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Li D, Xia L, Zhang X, Liu Y, Wang Z, Guo Q, Huang P, Leng W, Qin S. A new high-throughput screening methodology for the discovery of cancer-testis antigen using multi-omics data. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024; 250:108193. [PMID: 38678957 DOI: 10.1016/j.cmpb.2024.108193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/09/2024] [Accepted: 04/20/2024] [Indexed: 05/01/2024]
Abstract
BACKGROUND Cancer/testis antigens (CTAs), also known as tumor-specific antigens (TSAs) are specifically expressed in cancer cells and exhibit high immunogenicity, making them promising targets for immunotherapy and cancer vaccines. METHODS A new integrated high-throughput screening methodology for CTAs was proposed in this study through combining DNA methylation and RNA sequencing data. Briefly, the genes with increased transcript level and decreased DNA methylation were identified by multi-omics analysis. RNA sequencing studies in cell lines exposed to DNA methyltransferase (DNMT) inhibitors were performed to validate the inherent causal relationship between DNA hypomethylation and gene expression upregulation. RESULTS We proposed a new integrated high-throughput screening methodology for identification of CTAs using multi-omics analysis. In addition, we tested the feasibility of this method using gastric cancer (GC) as an example. In GC, we identified over 2000 primary candidate CTAs and ultimately identified 20 CTAs with significant tissue-specificity, including a testis-specific serine protease TESSP1/PRSS41. Integrated analysis confirmed that PRSS41 expression was reactivated in gastrointestinal cancers by promoter DNA hypomethylation at the CpG site (cg08104780). Additionally, DNA hypomethylation of PRSS41 predicted a poor prognosis in GC. CONCLUSION We propose a new high-throughput screening method for the identification of CTAs in cancer and validate its effectiveness. Our work emphasizes that serine protease PRSS41 is a novel TSA that is reactivated in GC due to promoter DNA hypomethylation.
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Affiliation(s)
- Dandan Li
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, Hubei, China; Laboratory of Tumor biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, PR China; Shiyan Key Laboratory of Natural Medicine Nanoformulation Research, Hubei University of Medicine, Shiyan, Hubei 442000, China
| | - Lingyun Xia
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Xiangang Zhang
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, Hubei, China; Laboratory of Tumor biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, PR China
| | - Yue Liu
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, Hubei, China; Laboratory of Tumor biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, PR China
| | - Zidi Wang
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, Hubei, China; Laboratory of Tumor biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, PR China
| | - Qiwei Guo
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, Hubei, China; Laboratory of Tumor biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, PR China
| | - Pan Huang
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, Hubei, China; Laboratory of Tumor biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, PR China
| | - Weidong Leng
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Shanshan Qin
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, Hubei, China; Laboratory of Tumor biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, PR China; Shiyan Key Laboratory of Natural Medicine Nanoformulation Research, Hubei University of Medicine, Shiyan, Hubei 442000, China.
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2
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Sueangoen N, Grove H, Chuangchot N, Prasopsiri J, Rungrotmongkol T, Sanachai K, Darai N, Thongchot S, Suriyaphol P, Sa-Nguanraksa D, Thuwajit P, Yenchitsomanus PT, Thuwajit C. Stimulating T cell responses against patient-derived breast cancer cells with neoantigen peptide-loaded peripheral blood mononuclear cells. Cancer Immunol Immunother 2024; 73:43. [PMID: 38349410 PMCID: PMC10864427 DOI: 10.1007/s00262-024-03627-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/06/2024] [Indexed: 02/15/2024]
Abstract
Breast cancer stands as a formidable global health challenge for women. While neoantigens exhibit efficacy in activating T cells specific to cancer and instigating anti-tumor immune responses, the accuracy of neoantigen prediction remains suboptimal. In this study, we identified neoantigens from the patient-derived breast cancer cells, PC-B-142CA and PC-B-148CA cells, utilizing whole-genome and RNA sequencing. The pVAC-Seq pipeline was employed, with minor modification incorporating criteria (1) binding affinity of mutant (MT) peptide with HLA (IC50 MT) ≤ 500 nm in 3 of 5 algorithms and (2) IC50 wild type (WT)/MT > 1. Sequencing results unveiled 2513 and 3490 somatic mutations, and 646 and 652 non-synonymous mutations in PC-B-142CA and PC-B-148CA, respectively. We selected the top 3 neoantigens to perform molecular dynamic simulation and synthesized 9-12 amino acid neoantigen peptides, which were then pulsed onto healthy donor peripheral blood mononuclear cells (PBMCs). Results demonstrated that T cells activated by ADGRL1E274K, PARP1E619K, and SEC14L2R43Q peptides identified from PC-B-142CA exhibited significantly increased production of interferon-gamma (IFN-γ), while PARP1E619K and SEC14L2R43Q peptides induced the expression of CD107a on T cells. The % tumor cell lysis was notably enhanced by T cells activated with MT peptides across all three healthy donors. Moreover, ALKBH6V83M and GAAI823T peptides from PC-B-148CA remarkably stimulated IFN-γ- and CD107a-positive T cells, displaying high cell-killing activity against target cancer cells. In summary, our findings underscore the successful identification of neoantigens with anti-tumor T cell functions and highlight the potential of personalized neoantigens as a promising avenue for breast cancer treatment.
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Grants
- R016341038 The Research and Innovation Grant, the National Research Council of Thailand, Ministry of Higher Education, Science, Research and Innovation
- R016341038 The Research and Innovation Grant, the National Research Council of Thailand, Ministry of Higher Education, Science, Research and Innovation
- R016334002 Siriraj Research Grant, Faculty of Medicine Siriraj Hospital, Mahidol University
- R016334002 Siriraj Research Grant, Faculty of Medicine Siriraj Hospital, Mahidol University
- Mahidol University
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Affiliation(s)
- Natthaporn Sueangoen
- Graduate Program in Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Harald Grove
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nisa Chuangchot
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jaturawitt Prasopsiri
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thanyada Rungrotmongkol
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Kamonpan Sanachai
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Nitchakan Darai
- ASEAN Institute for Health Development, Mahidol University, Nakon Pathom, Thailand
| | - Suyanee Thongchot
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Prapat Suriyaphol
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Doonyapat Sa-Nguanraksa
- Division of Head Neck and Breast Surgery, Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Peti Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pa-Thai Yenchitsomanus
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chanitra Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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3
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Rodriguez GM, Yakubovich E, Murshed H, Maranda V, Galpin KJ, Cudmore A, Hanna AMR, Macdonald E, Ramesh S, Garson K, Vanderhyden BC. NLRC5 overexpression in ovarian tumors remodels the tumor microenvironment and increases T-cell reactivity toward autologous tumor-associated antigens. Front Immunol 2024; 14:1295208. [PMID: 38235131 PMCID: PMC10791902 DOI: 10.3389/fimmu.2023.1295208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/04/2023] [Indexed: 01/19/2024] Open
Abstract
Introduction Epithelial ovarian cancer (OC) stands as one of the deadliest gynecologic malignancies, urgently necessitating novel therapeutic strategies. Approximately 60% of ovarian tumors exhibit reduced expression of major histocompatibility complex class I (MHC I), intensifying immune evasion mechanisms and rendering immunotherapies ineffective. NOD-like receptor CARD domain containing 5 (NLRC5) transcriptionally regulates MHC I genes and many antigen presentation machinery components. We therefore explored the therapeutic potential of NLRC5 in OC. Methods We generated OC cells overexpressing NLRC5 to rescue MHC I expression and antigen presentation and then assessed their capability to respond to PD-L1 blockade and an infected cell vaccine. Results Analysis of microarray datasets revealed a correlation between elevated NLRC5 expression and extended survival in OC patients; however, NLRC5 was scarcely detected in the OC tumor microenvironment. OC cells overexpressing NLRC5 exhibited slower tumor growth and resulted in higher recruitment of leukocytes in the TME with lower CD4/CD8 T-cell ratios and increased activation of T cells. Immune cells from peripheral blood, spleen, and ascites from these mice displayed heightened activation and interferon-gamma production when exposed to autologous tumor-associated antigens. Finally, as a proof of concept, NLRC5 overexpression within an infected cell vaccine platform enhanced responses and prolonged survival in comparison with control groups when challenged with parental tumors. Discussion These findings provide a compelling rationale for utilizing NLRC5 overexpression in "cold" tumor models to enhance tumor susceptibility to T-cell recognition and elimination by boosting the presentation of endogenous tumor antigens. This approach holds promise for improving antitumoral immune responses in OC.
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Affiliation(s)
- Galaxia M. Rodriguez
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Edward Yakubovich
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Humaira Murshed
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Vincent Maranda
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Kristianne J.C. Galpin
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Alison Cudmore
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Andrew M. R. Hanna
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Elizabeth Macdonald
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Shashankan Ramesh
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Kenneth Garson
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Barbara C. Vanderhyden
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
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4
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Custodio JM, Ayres CM, Rosales TJ, Brambley CA, Arbuiso AG, Landau LM, Keller GLJ, Srivastava PK, Baker BM. Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes. Proc Natl Acad Sci U S A 2023; 120:e2312057120. [PMID: 38085776 PMCID: PMC10742377 DOI: 10.1073/pnas.2312057120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/23/2023] [Indexed: 12/18/2023] Open
Abstract
Neoepitopes arising from amino acid substitutions due to single nucleotide polymorphisms are targets of T cell immune responses to cancer and are of significant interest in the development of cancer vaccines. However, understanding the characteristics of rare protective neoepitopes that truly control tumor growth has been a challenge, due to their scarcity as well as the challenge of verifying true, neoepitope-dependent tumor control in humans. Taking advantage of recent work in mouse models that circumvented these challenges, here, we compared the structural and physical properties of neoepitopes that range from fully protective to immunologically inactive. As neoepitopes are derived from self-peptides that can induce immune tolerance, we studied not only how the various neoepitopes differ from each other but also from their wild-type counterparts. We identified multiple features associated with protection, including features that describe how neoepitopes differ from self as well as features associated with recognition by diverse T cell receptor repertoires. We demonstrate both the promise and limitations of neoepitope structural analysis and predictive modeling and illustrate important aspects that can be incorporated into neoepitope prediction pipelines.
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Affiliation(s)
- Jean M. Custodio
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Cory M. Ayres
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Tatiana J. Rosales
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Chad A. Brambley
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Alyssa G. Arbuiso
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Lauren M. Landau
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Grant L. J. Keller
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Pramod K. Srivastava
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT06030
| | - Brian M. Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
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5
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Guerra C, Kalaitsidou M, Kueberuwa G, Hawkins R, Edmondson R. Engineering strategies to optimise adoptive cell therapy in ovarian cancer. Cancer Treat Rev 2023; 121:102632. [PMID: 37837788 DOI: 10.1016/j.ctrv.2023.102632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/16/2023]
Abstract
Ovarian cancer is amongst the ten most common cancer types in women, and it is one of the leading causes of death. Despite the promising results of targeted therapies, including anti-angiogenic agents and poly (ADP-ribose) polymerase inhibitors (PARPi), the majority of patients will relapse and develop treatment resistance, implying that novel therapeutic strategies are required. Adoptive cell therapy (ACT) refers to the process by which autologous immune cells are used to eliminate cancer. Examples include tumour infiltrating lymphocytes (TILs), T cells genetically engineered with T cell receptors (TCR), or chimeric antigen receptor (CAR)-T cells. Recently, ACT has revealed promising results in the treatment of haematological malignancies, however, its application to solid tumours is still limited due to lack of functionality and persistence of T cells, prevalence of an exhausted phenotype and impaired trafficking towards the tumour microenvironment (TME). In this review we explore the potential of ACT for the treatment of ovarian cancer and strategies to overcome its principal limitations.
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Affiliation(s)
- Catarina Guerra
- InstilBio UK, 48 Grafton St, Manchester M13 9XX, Manchester, United Kingdom; School of Medical Sciences, The University of Manchester, Oxford Rd, Manchester, United Kingdom.
| | - Milena Kalaitsidou
- InstilBio UK, 48 Grafton St, Manchester M13 9XX, Manchester, United Kingdom.
| | - Gray Kueberuwa
- InstilBio UK, 48 Grafton St, Manchester M13 9XX, Manchester, United Kingdom.
| | - Robert Hawkins
- InstilBio UK, 48 Grafton St, Manchester M13 9XX, Manchester, United Kingdom.
| | - Richard Edmondson
- School of Medical Sciences, The University of Manchester, Oxford Rd, Manchester, United Kingdom.
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6
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Annapragada A, Sikora AG, Marathe H, Liu S, Demetriou M, Fong L, Gao J, Kufe D, Morris ZS, Vilar E, Sharon E, Hutson A, Odunsi K. The Cancer Moonshot Immuno-Oncology Translational Network at 5: accelerating cancer immunotherapies. J Natl Cancer Inst 2023; 115:1262-1270. [PMID: 37572314 PMCID: PMC10637038 DOI: 10.1093/jnci/djad151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 07/29/2023] [Indexed: 08/14/2023] Open
Abstract
The Immuno-Oncology Translational Network (IOTN) was established in 2018 as part of the Cancer Moonshot. In 2022, President Joe Biden set new goals to reduce the cancer death rate by half within 25 years and improve the lives of people with cancer and cancer survivors. The IOTN is focused on accelerating translation of cancer immunology research, from bench to bedside, and improving immunotherapy outcomes across a wide array of cancers in the adult population. The unique structure and team science approach of the IOTN is designed to accelerate discovery and evaluation of novel immune-based therapeutic and prevention strategies. In this article, we describe IOTN progress to date, including new initiatives and the development of a robust set of resources to advance cancer immunology research. We summarize new insights by IOTN researchers, some of which are ripe for translation for several types of cancers. Looking to the future, we identify barriers to the translation of immuno-oncology concepts into clinical trials and key areas for action and improvements that are suitable for high-yield investments. Based on these experiences, we recommend novel National Institutes of Health funding mechanisms and development of new resources to address these barriers.
