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Olivera I, Etxeberria I, Luri-Rey C, Molero-Glez P, Melero I. Regional and intratumoral adoptive T-cell therapy. IMMUNO-ONCOLOGY TECHNOLOGY 2024; 24:100715. [PMID: 39055165 PMCID: PMC11269935 DOI: 10.1016/j.iotech.2024.100715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Adoptive T-cell therapies (ACTs) including tumor-infiltrating lymphocytes and engineered T cells (transgenic T-cell receptor and chimeric antigen receptor T cells), have made an important impact in the field of cancer treatment over the past years. Most of these therapies are typically administered systemically in approaches that facilitate the elimination of hematologic malignancies. Therapeutical efficacy against solid tumors, however, with the exception of tumor-infiltrating lymphocytes against melanoma, remains limited due to several barriers preventing lymphocyte access to the tumor bed. Building upon the experience of regional administration in other immunotherapies, the regional administration of adoptive cell therapies is being assessed to overcome this challenge, granting a first round of access of the transferred T cells to the tumor niche and thereby ensuring their activation and expansion. Intralesional and intracavitary routes of delivery have been tested with promising antitumor objective responses in preclinical and clinical studies. Additionally, several strategies are being developed to further improve T-cell activity after reinfusing them back to the patient such as combinations with other immunotherapy agents or direct engineering of the transferred T cells, achieving long-term immune memory. Clinical trials testing different regional adoptive T-cell therapies are ongoing but some issues related to methodology of administration and correct selection of the target antigen to avoid on-target/off-tumor side-effects need to be further evaluated and improved. Herein, we discuss the current preclinical and clinical landscape of intratumoral and locoregional delivery of adoptive T-cell therapies.
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Affiliation(s)
- I. Olivera
- Program of Immunology and Immunotherapy, Cima Universidad de Navarra, Pamplona
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
| | - I. Etxeberria
- Human Oncology and Pathogenesis Program (HOPP), Immuno-Oncology Service, Memorial Sloan Kettering Cancer Center, New York
- Parker Institute for Cancer Immunotherapy, New York, USA
| | - C. Luri-Rey
- Program of Immunology and Immunotherapy, Cima Universidad de Navarra, Pamplona
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
| | - P. Molero-Glez
- Program of Immunology and Immunotherapy, Cima Universidad de Navarra, Pamplona
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
| | - I. Melero
- Program of Immunology and Immunotherapy, Cima Universidad de Navarra, Pamplona
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
- Department of Immunology and Immunotherapy, Clínica Universidad de Navarra, Pamplona
- Department of Oncology, Clínica Universidad de Navarra, Madrid
- Centro del Cancer de la Universidad de Navarra (CCUN), Pamplona, Spain
- Nuffield Department of Medicine (NDM), University of Oxford, Oxford, UK
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2
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Golikova EA, Alshevskaya AA, Alrhmoun S, Sivitskaya NA, Sennikov SV. TCR-T cell therapy: current development approaches, preclinical evaluation, and perspectives on regulatory challenges. J Transl Med 2024; 22:897. [PMID: 39367419 PMCID: PMC11451006 DOI: 10.1186/s12967-024-05703-9] [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: 06/21/2024] [Accepted: 09/24/2024] [Indexed: 10/06/2024] Open
Abstract
TCR-T cell therapy represents a promising advancement in adoptive immunotherapy for cancer treatment. Despite its potential, the development and preclinical testing of TCR-T cells face significant challenges. This review provides a structured overview of the key stages in preclinical testing, including in silico, in vitro, and in vivo methods, within the context of the sequential development of novel therapies. This review aimed to systematically outline the processes for evaluating TCR-T cells at each stage: from in silico approaches used to predict target antigens, assess cross-reactivity, and minimize off-target effects, to in vitro assays designed to measure cell functionality, cytotoxicity, and activation. Additionally, the review discusses the limitations of in vivo testing in animal models, particularly in accurately reflecting the human tumor microenvironment and immune responses. Performed analysis emphasizes the importance of these preclinical stages in the safe and effective development of TCR-T cell therapies. While current models provide valuable insights, we identify critical gaps, particularly in in vivo biodistribution and toxicity assessments, and propose the need for enhanced standardization and the development of more representative models. This structured approach aims to improve the predictability and safety of TCR-T cell therapy as it advances towards clinical application.
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Affiliation(s)
- Elena A Golikova
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435, Moscow, Russia
| | - Alina A Alshevskaya
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435, Moscow, Russia.
| | - Saleh Alrhmoun
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435, Moscow, Russia
- Federal State Budgetary Scientific Institution, "Research Institute of Fundamental and Clinical Immunology" (RIFCI), 630099, Novosibirsk, Russia
| | - Natalia A Sivitskaya
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435, Moscow, Russia
| | - Sergey V Sennikov
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435, Moscow, Russia
- Federal State Budgetary Scientific Institution, "Research Institute of Fundamental and Clinical Immunology" (RIFCI), 630099, Novosibirsk, Russia
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3
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Anderson GSF, Chapman MA. T cell-redirecting therapies in hematological malignancies: Current developments and novel strategies for improved targeting. Mol Ther 2024; 32:2856-2891. [PMID: 39095991 PMCID: PMC11403239 DOI: 10.1016/j.ymthe.2024.07.028] [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: 03/25/2024] [Revised: 07/17/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024] Open
Abstract
T cell-redirecting therapies (TCRTs), such as chimeric antigen receptor (CAR) or T cell receptor (TCR) T cells and T cell engagers, have emerged as a highly effective treatment modality, particularly in the B and plasma cell-malignancy setting. However, many patients fail to achieve deep and durable responses; while the lack of truly unique tumor antigens, and concurrent on-target/off-tumor toxicities, have hindered the development of TCRTs for many other cancers. In this review, we discuss the recent developments in TCRT targets for hematological malignancies, as well as novel targeting strategies that aim to address these, and other, challenges.
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Affiliation(s)
| | - Michael A Chapman
- MRC Toxicology Unit, University of Cambridge, Cambridge CB2 1QR, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK; Addenbrooke's Hospital, Cambridge Universities Foundation Trust, Cambridge CB2 0QQ, UK.
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4
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Chiffelle J, Harari A. Personalized cancer T-cell therapy takes the stage, mirroring vaccine success. J Exp Med 2024; 221:e20240854. [PMID: 38861029 PMCID: PMC11167374 DOI: 10.1084/jem.20240854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024] Open
Abstract
Personalized T-cell therapy is emerging as a pivotal treatment of cancer care by tailoring cellular therapies to individual genetic and antigenic profiles, echoing the exciting success of personalized vaccines. We describe here the parallel evolution and analogies of cancer vaccines and T-cell therapies.
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Affiliation(s)
- Johanna Chiffelle
- Department of Oncology, Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Lausanne University Hospital-Ludwig Institute, Lausanne, Switzerland
| | - Alexandre Harari
- Department of Oncology, Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Lausanne University Hospital-Ludwig Institute, Lausanne, Switzerland
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5
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Meng W, Takeuchi Y, Ward JP, Sultan H, Arthur CD, Mardis ER, Artyomov MN, Lichti CF, Schreiber RD. Improvement of Tumor Neoantigen Detection by High-Field Asymmetric Waveform Ion Mobility Mass Spectrometry. Cancer Immunol Res 2024; 12:988-1006. [PMID: 38768391 PMCID: PMC11456315 DOI: 10.1158/2326-6066.cir-23-0900] [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: 10/26/2023] [Revised: 03/05/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Cancer neoantigens have been shown to elicit cancer-specific T-cell responses and have garnered much attention for their roles in both spontaneous and therapeutically induced antitumor responses. Mass spectrometry (MS) profiling of tumor immunopeptidomes has been used, in part, to identify MHC-bound mutant neoantigen ligands. However, under standard conditions, MS-based detection of such rare but clinically relevant neoantigens is relatively insensitive, requiring 300 million cells or more. Here, to quantitatively define the minimum detectable amounts of therapeutically relevant MHC-I and MHC-II neoantigen peptides, we analyzed different dilutions of immunopeptidomes isolated from the well-characterized T3 mouse methylcholanthrene (MCA)-induced cell line by MS. Using either data-dependent acquisition or parallel reaction monitoring (PRM), we established the minimum amount of material required to detect the major T3 neoantigens in the presence or absence of high field asymmetric waveform ion mobility spectrometry (FAIMS). This analysis yielded a 14-fold enhancement of sensitivity in detecting the major T3 MHC-I neoantigen (mLama4) with FAIMS-PRM compared with PRM without FAIMS, allowing ex vivo detection of this neoantigen from an individual 100 mg T3 tumor. These findings were then extended to two other independent MCA-sarcoma lines (1956 and F244). This study demonstrates that FAIMS substantially increases the sensitivity of MS-based characterization of validated neoantigens from tumors.
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Affiliation(s)
- Wei Meng
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, U.S.A
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63110, U.S.A
| | - Yoshiko Takeuchi
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, U.S.A
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63110, U.S.A
| | - Jeffrey P. Ward
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, U.S.A
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63110, U.S.A
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, U.S.A
| | - Hussein Sultan
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, U.S.A
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63110, U.S.A
| | - Cora D. Arthur
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, U.S.A
| | - Elaine R. Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children’s Hospital, Columbus, OH 43215, U.S.A
| | - Maxim N. Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, U.S.A
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63110, U.S.A
| | - Cheryl F. Lichti
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, U.S.A
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63110, U.S.A
| | - Robert D. Schreiber
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, U.S.A
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63110, U.S.A
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6
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Gurung HR, Heidersbach AJ, Darwish M, Chan PPF, Li J, Beresini M, Zill OA, Wallace A, Tong AJ, Hascall D, Torres E, Chang A, Lou K'HW, Abdolazimi Y, Hammer C, Xavier-Magalhães A, Marcu A, Vaidya S, Le DD, Akhmetzyanova I, Oh SA, Moore AJ, Uche UN, Laur MB, Notturno RJ, Ebert PJR, Blanchette C, Haley B, Rose CM. Systematic discovery of neoepitope-HLA pairs for neoantigens shared among patients and tumor types. Nat Biotechnol 2024; 42:1107-1117. [PMID: 37857725 PMCID: PMC11251992 DOI: 10.1038/s41587-023-01945-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 08/14/2023] [Indexed: 10/21/2023]
Abstract
The broad application of precision cancer immunotherapies is limited by the number of validated neoepitopes that are common among patients or tumor types. To expand the known repertoire of shared neoantigen-human leukocyte antigen (HLA) complexes, we developed a high-throughput platform that coupled an in vitro peptide-HLA binding assay with engineered cellular models expressing individual HLA alleles in combination with a concatenated transgene harboring 47 common cancer neoantigens. From more than 24,000 possible neoepitope-HLA combinations, biochemical and computational assessment yielded 844 unique candidates, of which 86 were verified after immunoprecipitation mass spectrometry analyses of engineered, monoallelic cell lines. To evaluate the potential for immunogenicity, we identified T cell receptors that recognized select neoepitope-HLA pairs and elicited a response after introduction into human T cells. These cellular systems and our data on therapeutically relevant neoepitopes in their HLA contexts will aid researchers studying antigen processing as well as neoepitope targeting therapies.
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Affiliation(s)
| | | | | | | | - Jenny Li
- Genentech, South San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Ana Marcu
- Genentech, South San Francisco, CA, USA
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Sueangoen N, Thuwajit P, Yenchitsomanus PT, Thuwajit C. Public neoantigens in breast cancer immunotherapy (Review). Int J Mol Med 2024; 54:65. [PMID: 38904202 PMCID: PMC11188978 DOI: 10.3892/ijmm.2024.5388] [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: 01/17/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024] Open
Abstract
Among women globally, breast cancer is the most prevalent cancer and the leading cause of cancer‑related death. Interestingly, though genetic mutations contribute to the disease, <15% of women diagnosed with breast cancer have a family history of the disease, suggesting a prevalence of sporadic genetic mutations in breast cancer development. In the rapidly rising field of cancer genomics, neoantigen‑based immunotherapy has come to the fore. The investigation of novel proteins arising from unique somatic mutations or neoantigens have opened a new pathway for both individualized and public cancer treatments. Because they are shared among individuals with similar genetic changes, public neoantigens provide an opportunity for 'off‑the‑shelf' anticancer therapies, potentially extending the benefits to a wider patient group. The present review aimed to highlight the role of shared or public neoantigens as therapeutic targets for patients with breast cancer, emphasizing common hotspot mutations of certain genes identified in breast cancer. The clinical utilization of public neoantigen‑based therapies for breast cancer treatment were also discussed.
