keeping high isolation yields of low-abundant target peptides. The subsequent targeted LC-MS3 detection allowed for increased sensitivity, which resulted in successful detection of the known HLA-A2-restricted epitope E711-19 and ten additional E7-derived peptides on the surface of HPV16-transformed cells. T-cell reactivity was shown for all the 11 detected peptides in ELISpot assays, which shows that detection by our approach has high predictive value for immunogenicity. The presented strategy is suitable for validating even low-abundant candidate epitopes to be true immunotherapy targets.
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Affiliation(s)
- Renata Blatnik
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Nitya Mohan
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
| | - Maria Bonsack
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Lasse G. Falkenby
- Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Stephanie Hoppe
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Kathrin Josef
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Alina Steinbach
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Sara Becker
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
| | - Wiebke M. Nadler
- Division of Stem Cells and CancerGerman Cancer Research Center (DKFZ) and Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI‐STEM)HeidelbergGermany
| | - Marijana Rucevic
- Massachusetts General HospitalCenter for Cancer ResearchCharlestownMAUSA
| | - Martin R. Larsen
- Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Mogjiborahman Salek
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Angelika B. Riemer
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
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13
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Dhanda SK, Usmani SS, Agrawal P, Nagpal G, Gautam A, Raghava GPS. Novel in silico tools for designing peptide-based subunit vaccines and immunotherapeutics. Brief Bioinform 2017; 18:467-478. [PMID: 27016393 DOI: 10.1093/bib/bbw025] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 12/19/2022] Open
Abstract
The conventional approach for designing vaccine against a particular disease involves stimulation of the immune system using the whole pathogen responsible for the disease. In the post-genomic era, a major challenge is to identify antigenic regions or epitopes that can stimulate different arms of the immune system. In the past two decades, numerous methods and databases have been developed for designing vaccine or immunotherapy against various pathogen-causing diseases. This review describes various computational resources important for designing subunit vaccines or epitope-based immunotherapy. First, different immunological databases are described that maintain epitopes, antigens and vaccine targets. This is followed by in silico tools used for predicting linear and conformational B-cell epitopes required for activating humoral immunity. Finally, information on T-cell epitope prediction methods is provided that includes indirect methods like prediction of Major Histocompatibility Complex and transporter-associated protein binders. Different studies for validating the predicted epitopes are also examined critically. This review enlists novel in silico resources and tools available for predicting humoral and cell-mediated immune potential. These predicted epitopes could be used for designing epitope-based vaccines or immunotherapy as they may activate the adaptive immunity. Authors emphasized the need to develop tools for the prediction of adjuvants to activate innate and adaptive immune system simultaneously. In addition, attention has also been given to novel prediction methods to predict general therapeutic properties of peptides like half-life, cytotoxicity and immune toxicity.
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14
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Reinherz EL. αβ TCR-mediated recognition: relevance to tumor-antigen discovery and cancer immunotherapy. Cancer Immunol Res 2016; 3:305-12. [PMID: 25847967 DOI: 10.1158/2326-6066.cir-15-0042] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
αβ T lymphocytes sense perturbations in host cellular body components induced by infectious pathogens, oncogenic transformation, or chemical or physical damage. Millions to billions of these lymphocytes are generated through T-lineage development in the thymus, each endowed with a clonally restricted surface T-cell receptor (TCR). An individual TCR has the capacity to recognize a distinct "foreign" peptide among the myriad of antigens that the mammalian host must be capable of detecting. TCRs explicitly distinguish foreign from self-peptides bound to major histocompatibility complex (MHC) molecules. This is a daunting challenge, given that the MHC-linked peptidome consists of thousands of distinct peptides with a relevant nonself target antigen often embedded at low number, among orders of magnitude higher frequency self-peptides. In this Masters of Immunology article, I review how TCR structure and attendant mechanobiology involving nonlinear responses affect sensitivity as well as specificity to meet this requirement. Assessment of human tumor-cell display using state-of-the-art mass spectrometry physical detection methods that quantify epitope copy number can help to provide information about requisite T-cell functional avidity affording protection and/or therapeutic immunity. Future rational CD8 cytotoxic T-cell-based vaccines may follow, targeting virally induced cancers, other nonviral immunogenic tumors, and potentially even nonimmunogenic tumors whose peptide display can be purposely altered by MHC-binding drugs to stimulate immune attack.