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Affiliation(s)
- Ananth Annapragada
- Edward B. Singleton Department of Radiology, Texas Children’s Hospital and Baylor College of Medicine, Houston, TX, USA
| | - Andrew G Sikora
- Department of Head and Neck Surgery, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Himangi Marathe
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Michael Demetriou
- Department of Neurology, University of California, Irvine, Irvine, CA, USA
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, USA
| | - Lawrence Fong
- Department Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Parker Institute of Cancer Immunotherapy, San Francisco, CA, USA
| | - Jinming Gao
- Department of Pharmacology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Otolaryngology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biomedical Engineering, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Donald Kufe
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Zachary S Morris
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, USA
| | - Eduardo Vilar
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elad Sharon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alan Hutson
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Kunle Odunsi
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA
- Department of Obstetrics and Gynecology, The University of Chicago, Chicago, IL, USA
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7
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Wu M, Zhou S. Harnessing tumor immunogenomics: Tumor neoantigens in ovarian cancer and beyond. Biochim Biophys Acta Rev Cancer 2023; 1878:189017. [PMID: 37935309 DOI: 10.1016/j.bbcan.2023.189017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
Ovarian cancer is a major cause of death among gynecological cancers due to its highly aggressive nature. Immunotherapy has emerged as a promising avenue for ovarian cancer treatment, offering targeted approaches with reduced off-target effects. With the advent of next-generation sequencing, it has become possible to identify genomic alterations that can serve as potential targets for immunotherapy. Furthermore, immunogenomics research has revealed the importance of genetic alterations in shaping the cancer immune responses. However, the heterogeneity of immunogenicity and the low tumor mutation burden pose challenges for neoantigen-based immunotherapies. Further research is needed to identify neoantigen-specific tumor-infiltrating lymphocytes (TIL) and establish guidelines for patient inclusion criteria in TIL-based therapy. The study of neoantigens and their implications in ovarian cancer immunotherapy holds great promise, and efforts focused on personalized treatment strategies, refined neoantigen selection, and optimized therapeutic combinations will contribute to improving patient outcomes in the future.
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Affiliation(s)
- Mengrui Wu
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, PR China
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, PR China.
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8
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Zhu Y, Li X, Chen T, Wang J, Zhou Y, Mu X, Du Y, Wang J, Tang J, Liu J. Personalised neoantigen-based therapy in colorectal cancer. Clin Transl Med 2023; 13:e1461. [PMID: 37921274 PMCID: PMC10623652 DOI: 10.1002/ctm2.1461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 11/04/2023] Open
Abstract
Colorectal cancer (CRC) has become one of the most common tumours with high morbidity, mortality and distinctive evolution mechanism. The neoantigens arising from the somatic mutations have become considerable treatment targets in the management of CRC. As cancer-specific aberrant peptides, neoantigens can trigger the robust host immune response and exert anti-tumour effects while minimising the emergence of adverse events commonly associated with alternative therapeutic regimens. In this review, we summarised the mechanism, generation, identification and prognostic significance of neoantigens, as well as therapeutic strategies challenges of neoantigen-based therapy in CRC. The evidence suggests that the establishment of personalised neoantigen-based therapy holds great promise as an effective treatment approach for patients with CRC.
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Affiliation(s)
- Ya‐Juan Zhu
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Xiong Li
- Department of GastroenterologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Ting‐Ting Chen
- The Second Clinical Medical College of Lanzhou UniversityLanzhouChina
| | - Jia‐Xiang Wang
- Department of Renal Cancer and MelanomaPeking University Cancer Hospital & InstituteBeijingChina
| | - Yi‐Xin Zhou
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Xiao‐Li Mu
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Yang Du
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Jia‐Ling Wang
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Jie Tang
- Clinical Trial CenterWest China HospitalSichuan UniversityChengduChina
| | - Ji‐Yan Liu
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
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9
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Molvi Z, Klatt MG, Dao T, Urraca J, Scheinberg DA, O'Reilly RJ. The landscape of MHC-presented phosphopeptides yields actionable shared tumor antigens for cancer immunotherapy across multiple HLA alleles. J Immunother Cancer 2023; 11:e006889. [PMID: 37775115 PMCID: PMC10546156 DOI: 10.1136/jitc-2023-006889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Certain phosphorylated peptides are differentially presented by major histocompatibility complex (MHC) molecules on cancer cells characterized by aberrant phosphorylation. Phosphopeptides presented in complex with the human leukocyte antigen HLA-A*02:01 provide a stability advantage over their non-phosphorylated counterparts. This stability is thought to contribute to enhanced immunogenicity. Whether tumor-associated phosphopeptides presented by other common alleles exhibit immunogenicity and structural characteristics similar to those presented by A*02:01 is unclear. Therefore, we determined the identity, structural features, and immunogenicity of phosphopeptides presented by the prevalent alleles HLA-A*03:01, HLA-A*11:01, HLA-C*07:01, and HLA-C*07:02. METHODS We isolated peptide-MHC complexes by immunoprecipitation from 11 healthy and neoplastic tissue samples using mass spectrometry, and then combined the resulting data with public immunopeptidomics data sets to assemble a curated set of phosphopeptides presented by 96 samples spanning 20 distinct healthy and neoplastic tissue types. We determined the biochemical features of selected phosphopeptides by in vitro binding assays and in silico docking, and their immunogenicity by analyzing healthy donor T cells for phosphopeptide-specific multimer binding and cytokine production. RESULTS We identified a subset of phosphopeptides presented by HLA-A*03:01, A*11:01, C*07:01 and C*07:02 on multiple tumor types, particularly lymphomas and leukemias, but not healthy tissues. These phosphopeptides are products of genes essential to lymphoma and leukemia survival. The presented phosphopeptides generally exhibited similar or worse binding to A*03:01 than their non-phosphorylated counterparts. HLA-C*07:01 generally presented phosphopeptides but not their unmodified counterparts. Phosphopeptide binding to HLA-C*07:01 was dependent on B-pocket interactions that were absent in HLA-C*07:02. While HLA-A*02:01 and HLA-A*11:01 phosphopeptide-specific T cells could be readily detected in an autologous setting even when the non-phosphorylated peptide was co-presented, HLA-A*03:01 or HLA-C*07:01 phosphopeptides were repeatedly non-immunogenic, requiring use of allogeneic T cells to induce phosphopeptide-specific T cells. CONCLUSIONS Phosphopeptides presented by multiple alleles that are differentially expressed on tumors constitute tumor-specific antigens that could be targeted for cancer immunotherapy, but the immunogenicity of such phosphopeptides is not a general feature. In particular, phosphopeptides presented by HLA-A*02:01 and A*11:01 exhibit consistent immunogenicity, while phosphopeptides presented by HLA-A*03:01 and C*07:01, although appropriately presented, are not immunogenic. Thus, to address an expanded patient population, phosphopeptide-targeted immunotherapies should be wary of allele-specific differences.
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Affiliation(s)
- Zaki Molvi
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Martin G Klatt
- Department of Hematology, Oncology and Tumor Immunology, Charite Universitatsmedizin Berlin, Berlin, Germany
- German Cancer Research Center, Heidelberg, Baden-Württemberg, Germany
- Berlin Institute of Health at Charité -Universitätsmedizin Berlin, BIH Biomedical 13 Innovation Academy, BIH Charité Clinician Scientist Program, Berlin, Germany
| | - Tao Dao
- Department of Pediatrics, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jessica Urraca
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David A Scheinberg
- Department of Pediatrics, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medicine, New York, New York, USA
| | - Richard J O'Reilly
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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10
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Millar DG, Yang SYC, Sayad A, Zhao Q, Nguyen LT, Warner K, Sangster AG, Nakatsugawa M, Murata K, Wang BX, Shaw P, Clarke B, Bernardini MQ, Pugh T, Thibault P, Hirano N, Perreault C, Ohashi PS. Identification of antigenic epitopes recognized by tumor infiltrating lymphocytes in high grade serous ovarian cancer by multi-omics profiling of the auto-antigen repertoire. Cancer Immunol Immunother 2023:10.1007/s00262-023-03413-7. [PMID: 36943460 DOI: 10.1007/s00262-023-03413-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/16/2023] [Indexed: 03/23/2023]
Abstract
Immunotherapeutic strategies aimed at enhancing tumor cell killing by tumor-specific T cells hold great potential for reducing tumor burden and prolonging survival of cancer patients. Although many potential tumor antigens have been described, identifying relevant targets when designing anti-cancer vaccines or targeted cell therapies remains a challenge. To identify novel, potentially immunogenic candidate tumor antigens, we performed integrated tumor transcriptomic, seromic, and proteomic analyses of high grade serous ovarian cancer (HGSC) patient tumor samples. We identified tumor neo-antigens and over-expressed antigens using whole exome and RNA sequencing and examined these in relation to patient-matched auto-antibody repertoires. Focusing on MHC class I epitopes recognized by CD8+ T cells, HLA-binding epitopes were identified or predicted from the highly expressed, mutated, or auto-antibody target antigen, or MHC-associated peptides (MAPs). Recognition of candidate antigenic peptides was assessed within the tumor-infiltrating T lymphocyte (TIL) population expanded from each patient. Known tumor-associated antigens (TAA) and cancer/testis antigens (CTA) were commonly found in the auto-antibody and MAP repertoires and CD8+ TILs recognizing epitopes from these antigens were detected, although neither expression level nor the presence of auto-antibodies correlated with TIL recognition. Auto-antibodies against tumor-mutated antigens were found in most patients, however, no TIL recognition of the highest predicted affinity neo-epitopes was detected. Using high expression level, auto-antibody recognition, and epitope prediction algorithms, we identified epitopes in 5 novel antigens (MOB1A, SOCS3, TUBB, PRKAR1A, CCDC6) recognized by HGSC patient TILs. Furthermore, selection of epitopes from the MAP repertoire identified 5 additional targets commonly recognized by multiple patient TILs. We find that the repertoire of TIL specificities includes recognition of highly expressed and immunogenic self-antigens that are processed and presented by tumors. These results indicate an ongoing autoimmune response against a range of self-antigens targeted by HGSC TILs.
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Affiliation(s)
- Douglas G Millar
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - S Y Cindy Yang
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Azin Sayad
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Qingchuan Zhao
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Linh T Nguyen
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Kathrin Warner
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Ami G Sangster
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Munehide Nakatsugawa
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Kenji Murata
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Ben X Wang
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Patricia Shaw
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Blaise Clarke
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Marcus Q Bernardini
- Division of Gynecologic Oncology, Cancer Clinical Research Unit (CCRU), Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Trevor Pugh
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Naoto Hirano
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Pamela S Ohashi
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada.
- Department of Immunology, University of Toronto, Toronto, ON, Canada.
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11
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Neoantigens: promising targets for cancer therapy. Signal Transduct Target Ther 2023; 8:9. [PMID: 36604431 PMCID: PMC9816309 DOI: 10.1038/s41392-022-01270-x] [Citation(s) in RCA: 139] [Impact Index Per Article: 139.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/14/2022] [Accepted: 11/27/2022] [Indexed: 01/07/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development and regulatory approval of tumor immunotherapies, including cancer vaccines, adoptive cell therapy and antibody-based therapies, especially for solid tumors. Neoantigens are newly formed antigens generated by tumor cells as a result of various tumor-specific alterations, such as genomic mutation, dysregulated RNA splicing, disordered post-translational modification, and integrated viral open reading frames. Neoantigens are recognized as non-self and trigger an immune response that is not subject to central and peripheral tolerance. The quick identification and prediction of tumor-specific neoantigens have been made possible by the advanced development of next-generation sequencing and bioinformatic technologies. Compared to tumor-associated antigens, the highly immunogenic and tumor-specific neoantigens provide emerging targets for personalized cancer immunotherapies, and serve as prospective predictors for tumor survival prognosis and immune checkpoint blockade responses. The development of cancer therapies will be aided by understanding the mechanism underlying neoantigen-induced anti-tumor immune response and by streamlining the process of neoantigen-based immunotherapies. This review provides an overview on the identification and characterization of neoantigens and outlines the clinical applications of prospective immunotherapeutic strategies based on neoantigens. We also explore their current status, inherent challenges, and clinical translation potential.
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12
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Castro A, Kaabinejadian S, Yari H, Hildebrand W, Zanetti M, Carter H. Subcellular location of source proteins improves prediction of neoantigens for immunotherapy. EMBO J 2022; 41:e111071. [PMID: 36314681 PMCID: PMC9753441 DOI: 10.15252/embj.2022111071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 12/23/2022] Open
Abstract
Antigen presentation via the major histocompatibility complex (MHC) is essential for anti-tumor immunity. However, the rules that determine which tumor-derived peptides will be immunogenic are still incompletely understood. Here, we investigated whether constraints on peptide accessibility to the MHC due to protein subcellular location are associated with peptide immunogenicity potential. Analyzing over 380,000 peptides from studies of MHC presentation and peptide immunogenicity, we find clear spatial biases in both eluted and immunogenic peptides. We find that including parent protein location improves the prediction of peptide immunogenicity in multiple datasets. In human immunotherapy cohorts, the location was associated with a neoantigen vaccination response, and immune checkpoint blockade responders generally had a higher burden of neopeptides from accessible locations. We conclude that protein subcellular location adds important information for optimizing cancer immunotherapies.
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Affiliation(s)
- Andrea Castro
- Bioinformatics and Systems Biology ProgramUniversity of California San DiegoLa JollaCAUSA
| | - Saghar Kaabinejadian
- Department of Microbiology and ImmunologyUniversity of Oklahoma Health Sciences CenterOklahoma CityOKUSA
- Pure MHC LLCOklahoma CityOKUSA
| | - Hooman Yari
- Department of Microbiology and ImmunologyUniversity of Oklahoma Health Sciences CenterOklahoma CityOKUSA
| | - William Hildebrand
- Department of Microbiology and ImmunologyUniversity of Oklahoma Health Sciences CenterOklahoma CityOKUSA
| | - Maurizio Zanetti
- The Laboratory of Immunology and Department of MedicineUniversity of California San DiegoLa JollaCAUSA
- Moores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
| | - Hannah Carter
- Moores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
- Department of Medicine, Division of Medical GeneticsUniversity of California San DiegoLa JollaCAUSA
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13
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Tian Y, Hu D, Li Y, Yang L. Development of therapeutic vaccines for the treatment of diseases. MOLECULAR BIOMEDICINE 2022; 3:40. [PMID: 36477638 PMCID: PMC9729511 DOI: 10.1186/s43556-022-00098-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/24/2022] [Indexed: 12/12/2022] Open
Abstract
Vaccines are one of the most effective medical interventions to combat newly emerging and re-emerging diseases. Prophylactic vaccines against rabies, measles, etc., have excellent effectiveness in preventing viral infection and associated diseases. However, the host immune response is unable to inhibit virus replication or eradicate established diseases in most infected people. Therapeutic vaccines, expressing specific endogenous or exogenous antigens, mainly induce or boost cell-mediated immunity via provoking cytotoxic T cells or elicit humoral immunity via activating B cells to produce specific antibodies. The ultimate aim of a therapeutic vaccine is to reshape the host immunity for eradicating a disease and establishing lasting memory. Therefore, therapeutic vaccines have been developed for the treatment of some infectious diseases and chronic noncommunicable diseases. Various technological strategies have been implemented for the development of therapeutic vaccines, including molecular-based vaccines (peptide/protein, DNA and mRNA vaccines), vector-based vaccines (bacterial vector vaccines, viral vector vaccines and yeast-based vaccines) and cell-based vaccines (dendritic cell vaccines and genetically modified cell vaccines) as well as combinatorial approaches. This review mainly summarizes therapeutic vaccine-induced immunity and describes the development and status of multiple types of therapeutic vaccines against infectious diseases, such as those caused by HPV, HBV, HIV, HCV, and SARS-CoV-2, and chronic noncommunicable diseases, including cancer, hypertension, Alzheimer's disease, amyotrophic lateral sclerosis, diabetes, and dyslipidemia, that have been evaluated in recent preclinical and clinical studies.