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Affiliation(s)
- Natthaporn Sueangoen
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Peti Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Pa-Thai Yenchitsomanus
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chanitra Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
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Hao Q, Long Y, Yang Y, Deng Y, Ding Z, Yang L, Shu Y, Xu H. Development and Clinical Applications of Therapeutic Cancer Vaccines with Individualized and Shared Neoantigens. Vaccines (Basel) 2024; 12:717. [PMID: 39066355 PMCID: PMC11281709 DOI: 10.3390/vaccines12070717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Neoantigens, presented as peptides on the surfaces of cancer cells, have recently been proposed as optimal targets for immunotherapy in clinical practice. The promising outcomes of neoantigen-based cancer vaccines have inspired enthusiasm for their broader clinical applications. However, the individualized tumor-specific antigens (TSA) entail considerable costs and time due to the variable immunogenicity and response rates of these neoantigens-based vaccines, influenced by factors such as neoantigen response, vaccine types, and combination therapy. Given the crucial role of neoantigen efficacy, a number of bioinformatics algorithms and pipelines have been developed to improve the accuracy rate of prediction through considering a series of factors involving in HLA-peptide-TCR complex formation, including peptide presentation, HLA-peptide affinity, and TCR recognition. On the other hand, shared neoantigens, originating from driver mutations at hot mutation spots (e.g., KRASG12D), offer a promising and ideal target for the development of therapeutic cancer vaccines. A series of clinical practices have established the efficacy of these vaccines in patients with distinct HLA haplotypes. Moreover, increasing evidence demonstrated that a combination of tumor associated antigens (TAAs) and neoantigens can also improve the prognosis, thus expand the repertoire of shared neoantigens for cancer vaccines. In this review, we provide an overview of the complex process involved in identifying personalized neoantigens, their clinical applications, advances in vaccine technology, and explore the therapeutic potential of shared neoantigen strategies.
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Affiliation(s)
- Qing Hao
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
| | - Yuhang Long
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
| | - Yi Yang
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
| | - Yiqi Deng
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
- Colorectal Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhenyu Ding
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
| | - Li Yang
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
| | - Yang Shu
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
- Gastric Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
- Institute of General Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Heng Xu
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
- Institute of General Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
- Research Center of Clinical Laboratory Medicine, Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
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Shen M, Chen S, Han X, Hao Y, Wang J, Li L, Chen T, Wang B, Zou L, Zhang T, Zhang W, Han X, Wang W, Yu H, Li K, Liu S, Jin A. Identification of an HLA-A*11:01-restricted neoepitope of mutant PIK3CA and its specific T cell receptors for cancer immunotherapy targeting hotspot driver mutations. Cancer Immunol Immunother 2024; 73:150. [PMID: 38832948 PMCID: PMC11150344 DOI: 10.1007/s00262-024-03729-y] [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: 04/10/2024] [Accepted: 05/10/2024] [Indexed: 06/06/2024]
Abstract
Hotspot driver mutations presented by human leukocyte antigens might be recognized by anti-tumor T cells. Based on their advantages of tumor-specificity and immunogenicity, neoantigens derived from hotspot mutations, such as PIK3CAH1047L, may serve as emerging targets for cancer immunotherapies. NetMHCpan V4.1 was utilized for predicting neoepitopes of PIK3CA hotspot mutation. Using in vitro stimulation, antigen-specific T cells targeting the HLA-A*11:01-restricted PIK3CA mutation were isolated from healthy donor-derived peripheral blood mononuclear cells. T cell receptors (TCRs) were cloned using single-cell PCR and sequencing. Their functionality was assessed through T cell activation markers, cytokine production and cytotoxic response to cancer cell lines pulsed with peptides or transduced genes of mutant PIK3CA. Immunogenic mutant antigens from PIK3CA and their corresponding CD8+ T cells were identified. These PIK3CA mutation-specific CD8+ T cells were subsequently enriched, and their TCRs were isolated. The TCR clones exhibited mutation-specific and HLA-restricted reactivity, demonstrating varying degrees of functional avidity. Identified TCR genes were transferred into CD8+ Jurkat cells and primary T cells deficient of endogenous TCRs. TCR-expressing cells demonstrated specific recognition and reactivity against the PIK3CAH1047L peptide presented by HLA-A*11:01-expressing K562 cells. Furthermore, mutation-specific TCR-T cells demonstrated an elevation in cytokine production and profound cytotoxic effects against HLA-A*11:01+ malignant cell lines harboring PIK3CAH1047L. Our data demonstrate the immunogenicity of an HLA-A*11:01-restricted PIK3CA hotspot mutation and its targeting therapeutic potential, together with promising candidates of TCR-T cell therapy.
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Affiliation(s)
- Meiying Shen
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Siyin Chen
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Xiaojian Han
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Yanan Hao
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Junfan Wang
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Luo Li
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Tong Chen
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Bozhi Wang
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Lin Zou
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Tong Zhang
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Wanli Zhang
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Xiaxia Han
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Wang Wang
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Haochen Yu
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Kang Li
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shengchun Liu
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Aishun Jin
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China.
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10
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Levin N, Kim SP, Marquardt CA, Vale NR, Yu Z, Sindiri S, Gartner JJ, Parkhurst M, Krishna S, Lowery FJ, Zacharakis N, Levy L, Prickett TD, Benzine T, Ray S, Masi RV, Gasmi B, Li Y, Islam R, Bera A, Goff SL, Robbins PF, Rosenberg SA. Neoantigen-specific stimulation of tumor-infiltrating lymphocytes enables effective TCR isolation and expansion while preserving stem-like memory phenotypes. J Immunother Cancer 2024; 12:e008645. [PMID: 38816232 PMCID: PMC11141192 DOI: 10.1136/jitc-2023-008645] [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: 04/22/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND Tumor-infiltrating lymphocytes (TILs) targeting neoantigens can effectively treat a selected set of metastatic solid cancers. However, harnessing TILs for cancer treatments remains challenging because neoantigen-reactive T cells are often rare and exhausted, and ex vivo expansion can further reduce their frequencies. This complicates the identification of neoantigen-reactive T-cell receptors (TCRs) and the development of TIL products with high reactivity for patient treatment. METHODS We tested whether TILs could be in vitro stimulated against neoantigens to achieve selective expansion of neoantigen-reactive TILs. Given their prevalence, mutant p53 or RAS were studied as models of human neoantigens. An in vitro stimulation method, termed "NeoExpand", was developed to provide neoantigen-specific stimulation to TILs. 25 consecutive patient TILs from tumors harboring p53 or RAS mutations were subjected to NeoExpand. RESULTS We show that neoantigenic stimulation achieved selective expansion of neoantigen-reactive TILs and broadened the neoantigen-reactive CD4+ and CD8+ TIL clonal repertoire. This allowed the effective isolation of novel neoantigen-reactive TCRs. Out of the 25 consecutive TIL samples, neoantigenic stimulation enabled the identification of 16 unique reactivities and 42 TCRs, while conventional TIL expansion identified 9 reactivities and 14 TCRs. Single-cell transcriptome analysis revealed that neoantigenic stimulation increased neoantigen-reactive TILs with stem-like memory phenotypes expressing IL-7R, CD62L, and KLF2. Furthermore, neoantigenic stimulation improved the in vivo antitumor efficacy of TILs relative to the conventional OKT3-induced rapid TIL expansion in p53-mutated or KRAS-mutated xenograft mouse models. CONCLUSIONS Taken together, neoantigenic stimulation of TILs selectively expands neoantigen-reactive TILs by frequencies and by their clonal repertoire. NeoExpand led to improved phenotypes and functions of neoantigen-reactive TILs. Our data warrant its clinical evaluation. TRIAL REGISTRATION NUMBER NCT00068003, NCT01174121, and NCT03412877.
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Affiliation(s)
- Noam Levin
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Sanghyun P Kim
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Charles A Marquardt
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Nolan R Vale
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Zhiya Yu
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Sivasish Sindiri
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Jared J Gartner
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Maria Parkhurst
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Sri Krishna
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Frank J Lowery
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Nikolaos Zacharakis
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Lior Levy
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Todd D Prickett
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Tiffany Benzine
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Satyajit Ray
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Robert V Masi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Billel Gasmi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Yong Li
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Rafiqul Islam
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Alakesh Bera
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Stephanie L Goff
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Paul F Robbins
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Steven A Rosenberg
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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11
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Ma J, Ayres CM, Brambley CA, Chandran SS, Rosales TJ, Corcelli SA, Kovrigin EL, Klebanoff CA, Baker BM. Dynamic allostery in the peptide/MHC complex enables TCR neoantigen selectivity. RESEARCH SQUARE 2024:rs.3.rs-4457195. [PMID: 38854019 PMCID: PMC11160895 DOI: 10.21203/rs.3.rs-4457195/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The inherent cross-reactivity of the T cell receptor (TCR) is balanced by high specificity, which often manifests in confounding ways not easily interpretable from static structures. We show here that TCR discrimination between an HLA-A*03:01 (HLA-A3)-restricted public neoantigen derived from mutant PIK3CA and its wild-type (WT) counterpart emerges from motions within the HLA binding groove that vary with the identity of the peptide's first primary anchor. The motions form a dynamic gate that in the complex with the WT peptide impedes a large conformational change required for TCR binding. The more rigid neoantigen is insusceptible to this limiting dynamic, and with the gate open, is able to transit its central tryptophan residue underneath the peptide backbone to the contralateral side of the HLA-A3 peptide binding groove, facilitating TCR binding. Our findings reveal a novel mechanism driving TCR specificity for a cancer neoantigen that is rooted in the dynamic and allosteric nature of peptide/MHC-I complexes, with implications for resolving long-standing and often confounding questions about the determinants of T cell specificity.
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Affiliation(s)
- Jiaqi Ma
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Chad A Brambley
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Smita S Chandran
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA
- Center for Cell Engineering, MSKCC, New York, NY, USA
| | - Tatiana J Rosales
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Evgenii L Kovrigin
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Christopher A Klebanoff
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA
- Center for Cell Engineering, MSKCC, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, New York, NY, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
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12
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Li Y, Zheng Y, Liu T, Liao C, Shen G, He Z. The potential and promise for clinical application of adoptive T cell therapy in cancer. J Transl Med 2024; 22:413. [PMID: 38693513 PMCID: PMC11064426 DOI: 10.1186/s12967-024-05206-7] [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: 02/06/2024] [Accepted: 04/15/2024] [Indexed: 05/03/2024] Open
Abstract
Adoptive cell therapy has revolutionized cancer treatment, especially for hematologic malignancies. T cells are the most extensively utilized cells in adoptive cell therapy. Currently, tumor-infiltrating lymphocytes, T cell receptor-transgenic T cells and chimeric antigen receptor T cells are the three main adoptive T cell therapies. Tumor-infiltrating lymphocytes kill tumors by reinfusing enlarged lymphocytes that naturally target tumor-specific antigens into the patient. T cell receptor-transgenic T cells have the ability to specifically destroy tumor cells via the precise recognition of exogenous T cell receptors with major histocompatibility complex. Chimeric antigen receptor T cells transfer genes with specific antigen recognition structural domains and T cell activation signals into T cells, allowing T cells to attack tumors without the assistance of major histocompatibility complex. Many barriers have been demonstrated to affect the clinical efficacy of adoptive T cell therapy, such as tumor heterogeneity and antigen loss, hard trafficking and infiltration, immunosuppressive tumor microenvironment and T cell exhaustion. Several strategies to improve the efficacy of adoptive T cell therapy have been explored, including multispecific chimeric antigen receptor T cell therapy, combination with immune checkpoint blockade, targeting the immunosuppressive tumor microenvironment, etc. In this review, we will summarize the current status and clinical application, followed by major bottlenecks in adoptive T cell therapy. In addition, we will discuss the promising strategies to improve adoptive T cell therapy. Adoptive T cell therapy will result in even more incredible advancements in solid tumors if the aforementioned problems can be handled.
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Affiliation(s)
- Yinqi Li
- Department of Pharmacy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, 610041, China
| | - Yeteng Zheng
- Department of Pharmacy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, 610041, China
| | - Taiqing Liu
- Department of Pharmacy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, 610041, China
| | - Chuanyun Liao
- Department of Pharmacy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, 610041, China
| | - Guobo Shen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, 610041, China.
| | - Zhiyao He
- Department of Pharmacy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, 610041, China.
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
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13
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Goldner Kabeli R, Zevin S, Abargel A, Zilberberg A, Efroni S. Self-supervised learning of T cell receptor sequences exposes core properties for T cell membership. SCIENCE ADVANCES 2024; 10:eadk4670. [PMID: 38669334 DOI: 10.1126/sciadv.adk4670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
The T cell receptor (TCR) repertoire is an extraordinarily diverse collection of TCRs essential for maintaining the body's homeostasis and response to threats. In this study, we compiled an extensive dataset of more than 4200 bulk TCR repertoire samples, encompassing 221,176,713 sequences, alongside 6,159,652 single-cell TCR sequences from over 400 samples. From this dataset, we then selected a representative subset of 5 million bulk sequences and 4.2 million single-cell sequences to train two specialized Transformer-based language models for bulk (CVC) and single-cell (scCVC) TCR repertoires, respectively. We show that these models successfully capture TCR core qualities, such as sharing, gene composition, and single-cell properties. These qualities are emergent in the encoded TCR latent space and enable classification into TCR-based qualities such as public sequences. These models demonstrate the potential of Transformer-based language models in TCR downstream applications.