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Affiliation(s)
- Ellis L Reinherz
- Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts.
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15
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Cross-Reactivity, Epitope Spreading, and De Novo Immune Stimulation Are Possible Mechanisms of Cross-Protection of Nonvaccine Human Papillomavirus (HPV) Types in Recipients of HPV Therapeutic Vaccines. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2015; 22:679-87. [PMID: 25947147 DOI: 10.1128/cvi.00149-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Numerous versions of human papillomavirus (HPV) therapeutic vaccines designed to treat individuals with established HPV infection, including those with cervical intraepithelial neoplasia (CIN), are in development because approved prophylactic vaccines are not effective once HPV infection is established. As human papillomavirus 16 (HPV-16) is the most commonly detected type worldwide, all versions of HPV therapeutic vaccines contain HPV-16, and some also contain HPV-18. While these two HPV types are responsible for approximately 70% of cervical cancer cases, there are other high-risk HPV types known to cause malignancy. Therefore, it would be of interest to assess whether these HPV therapeutic vaccines may confer cross-protection against other high-risk HPV types. Data available from a few clinical trials that enrolled subjects with CINs regardless of the HPV type(s) present demonstrated clinical responses, as measured by CIN regression, in subjects with both vaccine-matched and nonvaccine HPV types. The currently available evidence demonstrating cross-reactivity, epitope spreading, and de novo immune stimulation as possible mechanisms of cross-protection conferred by investigational HPV therapeutic vaccines is discussed.
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16
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Reinherz EL, Keskin DB, Reinhold B. Forward Vaccinology: CTL Targeting Based upon Physical Detection of HLA-Bound Peptides. Front Immunol 2014; 5:418. [PMID: 25237310 PMCID: PMC4154463 DOI: 10.3389/fimmu.2014.00418] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 08/18/2014] [Indexed: 12/22/2022] Open
Abstract
Vaccine-elicited cytotoxic T lymphocytes (CTL) recognizing conserved fragments of a pathogen's proteome could greatly impact infectious diseases and cancers. Enabling this potential are recent advances in mass spectrometry that identify specific target peptides among the myriad HLA-bound peptides on altered cells. Ultrasensitivity of these physical detection methods allows for the direct assessment of peptide presentation on small numbers of tissue-derived cells. In addition, concurrent advances in immunobiology suggest ways to induce CTLs with requisite functional avidity and tissue deployment. Elicitation of high-avidity resident-memory T cells through vaccination may shift the vaccinology paradigm both for preventive and therapeutic approaches to human disease control.
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Affiliation(s)
- Ellis L Reinherz
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute , Boston, MA , USA ; Department of Medicine, Harvard Medical School , Boston, MA , USA
| | - Derin B Keskin
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute , Boston, MA , USA ; Department of Medicine, Harvard Medical School , Boston, MA , USA
| | - Bruce Reinhold
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute , Boston, MA , USA ; Department of Medicine, Harvard Medical School , Boston, MA , USA
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17
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Big data analytics in immunology: a knowledge-based approach. BIOMED RESEARCH INTERNATIONAL 2014; 2014:437987. [PMID: 25045677 PMCID: PMC4090507 DOI: 10.1155/2014/437987] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/07/2014] [Indexed: 01/27/2023]
Abstract
With the vast amount of immunological data available, immunology research is entering the big data era. These data vary in granularity, quality, and complexity and are stored in various formats, including publications, technical reports, and databases. The challenge is to make the transition from data to actionable knowledge and wisdom and bridge the knowledge gap and application gap. We report a knowledge-based approach based on a framework called KB-builder that facilitates data mining by enabling fast development and deployment of web-accessible immunological data knowledge warehouses. Immunological knowledge discovery relies heavily on both the availability of accurate, up-to-date, and well-organized data and the proper analytics tools. We propose the use of knowledge-based approaches by developing knowledgebases combining well-annotated data with specialized analytical tools and integrating them into analytical workflow. A set of well-defined workflow types with rich summarization and visualization capacity facilitates the transformation from data to critical information and knowledge. By using KB-builder, we enabled streamlining of normally time-consuming processes of database development. The knowledgebases built using KB-builder will speed up rational vaccine design by providing accurate and well-annotated data coupled with tailored computational analysis tools and workflow.