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Affiliation(s)
- Yaomei Tian
- grid.412605.40000 0004 1798 1351College of Bioengineering, Sichuan University of Science & Engineering, No. 519, Huixing Road, Zigong, Sichuan 643000 The People’s Republic of China ,grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041 The People’s Republic of China
| | - Die Hu
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041 The People’s Republic of China
| | - Yuhua Li
- grid.410749.f0000 0004 0577 6238Department of Arboviral Vaccine, National Institutes for Food and Drug Control, Tiantan Xili, Dongcheng District, Beijing, 100050 The People’s Republic of China
| | - Li Yang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041 The People’s Republic of China
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14
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Kandalaft LE, Dangaj Laniti D, Coukos G. Immunobiology of high-grade serous ovarian cancer: lessons for clinical translation. Nat Rev Cancer 2022; 22:640-656. [PMID: 36109621 DOI: 10.1038/s41568-022-00503-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/28/2022] [Indexed: 11/09/2022]
Abstract
Treatment of high-grade serous ovarian cancer (HGSOC) remains challenging. Although HGSOC can potentially be responsive to immunotherapy owing to endogenous immunity at the molecular or T cell level, immunotherapy for this disease has fallen short of expectations to date. This Review proposes a working classification for HGSOC based on the presence or absence of intraepithelial T cells, and elaborates the putative mechanisms that give rise to such immunophenotypes. These differences might explain the failures of existing immunotherapies, and suggest that rational therapeutic approaches tailored to each immunophenotype might meet with improved success. In T cell-inflamed tumours, treatment could focus on mobilizing pre-existing immunity and strengthening the activation of T cells embedded in intraepithelial tumour myeloid niches. Conversely, in immune-excluded and immune-desert tumours, treatment could focus on restoring inflammation by reprogramming myeloid cells, stromal cells and vascular epithelial cells. Poly(ADP-ribose) polymerase (PARP) inhibitors, low-dose radiotherapy, epigenetic drugs and anti-angiogenesis therapy are among the tools available to restore T cell infiltration in HGSOC tumours and could be implemented in combination with vaccines and redirected T cells.
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Affiliation(s)
- Lana E Kandalaft
- Ludwig Institute for Cancer Research, Lausanne Branch, and Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Denarda Dangaj Laniti
- Ludwig Institute for Cancer Research, Lausanne Branch, and Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne Branch, and Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland.
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15
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Research progress of neoantigens in gynecologic cancers. Int Immunopharmacol 2022; 112:109236. [PMID: 36113318 DOI: 10.1016/j.intimp.2022.109236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 09/01/2022] [Accepted: 09/04/2022] [Indexed: 11/24/2022]
Abstract
The incidence and mortality of gynecological cancers have increased over the past decade. In the absence of effective treatment strategies, many advanced patients develop resistance to conventional therapies and have poor prognosis. Neoantigens have emerged as a novel tumor-specific antigen (TSA) that arises from genomic mutations in tumor cells. With higher immunogenicity than tumor-associated antigens (TAA), they have no risk of developing autoimmune response, leading them an attractive candidate for tumor therapeutic vaccines. With the development of next-generation sequencing (NGS) technology, the identification of neoantigens has been gradually improved, and the scope of application of neoantigen vaccines has continued to expand. Combined with other therapies such as immune-checkpoint inhibitors (ICIs) or adoptive cell therapy (ACT), the application of neoantigen in gynecological cancers has extended to clinical practice. Here, we reviewed the preclinical and clinical studies of neoantigens in gynecological cancers.
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16
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T-Cell Receptor Repertoire Sequencing and Its Applications: Focus on Infectious Diseases and Cancer. Int J Mol Sci 2022; 23:ijms23158590. [PMID: 35955721 PMCID: PMC9369427 DOI: 10.3390/ijms23158590] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/17/2022] Open
Abstract
The immune system is a dynamic feature of each individual and a footprint of our unique internal and external exposures. Indeed, the type and level of exposure to physical and biological agents shape the development and behavior of this complex and diffuse system. Many pathological conditions depend on how our immune system responds or does not respond to a pathogen or a disease or on how the regulation of immunity is altered by the disease itself. T-cells are important players in adaptive immunity and, together with B-cells, define specificity and monitor the internal and external signals that our organism perceives through its specific receptors, TCRs and BCRs, respectively. Today, high-throughput sequencing (HTS) applied to the TCR repertoire has opened a window of opportunity to disclose T-cell repertoire development and behavior down to the clonal level. Although TCR repertoire sequencing is easily accessible today, it is important to deeply understand the available technologies for choosing the best fit for the specific experimental needs and questions. Here, we provide an updated overview of TCR repertoire sequencing strategies, providers and applications to infectious diseases and cancer to guide researchers’ choice through the multitude of available options. The possibility of extending the TCR repertoire to HLA characterization will be of pivotal importance in the near future to understand how specific HLA genes shape T-cell responses in different pathological contexts and will add a level of comprehension that was unthinkable just a few years ago.
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17
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Wang W, Yuan T, Ma L, Zhu Y, Bao J, Zhao X, Zhao Y, Zong Y, Zhang Y, Yang S, Qiu X, Shen S, Wu R, Wu T, Wang H, Gao D, Wang P, Chen L. Hepatobiliary Tumor Organoids Reveal HLA Class I Neoantigen Landscape and Antitumoral Activity of Neoantigen Peptide Enhanced with Immune Checkpoint Inhibitors. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105810. [PMID: 35665491 PMCID: PMC9353440 DOI: 10.1002/advs.202105810] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/08/2022] [Indexed: 05/28/2023]
Abstract
Neoantigen-directed therapy lacks preclinical models recapitulating neoantigen characteristics of original tumors. It is urgent to develop a platform to assess T cell response for neoantigen screening. Here, immunogenic potential of neoantigen-peptides of tumor tissues and matched organoids (n = 27 pairs) are analyzed by Score tools with whole genome sequencing (WGS)-based human leukocyte antigen (HLA)-class-I algorithms. The comparisons between 9203 predicted neoantigen-peptides from 2449 mutations of tumor tissues and 9991 ones from 2637 mutations of matched organoids demonstrate that organoids preserved majority of genetic features, HLA alleles, and similar neoantigen landscape of original tumors. Higher neoantigen load is observed in tumors with early stage. Multiomics analysis combining WGS, RNA-seq, single-cell RNA-seq, mass spectrometry filters out 93 candidate neoantigen-peptides with strong immunogenic potential for functional validation in five organoids. Immunogenic peptides are defined by inducing increased CD107aCD137IFN-γ expressions and IFN-γ secretion of CD8 cells in flow cytometry and enzyme-linked immunosorbent assay assays. Nine immunogenic peptides shared by at least two individuals are validated, including peptide from TP53R90S . Organoid killing assay confirms the antitumor activity of validated immunogenic peptide-reactive CD8 cells, which is further enhanced in the presence of immune checkpoint inhibitors. The study characterizes HLA-class-I neoantigen landscape in hepatobiliary tumor, providing practical strategy with tumor organoid model for neoantigen-peptide identification in personalized immunotherapy.
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Affiliation(s)
- Wenwen Wang
- Fudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Tinggan Yuan
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
- CAS Key Laboratory of Computational BiologyShanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
| | - Lili Ma
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
- CAS Key Laboratory of Computational BiologyShanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yanjing Zhu
- The International Cooperation Laboratory on Signal TransductionEastern Hepatobiliary Surgery HospitalSecond Military Medical UniversityShanghai200438China
- National Center for Liver CancerShanghai200441China
| | - Jinxia Bao
- School of MedicineNanjing UniversityNanjing210093China
| | - Xiaofang Zhao
- Fudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Yan Zhao
- Institute of Metabolism and Integrative BiologyFudan UniversityShanghai200433China
| | - Yali Zong
- Institute of Metabolism and Integrative BiologyFudan UniversityShanghai200433China
| | - Yani Zhang
- Institute of Metabolism and Integrative BiologyFudan UniversityShanghai200433China
| | - Shuai Yang
- Fudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Xinyao Qiu
- Fudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Siyun Shen
- The International Cooperation Laboratory on Signal TransductionEastern Hepatobiliary Surgery HospitalSecond Military Medical UniversityShanghai200438China
- National Center for Liver CancerShanghai200441China
| | - Rui Wu
- Department of Biliary Surgery IEastern Hepatobiliary Surgery HospitalSecond Military Medical UniversityShanghai200438China
| | - Tong Wu
- The International Cooperation Laboratory on Signal TransductionEastern Hepatobiliary Surgery HospitalSecond Military Medical UniversityShanghai200438China
- National Center for Liver CancerShanghai200441China
| | - Hongyang Wang
- Fudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
- The International Cooperation Laboratory on Signal TransductionEastern Hepatobiliary Surgery HospitalSecond Military Medical UniversityShanghai200438China
- National Center for Liver CancerShanghai200441China
| | - Dong Gao
- University of Chinese Academy of SciencesBeijing100049China
- State Key Laboratory of Cell BiologyShanghai Key Laboratory of Molecular AndrologyShanghai Institute of Biochemistry and Cell BiologyCAS Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai200031China
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijing100101China
| | - Peng Wang
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
- CAS Key Laboratory of Computational BiologyShanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
| | - Lei Chen
- Fudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
- National Center for Liver CancerShanghai200441China
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU)Ministry of EducationShanghai200438China
- Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH)Shanghai200438China
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18
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Abstract
ABSTRACT The holy grail of cancer therapeutics is the destruction of cancer cells while avoiding harm to normal cells. Cancer is unique from normal tissues because of the presence of somatic mutations that accumulate during tumorigenesis. Some nonsynonymous mutations can give rise to mutated peptide antigens (hereafter referred to as neoantigens) that can be specifically recognized by T cells. Thus, the immunological targeting of neoantigens represents a safe and promising strategy to treat patients with cancer. This article reviews the clinical application of adoptive cell therapy targeting neoantigens in patients with epithelial cancers.
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Zhu S, Bao H, Zhang MC, Liu H, Wang Y, Lin C, Zhao X, Liu SL. KAZN as a diagnostic marker in ovarian cancer: a comprehensive analysis based on microarray, mRNA-sequencing, and methylation data. BMC Cancer 2022; 22:662. [PMID: 35710397 PMCID: PMC9204993 DOI: 10.1186/s12885-022-09747-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/09/2022] [Indexed: 11/29/2022] Open
Abstract
Background Ovarian cancer (OC) is among the deadliest malignancies in women and the lack of appropriate markers for early diagnosis leads to poor prognosis in most cases. Previous studies have shown that KAZN is involved in multiple biological processes during development, such as cell proliferation, differentiation, and apoptosis, so defects or aberrant expression of KAZN might cause queer cell behaviors such as malignancy. Here we evaluated the KAZN expression and methylation levels for possible use as an early diagnosis marker for OC. Methods We used data from Gene Expression Omnibus (GEO) microarrays, The Cancer Genome Atlas (TCGA), and Clinical Proteomic Tumor Analysis Consortium (CPTAC) to investigate the correlations between KAZN expression and clinical characteristics of OC by comparing methylation levels of normal and OC samples. The relationships among differentially methylated sites in the KAZN gene, corresponding KAZN mRNA expression levels and prognosis were analyzed. Results KAZN was up-regulated in ovarian epithelial tumors and the expression of KAZN was correlated with the patients’ survival time. KAZN CpG site cg17657618 was positively correlated with the expression of mRNA and the methylation levels were significantly differential between the group of stage “I and II” and the group of stage “III and IV”. This study also presents a new method to classify tumor and normal tissue in OC using DNA methylation pattern in the KAZN gene body region. Conclusions KAZN was involved in ovarian cancer pathogenesis. Our results demonstrate a new direction for ovarian cancer research and provide a potential diagnostic biomarker as well as a novel therapeutic target for clinical application. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09747-2.
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Affiliation(s)
- Songling Zhu
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Hongxia Bao
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Meng-Chun Zhang
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Huidi Liu
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yao Wang
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Caiji Lin
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Xingjuan Zhao
- Physical Examination Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China. .,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China. .,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China. .,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada.
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20
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Lu M, Xu L, Jian X, Tan X, Zhao J, Liu Z, Zhang Y, Liu C, Chen L, Lin Y, Xie L. dbPepNeo2.0: A Database for Human Tumor Neoantigen Peptides From Mass Spectrometry and TCR Recognition. Front Immunol 2022; 13:855976. [PMID: 35493528 PMCID: PMC9043652 DOI: 10.3389/fimmu.2022.855976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/17/2022] [Indexed: 12/04/2022] Open
Abstract
Neoantigens are widely reported to induce T-cell response and lead to tumor regression, indicating a promising potential to immunotherapy. Previously, we constructed an open-access database, i.e., dbPepNeo, providing a systematic resource for human tumor neoantigens to storage and query. In order to expand data volume and application scope, we updated dbPepNeo to version 2.0 (http://www.biostatistics.online/dbPepNeo2). Here, we provide about 801 high-confidence (HC) neoantigens (increased by 170%) and 842,289 low-confidence (LC) HLA immunopeptidomes (increased by 107%). Notably, 55 class II HC neoantigens and 630 neoantigen-reactive T-cell receptor-β (TCRβ) sequences were firstly included. Besides, two new analytical tools are developed, DeepCNN-Ineo and BLASTdb. DeepCNN-Ineo predicts the immunogenicity of class I neoantigens, and BLASTdb performs local alignments to look for sequence similarities in dbPepNeo2.0. Meanwhile, the web features and interface have been greatly improved and enhanced.