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Affiliation(s)
- Romi Goldner Kabeli
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Sarit Zevin
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Avital Abargel
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Alona Zilberberg
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Sol Efroni
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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14
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Sheikhlary S, Lopez DH, Moghimi S, Sun B. Recent Findings on Therapeutic Cancer Vaccines: An Updated Review. Biomolecules 2024; 14:503. [PMID: 38672519 PMCID: PMC11048403 DOI: 10.3390/biom14040503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/06/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Cancer remains one of the global leading causes of death and various vaccines have been developed over the years against it, including cell-based, nucleic acid-based, and viral-based cancer vaccines. Although many vaccines have been effective in in vivo and clinical studies and some have been FDA-approved, there are major limitations to overcome: (1) developing one universal vaccine for a specific cancer is difficult, as tumors with different antigens are different for different individuals, (2) the tumor antigens may be similar to the body's own antigens, and (3) there is the possibility of cancer recurrence. Therefore, developing personalized cancer vaccines with the ability to distinguish between the tumor and the body's antigens is indispensable. This paper provides a comprehensive review of different types of cancer vaccines and highlights important factors necessary for developing efficient cancer vaccines. Moreover, the application of other technologies in cancer therapy is discussed. Finally, several insights and conclusions are presented, such as the possibility of using cold plasma and cancer stem cells in developing future cancer vaccines, to tackle the major limitations in the cancer vaccine developmental process.
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Affiliation(s)
- Sara Sheikhlary
- Department of Biomedical Engineering, College of Engineering, The University of Arizona, Tucson, AZ 85721, USA
| | - David Humberto Lopez
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA; (D.H.L.); (S.M.)
| | - Sophia Moghimi
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA; (D.H.L.); (S.M.)
| | - Bo Sun
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA; (D.H.L.); (S.M.)
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15
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Chen M, Zhang X, Ming Z, Lingyu, Feng X, Han Z, An HX. Characterizing and forecasting neoantigens-resulting from MUC mutations in COAD. J Transl Med 2024; 22:315. [PMID: 38539235 PMCID: PMC10967086 DOI: 10.1186/s12967-024-05103-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/15/2024] [Indexed: 08/09/2024] Open
Abstract
BACKGROUND The treatment for colon adenocarcinoma (COAD) faces challenges in terms of immunotherapy effectiveness due to multiple factors. Because of the high tumor specificity and immunogenicity, neoantigen has been considered a pivotal target for cancer immunotherapy. Therefore, this study aims to identify and predict the potential tumor antigens of MUC somatic mutations (MUCmut) in COAD. METHODS Three databases of TCGA, TIMER2.0, and cBioPortal were used for a detailed evaluation of the association between MUCmut and multi-factors like tumor mutation burden (TMB), microsatellite instability (MSI), prognosis, and the tumor microenvironment within the context of total 2242 COAD patients. Next, TSNAdb and the differential agretopicity index (DAI) were utilized to predict high-confidence neopeptides for MUCmut based on 531 COAD patients' genomic information. DAI was calculated by subtraction of its predicted HLA binding affinity of the MUCmut peptide from the corresponding wild-type peptide. RESULTS The top six mutation frequencies (14 to 2.9%) were from MUC16, MUC17, MUC5B, MUC2, MUC4 and MUC6. COAD patients with MUC16 and MUC4 mutations had longer DFS and PFS. However, patients with MUC13 and MUC20 mutations had shorter OS. Patients with the mutation of MUC16, MUC5B, MUC2, MUC4, and MUC6 exhibited higher TMB and MSI. Moreover, these mutations from the MUC family were associated with the infiltration of diverse lymphocyte cells and the expression of immune checkpoint genes. Through TSNAdb 1.0/NetMHCpan v2.8, 452 single nucleotide variants (SNVs) of MUCmut peptides were identified. Moreover, through TSNAdb2.0/NetMHCpan v4.0, 57 SNVs, 1 Q-frame shift (TS), and 157 short insertions/deletions (INDELs) of MUCmut were identified. Finally, 10 high-confidence neopeptides of MUCmut were predicted by DAI. CONCLUSIONS Together, our findings establish the immunogenicity and therapeutic potential of mutant MUC family-derived neoantigens. Through combining the tools of TSNAdb and DAI, a group of novel MUCmut neoantigens were identified as potential targets for immunotherapy.
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Affiliation(s)
- Min Chen
- Clinical Central Research Core, Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan, Shanxi, China.
| | - Xin Zhang
- The Center Laboratory, Shanghai Medical College, Zhongshan Hospital (Xiamen Affiliated) of Fudan University, Fudan University, Xiamen, China
| | - Zihe Ming
- Cancer Center and Department of Breast and Thyroid Surgery, School of Medicine, Xiang'an Hospital of Xiamen University, Xiamen University, Xiamen, China
| | - Lingyu
- Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaorong Feng
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province, Chemistry and Chemical Engineering Guangdong Laboratory, Shantou University, Guangdong, China
| | - Zhenguo Han
- Department of Colorectal and Anal Surgery, Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Han-Xiang An
- Clinical Central Research Core, Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan, Shanxi, China.
- The Cancer Center, Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan, Shanxi, China.
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16
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Zhang W, Sun S, Zhu W, Meng D, Hu W, Yang S, Gao M, Yao P, Wang Y, Wang Q, Ji J. Birinapant Reshapes the Tumor Immunopeptidome and Enhances Antigen Presentation. Int J Mol Sci 2024; 25:3660. [PMID: 38612472 PMCID: PMC11011986 DOI: 10.3390/ijms25073660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
Birinapant, an antagonist of the inhibitor of apoptosis proteins, upregulates MHCs in tumor cells and displays a better tumoricidal effect when used in combination with immune checkpoint inhibitors, indicating that Birinapant may affect the antigen presentation pathway; however, the mechanism remains elusive. Based on high-resolution mass spectrometry and in vitro and in vivo models, we adopted integrated genomics, proteomics, and immunopeptidomics strategies to study the mechanism underlying the regulation of tumor immunity by Birinapant from the perspective of antigen presentation. Firstly, in HT29 and MCF7 cells, Birinapant increased the number and abundance of immunopeptides and source proteins. Secondly, a greater number of cancer/testis antigen peptides with increased abundance and more neoantigens were identified following Birinapant treatment. Moreover, we demonstrate the existence and immunogenicity of a neoantigen derived from insertion/deletion mutation. Thirdly, in HT29 cell-derived xenograft models, Birinapant administration also reshaped the immunopeptidome, and the tumor exhibited better immunogenicity. These data suggest that Birinapant can reshape the tumor immunopeptidome with respect to quality and quantity, which improves the presentation of CTA peptides and neoantigens, thus enhancing the immunogenicity of tumor cells. Such changes may be vital to the effectiveness of combination therapy, which can be further transferred to the clinic or aid in the development of new immunotherapeutic strategies to improve the anti-tumor immune response.
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Affiliation(s)
- Weiyan Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Shenghuan Sun
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA 94143, USA;
| | - Wenyuan Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Delan Meng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Weiyi Hu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Siqi Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Mingjie Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Pengju Yao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Yuhao Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Qingsong Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Jianguo Ji
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
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17
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Finnigan JP, Newman JH, Patskovsky Y, Patskovska L, Ishizuka AS, Lynn GM, Seder RA, Krogsgaard M, Bhardwaj N. Structural basis for self-discrimination by neoantigen-specific TCRs. Nat Commun 2024; 15:2140. [PMID: 38459027 PMCID: PMC10924104 DOI: 10.1038/s41467-024-46367-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/26/2024] [Indexed: 03/10/2024] Open
Abstract
T cell receptors (TCR) are pivotal in mediating tumour cell cytolysis via recognition of mutation-derived tumour neoantigens (neoAgs) presented by major histocompatibility class-I (MHC-I). Understanding the factors governing the emergence of neoAg from somatic mutations is a major focus of current research. However, the structural and cellular determinants controlling TCR recognition of neoAgs remain poorly understood. This study describes the multi-level analysis of a model neoAg from the B16F10 murine melanoma, H2-Db/Hsf2 p.K72N68-76, as well as its cognate TCR 47BE7. Through cellular, molecular and structural studies we demonstrate that the p.K72N mutation enhances H2-Db binding, thereby improving cell surface presentation and stabilizing the TCR 47BE7 epitope. Furthermore, TCR 47BE7 exhibited high functional avidity and selectivity, attributable to a broad, stringent, binding interface enabling recognition of native B16F10 despite low antigen density. Our findings provide insight into the generation of anchor-residue modified neoAg, and emphasize the value of molecular and structural investigations of neoAg in diverse MHC-I contexts for advancing the understanding of neoAg immunogenicity.
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Affiliation(s)
- John P Finnigan
- Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Pl., New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave., New York, NY, USA
- Department of Medicine, Division of Hematology and Medical Oncology, Mount Sinai Hospital, New York, NY, USA
- Department of Surgery, Division of Thoracic and Cardiac Surgery, Brigham and Women's Hospital, 75 Francis St., Boston, MA, USA
| | - Jenna H Newman
- Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Pl., New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave., New York, NY, USA
- Department of Medicine, Division of Hematology and Medical Oncology, Mount Sinai Hospital, New York, NY, USA
| | - Yury Patskovsky
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center at NYU Langone Health, New York, NY, USA
| | - Larysa Patskovska
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center at NYU Langone Health, New York, NY, USA
| | - Andrew S Ishizuka
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Barinthus Biotherapeutics, Germantown, MD, USA
| | - Geoffrey M Lynn
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Barinthus Biotherapeutics, Germantown, MD, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michelle Krogsgaard
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA.
- Laura and Isaac Perlmutter Cancer Center at NYU Langone Health, New York, NY, USA.
| | - Nina Bhardwaj
- Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Pl., New York, NY, USA.
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave., New York, NY, USA.
- Department of Medicine, Division of Hematology and Medical Oncology, Mount Sinai Hospital, New York, NY, USA.
- Parker Institute for Cancer Immunotherapy, Francisco, CA, USA.
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18
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Shafer P, Leung WK, Woods M, Choi JM, Rodriguez-Plata CM, Maknojia A, Mosquera A, Somes LK, Joubert J, Manliguez A, Ranjan R, Burt B, Lee HS, Zhang B, Fuqua S, Rooney C, Leen AM, Hoyos V. Incongruity between T cell receptor recognition of breast cancer hotspot mutations ESR1 Y537S and D538G following exogenous peptide loading versus endogenous antigen processing. Cytotherapy 2024; 26:266-275. [PMID: 38231165 PMCID: PMC10922969 DOI: 10.1016/j.jcyt.2023.12.002] [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: 08/14/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 01/18/2024]
Abstract
T cell receptor engineered T cell (TCR T) therapies have shown recent efficacy against certain types of solid metastatic cancers. However, to extend TCR T therapies to treat more patients across additional cancer types, new TCRs recognizing cancer-specific antigen targets are needed. Driver mutations in AKT1, ESR1, PIK3CA, and TP53 are common in patients with metastatic breast cancer (MBC) and if immunogenic could serve as ideal tumor-specific targets for TCR T therapy to treat this disease. Through IFN-γ ELISpot screening of in vitro expanded neopeptide-stimulated T cell lines from healthy donors and MBC patients, we identified reactivity towards 11 of 13 of the mutations. To identify neopeptide-specific TCRs, we then performed single-cell RNA sequencing of one of the T cell lines following neopeptide stimulation. Here, we identified an ESR1 Y537S specific T cell clone, clonotype 16, and an ESR1 Y537S/D538G dual-specific T cell clone, clonotype 21, which were HLA-B*40:02 and HLA-C*01:02 restricted, respectively. TCR Ts expressing these TCRs recognized and killed target cells pulsed with ESR1 neopeptides with minimal activity against ESR1 WT peptide. However, these TCRs failed to recognize target cells expressing endogenous mutant ESR1. To investigate the basis of this lack of recognition we performed immunopeptidomics analysis of a mutant-overexpressing lymphoblastoid cell line and found that the ESR1 Y537S neopeptide was not endogenously processed, despite binding to HLA-B*40:02 when exogenously pulsed onto the target cell. These results indicate that stimulation of T cells that likely derive from the naïve repertoire with pulsed minimal peptides may lead to the expansion of clones that recognize non-processed peptides, and highlights the importance of using methods that selectively expand T cells with specificity for antigens that are efficiently processed and presented.
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Affiliation(s)
- Paul Shafer
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Wingchi K Leung
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Mae Woods
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Jong Min Choi
- Systems Onco-Immunology Laboratory, David J. Sugarbaker Division of Thoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Carlos M Rodriguez-Plata
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Arushana Maknojia
- Division of Infectious Disease, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Andres Mosquera
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Lauren K Somes
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Jarrett Joubert
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Anthony Manliguez
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Rashi Ranjan
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Bryan Burt
- Systems Onco-Immunology Laboratory, David J. Sugarbaker Division of Thoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Hyun-Sung Lee
- Systems Onco-Immunology Laboratory, David J. Sugarbaker Division of Thoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Bing Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Suzanne Fuqua
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Cliona Rooney
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Ann M Leen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Valentina Hoyos
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA.