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18
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Zhang GL, Riemer AB, Keskin DB, Chitkushev L, Reinherz EL, Brusic V. HPVdb: a data mining system for knowledge discovery in human papillomavirus with applications in T cell immunology and vaccinology. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau031. [PMID: 24705205 PMCID: PMC3975992 DOI: 10.1093/database/bau031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
High-risk human papillomaviruses (HPVs) are the causes of many cancers, including cervical, anal, vulvar, vaginal, penile and oropharyngeal. To facilitate diagnosis, prognosis and characterization of these cancers, it is necessary to make full use of the immunological data on HPV available through publications, technical reports and databases. These data vary in granularity, quality and complexity. The extraction of knowledge from the vast amount of immunological data using data mining techniques remains a challenging task. To support integration of data and knowledge in virology and vaccinology, we developed a framework called KB-builder to streamline the development and deployment of web-accessible immunological knowledge systems. The framework consists of seven major functional modules, each facilitating a specific aspect of the knowledgebase construction process. Using KB-builder, we constructed the Human Papillomavirus T cell Antigen Database (HPVdb). It contains 2781 curated antigen entries of antigenic proteins derived from 18 genotypes of high-risk HPV and 18 genotypes of low-risk HPV. The HPVdb also catalogs 191 verified T cell epitopes and 45 verified human leukocyte antigen (HLA) ligands. Primary amino acid sequences of HPV antigens were collected and annotated from the UniProtKB. T cell epitopes and HLA ligands were collected from data mining of scientific literature and databases. The data were subject to extensive quality control (redundancy elimination, error detection and vocabulary consolidation). A set of computational tools for an in-depth analysis, such as sequence comparison using BLAST search, multiple alignments of antigens, classification of HPV types based on cancer risk, T cell epitope/HLA ligand visualization, T cell epitope/HLA ligand conservation analysis and sequence variability analysis, has been integrated within the HPVdb. Predicted Class I and Class II HLA binding peptides for 15 common HLA alleles are included in this database as putative targets. HPVdb is a knowledge-based system that integrates curated data and information with tailored analysis tools to facilitate data mining for HPV vaccinology and immunology. To our best knowledge, HPVdb is a unique data source providing a comprehensive list of HPV antigens and peptides. Database URL: http://cvc.dfci.harvard.edu/hpv/.
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Affiliation(s)
- Guang Lan Zhang
- Cancer Vaccine Center, Dana-Farber Cancer Institute, 77 Ave Louis Pasteur, Boston, MA 02115, USA, Department of Computer Science, Metropolitan College, Boston University, 808 Commonwealth Ave, Boston, MA 02215, USA, Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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Lank SM, Golbach BA, Creager HM, Wiseman RW, Keskin DB, Reinherz EL, Brusic V, O'Connor DH. Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing. BMC Genomics 2012; 13:378. [PMID: 22866951 PMCID: PMC3575390 DOI: 10.1186/1471-2164-13-378] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 07/07/2012] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND High-resolution HLA genotyping is a critical diagnostic and research assay. Current methods rarely achieve unambiguous high-resolution typing without making population-specific frequency inferences due to a lack of locus coverage and difficulty in exon-phase matching. Achieving high-resolution typing is also becoming more challenging with traditional methods as the database of known HLA alleles increases. RESULTS We designed a cDNA amplicon-based pyrosequencing method to capture 94% of the HLA class I open-reading-frame with only two amplicons per sample, and an analogous method for class II HLA genes, with a primary focus on sequencing the DRB loci. We present a novel Galaxy server-based analysis workflow for determining genotype. During assay validation, we performed two GS Junior sequencing runs to determine the accuracy of the HLA class I amplicons and DRB amplicon at different levels of multiplexing. When 116 amplicons were multiplexed, we unambiguously resolved 99%of class I alleles to four- or six-digit resolution, as well as 100% unambiguous DRB calls. The second experiment, with 271 multiplexed amplicons, missed some alleles, but generated high-resolution, concordant typing for 93% of class I alleles, and 96% for DRB1 alleles. In a third, preliminary experiment we attempted to sequence novel amplicons for other class II loci with mixed success. CONCLUSIONS The presented assay is higher-throughput and higher-resolution than existing HLA genotyping methods, and suitable for allele discovery or large cohort sampling. The validated class I and DRB primers successfully generated unambiguously high-resolution genotypes, while further work is needed to validate additional class II genotyping amplicons.
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Affiliation(s)
- Simon M Lank
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
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