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Affiliation(s)
- Manman Lu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Linfeng Xu
- Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.,School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xingxing Jian
- Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.,Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoxiu Tan
- Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.,Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Jingjing Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Zhenhao Liu
- Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Yu Zhang
- Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.,School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Chunyu Liu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Lanming Chen
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yong Lin
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Lu Xie
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.,Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
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21
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Song Q, Yang B, Sheng W, Zhou Z, Zhang T, Qin B, Ji L, Li P, Wang D, Zhang X, Sun S, Zhang G, Zhao X, Gan Q, Xiong Q, Guan Y, Xia X, Yi X, Chen X, Guo W, Jiao S. Safety and efficacy of mutant neoantigen-specific T-cell treatment combined anti-PD-1 therapy in stage IV solid tumors. Immunotherapy 2022; 14:553-565. [PMID: 35321561 DOI: 10.2217/imt-2021-0105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aims: This trial explored the safety and efficacy of neoantigen-specific T cells (Nas-Ts) combined with anti-PD-1 (Nas-T + anti-PD-1). Patients & methods: This non-randomized trial recruited participants with solid tumors treated with at least two prior systemic treatment lines. For comparison, 1:1-matched controls who received anti-PD-1 alone were recruited. The primary end point was safety. Results: 15 participants were enrolled in the Nas-T + anti-PD-1 group, the objective response rate was 33.3%, and the disease control rate was 93.3%. The median progression-free survival was significantly different between the Nas-T + anti-PD-1 and control groups (13.8 vs 4.2 months; p = 0.024), but no difference in overall survival was found (p = 0.126). The most common adverse events were maculopapular skin reaction (53.3%), rash (53.3%), hepatotoxicity (53.3%) and fever (53.3%) in the Nas-T + anti-PD-1 group. No serious safety issues were experienced. Conclusion: Nas-Ts combined with anti-PD-1 could be more effective than anti-PD-1 alone in prolonging progression-free survival, with good safety.
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Affiliation(s)
- Qi Song
- Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Bo Yang
- Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Wei Sheng
- Department of Tissue Repair & Regeneration, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing, China
| | - Zishan Zhou
- Beijing DCTY Biotech Co., Ltd, Beijing, China
| | | | - Boyu Qin
- Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | | | | | - Dan Wang
- Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xiaoling Zhang
- Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Shengjie Sun
- Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Guoqing Zhang
- Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xiao Zhao
- Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Quan Gan
- Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Qi Xiong
- Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | | | | | | | | | - Wei Guo
- BeiGene Co., Ltd, Beijing, China
| | - Shunchang Jiao
- Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
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22
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Genetic Modification of T Cells for the Immunotherapy of Cancer. Vaccines (Basel) 2022; 10:vaccines10030457. [PMID: 35335089 PMCID: PMC8949949 DOI: 10.3390/vaccines10030457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/05/2022] [Accepted: 03/11/2022] [Indexed: 02/01/2023] Open
Abstract
Immunotherapy is a beneficial treatment approach for multiple cancers, however, current therapies are effective only in a small subset of patients. Adoptive cell transfer (ACT) is a facet of immunotherapy where T cells targeting the tumor cells are transferred to the patient with several primary forms, utilizing unmodified or modified T cells: tumor-infiltrating lymphocytes (TIL), genetically modified T cell receptor transduced T cells, and chimeric antigen receptor (CAR) transduced T cells. Many clinical trials are underway investigating the efficacy and safety of these different subsets of ACT, as well as trials that combine one of these subsets with another type of immunotherapy. The main challenges existing with ACT are improving clinical responses and decreasing adverse events. Current research focuses on identifying novel tumor targeting T cell receptors, improving safety and efficacy, and investigating ACT in combination with other immunotherapies.
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23
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Matsuzaki J, Lele S, Odunsi K, Tsuji T. Identification of Claudin 6-specific HLA class I- and HLA class II-restricted T cell receptors for cellular immunotherapy in ovarian cancer. Oncoimmunology 2022; 11:2020983. [PMID: 35003898 PMCID: PMC8741298 DOI: 10.1080/2162402x.2021.2020983] [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] [Indexed: 11/16/2022] Open
Abstract
Adoptive cell therapy (ACT) is one of promising immunotherapies for cancer patients by providing a large amount of cancer antigen-specific effector T cells that can be manufactured rapidly by ex vivo gene engineering. To provide antigen-specificity to patients’ autologous T cells in a short-term culture, T-cell receptors (TCRs) or chimeric antigen receptors (CARs) are transduced to bulk T cells. Because of intra- and inter-tumoral heterogeneity in tumor antigen expression, a repertoire of TCR or CAR genes targeting a wide range of tumor antigens are required for a broad and effective treatment by ACT. Here, we characterized immunogenicity of claudin 6 (CLDN6) in ovarian cancer patients and identified specific TCR genes from CD8+ and CD4+ T cells. CLDN6 protein was frequently expressed on EpCAM+ ovarian cancer cells but not CD45+ lymphocytes in tumor ascites of ovarian cancer patients. Spontaneous CLDN6-specific CD4+ and CD8+ T-cell response was detected in peripheral blood mononuclear cells (PBMCs) from 1 out of 17 ovarian cancer patients. HLA-A*02:01 (A2) and DR*04:04 (DR4)-restricted TCR genes were isolated from CLDN6-specific CD8+ and CD4+ T cells, respectively. T cells that were engineered with A2-restricted TCR gene recognized and killed A2+CLDN6+ cancer cells. DR4-restricted TCR-transduced T cells directly recognized DR4+CLDN6+-overexpressed cancer cells. Our results demonstrate that these CLDN6-specific TCR genes are useful as therapeutic genes for ACT to patients with ovarian and other solid tumors expressing CLDN6.
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Affiliation(s)
- Junko Matsuzaki
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL, USA.,University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA
| | - Shashikant Lele
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Kunle Odunsi
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL, USA.,University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA.,Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Takemasa Tsuji
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL, USA.,University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA
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24
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Hu S, Alimire A, Lai Y, Hu H, Chen Z, Li Y. Trends and Frontiers of Research on Cancer Gene Therapy From 2016 to 2020: A Bibliometric Analysis. Front Med (Lausanne) 2021; 8:740710. [PMID: 34765618 PMCID: PMC8576170 DOI: 10.3389/fmed.2021.740710] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/24/2021] [Indexed: 02/05/2023] Open
Abstract
Background: With rapid development in molecular biology techniques and a greater understanding of cancer pathogenesis, the growing attention has been concentrated on cancer gene therapy, with numerous articles on this topic published in recent 5 years. However, there is lacking a bibliometric analysis of research on cancer gene therapy. Therefore, the aim of the present study was to conduct a bibliometric analysis to provide the trends and frontiers of research on cancer gene therapy during 2016-2020. Methods: We utilized CiteSpace 5.7.R5 software to conduct a bibliometric analysis of publications on cancer gene therapy published during 2016-2020. The bibliometric records were obtained from the Web of Science Core Collection. Results: A total of 4,392 papers were included in the bibliometric analysis. Materials Science and Nanoscience and Nanotechnology took an increasing part in the field of cancer gene therapy. Additionally, WANG W was the most productive author, while ZHANG Y ranked top in terms of citations. Harvard Medical School and Sichuan University ranked top in the active institutions. P NATL ACAD SCI USA was identified as the core journal in the field of cancer gene therapy. "Ovarian cancer" was found to be the latest keyword with the strongest burst. The keyword analysis suggested that the top three latest clusters were labeled "gene delivery," "drug delivery," and "gene therapy." In the reference analysis, cluster#2 labeled "gene delivery" held a dominant place considering both the node volume and mean year. Conclusion: The academic attention on cancer gene therapy was growing at a dramatically high speed. Materials Science and Nanoscience and Nanotechnology might become promising impetus for the development of this field. "Gene delivery" was thought to best reflect the research frontier on cancer gene therapy. The top-cited articles on gene delivery were focused on several novel non-viral vectors due to their specialty compared with viral vectors. "Ovarian cancer" was likely to be the potential research direction. These findings would help medical workers conduct further investigations on cancer gene therapy.
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Affiliation(s)
- Shoushan Hu
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Alifu Alimire
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yancheng Lai
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Haonan Hu
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhuo Chen
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yi Li
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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25
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Ebrahimi-Nik H, Moussa M, Englander RP, Singhaviranon S, Michaux J, Pak H, Miyadera H, Corwin WL, Keller GLJ, Hagymasi AT, Shcheglova TV, Coukos G, Baker BM, Mandoiu II, Bassani-Sternberg M, Srivastava PK. Reversion analysis reveals the in vivo immunogenicity of a poorly MHC I-binding cancer neoepitope. Nat Commun 2021; 12:6423. [PMID: 34741035 PMCID: PMC8571378 DOI: 10.1038/s41467-021-26646-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 09/27/2021] [Indexed: 12/30/2022] Open
Abstract
High-affinity MHC I-peptide interactions are considered essential for immunogenicity. However, some neo-epitopes with low affinity for MHC I have been reported to elicit CD8 T cell dependent tumor rejection in immunization-challenge studies. Here we show in a mouse model that a neo-epitope that poorly binds to MHC I is able to enhance the immunogenicity of a tumor in the absence of immunization. Fibrosarcoma cells with a naturally occurring mutation are edited to their wild type counterpart; the mutation is then re-introduced in order to obtain a cell line that is genetically identical to the wild type except for the neo-epitope-encoding mutation. Upon transplantation into syngeneic mice, all three cell lines form tumors that are infiltrated with activated T cells. However, lymphocytes from the two tumors that harbor the mutation show significantly stronger transcriptional signatures of cytotoxicity and TCR engagement, and induce greater breadth of TCR reactivity than those of the wild type tumors. Structural modeling of the neo-epitope peptide/MHC I pairs suggests increased hydrophobicity of the neo-epitope surface, consistent with higher TCR reactivity. These results confirm the in vivo immunogenicity of low affinity or ‘non-binding’ epitopes that do not follow the canonical concept of MHC I-peptide recognition. The immunogenicity of peptides is believed to be determined by their high-affinity binding to MHC I. Here authors show that low-affinity MHC I-peptide interactions are also able to trigger robust T cell response and anti-tumour immunity in vivo.
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Affiliation(s)
- Hakimeh Ebrahimi-Nik
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA.,Broad Institute of MIT and Harvard, 105 Broadway, Cambridge, MA, USA
| | - Marmar Moussa
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Ryan P Englander
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Summit Singhaviranon
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Justine Michaux
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Lausanne, Switzerland
| | - HuiSong Pak
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Lausanne, Switzerland
| | - Hiroko Miyadera
- Department of Medical Genetics, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Genome Medical Science Project, National Center for Global Health and Medicine, Chiba, Japan
| | - William L Corwin
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA.,Arvinas, 5 science park, 395 Winchester Ave, New Haven, CT, USA
| | - Grant L J Keller
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Adam T Hagymasi
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Tatiana V Shcheglova
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - George Coukos
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Lausanne, Switzerland
| | - Brian M Baker
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Ion I Mandoiu
- Department of Computer Sciences, University of Connecticut School of Engineering, Storrs, CT, USA
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Lausanne, Switzerland
| | - Pramod K Srivastava
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA.
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26
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Verdon DJ, Jenkins MR. Identification and Targeting of Mutant Peptide Neoantigens in Cancer Immunotherapy. Cancers (Basel) 2021; 13:4245. [PMID: 34439399 PMCID: PMC8391927 DOI: 10.3390/cancers13164245] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 12/30/2022] Open
Abstract
In recent decades, adoptive cell transfer and checkpoint blockade therapies have revolutionized immunotherapeutic approaches to cancer treatment. Advances in whole exome/genome sequencing and bioinformatic detection of tumour-specific genetic variations and the amino acid sequence alterations they induce have revealed that T cell mediated anti-tumour immunity is substantially directed at mutated peptide sequences, and the identification and therapeutic targeting of patient-specific mutated peptide antigens now represents an exciting and rapidly progressing frontier of personalized medicine in the treatment of cancer. This review outlines the historical identification and validation of mutated peptide neoantigens as a target of the immune system, and the technical development of bioinformatic and experimental strategies for detecting, confirming and prioritizing both patient-specific or "private" and frequently occurring, shared "public" neoantigenic targets. Further, we examine the range of therapeutic modalities that have demonstrated preclinical and clinical anti-tumour efficacy through specifically targeting neoantigens, including adoptive T cell transfer, checkpoint blockade and neoantigen vaccination.
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Affiliation(s)
- Daniel J. Verdon
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
| | - Misty R. Jenkins
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
- La Trobe Institute of Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
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27
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Nilsson JB, Grifoni A, Tarke A, Sette A, Nielsen M. PopCover-2.0. Improved Selection of Peptide Sets With Optimal HLA and Pathogen Diversity Coverage. Front Immunol 2021; 12:728936. [PMID: 34484239 PMCID: PMC8416060 DOI: 10.3389/fimmu.2021.728936] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/30/2021] [Indexed: 12/30/2022] Open
Abstract
The use of minimal peptide sets offers an appealing alternative for design of vaccines and T cell diagnostics compared to conventional whole protein approaches. T cell immunogenicity towards peptides is contingent on binding to human leukocyte antigen (HLA) molecules of the given individual. HLA is highly polymorphic, and each variant typically presents a different repertoire of peptides. This polymorphism combined with pathogen diversity challenges the rational selection of peptide sets with broad immunogenic potential and population coverage. Here we propose PopCover-2.0, a simple yet highly effective method, for resolving this challenge. The method takes as input a set of (predicted) CD8 and/or CD4 T cell epitopes with associated HLA restriction and pathogen strain annotation together with information on HLA allele frequencies, and identifies peptide sets with optimal pathogen and HLA (class I and II) coverage. PopCover-2.0 was benchmarked on historic data in the context of HIV and SARS-CoV-2. Further, the immunogenicity of the selected SARS-CoV-2 peptides was confirmed by experimentally validating the peptide pools for T cell responses in a panel of SARS-CoV-2 infected individuals. In summary, PopCover-2.0 is an effective method for rational selection of peptide subsets with broad HLA and pathogen coverage. The tool is available at https://services.healthtech.dtu.dk/service.php?PopCover-2.0.