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19
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Katsikis PD, Ishii KJ, Schliehe C. Challenges in developing personalized neoantigen cancer vaccines. Nat Rev Immunol 2024; 24:213-227. [PMID: 37783860 DOI: 10.1038/s41577-023-00937-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2023] [Indexed: 10/04/2023]
Abstract
The recent success of cancer immunotherapies has highlighted the benefit of harnessing the immune system for cancer treatment. Vaccines have a long history of promoting immunity to pathogens and, consequently, vaccines targeting cancer neoantigens have been championed as a tool to direct and amplify immune responses against tumours while sparing healthy tissue. In recent years, extensive preclinical research and more than one hundred clinical trials have tested different strategies of neoantigen discovery and vaccine formulations. However, despite the enthusiasm for neoantigen vaccines, proof of unequivocal efficacy has remained beyond reach for the majority of clinical trials. In this Review, we focus on the key obstacles pertaining to vaccine design and tumour environment that remain to be overcome in order to unleash the true potential of neoantigen vaccines in cancer therapy.
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Affiliation(s)
- Peter D Katsikis
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands.
| | - Ken J Ishii
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo, Japan
- International Vaccine Design Center (vDesC), The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo, Japan
| | - Christopher Schliehe
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
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20
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Addala V, Newell F, Pearson JV, Redwood A, Robinson BW, Creaney J, Waddell N. Computational immunogenomic approaches to predict response to cancer immunotherapies. Nat Rev Clin Oncol 2024; 21:28-46. [PMID: 37907723 DOI: 10.1038/s41571-023-00830-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/02/2023]
Abstract
Cancer immunogenomics is an emerging field that bridges genomics and immunology. The establishment of large-scale genomic collaborative efforts along with the development of new single-cell transcriptomic techniques and multi-omics approaches have enabled characterization of the mutational and transcriptional profiles of many cancer types and helped to identify clinically actionable alterations as well as predictive and prognostic biomarkers. Researchers have developed computational approaches and machine learning algorithms to accurately obtain clinically useful information from genomic and transcriptomic sequencing data from bulk tissue or single cells and explore tumours and their microenvironment. The rapid growth in sequencing and computational approaches has resulted in the unmet need to understand their true potential and limitations in enabling improvements in the management of patients with cancer who are receiving immunotherapies. In this Review, we describe the computational approaches currently available to analyse bulk tissue and single-cell sequencing data from cancer, stromal and immune cells, as well as how best to select the most appropriate tool to address various clinical questions and, ultimately, improve patient outcomes.
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Affiliation(s)
- Venkateswar Addala
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
| | - Felicity Newell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - John V Pearson
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Alec Redwood
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- School of Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
| | - Bruce W Robinson
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
- Medical School, University of Western Australia, Perth, Western Australia, Australia
| | - Jenette Creaney
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- School of Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Nicola Waddell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
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21
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Li X, You J, Hong L, Liu W, Guo P, Hao X. Neoantigen cancer vaccines: a new star on the horizon. Cancer Biol Med 2023; 21:j.issn.2095-3941.2023.0395. [PMID: 38164734 PMCID: PMC11033713 DOI: 10.20892/j.issn.2095-3941.2023.0395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024] Open
Abstract
Immunotherapy represents a promising strategy for cancer treatment that utilizes immune cells or drugs to activate the patient's own immune system and eliminate cancer cells. One of the most exciting advances within this field is the targeting of neoantigens, which are peptides derived from non-synonymous somatic mutations that are found exclusively within cancer cells and absent in normal cells. Although neoantigen-based therapeutic vaccines have not received approval for standard cancer treatment, early clinical trials have yielded encouraging outcomes as standalone monotherapy or when combined with checkpoint inhibitors. Progress made in high-throughput sequencing and bioinformatics have greatly facilitated the precise and efficient identification of neoantigens. Consequently, personalized neoantigen-based vaccines tailored to each patient have been developed that are capable of eliciting a robust and long-lasting immune response which effectively eliminates tumors and prevents recurrences. This review provides a concise overview consolidating the latest clinical advances in neoantigen-based therapeutic vaccines, and also discusses challenges and future perspectives for this innovative approach, particularly emphasizing the potential of neoantigen-based therapeutic vaccines to enhance clinical efficacy against advanced solid tumors.
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Affiliation(s)
- Xiaoling Li
- Cell Biotechnology Laboratory, Tianjin Cancer Hospital Airport Hospital, Tianjin 300308, China
- National Clinical Research Center for Cancer, Tianjin 300060, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300090, China
| | - Jian You
- Department of Thoracic Oncology, Tianjin Cancer Hospital Airport Hospital, Tianjin 300308, China
- Department of Thoracic Oncology Surgery, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China
| | - Liping Hong
- Cell Biotechnology Laboratory, Tianjin Cancer Hospital Airport Hospital, Tianjin 300308, China
- National Clinical Research Center for Cancer, Tianjin 300060, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300090, China
| | - Weijiang Liu
- Cell Biotechnology Laboratory, Tianjin Cancer Hospital Airport Hospital, Tianjin 300308, China
- National Clinical Research Center for Cancer, Tianjin 300060, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300090, China
| | - Peng Guo
- Cell Biotechnology Laboratory, Tianjin Cancer Hospital Airport Hospital, Tianjin 300308, China
- National Clinical Research Center for Cancer, Tianjin 300060, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300090, China
| | - Xishan Hao
- Cell Biotechnology Laboratory, Tianjin Cancer Hospital Airport Hospital, Tianjin 300308, China
- National Clinical Research Center for Cancer, Tianjin 300060, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300090, China
- Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China
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22
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Chamorro DF, Somes LK, Hoyos V. Engineered Adoptive T-Cell Therapies for Breast Cancer: Current Progress, Challenges, and Potential. Cancers (Basel) 2023; 16:124. [PMID: 38201551 PMCID: PMC10778447 DOI: 10.3390/cancers16010124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Breast cancer remains a significant health challenge, and novel treatment approaches are critically needed. This review presents an in-depth analysis of engineered adoptive T-cell therapies (E-ACTs), an innovative frontier in cancer immunotherapy, focusing on their application in breast cancer. We explore the evolving landscape of chimeric antigen receptor (CAR) and T-cell receptor (TCR) T-cell therapies, highlighting their potential and challenges in targeting breast cancer. The review addresses key obstacles such as target antigen selection, the complex breast cancer tumor microenvironment, and the persistence of engineered T-cells. We discuss the advances in overcoming these barriers, including strategies to enhance T-cell efficacy. Finally, our comprehensive analysis of the current clinical trials in this area provides insights into the future possibilities and directions of E-ACTs in breast cancer treatment.
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Affiliation(s)
- Diego F. Chamorro
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; (D.F.C.); (L.K.S.)
| | - Lauren K. Somes
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; (D.F.C.); (L.K.S.)
| | - Valentina Hoyos
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; (D.F.C.); (L.K.S.)
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
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23
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Yang D, Duan Z, Yuan P, Ding C, Dai X, Chen G, Wu D. How does TCR-T cell therapy exhibit a superior anti-tumor efficacy. Biochem Biophys Res Commun 2023; 687:149209. [PMID: 37944471 DOI: 10.1016/j.bbrc.2023.149209] [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: 08/18/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023]
Abstract
TCR-engineered T cells have achieved great progress in solid tumor therapy, some of which have been applicated in clinical trials. Deep knowledge about the current progress of TCR-T in tumor therapy would be beneficial to understand the direction. Here, we classify tumor antigens into tumor-associated antigens, tumor-specific antigens, tumor antigens expressed by oncogenic viruses, and tumor antigens caused by abnormal protein modification; Then we detail the TCR-T cell therapy effects targeting those tumor antigens in clinical or preclinical trials, and propose that neoantigen specific TCR-T cell therapy is expected to be a promising approach for solid tumors; Furthermore, we summarize the optimization strategies, such as tumor microenvironment, TCR pairing and affinity, to improve the therapeutic effect of TCR-T. Overall, this review provides inspiration for the antigen selection and therapy strategies of TCR-T in the future.
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Affiliation(s)
- Dandan Yang
- Laboratory of Structural Immunology, Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Zhihui Duan
- Laboratory of Structural Immunology, Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Ping Yuan
- Laboratory of Structural Immunology, Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Chengming Ding
- Laboratory of Structural Immunology, Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Xiaoming Dai
- Laboratory of Structural Immunology, Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Guodong Chen
- Laboratory of Structural Immunology, Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| | - Daichao Wu
- Laboratory of Structural Immunology, Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
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24
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Vos JL, Burman B, Jain S, Fitzgerald CWR, Sherman EJ, Dunn LA, Fetten JV, Michel LS, Kriplani A, Ng KK, Eng J, Tchekmedyian V, Haque S, Katabi N, Kuo F, Han CY, Nadeem Z, Yang W, Makarov V, Srivastava RM, Ostrovnaya I, Prasad M, Zuur CL, Riaz N, Pfister DG, Klebanoff CA, Chan TA, Ho AL, Morris LGT. Nivolumab plus ipilimumab in advanced salivary gland cancer: a phase 2 trial. Nat Med 2023; 29:3077-3089. [PMID: 37620627 PMCID: PMC11293616 DOI: 10.1038/s41591-023-02518-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023]
Abstract
Salivary gland cancers (SGCs) are rare, aggressive cancers without effective treatments when metastasized. We conducted a phase 2 trial evaluating nivolumab (nivo, anti-PD-1) and ipilimumab (ipi, anti-CTLA-4) in 64 patients with metastatic SGC enrolled in two histology-based cohorts (32 patients each): adenoid cystic carcinoma (ACC; cohort 1) and other SGCs (cohort 2). The primary efficacy endpoint (≥4 objective responses) was met in cohort 2 (5/32, 16%) but not in cohort 1 (2/32, 6%). Treatment safety/tolerability and progression-free survival (PFS) were secondary endpoints. Treatment-related adverse events grade ≥3 occurred in 24 of 64 (38%) patients across both cohorts, and median PFS was 4.4 months (95% confidence interval (CI): 2.4, 8.3) and 2.2 months (95% CI: 1.8, 5.3) for cohorts 1 and 2, respectively. We present whole-exome, RNA and T cell receptor (TCR) sequencing data from pre-treatment and on-treatment tumors and immune cell flow cytometry and TCR sequencing from peripheral blood at serial timepoints. Responding tumors universally demonstrated clonal expansion of pre-existing T cells and mutational contraction. Responding ACCs harbored neoantigens, including fusion-derived neoepitopes, that induced T cell responses ex vivo. This study shows that nivo+ipi has limited efficacy in ACC, albeit with infrequent, exceptional responses, and that it could be promising for non-ACC SGCs, particularly salivary duct carcinomas. ClinicalTrials.gov identifier: NCT03172624 .
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Affiliation(s)
- Joris L Vos
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bharat Burman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Swati Jain
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Conall W R Fitzgerald
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric J Sherman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lara A Dunn
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James V Fetten
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Loren S Michel
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anuja Kriplani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth K Ng
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juliana Eng
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vatche Tchekmedyian
- Department of Medicine, Maine Medical Center-Tufts University School of Medicine, Portland, ME, USA
| | - Sofia Haque
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nora Katabi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fengshen Kuo
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Catherine Y Han
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zaineb Nadeem
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Yang
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vladimir Makarov
- Center for Immunotherapy and Precision Immuno-oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Raghvendra M Srivastava
- Center for Immunotherapy and Precision Immuno-oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Manu Prasad
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlotte L Zuur
- Department of Head and Neck Oncology and Surgery, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Department of Otorhinolaryngology Head and Neck Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David G Pfister
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher A Klebanoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy A Chan
- Center for Immunotherapy and Precision Immuno-oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Alan L Ho
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Luc G T Morris
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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25
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Klebanoff CA, Chandran SS, Baker BM, Quezada SA, Ribas A. T cell receptor therapeutics: immunological targeting of the intracellular cancer proteome. Nat Rev Drug Discov 2023; 22:996-1017. [PMID: 37891435 PMCID: PMC10947610 DOI: 10.1038/s41573-023-00809-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2023] [Indexed: 10/29/2023]
Abstract
The T cell receptor (TCR) complex is a naturally occurring antigen sensor that detects, amplifies and coordinates cellular immune responses to epitopes derived from cell surface and intracellular proteins. Thus, TCRs enable the targeting of proteins selectively expressed by cancer cells, including neoantigens, cancer germline antigens and viral oncoproteins. As such, TCRs have provided the basis for an emerging class of oncology therapeutics. Herein, we review the current cancer treatment landscape using TCRs and TCR-like molecules. This includes adoptive cell transfer of T cells expressing endogenous or engineered TCRs, TCR bispecific engagers and antibodies specific for human leukocyte antigen (HLA)-bound peptides (TCR mimics). We discuss the unique complexities associated with the clinical development of these therapeutics, such as HLA restriction, TCR retrieval, potency assessment and the potential for cross-reactivity. In addition, we highlight emerging clinical data that establish the antitumour potential of TCR-based therapies, including tumour-infiltrating lymphocytes, for the treatment of diverse human malignancies. Finally, we explore the future of TCR therapeutics, including emerging genome editing methods to safely enhance potency and strategies to streamline patient identification.