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Affiliation(s)
- Jonas Birkelund Nilsson
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Alison Tarke
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
- Department of Internal Medicine, University of Genoa, Genoa, Italy
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Morten Nielsen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark
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28
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de Sousa E, Lérias JR, Beltran A, Paraschoudi G, Condeço C, Kamiki J, António PA, Figueiredo N, Carvalho C, Castillo-Martin M, Wang Z, Ligeiro D, Rao M, Maeurer M. Targeting Neoepitopes to Treat Solid Malignancies: Immunosurgery. Front Immunol 2021; 12:592031. [PMID: 34335558 PMCID: PMC8320363 DOI: 10.3389/fimmu.2021.592031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 05/07/2021] [Indexed: 12/26/2022] Open
Abstract
Successful outcome of immune checkpoint blockade in patients with solid cancers is in part associated with a high tumor mutational burden (TMB) and the recognition of private neoantigens by T-cells. The quality and quantity of target recognition is determined by the repertoire of ‘neoepitope’-specific T-cell receptors (TCRs) in tumor-infiltrating lymphocytes (TIL), or peripheral T-cells. Interferon gamma (IFN-γ), produced by T-cells and other immune cells, is essential for controlling proliferation of transformed cells, induction of apoptosis and enhancing human leukocyte antigen (HLA) expression, thereby increasing immunogenicity of cancer cells. TCR αβ-dependent therapies should account for tumor heterogeneity and availability of the TCR repertoire capable of reacting to neoepitopes and functional HLA pathways. Immunogenic epitopes in the tumor-stroma may also be targeted to achieve tumor-containment by changing the immune-contexture in the tumor microenvironment (TME). Non protein-coding regions of the tumor-cell genome may also contain many aberrantly expressed, non-mutated tumor-associated antigens (TAAs) capable of eliciting productive anti-tumor immune responses. Whole-exome sequencing (WES) and/or RNA sequencing (RNA-Seq) of cancer tissue, combined with several layers of bioinformatic analysis is commonly used to predict possible neoepitopes present in clinical samples. At the ImmunoSurgery Unit of the Champalimaud Centre for the Unknown (CCU), a pipeline combining several tools is used for predicting private mutations from WES and RNA-Seq data followed by the construction of synthetic peptides tailored for immunological response assessment reflecting the patient’s tumor mutations, guided by MHC typing. Subsequent immunoassays allow the detection of differential IFN-γ production patterns associated with (intra-tumoral) spatiotemporal differences in TIL or peripheral T-cells versus TIL. These bioinformatics tools, in addition to histopathological assessment, immunological readouts from functional bioassays and deep T-cell ‘adaptome’ analyses, are expected to advance discovery and development of next-generation personalized precision medicine strategies to improve clinical outcomes in cancer in the context of i) anti-tumor vaccination strategies, ii) gauging mutation-reactive T-cell responses in biological therapies and iii) expansion of tumor-reactive T-cells for the cellular treatment of patients with cancer.
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Affiliation(s)
- Eric de Sousa
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Joana R Lérias
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Antonio Beltran
- Department of Pathology, Champalimaud Clinical Centre, Lisbon, Portugal
| | | | - Carolina Condeço
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Jéssica Kamiki
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | | | - Nuno Figueiredo
- Digestive Unit, Champalimaud Clinical Centre, Lisbon, Portugal
| | - Carlos Carvalho
- Digestive Unit, Champalimaud Clinical Centre, Lisbon, Portugal
| | | | - Zhe Wang
- Jiangsu Industrial Technology Research Institute (JITRI), Applied Adaptome Immunology Institute, Nanjing, China
| | - Dário Ligeiro
- Lisbon Centre for Blood and Transplantation, Instituto Português do Sangue e Transplantação (IPST), Lisbon, Portugal
| | - Martin Rao
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Markus Maeurer
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal.,I Medical Clinic, Johannes Gutenberg University of Mainz, Mainz, Germany
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29
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Udumula MP, Sakr S, Dar S, Alvero AB, Ali-Fehmi R, Abdulfatah E, Li J, Jiang J, Tang A, Buekers T, Morris R, Munkarah A, Giri S, Rattan R. Ovarian cancer modulates the immunosuppressive function of CD11b +Gr1 + myeloid cells via glutamine metabolism. Mol Metab 2021; 53:101272. [PMID: 34144215 PMCID: PMC8267600 DOI: 10.1016/j.molmet.2021.101272] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/03/2021] [Accepted: 06/11/2021] [Indexed: 12/20/2022] Open
Abstract
Objective Immature CD11b + Gr1+ myeloid cells that acquire immunosuppressive capability, also known as myeloid-derived suppressor cells (MDSCs), are a heterogeneous population of cells that regulate immune responses. Our study's objective was to elucidate the role of ovarian cancer microenvironment in regulating the immunosuppressive function of CD11b+Gr1+ myeloid cells. Methods All studies were performed using the intraperitoneal ID8 syngeneic epithelial ovarian cancer mouse model. Myeloid cell depletion and immunotherapy were carried out using anti-Gr1 mAb, gemcitabine treatments, and/or anti-PD1 mAb. The treatment effect was assessed by a survival curve, in situ luciferase-guided imaging, and histopathologic evaluation. Adoptive transfer assays were carried out between congenic CD45.2 and CD45.1 mice. Immune surface and intracellular markers were assessed by flow cytometry. ELISA, western blot, and RT-PCR techniques were employed to assess the protein and RNA expression of various markers. Bone marrow-derived myeloid cells were used for ex-vivo studies. Results The depletion of Gr1+ immunosuppressive myeloid cells alone and in combination with anti-PD1 immunotherapy inhibited ovarian cancer growth. In addition to the adoptive transfer studies, these findings validate the role of immunosuppressive CD11b+Gr1+ myeloid cells in promoting ovarian cancer. Mechanistic investigations showed that ID8 tumor cells and their microenvironments produced recruitment and regulatory factors for immunosuppressive CD11b+Gr1+ myeloid cells. CD11b+Gr1+ myeloid cells primed by ID8 tumors showed increased immunosuppressive marker expression and acquired an energetic metabolic phenotype promoted primarily by increased oxidative phosphorylation fueled by glutamine. Inhibiting the glutamine metabolic pathway reduced the increased oxidative phosphorylation and decreased immunosuppressive markers’ expression and function. Dihydrolipoamide succinyl transferase (DLST), a subunit of α-KGDC in the TCA cycle, was found to be the most significantly elevated gene in tumor-primed myeloid cells. The inhibition of DLST reduced oxidative phosphorylation, immunosuppressive marker expression and function in myeloid cells. Conclusion Our study shows that the ovarian cancer microenvironment can regulate the metabolism and function of immunosuppressive CD11b + Gr1+ myeloid cells and modulate its immune microenvironment. Targeting glutamine metabolism via DLST in immunosuppressive myeloid cells decreased their activity, leading to a reduction in the immunosuppressive tumor microenvironment. Thus, targeting glutamine metabolism has the potential to enhance the success of immunotherapy in ovarian cancer. Ovarian cancer microenvironment increases the immunosuppressive ability of myeloid cells. Ovarian cancer microenvironment can induce metabolic reprogramming in the immunosuppressive myeloid cells. Immunosuppressive myeloid cells upsurge their oxidative metabolism fueled by glutamine in ovarian cancer. DLST, a component of alpha-ketoglutarate dehydrogenase complex plays a key role in the immunometabolic regulation of immunosuppressive myeloid cells in ovarian cancer.
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Affiliation(s)
- Mary P Udumula
- Division of Gynecology Oncology, Department of Women's Health Services, Henry Ford Cancer Institute and Henry Ford Health System, Detroit, MI, USA
| | - Sharif Sakr
- Department of Gynecology Oncology, Barbara Ann Karmanos Cancer Institute and Wayne State University, Detroit, MI, USA
| | - Sajad Dar
- Division of Gynecology Oncology, Department of Women's Health Services, Henry Ford Cancer Institute and Henry Ford Health System, Detroit, MI, USA
| | - Ayesha B Alvero
- Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Rouba Ali-Fehmi
- Department of Pathology, Wayne State University and Barbara Ann Karmanos Cancer Institute, Detroit, MI, USA
| | - Eman Abdulfatah
- Department of Pathology, Wayne State University and Barbara Ann Karmanos Cancer Institute, Detroit, MI, USA
| | - Jing Li
- Metabolomics Core, Barbara Ann Karmanos Cancer Institute and Wayne State University, Detroit, MI, USA
| | - Jun Jiang
- Metabolomics Core, Barbara Ann Karmanos Cancer Institute and Wayne State University, Detroit, MI, USA
| | - Amy Tang
- Department of Public Health Services, Henry Ford Health System, Detroit, MI, USA
| | - Thomas Buekers
- Division of Gynecology Oncology, Department of Women's Health Services, Henry Ford Cancer Institute and Henry Ford Health System, Detroit, MI, USA; Department of Gynecology Oncology, Barbara Ann Karmanos Cancer Institute and Wayne State University, Detroit, MI, USA
| | - Robert Morris
- Department of Gynecology Oncology, Barbara Ann Karmanos Cancer Institute and Wayne State University, Detroit, MI, USA
| | - Adnan Munkarah
- Division of Gynecology Oncology, Department of Women's Health Services, Henry Ford Cancer Institute and Henry Ford Health System, Detroit, MI, USA
| | - Shailendra Giri
- Department of Neurology, Henry Ford Health System, Detroit, MI, USA
| | - Ramandeep Rattan
- Division of Gynecology Oncology, Department of Women's Health Services, Henry Ford Cancer Institute and Henry Ford Health System, Detroit, MI, USA; Department of Oncology, Wayne State University, Detroit, MI, USA.
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30
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Pasetto A, Lu YC. Single-Cell TCR and Transcriptome Analysis: An Indispensable Tool for Studying T-Cell Biology and Cancer Immunotherapy. Front Immunol 2021; 12:689091. [PMID: 34163487 PMCID: PMC8215674 DOI: 10.3389/fimmu.2021.689091] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/10/2021] [Indexed: 12/18/2022] Open
Abstract
T cells have been known to be the driving force for immune response and cancer immunotherapy. Recent advances on single-cell sequencing techniques have empowered scientists to discover new biology at the single-cell level. Here, we review the single-cell techniques used for T-cell studies, including T-cell receptor (TCR) and transcriptome analysis. In addition, we summarize the approaches used for the identification of T-cell neoantigens, an important aspect for T-cell mediated cancer immunotherapy. More importantly, we discuss the applications of single-cell techniques for T-cell studies, including T-cell development and differentiation, as well as the role of T cells in autoimmunity, infectious disease and cancer immunotherapy. Taken together, this powerful tool not only can validate previous observation by conventional approaches, but also can pave the way for new discovery, such as previous unidentified T-cell subpopulations that potentially responsible for clinical outcomes in patients with autoimmunity or cancer.
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Affiliation(s)
- Anna Pasetto
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA FUTURA, Karolinska Institutet, Stockholm, Sweden
| | - Yong-Chen Lu
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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31
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Poorebrahim M, Mohammadkhani N, Mahmoudi R, Gholizadeh M, Fakhr E, Cid-Arregui A. TCR-like CARs and TCR-CARs targeting neoepitopes: an emerging potential. Cancer Gene Ther 2021; 28:581-589. [PMID: 33654227 PMCID: PMC8203496 DOI: 10.1038/s41417-021-00307-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/21/2021] [Accepted: 02/03/2021] [Indexed: 01/31/2023]
Abstract
Neoepitopes or neoantigens are a spectrum of unique mutations presented in a particular patient's tumor. Neoepitope-based adoptive therapies have the potential of tumor eradication without undue damaging effect on normal tissues. In this context, methods based on the T cell receptor (TCR) engineering or chimeric antigen receptors (CARs) have shown great promise. This review focuses on the TCR-like CARs and TCR-CARs directed against tumor-derived epitopes, with a concerted view on neoepitopes. We also address the current limitations of the field to know how to harness the full benefits of this approach and thereby design a sustained and specific antitumor therapy.
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MESH Headings
- Antigens, Neoplasm/immunology
- Antigens, Neoplasm/therapeutic use
- Humans
- Immunotherapy, Adoptive
- Neoplasms/genetics
- Neoplasms/immunology
- Neoplasms/therapy
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/therapeutic use
- Receptors, Chimeric Antigen/genetics
- T-Lymphocytes/immunology
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Affiliation(s)
- Mansour Poorebrahim
- Targeted Tumor Vaccines Group, Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Niloufar Mohammadkhani
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cancer Immunology Project (CIP), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Reza Mahmoudi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Monireh Gholizadeh
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Immunology, Pasteur Institute of Iran, Tehran, Iran
| | - Elham Fakhr
- Targeted Tumor Vaccines Group, Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Angel Cid-Arregui
- Targeted Tumor Vaccines Group, Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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32
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Tay BQ, Wright Q, Ladwa R, Perry C, Leggatt G, Simpson F, Wells JW, Panizza BJ, Frazer IH, Cruz JLG. Evolution of Cancer Vaccines-Challenges, Achievements, and Future Directions. Vaccines (Basel) 2021; 9:vaccines9050535. [PMID: 34065557 PMCID: PMC8160852 DOI: 10.3390/vaccines9050535] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 02/06/2023] Open
Abstract
The development of cancer vaccines has been intensively pursued over the past 50 years with modest success. However, recent advancements in the fields of genetics, molecular biology, biochemistry, and immunology have renewed interest in these immunotherapies and allowed the development of promising cancer vaccine candidates. Numerous clinical trials testing the response evoked by tumour antigens, differing in origin and nature, have shed light on the desirable target characteristics capable of inducing strong tumour-specific non-toxic responses with increased potential to bring clinical benefit to patients. Novel delivery methods, ranging from a patient’s autologous dendritic cells to liposome nanoparticles, have exponentially increased the abundance and exposure of the antigenic payloads. Furthermore, growing knowledge of the mechanisms by which tumours evade the immune response has led to new approaches to reverse these roadblocks and to re-invigorate previously suppressed anti-tumour surveillance. The use of new drugs in combination with antigen-based therapies is highly targeted and may represent the future of cancer vaccines. In this review, we address the main antigens and delivery methods used to develop cancer vaccines, their clinical outcomes, and the new directions that the vaccine immunotherapy field is taking.
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Affiliation(s)
- Ban Qi Tay
- Faculty of Medicine, Diamantina Institute, University of Queensland, Brisbane, QLD 4102, Australia; (B.Q.T.); (Q.W.); (G.L.); (F.S.); (J.W.W.); (I.H.F.)
| | - Quentin Wright
- Faculty of Medicine, Diamantina Institute, University of Queensland, Brisbane, QLD 4102, Australia; (B.Q.T.); (Q.W.); (G.L.); (F.S.); (J.W.W.); (I.H.F.)
| | - Rahul Ladwa
- Department of Medical Oncology, Princess Alexandra Hospital, Brisbane, QLD 4102, Australia;
- Faculty of Medicine, University of Queensland, Woolloongabba, QLD 4102, Australia; (C.P.); (B.J.P.)
| | - Christopher Perry
- Faculty of Medicine, University of Queensland, Woolloongabba, QLD 4102, Australia; (C.P.); (B.J.P.)
- Department of Otolaryngology, Princess Alexandra Hospital, Brisbane, QLD 4102, Australia
| | - Graham Leggatt
- Faculty of Medicine, Diamantina Institute, University of Queensland, Brisbane, QLD 4102, Australia; (B.Q.T.); (Q.W.); (G.L.); (F.S.); (J.W.W.); (I.H.F.)
| | - Fiona Simpson
- Faculty of Medicine, Diamantina Institute, University of Queensland, Brisbane, QLD 4102, Australia; (B.Q.T.); (Q.W.); (G.L.); (F.S.); (J.W.W.); (I.H.F.)
| | - James W. Wells
- Faculty of Medicine, Diamantina Institute, University of Queensland, Brisbane, QLD 4102, Australia; (B.Q.T.); (Q.W.); (G.L.); (F.S.); (J.W.W.); (I.H.F.)
| | - Benedict J. Panizza
- Faculty of Medicine, University of Queensland, Woolloongabba, QLD 4102, Australia; (C.P.); (B.J.P.)
- Department of Otolaryngology, Princess Alexandra Hospital, Brisbane, QLD 4102, Australia
| | - Ian H. Frazer
- Faculty of Medicine, Diamantina Institute, University of Queensland, Brisbane, QLD 4102, Australia; (B.Q.T.); (Q.W.); (G.L.); (F.S.); (J.W.W.); (I.H.F.)
| | - Jazmina L. G. Cruz
- Faculty of Medicine, Diamantina Institute, University of Queensland, Brisbane, QLD 4102, Australia; (B.Q.T.); (Q.W.); (G.L.); (F.S.); (J.W.W.); (I.H.F.)
- Correspondence: ; Tel.: +61-0478912737
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Basu A, Ramamoorthi G, Albert G, Gallen C, Beyer A, Snyder C, Koski G, Disis ML, Czerniecki BJ, Kodumudi K. Differentiation and Regulation of T H Cells: A Balancing Act for Cancer Immunotherapy. Front Immunol 2021; 12:669474. [PMID: 34012451 PMCID: PMC8126720 DOI: 10.3389/fimmu.2021.669474] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/19/2021] [Indexed: 12/22/2022] Open
Abstract
Current success of immunotherapy in cancer has drawn attention to the subsets of TH cells in the tumor which are critical for activation of anti-tumor response either directly by themselves or by stimulating cytotoxic T cell activity. However, presence of immunosuppressive pro-tumorigenic TH subsets in the tumor milieu further contributes to the complexity of regulation of TH cell-mediated immune response. In this review, we present an overview of the multifaceted positive and negative effects of TH cells, with an emphasis on regulation of different TH cell subtypes by various immune cells, and how a delicate balance of contradictory signals can influence overall success of cancer immunotherapy. We focus on the regulatory network that encompasses dendritic cell-induced activation of CD4+ TH1 cells and subsequent priming of CD8+ cytotoxic T cells, along with intersecting anti-inflammatory and pro-tumorigenic TH2 cell activity. We further discuss how other tumor infiltrating immune cells such as immunostimulatory TH9 and Tfh cells, immunosuppressive Treg cells, and the duality of TH17 function contribute to tip the balance of anti- vs pro-tumorigenic TH responses in the tumor. We highlight the developing knowledge of CD4+ TH1 immune response against neoantigens/oncodrivers, impact of current immunotherapy strategies on CD4+ TH1 immunity, and how opposing action of TH cell subtypes can be explored further to amplify immunotherapy success in patients. Understanding the nuances of CD4+ TH cells regulation and the molecular framework undergirding the balancing act between anti- vs pro-tumorigenic TH subtypes is critical for rational designing of immunotherapies that can bypass therapeutic escape to maximize the potential of immunotherapy.
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Affiliation(s)
- Amrita Basu
- Clinical Science Division, Moffitt Cancer Center, Tampa, FL, United States
| | | | - Gabriella Albert
- Clinical Science Division, Moffitt Cancer Center, Tampa, FL, United States
| | - Corey Gallen
- Clinical Science Division, Moffitt Cancer Center, Tampa, FL, United States
| | - Amber Beyer
- Clinical Science Division, Moffitt Cancer Center, Tampa, FL, United States
| | - Colin Snyder
- Clinical Science Division, Moffitt Cancer Center, Tampa, FL, United States
| | - Gary Koski
- Department of Biological Sciences, Kent State University, Kent, OH, United States
| | - Mary L Disis
- UW Medicine Cancer Vaccine Institute, University of Washington, Seattle, WA, United States
| | - Brian J Czerniecki
- Clinical Science Division, Moffitt Cancer Center, Tampa, FL, United States.,Department of Oncological Sciences, University of South Florida, Tampa, FL, United States.,Department of Breast Cancer Program, Moffitt Cancer Center, Tampa, FL, United States
| | - Krithika Kodumudi
- Clinical Science Division, Moffitt Cancer Center, Tampa, FL, United States.,Department of Biological Sciences, Kent State University, Kent, OH, United States
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McGray AJR, Eppolito C, Miliotto A, Singel KL, Stephenson K, Lugade A, Segal BH, Keler T, Webster G, Lichty B, Kozbor D, Odunsi K. A prime/boost vaccine platform efficiently identifies CD27 agonism and depletion of myeloid-derived suppressor cells as therapies that rationally combine with checkpoint blockade in ovarian cancer. Cancer Immunol Immunother 2021; 70:3451-3460. [PMID: 33880648 PMCID: PMC8057655 DOI: 10.1007/s00262-021-02936-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/31/2021] [Indexed: 12/30/2022]
Abstract
Cancer immunotherapies have generated remarkable clinical responses for some patients with advanced/metastatic disease, prompting exploration of rational combination therapies to bolster anti-tumor immunity in patients with limited response or those who experience tumor progression following an initial response to immunotherapy. In contrast to other tumor indications, objective response rates to single-agent PD-1/PD-L1 blockade in ovarian cancer are limited, suggesting a need to identify combinatorial approaches that lead to tumor regression in a setting where checkpoint blockade alone is ineffective. Using a pre-clinical model of aggressive intraperitoneal ovarian cancer, we have previously reported on a heterologous prime/boost cancer vaccine that elicits robust anti-tumor immunity, prolongs survival of tumor-bearing mice, and which is further improved when combined with checkpoint blockade. As tumor control in this model is CD8 + T cell dependent, we reasoned that the prime/boost vaccine platform could be used to explore additional treatment combinations intended to bolster the effects of CD8 + T cells. Using whole tumor transcriptomic data, we identified candidate therapeutic targets anticipated to rationally combine with prime/boost vaccination. In the context of a highly effective cancer vaccine, CD27 agonism or antibody-mediated depletion of granulocytic cells each modestly increased tumor control following vaccination, with anti-PD-1 therapy further improving treatment efficacy. These findings support the use of immunotherapies with well-defined mechanisms(s) of action as a valuable platform for identifying candidate combination approaches for further therapeutic testing in ovarian cancer.
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Affiliation(s)
- A J R McGray
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Roswell Park Cancer Institute, Elm and Carlton Sts, Buffalo, NY, 14263, USA.
| | - C Eppolito
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Roswell Park Cancer Institute, Elm and Carlton Sts, Buffalo, NY, 14263, USA
| | - A Miliotto
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Roswell Park Cancer Institute, Elm and Carlton Sts, Buffalo, NY, 14263, USA
| | - K L Singel
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Office of Evaluation, Performance, and Reporting, National Institutes of Health, Bethesda, MD, USA
| | - K Stephenson
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
- Turnstone Biologics, Ottawa, ON, Canada
| | - A Lugade
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Roswell Park Cancer Institute, Elm and Carlton Sts, Buffalo, NY, 14263, USA
| | - B H Segal
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Department of Internal Medicine, Roswell Park Comprehensive Cancer Center and Jacobs School of Medicine and Biomedical Sciences, University At Buffalo, Buffalo, NY, USA
| | - T Keler
- Celldex Therapeutics, Hampton, NJ, USA
| | - G Webster
- Innate Immunotherapeutics, Auckland, New Zealand
| | - B Lichty
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - D Kozbor
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - K Odunsi
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Roswell Park Cancer Institute, Elm and Carlton Sts, Buffalo, NY, 14263, USA.
- University of Chicago Comprehensive Cancer Center, 5841 South Maryland Avenue, MC1140, Chicago, IL, 60637, USA.
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FU J, SHANG Y, QIAN Z, HOU J, YAN F, LIU G, DEHUA L, TIAN X. Chimeric Antigen receptor-T (CAR-T) cells targeting Epithelial cell adhesion molecule (EpCAM) can inhibit tumor growth in ovarian cancer mouse model. J Vet Med Sci 2021; 83:241-247. [PMID: 33328392 PMCID: PMC7972873 DOI: 10.1292/jvms.20-0455] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/05/2020] [Indexed: 12/27/2022] Open
Abstract
Ovarian cancer (OC) is one of the most lethal solid tumors with poor prognosis. In 2017, two chimeric antigen receptor-T (CAR-T) cell drugs were approved by the U.S. Food and Drug Administration (FDA), and continuously optimized CAR-T cells therapy might be the novel hope for OC patient. EpCAM are known to be over-expressed in OC cells and could be targeted by CAR-T cells. However, the feasibility of using EpCAM-CAR-T cells to treat OC still needs to be verified. We engineered the 3rd-generation EpCAM-CAR containing a single-chain variable fragment (scFv) EpCAM-scFv that targeting EpCAM, a CD8 transmembrane domain, the costimulatory domains from both CD28 and 4-1BB, and activating domain CD3ζ and then transduced the CAR into T-cells via lentivirus. In addition, the cytotoxicity and cytokine releasing ability of the EpCAM-CAR-T cells against OC cell SKOV3 were verified in vitro. The in vivo data also showed that EpCAM-CAR-T cells significantly reduced the tumor size in OC xenograft mouse models. The anti-tumor activity of EpCAM-CAR-T cells against OC in vitro and in vivo indicated that the CAR-T might provide a promising therapeutic approach to OC.
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Affiliation(s)
- Juan FU
- Department of Obstetrics and Gynecology, the First
Affiliated Hospital of Dalian Medical University, Dalian, 116000, China
| | - Yuhong SHANG
- Department of Obstetrics and Gynecology, the First
Affiliated Hospital of Dalian Medical University, Dalian, 116000, China
| | - Zhang QIAN
- Shanghai Yihao Biological Technology Co., Ltd., Shanghai,
200231, China
| | - Jinping HOU
- Department of Pathology, the First Affiliated Hospital of
Dalian Medical University, Dalian, 116000, China
| | - Feng YAN
- Department of Pathology, the First Affiliated Hospital of
Dalian Medical University, Dalian, 116000, China
| | - Guodi LIU
- Shanghai Yihao Biological Technology Co., Ltd., Shanghai,
200231, China
| | - Li DEHUA
- Shanghai Yihao Biological Technology Co., Ltd., Shanghai,
200231, China
| | - Xiaoli TIAN
- Shanghai Yihao Biological Technology Co., Ltd., Shanghai,
200231, China
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36
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Want MY, Tsuji T, Singh PK, Thorne JL, Matsuzaki J, Karasik E, Gillard B, Cortes Gomez E, Koya RC, Lugade A, Odunsi K, Battaglia S. WHSC1/NSD2 regulates immune infiltration in prostate cancer. J Immunother Cancer 2021; 9:jitc-2020-001374. [PMID: 33589522 PMCID: PMC7887377 DOI: 10.1136/jitc-2020-001374] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Immunotherapy in prostate cancer (PCa) lags behind the progresses obtained in other cancer types partially because of its limited immune infiltration. Tumor-resident immune cells have been detected in the prostate, but the regulatory mechanisms that govern tumor infiltration are still poorly understood. To address this gap, we investigated the role of Wolf-Hirschhorn syndrome candidate 1 (WHSC1), a histone methyltransferase enzyme that targets dimethyl and trimethyl H3K36. WHSC1 is known to promote malignant growth and progression in multiple tumors, but its role in the interface between PCa and immune system is unknown. METHODS RNA Sequencing (RNASeq) data from patients with PCa from The Cancer Genome Atlas (TCGA) were collected and divided into top/bottom 30% based on the expression of WHSC1 and disease-free survival was calculated. Publicly available chromatin immunoprecipitation (ChIPSeq) data were obtained from Cistrome and integrated with the available RNASeq data. RNASeq, ATACSeq and methylomic were analyzed using R Bioconductor packages comparing C42 cells with or without stable knockdown on WHSC1. Flow cytometry was used to measure Major Histocompatibility complex (MHC) levels, MHC-bound ovalbumin and tumor infiltration. C57B6 and NOD scid gamma (NSG) mice were subcutaneously grafted with TRansgenic Adenocarcinoma of the Mouse Prostate (TRAMP) C2 cells and treated with MCTP39 (10 mg/kg); tumor size was monitored over time and curves were compared using permutation analyses. All analyses used a significance threshold of 0.05. RESULTS Leveraging TCGA data, we demonstrated that elevated WHSC1 levels positively correlate with the presence of an immunosuppressive microenvironment. We validated those results in vitro, demonstrating that genetic and pharmacological inhibition of WHSC1 restores antigen presentation. This occurs via an elegant epigenetic regulation of gene expression at the chromatin and DNA methylation levels. In vivo studies in immunocompetent mice also show an increased frequency of CD8+ T cells in tumors from mice treated with WHSC1 inhibitor, supporting the hypothesis that the antitumor effect following WHSC1 inhibition requires a fully functional immune system. CONCLUSIONS This study demonstrates a novel role for WHSC1 in defining immune infiltration in PCa, with significant future implications for the use of immunotherapies in prostate malignancies.