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Affiliation(s)
- Christopher A Klebanoff
- Memorial Sloan Kettering Cancer Center (MSKCC), Human Oncology and Pathogenesis Program, New York, NY, USA.
| | - Smita S Chandran
- Memorial Sloan Kettering Cancer Center (MSKCC), Human Oncology and Pathogenesis Program, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, New York, NY, USA
- Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, ID, USA
- The Harper Cancer Research Institute, University of Notre Dame, Notre Dame, ID, USA
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Achilles Therapeutics, London, UK
| | - Antoni Ribas
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
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26
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Mariuzza RA, Wu D, Pierce BG. Structural basis for T cell recognition of cancer neoantigens and implications for predicting neoepitope immunogenicity. Front Immunol 2023; 14:1303304. [PMID: 38045695 PMCID: PMC10693334 DOI: 10.3389/fimmu.2023.1303304] [Citation(s) in RCA: 1] [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: 09/27/2023] [Accepted: 11/03/2023] [Indexed: 12/05/2023] Open
Abstract
Adoptive cell therapy (ACT) with tumor-specific T cells has been shown to mediate durable cancer regression. Tumor-specific T cells are also the basis of other therapies, notably cancer vaccines. The main target of tumor-specific T cells are neoantigens resulting from mutations in self-antigens over the course of malignant transformation. The detection of neoantigens presents a major challenge to T cells because of their high structural similarity to self-antigens, and the need to avoid autoimmunity. How different a neoantigen must be from its wild-type parent for it to induce a T cell response is poorly understood. Here we review recent structural and biophysical studies of T cell receptor (TCR) recognition of shared cancer neoantigens derived from oncogenes, including p53R175H, KRASG12D, KRASG12V, HHATp8F, and PIK3CAH1047L. These studies have revealed that, in some cases, the oncogenic mutation improves antigen presentation by strengthening peptide-MHC binding. In other cases, the mutation is detected by direct interactions with TCR, or by energetically driven or other indirect strategies not requiring direct TCR contacts with the mutation. We also review antibodies designed to recognize peptide-MHC on cell surfaces (TCR-mimic antibodies) as an alternative to TCRs for targeting cancer neoantigens. Finally, we review recent computational advances in this area, including efforts to predict neoepitope immunogenicity and how these efforts may be advanced by structural information on peptide-MHC binding and peptide-MHC recognition by TCRs.
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Affiliation(s)
- Roy A. Mariuzza
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
| | - Daichao Wu
- Laboratory of Structural Immunology, Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Brian G. Pierce
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
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Zhou R, Tong F, Zhang Y, Zhang R, Bin Y, Zhang S, Yang N, Dong X. Genomic alterations associated with pseudoprogression and hyperprogressive disease during anti-PD1 treatment for advanced non-small-cell lung cancer. Front Oncol 2023; 13:1231094. [PMID: 38023206 PMCID: PMC10667039 DOI: 10.3389/fonc.2023.1231094] [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: 05/30/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction This study aimed to elucidate the relationship between dynamic genomic mutation alteration and pseudoprogression (PsPD)/hyperprogressive disease (HPD) in immunotherapy-treated advanced non-small-cell lung cancer (NSCLC), to provide clinical evidence for identifying and distinguishing between PsPD and HPD. Method Patients with advanced NSCLC who were treated with anti-PD1 were enrolled. Whole blood was collected at baseline and post image progression. Serum was separated and sequenced using 425-panel next-generation sequencing analysis (NGS). Results NGS revealed that not only single gene mutations were associated with PsPD/HPD before treatment, dynamic monitoring of the whole-blood genome mutation spectrum also varied greatly. Mutational burden, allele frequency%, and relative circulating tumor DNA abundance indicated that the fold change after image progression was much higher in the HPD group. Discussion The gene mutation profiles of PsPD and HPD not only differed before treatment, but higher genome mutation spectrum post image progression indicated true disease progression in patients with HPD. This suggests that dynamic whole-genome mutation profile monitoring as NGS can distinguish PsPD from HPD more effectively than single gene detection, providing a novel method for guiding clinical immune treatment.
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Affiliation(s)
- Rui Zhou
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fan Tong
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yongchang Zhang
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Ruigang Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yawen Bin
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sheng Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Nong Yang
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Xiaorong Dong
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Meng W, Schreiber RD, Lichti CF. Recent advances in immunopeptidomic-based tumor neoantigen discovery. Adv Immunol 2023; 160:1-36. [PMID: 38042584 DOI: 10.1016/bs.ai.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2023]
Abstract
The role of aberrantly expressed proteins in tumors in driving immune-mediated control of cancer has been well documented for more than five decades. Today, we know that both aberrantly expressed normal proteins as well as mutant proteins (neoantigens) can function as tumor antigens in both humans and mice. Next-generation sequencing (NGS) and high-resolution mass spectrometry (MS) technologies have made significant advances since the early 2010s, enabling detection of rare but clinically relevant neoantigens recognized by T cells. MS profiling of tumor-specific immunopeptidomes remains the most direct method to identify mutant peptides bound to cellular MHC. However, the need for use of large numbers of cells or significant amounts of tumor tissue to achieve neoantigen detection has historically limited the application of MS. Newer, more sensitive MS technologies have recently demonstrated the capacities to detect neoantigens from fewer cells. Here, we highlight recent advancements in immunopeptidomics-based characterization of tumor-specific neoantigens. Various tumor antigen categories and neoantigen identification approaches are also discussed. Furthermore, we summarize recent reports that achieved successful tumor neoantigen detection by MS using a variety of starting materials, MS acquisition modes, and novel ion mobility devices.
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Affiliation(s)
- Wei Meng
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, United States
| | - Robert D Schreiber
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, United States.
| | - Cheryl F Lichti
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, United States.
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Giordano Attianese GMP, Ash S, Irving M. Coengineering specificity, safety, and function into T cells for cancer immunotherapy. Immunol Rev 2023; 320:166-198. [PMID: 37548063 DOI: 10.1111/imr.13252] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023]
Abstract
Adoptive T-cell transfer (ACT) therapies, including of tumor infiltrating lymphocytes (TILs) and T cells gene-modified to express either a T cell receptor (TCR) or a chimeric antigen receptor (CAR), have demonstrated clinical efficacy for a proportion of patients and cancer-types. The field of ACT has been driven forward by the clinical success of CD19-CAR therapy against various advanced B-cell malignancies, including curative responses for some leukemia patients. However, relapse remains problematic, in particular for lymphoma. Moreover, for a variety of reasons, relative limited efficacy has been demonstrated for ACT of non-hematological solid tumors. Indeed, in addition to pre-infusion challenges including lymphocyte collection and manufacturing, ACT failure can be attributed to several biological processes post-transfer including, (i) inefficient tumor trafficking, infiltration, expansion and retention, (ii) chronic antigen exposure coupled with insufficient costimulation resulting in T-cell exhaustion, (iii) a range of barriers in the tumor microenvironment (TME) mediated by both tumor cells and suppressive immune infiltrate, (iv) tumor antigen heterogeneity and loss, or down-regulation of antigen presentation machinery, (v) gain of tumor intrinsic mechanisms of resistance such as to apoptosis, and (vi) various forms of toxicity and other adverse events in patients. Affinity-optimized TCRs can improve T-cell function and innovative CAR designs as well as gene-modification strategies can be used to coengineer specificity, safety, and function into T cells. Coengineering strategies can be designed not only to directly support the transferred T cells, but also to block suppressive barriers in the TME and harness endogenous innate and adaptive immunity. Here, we review a selection of the remarkable T-cell coengineering strategies, including of tools, receptors, and gene-cargo, that have been developed in recent years to augment tumor control by ACT, more and more of which are advancing to the clinic.
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Affiliation(s)
- Greta Maria Paola Giordano Attianese
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Sarah Ash
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Melita Irving
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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Malviya M, Aretz Z, Molvi Z, Lee J, Pierre S, Wallisch P, Dao T, Scheinberg DA. Challenges and solutions for therapeutic TCR-based agents. Immunol Rev 2023; 320:58-82. [PMID: 37455333 PMCID: PMC11141734 DOI: 10.1111/imr.13233] [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: 05/30/2023] [Accepted: 06/18/2023] [Indexed: 07/18/2023]
Abstract
Recent development of methods to discover and engineer therapeutic T-cell receptors (TCRs) or antibody mimics of TCRs, and to understand their immunology and pharmacology, lag two decades behind therapeutic antibodies. Yet we have every expectation that TCR-based agents will be similarly important contributors to the treatment of a variety of medical conditions, especially cancers. TCR engineered cells, soluble TCRs and their derivatives, TCR-mimic antibodies, and TCR-based CAR T cells promise the possibility of highly specific drugs that can expand the scope of immunologic agents to recognize intracellular targets, including mutated proteins and undruggable transcription factors, not accessible by traditional antibodies. Hurdles exist regarding discovery, specificity, pharmacokinetics, and best modality of use that will need to be overcome before the full potential of TCR-based agents is achieved. HLA restriction may limit each agent to patient subpopulations and off-target reactivities remain important barriers to widespread development and use of these new agents. In this review we discuss the unique opportunities for these new classes of drugs, describe their unique antigenic targets, compare them to traditional antibody therapeutics and CAR T cells, and review the various obstacles that must be overcome before full application of these drugs can be realized.
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Affiliation(s)
- Manish Malviya
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
| | - Zita Aretz
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
- Physiology, Biophysics & Systems Biology Program, Weill Cornell Graduate School of Medical Sciences, 1300 York Avenue, New York, NY 10021
| | - Zaki Molvi
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
- Physiology, Biophysics & Systems Biology Program, Weill Cornell Graduate School of Medical Sciences, 1300 York Avenue, New York, NY 10021
| | - Jayop Lee
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
| | - Stephanie Pierre
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
- Tri-Institutional Medical Scientist Program, 1300 York Avenue, New York, NY 10021
| | - Patrick Wallisch
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, 1300 York Avenue, New York, NY 10021
| | - Tao Dao
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
| | - David A. Scheinberg
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, 1300 York Avenue, New York, NY 10021
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31
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Kohn DB, Chen YY, Spencer MJ. Successes and challenges in clinical gene therapy. Gene Ther 2023; 30:738-746. [PMID: 37935854 PMCID: PMC10678346 DOI: 10.1038/s41434-023-00390-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/20/2023] [Accepted: 02/07/2023] [Indexed: 11/09/2023]
Abstract
Despite the ups and downs in the field over three decades, the science of gene therapy has continued to advance and provide enduring treatments for increasing number of diseases. There are active clinical trials approaching a variety of inherited and acquired disorders of different organ systems. Approaches include ex vivo modification of hematologic stem cells (HSC), T lymphocytes and other immune cells, as well as in vivo delivery of genes or gene editing reagents to the relevant target cells by either local or systemic administration. In this article, we highlight success and ongoing challenges in three areas of high activity in gene therapy: inherited blood cell diseases by targeting hematopoietic stem cells, malignant disorders using immune effector cells genetically modified with chimeric antigen receptors, and ophthalmologic, neurologic, and coagulation disorders using in vivo administration of adeno-associated virus (AAV) vectors. In recent years, there have been true cures for many of these diseases, with sustained clinical benefit that exceed those from other medical approaches. Each of these treatments faces ongoing challenges, namely their high one-time costs and the complexity of manufacturing the therapeutic agents, which are biological viruses and cell products, at pharmacologic standards of quality and consistency. New models of reimbursement are needed to make these innovative treatments widely available to patients in need.
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Affiliation(s)
- Donald B Kohn
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Yvonne Y Chen
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Chemical and Biomolecular Engineering, Henry Samueli School of Engineering, University of California, Los Angeles, Los Angeles, CA, USA
- Parker Institute for Cancer Immunotherapy Center at UCLA, University of California, Los Angeles, Los Angeles, CA, USA
| | - Melissa J Spencer
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
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Kwok DW, Stevers NO, Nejo T, Chen LH, Etxeberria I, Jung J, Okada K, Cove MC, Lakshmanachetty S, Gallus M, Barpanda A, Hong C, Chan GKL, Wu SH, Ramos E, Yamamichi A, Liu J, Watchmaker P, Ogino H, Saijo A, Du A, Grishanina N, Woo J, Diaz A, Chang SM, Phillips JJ, Wiita AP, Klebanoff CA, Costello JF, Okada H. Tumor-wide RNA splicing aberrations generate immunogenic public neoantigens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563178. [PMID: 37904942 PMCID: PMC10614978 DOI: 10.1101/2023.10.19.563178] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
T-cell-mediated immunotherapies are limited by the extent to which cancer-specific antigens are homogenously expressed throughout a tumor. We reasoned that recurrent splicing aberrations in cancer represent a potential source of tumor-wide and public neoantigens, and to test this possibility, we developed a novel pipeline for identifying neojunctions expressed uniformly within a tumor across diverse cancer types. Our analyses revealed multiple neojunctions that recur across patients and either exhibited intratumor heterogeneity or, in some cases, were tumor-wide. We identified CD8+ T-cell clones specific for neoantigens derived from tumor-wide and conserved neojunctions in GNAS and RPL22 , respectively. TCR-engineered CD8 + T-cells targeting these mutations conferred neoantigen-specific tumor cell eradication. Furthermore, we revealed that cancer-specific dysregulation in splicing factor expression leads to recurrent neojunction expression. Together, these data reveal that a subset of neojunctions are both intratumorally conserved and public, providing the molecular basis for novel T-cell-based immunotherapies that address intratumoral heterogeneity.
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33
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Gupta S, Nerli S, Kutti Kandy S, Mersky GL, Sgourakis NG. HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes. Nat Commun 2023; 14:6349. [PMID: 37816745 PMCID: PMC10564892 DOI: 10.1038/s41467-023-42163-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 09/29/2023] [Indexed: 10/12/2023] Open
Abstract
The class I proteins of the major histocompatibility complex (MHC-I) display epitopic peptides derived from endogenous proteins on the cell surface for immune surveillance. Accurate modeling of peptides bound to the human MHC, HLA, has been mired by conformational diversity of the central peptide residues, which are critical for recognition by T cell receptors. Here, analysis of X-ray crystal structures within our curated database (HLA3DB) shows that pHLA complexes encompassing multiple HLA allotypes present a discrete set of peptide backbone conformations. Leveraging these backbones, we employ a regression model trained on terms of a physically relevant energy function to develop a comparative modeling approach for nonamer pHLA structures named RepPred. Our method outperforms the top pHLA modeling approach by up to 19% in structural accuracy, and consistently predicts blind targets not included in our training set. Insights from our work may be applied towards predicting antigen immunogenicity, and receptor cross-reactivity.
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Affiliation(s)
- Sagar Gupta
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Santrupti Nerli
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sreeja Kutti Kandy
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Glenn L Mersky
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nikolaos G Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Zhang H, Zhang R, Su Y, Zheng J, Li H, Han Z, Kong Y, Liu H, Zhang Z, Sai C. Anti-cervical cancer mechanism of bioactive compounds from Alangium platanifolium based on the 'compound-target-disease' network. Heliyon 2023; 9:e20747. [PMID: 37860565 PMCID: PMC10582369 DOI: 10.1016/j.heliyon.2023.e20747] [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: 08/08/2023] [Revised: 10/01/2023] [Accepted: 10/05/2023] [Indexed: 10/21/2023] Open
Abstract
In this study, we analyzed the chemical compositions of Alangium platanifolium (Sieb. et Zucc.) Harms (AP) using ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) non-targeted plant metabolomics integration MolNetEnhancer strategy. A total of 75 compounds, including flavonoids, alkaloids, terpenes, C21 steroids, among others, were identified by comparing accurate mass-to-charge ratios, MS2 cleavage fragments, retention times, and MolNetenhancer-integrated analytical data, and the cleavage rules of the characteristic compounds were analyzed. A total of 125 potential cervical cancer (CC) therapeutic targets were obtained through Gene Expression Omnibus (GEO) data mining, differential analysis, and database screening. Hub targets were obtained by constructing protein-protein interaction (PPI) networks and CytoNCA topology analysis, including SRC, STAT3, TP53, PIK3R1, MAPK3, and PIK3CA. According to Gene ontology (GO) analysis, AP was primarily against CC by influencing gland development, oxidative stress processes, serine/threonine kinase, and tyrosine kinase activity. Enrichment analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated that the PI3K/AKT and MAPK signaling pathways play a crucial role in AP treatment for CC. The compound-target-pathway (C-T-P) network revealed that quercetin, methylprednisolone, and caudatin may play key roles in the treatment of CC. The results of molecular docking revealed that the core compound could bind significantly to the core target. In this study, the compounds in AP were systematically analyzed qualitatively, and the core components, core targets, and mechanisms of action of AP in the treatment of CC were screened through a combination of network pharmacology tools. Providing a scientific reference for the therapeutic material basis and quality control of AP.
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Affiliation(s)
- Hao Zhang
- College of Pharmacy, Weifang Medical University, Weifang, 261053, China
- College of Pharmacy, Jining Medical University, Rizhao, 276826, China
| | - Ruiming Zhang
- College of Pharmacy, Jining Medical University, Rizhao, 276826, China
| | - Yuefen Su
- College of Pharmacy, Jining Medical University, Rizhao, 276826, China
| | - Jingrou Zheng
- College of Pharmacy, Jining Medical University, Rizhao, 276826, China
| | - Hui Li
- College of Pharmacy, Jining Medical University, Rizhao, 276826, China
| | - Zhichao Han
- College of Pharmacy, Jining Medical University, Rizhao, 276826, China
- College of Agriculture, Yanbian University, Yanji, 133002, China
| | - Yunzhen Kong
- College of Pharmacy, Jining Medical University, Rizhao, 276826, China
| | - Han Liu
- College of Pharmacy, Jining Medical University, Rizhao, 276826, China
| | - Zhen Zhang
- College of Pharmacy, Jining Medical University, Rizhao, 276826, China
| | - Chunmei Sai
- College of Pharmacy, Jining Medical University, Rizhao, 276826, China
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Bolivar AM, Duzagac F, Sinha KM, Vilar E. Advances in vaccine development for cancer prevention and treatment in Lynch Syndrome. Mol Aspects Med 2023; 93:101204. [PMID: 37478804 PMCID: PMC10528439 DOI: 10.1016/j.mam.2023.101204] [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: 04/13/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023]
Abstract
Lynch Syndrome (LS) is one of the most common hereditary cancer syndromes, and is caused by mutations in one of the four DNA mismatch repair (MMR) genes, namely MLH1, MSH2, MSH6 and PMS2. Tumors developed by LS carriers display high levels of microsatellite instability, which leads to the accumulation of large numbers of mutations, among which frameshift insertion/deletions (indels) within microsatellite (MS) loci are the most common. As a result, MMR-deficient (MMRd) cells generate increased rates of tumor-specific neoantigens (neoAgs) that can be recognized by the immune system to activate cancer cell killing. In this context, LS is an ideal disease to leverage immune-interception strategies. Therefore, the identification of these neoAgs is an ongoing effort for the development of LS cancer preventive vaccines. In this review, we summarize the computational methods used for in silico neoAg prediction, including their challenges, and the experimental techniques used for in vitro validation of their immunogenicity. In addition, we outline results from past and on-going vaccine clinical trials and highlight avenues for improvement and future directions.
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Affiliation(s)
- Ana M Bolivar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fahriye Duzagac
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Krishna M Sinha
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Giannakopoulou E, Lehander M, Virding Culleton S, Yang W, Li Y, Karpanen T, Yoshizato T, Rustad EH, Nielsen MM, Bollineni RC, Tran TT, Delic-Sarac M, Gjerdingen TJ, Douvlataniotis K, Laos M, Ali M, Hillen A, Mazzi S, Chin DWL, Mehta A, Holm JS, Bentzen AK, Bill M, Griffioen M, Gedde-Dahl T, Lehmann S, Jacobsen SEW, Woll PS, Olweus J. A T cell receptor targeting a recurrent driver mutation in FLT3 mediates elimination of primary human acute myeloid leukemia in vivo. NATURE CANCER 2023; 4:1474-1490. [PMID: 37783807 PMCID: PMC10597840 DOI: 10.1038/s43018-023-00642-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 08/28/2023] [Indexed: 10/04/2023]
Abstract
Acute myeloid leukemia (AML), the most frequent leukemia in adults, is driven by recurrent somatically acquired genetic lesions in a restricted number of genes. Treatment with tyrosine kinase inhibitors has demonstrated that targeting of prevalent FMS-related receptor tyrosine kinase 3 (FLT3) gain-of-function mutations can provide significant survival benefits for patients, although the efficacy of FLT3 inhibitors in eliminating FLT3-mutated clones is variable. We identified a T cell receptor (TCR) reactive to the recurrent D835Y driver mutation in the FLT3 tyrosine kinase domain (TCRFLT3D/Y). TCRFLT3D/Y-redirected T cells selectively eliminated primary human AML cells harboring the FLT3D835Y mutation in vitro and in vivo. TCRFLT3D/Y cells rejected both CD34+ and CD34- AML in mice engrafted with primary leukemia from patients, reaching minimal residual disease-negative levels, and eliminated primary CD34+ AML leukemia-propagating cells in vivo. Thus, T cells targeting a single shared mutation can provide efficient immunotherapy toward selective elimination of clonally involved primary AML cells in vivo.
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Grants
- G0801073 Medical Research Council
- MC_UU_00016/5 Medical Research Council
- MC_UU_12009/5 Medical Research Council
- South-Eastern Regional Health Authority Norway, the Research Council of Norway, the Norwegian Cancer Society, the Norwegian Childhood Cancer Foundation, Stiftelsen Kristian Gerhard Jebsen, European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 865805), the University of Oslo and Oslo University Hospital and Novo Nordisk Foundation.
- Knut and Alice Wallenberg Foundation, The Swedish Research Council, Tobias Foundation, Torsten Söderberg Foundation, Center for Innovative Medicine (CIMED) at Karolinska Institutet, and The UK Medical Research Council
- Technical University of Denmark (DTU)
- Aarhus University Hospital
- Leiden University Medical Center
- Oslo University Hospital
- Karolinska University Hospital
- University of Oslo and Oslo University Hospital
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Affiliation(s)
- Eirini Giannakopoulou
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Madeleine Lehander
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Stina Virding Culleton
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Weiwen Yang
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Yingqian Li
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Terhi Karpanen
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Tetsuichi Yoshizato
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Even H Rustad
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Morten Milek Nielsen
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ravi Chand Bollineni
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Trung T Tran
- Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Marina Delic-Sarac
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Thea Johanne Gjerdingen
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Karolos Douvlataniotis
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Maarja Laos
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Muhammad Ali
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Amy Hillen
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Stefania Mazzi
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Desmond Wai Loon Chin
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Adi Mehta
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Jeppe Sejerø Holm
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Amalie Kai Bentzen
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Marie Bill
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Tobias Gedde-Dahl
- Hematology Department, Section for Stem Cell Transplantation, Oslo University Hospital, Rikshospitalet, Clinic for Cancer Medicine, Oslo, Norway
| | - Sören Lehmann
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Karolinska University Hospital, Stockholm, Sweden
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Sten Eirik W Jacobsen
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Karolinska University Hospital, Stockholm, Sweden.
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | - Petter S Woll
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Johanna Olweus
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway.
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
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Cao Y, Wang D, Wu J, Yao Z, Shen S, Niu C, Liu Y, Zhang P, Wang Q, Wang J, Li H, Wei X, Wang X, Dong Q. MSI-XGNN: an explainable GNN computational framework integrating transcription- and methylation-level biomarkers for microsatellite instability detection. Brief Bioinform 2023; 24:bbad362. [PMID: 37833839 DOI: 10.1093/bib/bbad362] [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: 06/29/2023] [Revised: 09/05/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Microsatellite instability (MSI) is a hypermutator phenotype caused by DNA mismatch repair deficiency. MSI has been reported in various human cancers, particularly colorectal, gastric and endometrial cancers. MSI is a promising biomarker for cancer prognosis and immune checkpoint blockade immunotherapy. Several computational methods have been developed for MSI detection using DNA- or RNA-based approaches based on next-generation sequencing. Epigenetic mechanisms, such as DNA methylation, regulate gene expression and play critical roles in the development and progression of cancer. We here developed MSI-XGNN, a new computational framework for predicting MSI status using bulk RNA-sequencing and DNA methylation data. MSI-XGNN is an explainable deep learning model that combines a graph neural network (GNN) model to extract features from the gene-methylation probe network with a CatBoost model to classify MSI status. MSI-XGNN, which requires tumor-only samples, exhibited comparable performance with two well-known methods that require tumor-normal paired sequencing data, MSIsensor and MANTIS and better performance than several other tools. MSI-XGNN also showed good generalizability on independent validation datasets. MSI-XGNN identified six MSI markers consisting of four methylation probes (EPM2AIP1|MLH1:cg14598950, EPM2AIP1|MLH1:cg27331401, LNP1:cg05428436 and TSC22D2:cg15048832) and two genes (RPL22L1 and MSH4) constituting the optimal feature subset. All six markers were significantly associated with beneficial tumor microenvironment characteristics for immunotherapy, such as tumor mutation burden, neoantigens and immune checkpoint molecules such as programmed cell death-1 and cytotoxic T-lymphocyte antigen-4. Overall, our study provides a powerful and explainable deep learning model for predicting MSI status and identifying MSI markers that can potentially be used for clinical MSI evaluation.