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Affiliation(s)
- Muzamil Y Want
- Center For Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Takemasa Tsuji
- Center For Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Prashant K Singh
- Genomics Shared Resource, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - James L Thorne
- School of Food Science and Nutrition, Faculty of Environment, University of Leeds, Leeds, West Yorkshire, UK
| | - Junko Matsuzaki
- Center For Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Ellen Karasik
- Department of Pharmacology and Experimental Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Bryan Gillard
- Department of Pharmacology and Experimental Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Eduardo Cortes Gomez
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Richard C Koya
- Center For Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Amit Lugade
- Center For Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Kunle Odunsi
- Center For Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Sebastiano Battaglia
- Center For Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
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37
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Nanoparticles in precision medicine for ovarian cancer: From chemotherapy to immunotherapy. Int J Pharm 2020; 591:119986. [DOI: 10.1016/j.ijpharm.2020.119986] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/23/2020] [Accepted: 10/11/2020] [Indexed: 12/24/2022]
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38
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Wang C, Ding Y, Liu Y, Zhang Q, Xu S, Xia L, Duan H, Wang S, Ji P, Huang W, Zhao G, Cao Z, Shen H, Wang Y. Identification of Mutated Peptides in Bladder Cancer From Exomic Sequencing Data Reveals Negative Correlation Between Mutation-Specific Immunoreactivity and Inflammation. Front Immunol 2020; 11:576603. [PMID: 33329543 PMCID: PMC7734250 DOI: 10.3389/fimmu.2020.576603] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022] Open
Abstract
Introduction and Objective Neoantigen-based immunotherapy is one of the breakthroughs in cancer immunotherapy. Benefit from the Cancer Genome Atlas database, we intended to identify mutant peptides with neoantigen property in bladder cancer (BC). Correlations between the immunoreactivity of candidate neoantigens and clinical manifestations were further analyzed. Methods HLA-A*02:01 restricted mutant (MT) and wildtype (WT) peptides were predicted by using whole exome sequencing data of 412 BC patients in the TCGA database. Binding affinity to HLA-A2 molecules was determined by using T2 cell-based binding assay. The immunoreactivity to WT and MT peptides in HLA-A2+ BC patients was determined by using an ELISPOT assay upon in vitro stimulation with MT and WT peptides individually. Clinical relevance to peptide-specific immunoreactivity was analyzed by Pearson correlation analysis. The disease free survival (DFS) curves were plotted using the Kaplan–Meier method in BC patients with or without mutations and compared using the log-rank test online. Results Fifty-seven HLA-A*02:01 restricted WT and MT peptides were selected based on predicted high affinity and expression frequency, among which 12 MT peptides from 12 individual genes exhibited strong affinity to HLA-A2 molecules when compared to WT counterparts. MT peptides induced more peptide-specific IFNγ spot forming units (SFUs) than WT counterparts in HLA-A2+ BC patients upon in vitro stimulation. They were negatively correlated to the counts of peripheral leukocytes and platelets. Patients with higher C-reactive protein level exhibited lower immunoreactivity to MT peptides. Combination of MT peptides from 6 genes, including CDKN1AG61V, RHOBP75L, DDB1S25L, AHNAKD4855Y, ANP32AS56L and MKI67H84L covered 47.5% of the patients under investigation. Patients harboring combinational mutations in these genes were associated with a longer DFS according to the cBioportal online analysis. Conclusion Twelve HLA-A*02:01 restricted MT peptides have been identified exhibiting higher binding affinity to HLA-A2 molecules and stronger immunoreactivity than WT counterparts in BC patients. Combination of MT peptides from six genes might be potential as neoantigen candidates in cancer immunotherapy against BC in the future. Inflammatory modulation is inclined to be a strategy to enhance the efficacy of neoantigen-based immunotherapy.
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Affiliation(s)
- Chen Wang
- Department of Urology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yu Ding
- Department of Urology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yuanyong Liu
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qingchen Zhang
- Deparment of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shiqiang Xu
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Liliang Xia
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Huangqi Duan
- Department of Urology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Shujun Wang
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ping Ji
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Weiren Huang
- State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Guoping Zhao
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Zhiwei Cao
- Deparment of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Haibo Shen
- Department of Urology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ying Wang
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
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Odunsi A, McGray AJR, Miliotto A, Zhang Y, Wang J, Abiola A, Eppolito C, Huang RY. Fidelity of human ovarian cancer patient-derived xenografts in a partially humanized mouse model for preclinical testing of immunotherapies. J Immunother Cancer 2020; 8:jitc-2020-001237. [PMID: 33177175 PMCID: PMC7661374 DOI: 10.1136/jitc-2020-001237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2020] [Indexed: 12/27/2022] Open
Abstract
Background Immune checkpoint blockers (ICBs) have been approved by the Food and Drug Administration to be used alone in front-line therapies or in combination with other regimens for certain advanced cancers. Since ICB only works in a subset of patients and has limited efficacy in treating ovarian cancer (OVC), developing preclinical models that help to understand which patients may derive benefit from ICB would be of tremendous benefit in OVC. Methods Here, we generated preclinical human OVC models from freshly resected tumors, which include six patient-derived xenografts (PDXs) from six different patient tumors, three transplantable OVC PD spheroid lines (PD-sphs), and 3 cell lines (PD-CLs). We tested the therapeutic combination of anti-PD1/CTLA4 antibodies with (1) autologous tumor-associated leukocytes (TALs) on the growth of PD-sphs in a coculture system in vitro, (2) with adoptively transferred autologous peripheral blood mononuclear cells or TALs in patient-derived OVC models using partially humanized mice, NSG-HHDxSGM3 (N-HSGM3). Results We show that PD-1 and CTLA-4 dual blockade when combined with autologous TALs effectively reduced PD-sph number in a co-culture system and led to regression of established PD-CLs and PDXs in the N-HSGM3 mice. Combinatorial PD-1 and CTLA-4 blockade increased the frequency and function of tumor-specific CD8 T cells. These CD8 T cells persisted in the tumor microenvironment, exhibited memory phenotype and protected animals from tumor growth on tumor rechallenge. Gene expression analysis of tumors resistant to dual PD1/CTLA4 blockade treatment identified upregulation of antigen processing and presentation pathways and downregulation of extracellular matrix organization genes. Conclusions These findings describe a novel platform for developing patient-derived preclinical tumor models suitable for rationally testing combinatorial ICB in the context of autologous tumor-reactive T cells. This platform can be further developed for testing additional targeted therapies relevant to OVC.
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Affiliation(s)
- Adekunle Odunsi
- Center For Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA.,Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - A J Robert McGray
- Center For Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Anthony Miliotto
- Center For Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Yali Zhang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Jianming Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Adebukola Abiola
- Center For Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Cheryl Eppolito
- Center For Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Ruea-Yea Huang
- Center For Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
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D’Ippolito E, Wagner KI, Busch DH. Needle in a Haystack: The Naïve Repertoire as a Source of T Cell Receptors for Adoptive Therapy with Engineered T Cells. Int J Mol Sci 2020; 21:E8324. [PMID: 33171940 PMCID: PMC7664211 DOI: 10.3390/ijms21218324] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 12/11/2022] Open
Abstract
T cell engineering with antigen-specific T cell receptors (TCRs) has allowed the generation of increasingly specific, reliable, and versatile T cell products with near-physiological features. However, a broad applicability of TCR-based therapies in cancer is still limited by the restricted number of TCRs, often also of suboptimal potency, available for clinical use. In addition, targeting of tumor neoantigens with TCR-engineered T cell therapy moves the field towards a highly personalized treatment, as tumor neoantigens derive from somatic mutations and are extremely patient-specific. Therefore, relevant TCRs have to be de novo identified for each patient and within a narrow time window. The naïve repertoire of healthy donors would represent a reliable source due to its huge diverse TCR repertoire, which theoretically entails T cells for any antigen specificity, including tumor neoantigens. As a challenge, antigen-specific naïve T cells are of extremely low frequency and mostly of low functionality, making the identification of highly functional TCRs finding a "needle in a haystack." In this review, we present the technological advancements achieved in high-throughput mapping of patient-specific neoantigens and corresponding cognate TCRs and how these platforms can be used to interrogate the naïve repertoire for a fast and efficient identification of rare but therapeutically valuable TCRs for personalized adoptive T cell therapy.
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MESH Headings
- Antigens, Neoplasm/genetics
- CD4-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/immunology
- Humans
- Immunotherapy, Adoptive/methods
- Immunotherapy, Adoptive/trends
- Neoplasms/genetics
- Precision Medicine/methods
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/physiology
- Receptors, Chimeric Antigen/genetics
- Receptors, Chimeric Antigen/immunology
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Affiliation(s)
- Elvira D’Ippolito
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), 81675 Munich, Germany; (E.D.); (K.I.W.)
| | - Karolin I. Wagner
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), 81675 Munich, Germany; (E.D.); (K.I.W.)
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), 81675 Munich, Germany; (E.D.); (K.I.W.)
- German Center for Infection Research (DZIF), Partner Site Munich, 81675 Munich, Germany
- Focus Group ‘‘Clinical Cell Processing and Purification”, Institute for Advanced Study, Technische Universität München (TUM), 81675 Munich, Germany
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Gaissmaier L, Elshiaty M, Christopoulos P. Breaking Bottlenecks for the TCR Therapy of Cancer. Cells 2020; 9:E2095. [PMID: 32937956 PMCID: PMC7564186 DOI: 10.3390/cells9092095] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/03/2020] [Accepted: 09/11/2020] [Indexed: 12/26/2022] Open
Abstract
Immune checkpoint inhibitors have redefined the treatment of cancer, but their efficacy depends critically on the presence of sufficient tumor-specific lymphocytes, and cellular immunotherapies develop rapidly to fill this gap. The paucity of suitable extracellular and tumor-associated antigens in solid cancers necessitates the use of neoantigen-directed T-cell-receptor (TCR)-engineered cells, while prevention of tumor evasion requires combined targeting of multiple neoepitopes. These can be currently identified within 2 weeks by combining cutting-edge next-generation sequencing with bioinformatic pipelines and used to select tumor-reactive TCRs in a high-throughput manner for expeditious scalable non-viral gene editing of autologous or allogeneic lymphocytes. "Young" cells with a naive, memory stem or central memory phenotype can be additionally armored with "next-generation" features against exhaustion and the immunosuppressive tumor microenvironment, where they wander after reinfusion to attack heavily pretreated and hitherto hopeless neoplasms. Facilitated by major technological breakthroughs in critical manufacturing steps, based on a solid preclinical rationale, and backed by rapidly accumulating evidence, TCR therapies break one bottleneck after the other and hold the promise to become the next immuno-oncological revolution.
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Affiliation(s)
- Lena Gaissmaier
- Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany; (L.G.); (M.E.)
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Mariam Elshiaty
- Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany; (L.G.); (M.E.)
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Petros Christopoulos
- Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany; (L.G.); (M.E.)
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
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Xu P, Luo H, Kong Y, Lai WF, Cui L, Zhu X. Cancer neoantigen: Boosting immunotherapy. Biomed Pharmacother 2020; 131:110640. [PMID: 32836075 DOI: 10.1016/j.biopha.2020.110640] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/13/2020] [Accepted: 08/16/2020] [Indexed: 12/21/2022] Open
Abstract
Tumor neoantigen has a high degree of immunogenicity. As one of the emerging methods of tumor immunotherapy, the vaccine developed against it has served to clinical trials of various solid tumors, especially in the treatment of melanoma. Currently, a variety of immunotherapy methods have been applied to the treatment of the tumor. However, other therapeutic methods have the disadvantages of low specificity and prominent side effects. Treatments require tumor antigen with higher immunogenicity as the target of immune attack. This review will recommend the identification of neoantigen, the influencing factors of neoantigen, and the application of personalized vaccines for neoantigen in metastatic tumors such as malignant melanoma.
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Affiliation(s)
- Peijia Xu
- Guangdong Key Laboratory for Research and Development of Natural Drugs, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, 524023, China; The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China; The Key Lab of Zhanjiang for R&D Marine Microbial Resources in the Beibu Gulf Rim, Guangdong Medical University, Zhanjiang, 524023, China
| | - Haiqing Luo
- Cancer Center, Affiliated Hospital, Guangdong Medical University, Zhanjiang, 524023, China
| | - Ying Kong
- Department of Clinical Laboratory, Hubei No. 3 People's Hospital of Jianghan University, Wuhan, 430033, China
| | - Wing-Fu Lai
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China; School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen, China.
| | - Liao Cui
- Guangdong Key Laboratory for Research and Development of Natural Drugs, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, 524023, China; The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China.
| | - Xiao Zhu
- Guangdong Key Laboratory for Research and Development of Natural Drugs, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, 524023, China; The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China; The Key Lab of Zhanjiang for R&D Marine Microbial Resources in the Beibu Gulf Rim, Guangdong Medical University, Zhanjiang, 524023, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524023, China.
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Shu S, Matsuzaki J, Want MY, Conway A, Benjamin-Davalos S, Allen CL, Koroleva M, Battaglia S, Odunsi A, Minderman H, Ernstoff MS. An Immunosuppressive Effect of Melanoma-derived Exosomes on NY-ESO-1 Antigen-specific Human CD8 + T Cells is Dependent on IL-10 and Independent of BRAF V600E Mutation in Melanoma Cell Lines. Immunol Invest 2020; 49:744-757. [PMID: 32799717 DOI: 10.1080/08820139.2020.1803353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Exosomes, including human melanoma-derived exosomes (HMEX), are known to suppress the function of immune effector cells, which for HMEX has been associated with the surface presence of the immune checkpoint ligand PD-L1. This study investigated the relationship between the BRAF mutational status of melanoma cells and the inhibition of secreted HMEX exosomes on antigen-specific human T cells. Exosomes were isolated from two melanoma cell lines, 2183-Her4 and 888-mel, which are genetically wild-type BRAFWT and BRAFV600E, respectively. HMEX were isolated using a modified, size-exclusion chromatography (SEC) method shown to reduce co-isolation of non-exosome-associated cytokines compared to ultracentrifugation isolation. The immunoinhibitory effect of the exosomes was tested in vitro on patient-derived NY-ESO-1-specific CD8+ T cells challenged with NY-ESO-1 antigen. HMEX from both cell lines inhibited the immune response of antigen-specific T cells comparably, as evidenced by the reduction of IFN-γ and TNF-α in NY-ESO-1 tetramer-positive cells. This inhibition could be partially reversed by the presence of anti-PD-L1 and anti-IL-10 antibodies. IL-10 has been demonstrated to be a critical pathway for sustaining enhanced tumorigenesis in BRAFV600E mutant cells compared to BRAFWT melanoma cells. Thus, we demonstrate that HMEX inhibit antigen-specific T cell responses independent of the BRAF mutational status of the parent cells. In addition, PD-L1 and IL-10 contribute to the HMEX-mediated immunosuppression of antigen-specific human T cells. The inhibitory capacity of exosomes should be taken into consideration when developing therapies that are reliant upon the potency of customized, antigen-specific effector T cells.
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Affiliation(s)
- ShinLa Shu
- Department of Medicine, Roswell Park Comprehensive Cancer Center , Buffalo, NY, USA
| | - Junko Matsuzaki
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center , Buffalo, NY, USA
| | - Muzamil Y Want
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center , Buffalo, NY, USA
| | - Alexis Conway
- Flow and Image Cytometry Shared Resource, Roswell Park Comprehensive Cancer Center , Buffalo, NY, USA
| | | | - Cheryl L Allen
- Department of Medicine, Roswell Park Comprehensive Cancer Center , Buffalo, NY, USA
| | - Marina Koroleva
- Department of Medicine, Roswell Park Comprehensive Cancer Center , Buffalo, NY, USA
| | - Sebastiano Battaglia
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center , Buffalo, NY, USA
| | - Adekunle Odunsi
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center , Buffalo, NY, USA
| | - Hans Minderman
- Flow and Image Cytometry Shared Resource, Roswell Park Comprehensive Cancer Center , Buffalo, NY, USA
| | - Marc S Ernstoff
- Department of Medicine, Roswell Park Comprehensive Cancer Center , Buffalo, NY, USA
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The Quest for the Best: How TCR Affinity, Avidity, and Functional Avidity Affect TCR-Engineered T-Cell Antitumor Responses. Cells 2020; 9:cells9071720. [PMID: 32708366 PMCID: PMC7408146 DOI: 10.3390/cells9071720] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022] Open
Abstract
Over the past decades, adoptive transfer of T cells has revolutionized cancer immunotherapy. In particular, T-cell receptor (TCR) engineering of T cells has marked important milestones in developing more precise and personalized cancer immunotherapies. However, to get the most benefit out of this approach, understanding the role that TCR affinity, avidity, and functional avidity play on how TCRs and T cells function in the context of tumor-associated antigen (TAA) recognition is vital to keep generating improved adoptive T-cell therapies. Aside from TCR-related parameters, other critical factors that govern T-cell activation are the effect of TCR co-receptors on TCR–peptide-major histocompatibility complex (pMHC) stabilization and TCR signaling, tumor epitope density, and TCR expression levels in TCR-engineered T cells. In this review, we describe the key aspects governing TCR specificity, T-cell activation, and how these concepts can be applied to cancer-specific TCR redirection of T cells.
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45
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Rus Bakarurraini NAA, Ab Mutalib NS, Jamal R, Abu N. The Landscape of Tumor-Specific Antigens in Colorectal Cancer. Vaccines (Basel) 2020; 8:E371. [PMID: 32664247 PMCID: PMC7565947 DOI: 10.3390/vaccines8030371] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/22/2020] [Accepted: 06/22/2020] [Indexed: 12/24/2022] Open
Abstract
Over the last few decades, major efforts in cancer research and treatment have intensified. Apart from standard chemotherapy approaches, immunotherapy has gained substantial traction. Personalized immunotherapy has become an important tool for cancer therapy with the discovery of immune checkpoint inhibitors. Traditionally, tumor-associated antigens are used in immunotherapy-based treatments. Nevertheless, these antigens lack specificity and may have increased toxicity. With the advent of next-generation technologies, the identification of new tumor-specific antigens is becoming more important. In colorectal cancer, several tumor-specific antigens were identified and functionally validated. Multiple clinical trials from vaccine-based and adoptive cell therapy utilizing tumor-specific antigens have commenced. Herein, we will summarize the current landscape of tumor-specific antigens particularly in colorectal cancer.
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Affiliation(s)
| | | | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (N.A.A.R.B.); (N.S.A.M.)
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (N.A.A.R.B.); (N.S.A.M.)
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Nielsen AY, Ormhøj M, Traynor S, Gjerstorff MF. Augmenting engineered T-cell strategies in solid cancers through epigenetic priming. Cancer Immunol Immunother 2020; 69:2169-2178. [PMID: 32648166 DOI: 10.1007/s00262-020-02661-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/03/2020] [Indexed: 02/06/2023]
Abstract
T-cell receptor (TCR)- and chimeric antigen receptor (CAR)-based adoptive cell transfer (ACT) has shown promising results in hematological malignancies, but remains immature in solid cancers. The challenges associated with identification of tumor-specific targets, the heterogenic antigen expression, limited T-cell trafficking to tumor sites and the hostile tumor microenvironment (TME), are all factors contributing to the limited efficacy of ACT therapies against solid tumors. Epigenetic priming of tumor cells and the microenvironment may be a way of overcoming these obstacles and improving the clinical efficacy of adoptive T-cell therapies in the future. Here, we review the current literature and suggest combining epigenetic modulators and ACT strategies as a way of augmenting the efficacy of TCR- and CAR-engineered T cells against solid tumors.
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Affiliation(s)
- Aaraby Y Nielsen
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Maria Ormhøj
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Sofie Traynor
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Morten F Gjerstorff
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark. .,Department of Oncology, Odense University Hospital, Odense, Denmark. .,Academy of Geriatric Cancer Research (AgeCare), Odense University Hospital, Odense, Denmark.
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Adoptive Cell Therapy-Harnessing Antigen-Specific T Cells to Target Solid Tumours. Cancers (Basel) 2020; 12:cancers12030683. [PMID: 32183246 PMCID: PMC7140076 DOI: 10.3390/cancers12030683] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/06/2020] [Accepted: 03/10/2020] [Indexed: 12/26/2022] Open
Abstract
In recent years, much research has been focused on the field of adoptive cell therapies (ACT) that use native or genetically modified T cells as therapeutic tools. Immunotherapy with T cells expressing chimeric antigen receptors (CARs) demonstrated great success in the treatment of haematologic malignancies, whereas adoptive transfer of autologous tumour infiltrating lymphocytes (TILs) proved to be highly effective in metastatic melanoma. These encouraging results initiated many studies where ACT was tested as a treatment for various solid tumours. In this review, we provide an overview of the challenges of T cell-based immunotherapies of solid tumours. We describe alternative approaches for choosing the most efficient T cells for cancer treatment in terms of their tumour-specificity and phenotype. Finally, we present strategies for improvement of anti-tumour potential of T cells, including combination therapies.
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Lazarou G, Chelliah V, Small BG, Walker M, van der Graaf PH, Kierzek AM. Integration of Omics Data Sources to Inform Mechanistic Modeling of Immune-Oncology Therapies: A Tutorial for Clinical Pharmacologists. Clin Pharmacol Ther 2020; 107:858-870. [PMID: 31955413 PMCID: PMC7158209 DOI: 10.1002/cpt.1786] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/03/2020] [Indexed: 12/15/2022]
Abstract
Application of contemporary molecular biology techniques to clinical samples in oncology resulted in the accumulation of unprecedented experimental data. These “omics” data are mined for discovery of therapeutic target combinations and diagnostic biomarkers. It is less appreciated that omics resources could also revolutionize development of the mechanistic models informing clinical pharmacology quantitative decisions about dose amount, timing, and sequence. We discuss the integration of omics data to inform mechanistic models supporting drug development in immuno‐oncology. To illustrate our arguments, we present a minimal clinical model of the Cancer Immunity Cycle (CIC), calibrated for non‐small cell lung carcinoma using tumor microenvironment composition inferred from transcriptomics of clinical samples. We review omics data resources, which can be integrated to parameterize mechanistic models of the CIC. We propose that virtual trial simulations with clinical Quantitative Systems Pharmacology platforms informed by omics data will be making increasing impact in the development of cancer immunotherapies.
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Affiliation(s)
| | | | - Ben G Small
- Certara QSP, Certara UK Limited, Sheffield, UK
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Zhao Q, Laverdure JP, Lanoix J, Durette C, Côté C, Bonneil É, Laumont CM, Gendron P, Vincent K, Courcelles M, Lemieux S, Millar DG, Ohashi PS, Thibault P, Perreault C. Proteogenomics Uncovers a Vast Repertoire of Shared Tumor-Specific Antigens in Ovarian Cancer. Cancer Immunol Res 2020; 8:544-555. [PMID: 32047025 DOI: 10.1158/2326-6066.cir-19-0541] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/03/2019] [Accepted: 02/07/2020] [Indexed: 11/16/2022]
Abstract
High-grade serous ovarian cancer (HGSC), the principal cause of death from gynecologic malignancies in the world, has not significantly benefited from advances in cancer immunotherapy. Although HGSC infiltration by lymphocytes correlates with superior survival, the nature of antigens that can elicit anti-HGSC immune responses is unknown. The goal of this study was to establish the global landscape of HGSC tumor-specific antigens (TSA) using a mass spectrometry pipeline that interrogated all reading frames of all genomic regions. In 23 HGSC tumors, we identified 103 TSAs. Classic TSA discovery approaches focusing only on mutated exonic sequences would have uncovered only three of these TSAs. Other mutated TSAs resulted from out-of-frame exonic translation (n = 2) or from noncoding sequences (n = 7). One group of TSAs (n = 91) derived from aberrantly expressed unmutated genomic sequences, which were not expressed in normal tissues. These aberrantly expressed TSAs (aeTSA) originated primarily from nonexonic sequences, in particular intronic (29%) and intergenic (22%) sequences. Their expression was regulated at the transcriptional level by variations in gene copy number and DNA methylation. Although mutated TSAs were unique to individual tumors, aeTSAs were shared by a large proportion of HGSCs. Taking into account the frequency of aeTSA expression and HLA allele frequencies, we calculated that, in Caucasians, the median number of aeTSAs per tumor would be five. We conclude that, in view of their number and the fact that they are shared by many tumors, aeTSAs may be the most attractive targets for HGSC immunotherapy.
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Affiliation(s)
- Qingchuan Zhao
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada.,Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Jean-Philippe Laverdure
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Joël Lanoix
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Caroline Côté
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Éric Bonneil
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Céline M Laumont
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada.,Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Patrick Gendron
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Krystel Vincent
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Mathieu Courcelles
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada.,Department of Computer Science and Operations Research, Université de Montréal, Montreal, Quebec, Canada
| | - Douglas G Millar
- Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Pamela S Ohashi
- Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics and Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada. .,Department of Chemistry, Université de Montréal, Montreal, Quebec, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada. .,Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
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50
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Malekzadeh P, Yossef R, Cafri G, Paria BC, Lowery FJ, Jafferji M, Good ML, Sachs A, Copeland AR, Kim SP, Kivitz S, Parkhurst MR, Robbins PF, Ray S, Xi L, Raffeld M, Yu Z, Restifo NP, Somerville RPT, Rosenberg SA, Deniger DC. Antigen Experienced T Cells from Peripheral Blood Recognize p53 Neoantigens. Clin Cancer Res 2020; 26:1267-1276. [PMID: 31996390 DOI: 10.1158/1078-0432.ccr-19-1874] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/30/2019] [Accepted: 11/12/2019] [Indexed: 01/21/2023]
Abstract
PURPOSE The purpose of this study was to evaluate antigen experienced T cells in peripheral blood lymphocytes (PBL) for responses to p53 neoantigens. EXPERIMENTAL DESIGN PBLs from patients with a mutated TP53 tumor were sorted for antigen-experienced T cells and in vitro stimulation (IVS) was performed with p53 neoantigens. The IVS cultures were stimulated with antigen-presenting cells expressing p53 neoantigens, enriched for 41BB/OX40 and grown with rapid expansion protocol. RESULTS T-cell responses were not observed in the PBLs of 4 patients who did not have tumor-infiltrating lymphocyte (TIL) responses to mutated TP53. In contrast, 5 patients with TIL responses to mutated TP53 also had similar T-cell responses in their PBLs, indicating that the PBLs and TILs were congruent in p53 neoantigen reactivity. CD4+ and CD8+ T cells were specific for p53R175H, p53Y220C, or p53R248W neoantigens, including a 78% reactive T-cell culture against p53R175H and HLA-A*02:01. Tracking TCRB clonotypes (clonality, top ranked, and TP53 mutation-specific) supported the enrichment of p53 neoantigen-reactive T cells from PBLs. The same T-cell receptor (TCR) from the TIL was found in the IVS cultures in three cases and multiple unique TCRs were found in another patient. TP53 mutation-specific T cells also recognized tumor cell lines bearing the appropriate human leukocyte antigen restriction element and TP53 mutation, indicating these T cells could recognize processed and presented p53 neoantigens. CONCLUSIONS PBL was a noninvasive source of T cells targeting TP53 mutations for cell therapy and can provide a window into intratumoral p53 neoantigen immune responses.See related commentary by Olivera et al., p. 1203.
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Affiliation(s)
| | - Rami Yossef
- Surgery Branch, National Cancer Institute, Bethesda, Maryland
| | - Gal Cafri
- Surgery Branch, National Cancer Institute, Bethesda, Maryland
| | - Biman C Paria
- Surgery Branch, National Cancer Institute, Bethesda, Maryland
| | - Frank J Lowery
- Surgery Branch, National Cancer Institute, Bethesda, Maryland
| | | | - Meghan L Good
- Surgery Branch, National Cancer Institute, Bethesda, Maryland
| | - Abraham Sachs
- Surgery Branch, National Cancer Institute, Bethesda, Maryland
| | - Amy R Copeland
- Surgery Branch, National Cancer Institute, Bethesda, Maryland
| | - Sanghyun P Kim
- Surgery Branch, National Cancer Institute, Bethesda, Maryland
| | - Scott Kivitz
- Surgery Branch, National Cancer Institute, Bethesda, Maryland
| | | | - Paul F Robbins
- Surgery Branch, National Cancer Institute, Bethesda, Maryland
| | - Satyajit Ray
- Surgery Branch, National Cancer Institute, Bethesda, Maryland
| | - Liqiang Xi
- Hematopathology Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Mark Raffeld
- Hematopathology Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Zhiya Yu
- Surgery Branch, National Cancer Institute, Bethesda, Maryland
| | | | | | | | - Drew C Deniger
- Surgery Branch, National Cancer Institute, Bethesda, Maryland
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