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Affiliation(s)
- Yang Cao
- Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Dan Wang
- Department of Bioinformatics, Yicon (Beijing) Biomedical Technology Inc
| | - Jin Wu
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Zhanxin Yao
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Si Shen
- School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300050, China
| | - Chao Niu
- Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Ying Liu
- Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Pengcheng Zhang
- Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | | | - Jinhao Wang
- Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Hua Li
- Department of Diagnostic and Therapeutic Ultrasonography, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Xi Wei
- Department of Diagnostic and Therapeutic Ultrasonography, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Xinxing Wang
- Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Qingyang Dong
- Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
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Pu T, Peddle A, Zhu J, Tejpar S, Verbandt S. Neoantigen identification: Technological advances and challenges. Methods Cell Biol 2023; 183:265-302. [PMID: 38548414 DOI: 10.1016/bs.mcb.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Neoantigens have emerged as promising targets for cutting-edge immunotherapies, such as cancer vaccines and adoptive cell therapy. These neoantigens are unique to tumors and arise exclusively from somatic mutations or non-genomic aberrations in tumor proteins. They encompass a wide range of alterations, including genomic mutations, post-transcriptomic variants, and viral oncoproteins. With the advancements in technology, the identification of immunogenic neoantigens has seen rapid progress, raising new opportunities for enhancing their clinical significance. Prediction of neoantigens necessitates the acquisition of high-quality samples and sequencing data, followed by mutation calling. Subsequently, the pipeline involves integrating various tools that can predict the expression, processing, binding, and recognition potential of neoantigens. However, the continuous improvement of computational tools is constrained by the availability of datasets which contain validated immunogenic neoantigens. This review article aims to provide a comprehensive summary of the current knowledge as well as limitations in neoantigen prediction and validation. Additionally, it delves into the origin and biological role of neoantigens, offering a deeper understanding of their significance in the field of cancer immunotherapy. This article thus seeks to contribute to the ongoing efforts to harness neoantigens as powerful weapons in the fight against cancer.
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Affiliation(s)
- Ting Pu
- Digestive Oncology Unit, KULeuven, Leuven, Belgium
| | | | - Jingjing Zhu
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
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Carabaño M, Liu T, Liu A, Lee JC, Cheng L, Wang LJ, Huang CK, Lu S. Association of HLA-A, B, and C alleles and cancer susceptibility in 179 solid malignancies. Am J Transl Res 2023; 15:5642-5652. [PMID: 37854217 PMCID: PMC10579009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/04/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND The major histocompatibility complex (MHC) genes are known to be capable of influencing the susceptibility of many cancers. All mammalian cells, including cancer cells, express MHC class I molecules consisting of human leukocyte antigens (HLA) A, B, and C. The tumor susceptibility of HLA-A, B, and C alleles has not been studied extensively in solid tumors. METHODS HLA-A, B, and C genotypes of 179 solid tumors were collected from Caris Comprehensive Tumor Profiling reports, including 45 GU, 44 GI, 28 pancreaticobiliary, 21 thoracic, 15 breast, 13 Gyn, among others. The tumors were mainly from Caucasians (82%). The HLA allele frequencies in the tumors were compared to those of respective ethnic populations in the US National Marrow Donor Program (NMDP) database. Fisher's exact tests were performed, adjusted P values were calculated using Benjamini-Hochberg's method for false discovery rate (FDR), and Prevalence ratios (PRs) were calculated to quantify associations. RESULTS Twenty-one alleles were not listed in the NMDP. Among them, A*11:303 alone was present in 11 carcinomas, and B*08:222 was seen in 4 tumors. Among the alleles listed in the NMDP, C*08:02, B*14:02, A*03:02, and B*44:06 were significantly associated with tumors in Caucasian Americans (PR: 2.50-170), while B*44:02 appeared protective (PR: 0.36). Alleles with less significant associations were listed. CONCLUSIONS From the HLA-A, B, and C data of the 179 tumors, we identified several susceptible alleles and one protective allele. Of interest, 21 alleles were not listed in the NMDP. The limited cases prevented our analysis from identifying cancer-susceptible alleles in other races.
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Affiliation(s)
- Miguel Carabaño
- Department of Pathology and Laboratory Medicine, Alpert Medical School of Brown UniversityProvidence, RI 02903, USA
| | - Tao Liu
- Department of Biostatistics, Brown UniversityProvidence, RI 02912, USA
| | - Abraham Liu
- Department of Biostatistics, Brown UniversityProvidence, RI 02912, USA
| | - Jim ChunHao Lee
- Department of Pathology and Laboratory Medicine, Alpert Medical School of Brown UniversityProvidence, RI 02903, USA
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Alpert Medical School of Brown UniversityProvidence, RI 02903, USA
| | - Li-Juan Wang
- Department of Pathology and Laboratory Medicine, Alpert Medical School of Brown UniversityProvidence, RI 02903, USA
| | - Chiung-Kuei Huang
- Department of Pathology and Laboratory Medicine, Tulane University School of MedicineNew Orleans, LA 70112, USA
| | - Shaolei Lu
- Department of Pathology and Laboratory Medicine, Alpert Medical School of Brown UniversityProvidence, RI 02903, USA
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Fast E, Dhar M, Chen B. TAPIR: a T-cell receptor language model for predicting rare and novel targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557285. [PMID: 37745475 PMCID: PMC10515850 DOI: 10.1101/2023.09.12.557285] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
T-cell receptors (TCRs) are involved in most human diseases, but linking their sequences with their targets remains an unsolved grand challenge in the field. In this study, we present TAPIR (T-cell receptor and Peptide Interaction Recognizer), a T-cell receptor (TCR) language model that predicts TCR-target interactions, with a focus on novel and rare targets. TAPIR employs deep convolutional neural network (CNN) encoders to process TCR and target sequences across flexible representations (e.g., beta-chain only, unknown MHC allele, etc.) and learns patterns of interactivity via several training tasks. This flexibility allows TAPIR to train on more than 50k either paired (alpha and beta chain) or unpaired TCRs (just alpha or beta chain) from public and proprietary databases against 1933 unique targets. TAPIR demonstrates state-of-the-art performance when predicting TCR interactivity against common benchmark targets and is the first method to demonstrate strong performance when predicting TCR interactivity against novel targets, where no examples are provided in training. TAPIR is also capable of predicting TCR interaction against MHC alleles in the absence of target information. Leveraging these capabilities, we apply TAPIR to cancer patient TCR repertoires and identify and validate a novel and potent anti-cancer T-cell receptor against a shared cancer neoantigen target (PIK3CA H1047L). We further show how TAPIR, when extended with a generative neural network, is capable of directly designing T-cell receptor sequences that interact with a target of interest.
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Affiliation(s)
- Ethan Fast
- Vcreate, Inc., Menlo Park, CA, 94025, USA
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Ade CM, Sporn MJ, Das S, Yu Z, Hanada KI, Qi YA, Maity T, Zhang X, Guha U, Andresson T, Yang JC. Identification of neoepitope reactive T-cell receptors guided by HLA-A*03:01 and HLA-A*11:01 immunopeptidomics. J Immunother Cancer 2023; 11:e007097. [PMID: 37758652 PMCID: PMC10537849 DOI: 10.1136/jitc-2023-007097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Tumor-specific mutated proteins can create immunogenic non-self, mutation-containing 'neoepitopes' that are attractive targets for adoptive T-cell therapies. To avoid the complexity of defining patient-specific, private neoepitopes, there has been major interest in targeting common shared mutations in driver genes using off-the-shelf T-cell receptors (TCRs) engineered into autologous lymphocytes. However, identifying the precise naturally processed neoepitopes to pursue is a complex and challenging process. One method to definitively demonstrate whether an epitope is presented at the cell surface is to elute peptides bound to a specific major histocompatibility complex (MHC) allele and analyze them by mass spectrometry (MS). These MS data can then be prospectively applied to isolate TCRs specific to the neoepitope. METHODS We created mono-allelic cell lines expressing one class I HLA allele and one common mutated oncogene in order to eliminate HLA deconvolution requirements and increase the signal of recovered peptides. MHC-bound peptides on the surface of these cell lines were immunoprecipitated, purified, and analyzed using liquid chromatography-tandem mass spectrometry, producing a list of mutation-containing minimal epitopes. To validate the immunogenicity of these neoepitopes, HLA-transgenic mice were vaccinated using the minimal peptides identified by MS in order to generate neoepitope-reactive TCRs. Specificity of these candidate TCRs was confirmed by peptide titration and recognition of transduced targets. RESULTS We identified precise neoepitopes derived from mutated isoforms of KRAS, EGFR, BRAF, and PIK3CA presented by HLA-A*03:01 and/or HLA-A*11:01 across multiple biological replicates. From our MS data, we were able to successfully isolate murine TCRs that specifically recognize four HLA-A*11:01 restricted neoepitopes (KRAS G13D, PIK3CA E545K, EGFR L858R and BRAF V600E) and three HLA-A*03:01 restricted neoepitopes (KRAS G12V, EGFR L858R and BRAF V600E). CONCLUSIONS Our data show that an MS approach can be used to demonstrate which shared oncogene-derived neoepitopes are processed and presented by common HLA alleles, and those MS data can rapidly be used to develop TCRs against these common tumor-specific antigens. Although further characterization of these neoepitope-specific murine TCRs is required, ultimately, they have the potential to be used clinically for adoptive cell therapy.
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Affiliation(s)
- Catherine M Ade
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Matthew J Sporn
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Sudipto Das
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Zhiya Yu
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Ken-Ichi Hanada
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Yue A Qi
- Thoracic and GI Malignancies Branch, National Cancer Institute, Bethesda, Maryland, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Tapan Maity
- Thoracic and GI Malignancies Branch, National Cancer Institute, Bethesda, Maryland, USA
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD, USA
| | - Xu Zhang
- Thoracic and GI Malignancies Branch, National Cancer Institute, Bethesda, Maryland, USA
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Udayan Guha
- Thoracic and GI Malignancies Branch, National Cancer Institute, Bethesda, Maryland, USA
- NextCure Inc, Beltsville, MD, USA
| | - Thorkell Andresson
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - James C Yang
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
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Bonini C, Chapuis AG, Hudecek M, Guedan S, Magnani CF, Qasim W. Genome Editing in Engineered T Cells for Cancer Immunotherapy. Hum Gene Ther 2023; 34:853-869. [PMID: 37694593 PMCID: PMC10623081 DOI: 10.1089/hum.2023.128] [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: 08/01/2023] [Accepted: 09/10/2023] [Indexed: 09/12/2023] Open
Abstract
Advanced gene transfer technologies and profound immunological insights have enabled substantial increases in the efficacy of anticancer adoptive cellular therapy (ACT). In recent years, the U.S. Food and Drug Administration and European Medicines Agency have approved six engineered T cell therapeutic products, all chimeric antigen receptor-engineered T cells directed against B cell malignancies. Despite encouraging clinical results, engineered T cell therapy is still constrained by challenges, which could be addressed by genome editing. As RNA-guided Clustered Regularly Interspaced Short Palindromic Repeats technology passes its 10-year anniversary, we review emerging applications of genome editing approaches designed to (1) overcome resistance to therapy, including cancer immune evasion mechanisms; (2) avoid unwanted immune reactions related to allogeneic T cell products; (3) increase fitness, expansion capacity, persistence, and potency of engineered T cells, while preserving their safety profile; and (4) improve the ability of therapeutic cells to resist immunosuppressive signals active in the tumor microenvironment. Overall, these innovative approaches should widen the safe and effective use of ACT to larger number of patients affected by cancer.
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Affiliation(s)
- Chiara Bonini
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Aude G. Chapuis
- Program in Immunology, Division of Translational Sciences and Therapeutics, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Oncology, University of Washington, Seattle, Washington, USA
| | - Michael Hudecek
- Lehrstuhl für Zelluläre Immuntherapie, Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Sonia Guedan
- Department of Hematology and Oncology, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Chiara F. Magnani
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), Zurich, Switzerland
| | - Waseem Qasim
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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Li J, Xiao Z, Wang D, Jia L, Nie S, Zeng X, Hu W. The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells. Mol Cancer 2023; 22:141. [PMID: 37649123 PMCID: PMC10466891 DOI: 10.1186/s12943-023-01844-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development of tumor immunotherapies, including adoptive cell therapies (ACTs), cancer vaccines and antibody-based therapies, particularly for solid tumors. With the development of next-generation sequencing and bioinformatics technology, the rapid identification and prediction of tumor-specific antigens (TSAs) has become possible. Compared with tumor-associated antigens (TAAs), highly immunogenic TSAs provide new targets for personalized tumor immunotherapy and can be used as prospective indicators for predicting tumor patient survival, prognosis, and immune checkpoint blockade response. Here, the identification and characterization of neoantigens and the clinical application of neoantigen-based TCR-T immunotherapy strategies are summarized, and the current status, inherent challenges, and clinical translational potential of these strategies are discussed.
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Affiliation(s)
- Jiangping Li
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
| | - Zhiwen Xiao
- Department of Otolaryngology Head and Neck Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, People's Republic of China
| | - Donghui Wang
- Department of Radiation Oncology, The Third Affiliated Hospital Sun Yat-Sen University, Guangzhou, 510630, People's Republic of China
| | - Lei Jia
- International Health Medicine Innovation Center, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Shihong Nie
- Department of Radiation Oncology, West China Hospital, Sichuan University, Cancer Center, Chengdu, 610041, People's Republic of China
| | - Xingda Zeng
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Wei Hu
- Division of Vascular Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, People's Republic of China
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Iizuka A, Akiyama Y, Sakura N, Kanematsu A, Kikuchi Y, Nagashima T, Urakami K, Shimoda Y, Ohshima K, Shiomi A, Ohde Y, Terashima M, Uesaka K, Mukaigawa T, Hirashima Y, Yoshikawa S, Katagiri H, Sugino T, Takahashi M, Kenmotsu H, Yamaguchi K. Generation of novel complete HLA class I monoallelic cell lines used in an MHC stabilization assay for neoantigen evaluation. Oncol Lett 2023; 26:324. [PMID: 37415627 PMCID: PMC10320429 DOI: 10.3892/ol.2023.13910] [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: 01/17/2023] [Accepted: 05/16/2023] [Indexed: 07/08/2023] Open
Abstract
Immunogenic neoantigens derived from somatic mutations in cancer have been identified through clinical studies with the cloning of tumor-infiltrating T cells, and cancer driver gene mutation-derived epitopes have been reported; however, these are rare. At present, the validation of epitopes predicted in silico is difficult as human T-cell clonal diversity cannot be reproduced in vitro or in experimental animal models. To confirm the epitope peptides presented by human leukocyte antigen (HLA) class I molecules predicted in silico, biochemical methods such as major histocompatibility complex (MHC) stabilization assays and mass spectrometry-mediated identification have been developed based on HLA-A*02:01 monoallelic T2 cells and HLA-C*01:02 monoallelic LCL721.221 cells. Therefore, in the present study, to prevent confusion due to peptide cross-presentation among HLA molecules, HLA class I monoallelic B-cell clones were generated from the TISI cell line by knocking out HLA-ABC and TAP2, and knocking in HLA alleles. To explore cancer driver mutations as potential targets for immunotherapy, exome sequencing data from 5,143 patients with cancer enrolled in a comprehensive genome analysis project at the Shizuoka Cancer Center were used to identify somatic amino acid substituted mutations and the 50 most frequent mutations in five genes, TP53, EGFR, PIK3CA, KRAS and BRAF, were identified. Using NetMHC4.1, the present study predicted whether epitopes derived from these mutations are presented on major HLA-ABC alleles in Japanese individuals and synthesized 138 peptides for MHC stabilization assays. The authors also attempted to examine the candidate epitopes at physiological temperatures by using antibody clone G46-2.6, which can detect HLA-ABC, independent of β2-microglobulin association. In the assays, although the peptide-induced HLA expression levels were associated with the predicted affinities, the respective HLA alleles exhibited varying degrees of responsiveness, and unexpectedly, p53-mutant epitopes with predicted weak affinities exhibited strong responses. These results suggested that MHC stabilization assays using completely monoallelic HLA-expressing B-cell lines are useful for evaluating the presentation of neoantigen epitopes.
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Affiliation(s)
- Akira Iizuka
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Naoki Sakura
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Akari Kanematsu
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Yasufumi Kikuchi
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
- SRL, Inc., Tokyo 163-0409, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Yuji Shimoda
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Akio Shiomi
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Yasuhisa Ohde
- Division of Thoracic Surgery, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Masanori Terashima
- Division of Gastric Surgery, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Katsuhiko Uesaka
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Takashi Mukaigawa
- Division of Head and Neck Surgery, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Yasuyuki Hirashima
- Division of Gynecology, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Shusuke Yoshikawa
- Division of Dermatology, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Hirohisa Katagiri
- Division of Orthopedic Oncology, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Takashi Sugino
- Division of Pathology, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Mitsuru Takahashi
- Division of Orthopedic Oncology, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Hirotsugu Kenmotsu
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Ken Yamaguchi
- Office of The President, Shizuoka Cancer Center, Shizuoka 411-8777, Japan
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Ascierto PA, Avallone A, Bifulco C, Bracarda S, Brody JD, Emens LA, Ferris RL, Formenti SC, Hamid O, Johnson DB, Kirchhoff T, Klebanoff CA, Lesinski GB, Monette A, Neyns B, Odunsi K, Paulos CM, Powell DJ, Rezvani K, Segal BH, Singh N, Sullivan RJ, Fox BA, Puzanov I. Perspectives in Immunotherapy: meeting report from Immunotherapy Bridge (Naples, November 30th-December 1st, 2022). J Transl Med 2023; 21:488. [PMID: 37475035 PMCID: PMC10360352 DOI: 10.1186/s12967-023-04329-7] [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: 06/22/2023] [Accepted: 07/06/2023] [Indexed: 07/22/2023] Open
Abstract
The discovery and development of novel treatments that harness the patient's immune system and prevent immune escape has dramatically improved outcomes for patients across cancer types. However, not all patients respond to immunotherapy, acquired resistance remains a challenge, and responses are poor in certain tumors which are considered to be immunologically cold. This has led to the need for new immunotherapy-based approaches, including adoptive cell transfer (ACT), therapeutic vaccines, and novel immune checkpoint inhibitors. These new approaches are focused on patients with an inadequate response to current treatments, with emerging evidence of improved responses in various cancers with new immunotherapy agents, often in combinations with existing agents. The use of cell therapies, drivers of immune response, and trends in immunotherapy were the focus of the Immunotherapy Bridge (November 30th-December 1st, 2022), organized by the Fondazione Melanoma Onlus, Naples, Italy, in collaboration with the Society for Immunotherapy of Cancer.
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Affiliation(s)
- Paolo A Ascierto
- Department of Melanoma, Cancer Immunotherapy and Innovative Therapy, Istituto Nazionale Tumor IRCCS "Fondazione G. Pascale", Naples, Italy.
| | - Antonio Avallone
- Experimental Clinical Abdominal Oncology Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples, Italy
| | - Carlo Bifulco
- Translational Molecular Pathology and Molecular Genomics, Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | - Sergio Bracarda
- Department of Oncology, Medical and Translational Oncology, Azienda Ospedaliera Santa Maria, Terni, Italy
| | - Joshua D Brody
- Tisch Cancer Institute, Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Leisha A Emens
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Ankyra Therapeutics, Cambridge, MA, USA
| | - Robert L Ferris
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Omid Hamid
- The Angeles Clinic and Research Institute, A Cedars-Sinai Affiliate, Los Angeles, CA, USA
| | - Douglas B Johnson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Tomas Kirchhoff
- Laura and Isaac Perlmutter Cancer Center, New York University (NYU) School of Medicine, NYU Langone Health, New York, NY, USA
| | - Christopher A Klebanoff
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Gregory B Lesinski
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Anne Monette
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Bart Neyns
- Department of Medical Oncology, University Hospital Brussel, Brussels, Belgium
| | - Kunle Odunsi
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA
| | - Chrystal M Paulos
- Department of Surgery and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Translational Research for Cutaneous Malignancies, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Daniel J Powell
- Center for Cellular Immunotherapies, Department of Pathology and Laboratory Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brahm H Segal
- Department of Internal Medicine and Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Nathan Singh
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Ryan J Sullivan
- Melanoma Program, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Bernard A Fox
- Robert W. Franz Cancer Research Center, Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | - Igor Puzanov
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
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46
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Peri A, Salomon N, Wolf Y, Kreiter S, Diken M, Samuels Y. The landscape of T cell antigens for cancer immunotherapy. NATURE CANCER 2023:10.1038/s43018-023-00588-x. [PMID: 37415076 DOI: 10.1038/s43018-023-00588-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/18/2023] [Indexed: 07/08/2023]
Abstract
The remarkable capacity of immunotherapies to induce durable regression in some patients with metastatic cancer relies heavily on T cell recognition of tumor-presented antigens. As checkpoint-blockade therapy has limited efficacy, tumor antigens have the potential to be exploited for complementary treatments, many of which are already in clinical trials. The surge of interest in this topic has led to the expansion of the tumor antigen landscape with the emergence of new antigen categories. Nonetheless, how different antigens compare in their ability to elicit efficient and safe clinical responses remains largely unknown. Here, we review known cancer peptide antigens, their attributes and the relevant clinical data and discuss future directions.
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Affiliation(s)
- Aviyah Peri
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nadja Salomon
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| | - Yochai Wolf
- Ella Lemelbaum Institute for Immuno-oncology and Skin Cancer, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Sebastian Kreiter
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany.
| | - Mustafa Diken
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany.
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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Abstract
Recent advances in cancer immunotherapy - ranging from immune-checkpoint blockade therapy to adoptive cellular therapy and vaccines - have revolutionized cancer treatment paradigms, yet the variability in clinical responses to these agents has motivated intense interest in understanding how the T cell landscape evolves with respect to response to immune intervention. Over the past decade, the advent of multidimensional single-cell technologies has provided the unprecedented ability to dissect the constellation of cell states of lymphocytes within a tumour microenvironment. In particular, the rapidly expanding capacity to definitively link intratumoural phenotypes with the antigen specificity of T cells provided by T cell receptors (TCRs) has now made it possible to focus on investigating the properties of T cells with tumour-specific reactivity. Moreover, the assessment of TCR clonality has enabled a molecular approach to track the trajectories, clonal dynamics and phenotypic changes of antitumour T cells over the course of immunotherapeutic intervention. Here, we review the current knowledge on the cellular states and antigen specificities of antitumour T cells and examine how fine characterization of T cell dynamics in patients has provided meaningful insights into the mechanisms underlying effective cancer immunotherapy. We highlight those T cell subsets associated with productive T cell responses and discuss how diverse immunotherapies might leverage the pre-existing tumour-reactive T cell pool or instruct de novo generation of antitumour specificities. Future studies aimed at elucidating the factors associated with the elicitation of productive antitumour T cell immunity are anticipated to instruct the design of more efficacious treatment strategies.
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Affiliation(s)
- Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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48
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Genolet R, Bobisse S, Chiffelle J, Arnaud M, Petremand R, Queiroz L, Michel A, Reichenbach P, Cesbron J, Auger A, Baumgaertner P, Guillaume P, Schmidt J, Irving M, Kandalaft LE, Speiser DE, Coukos G, Harari A. TCR sequencing and cloning methods for repertoire analysis and isolation of tumor-reactive TCRs. CELL REPORTS METHODS 2023; 3:100459. [PMID: 37159666 PMCID: PMC10163020 DOI: 10.1016/j.crmeth.2023.100459] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/27/2023] [Accepted: 03/27/2023] [Indexed: 05/11/2023]
Abstract
T cell receptor (TCR) technologies, including repertoire analyses and T cell engineering, are increasingly important in the clinical management of cellular immunity in cancer, transplantation, and other immune diseases. However, sensitive and reliable methods for repertoire analyses and TCR cloning are still lacking. Here, we report on SEQTR, a high-throughput approach to analyze human and mouse repertoires that is more sensitive, reproducible, and accurate as compared with commonly used assays, and thus more reliably captures the complexity of blood and tumor TCR repertoires. We also present a TCR cloning strategy to specifically amplify TCRs from T cell populations. Positioned downstream of single-cell or bulk TCR sequencing, it allows time- and cost-effective discovery, cloning, screening, and engineering of tumor-specific TCRs. Together, these methods will accelerate TCR repertoire analyses in discovery, translational, and clinical settings and permit fast TCR engineering for cellular therapies.
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Affiliation(s)
- Raphael Genolet
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Corresponding author
| | - Sara Bobisse
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Johanna Chiffelle
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Marion Arnaud
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Rémy Petremand
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Lise Queiroz
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Alexandra Michel
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Patrick Reichenbach
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
| | - Julien Cesbron
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Aymeric Auger
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Petra Baumgaertner
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Philippe Guillaume
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Julien Schmidt
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Melita Irving
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
| | - Lana E. Kandalaft
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Daniel E. Speiser
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Corresponding author
| | - Alexandre Harari
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Corresponding author
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49
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Cole K, Al-Kadhimi Z, Talmadge JE. Highlights into historical and current immune interventions for cancer. Int Immunopharmacol 2023; 117:109882. [PMID: 36848790 PMCID: PMC10355273 DOI: 10.1016/j.intimp.2023.109882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 03/01/2023]
Abstract
Immunotherapy is an additional pillar when combined with traditional standards of care such as chemotherapy, radiotherapy, and surgery for cancer patients. It has revolutionized cancer treatment and rejuvenated the field of tumor immunology. Several types of immunotherapies, including adoptive cellular therapy (ACT) and checkpoint inhibitors (CPIs), can induce durable clinical responses. However, their efficacies vary, and only subsets of cancer patients benefit from their use. In this review, we address three goals: to provide insight into the history of these approaches, broaden our understanding of immune interventions, and discuss current and future approaches. We highlight how cancer immunotherapy has evolved and discuss how personalization of immune intervention may address present limitations. Cancer immunotherapy is considered a recent medical achievement and in 2013 was selected as the "Breakthrough of the Year" by Science. While the breadth of immunotherapeutics has been rapidly expanding, to include the use of chimeric antigen receptor (CAR) T-cell therapy and immune checkpoint inhibitor (ICI) therapy, immunotherapy dates back over 3000 years. The expansive history of immunotherapy, and related observations, have resulted in several approved immune therapeutics beyond the recent emphasis on CAR-T and ICI therapies. In addition to other classical forms of immune intervention, including human papillomavirus (HPV), hepatitis B, and the Mycobacterium bovis Bacillus Calmette-Guérin (BCG) tuberculosis vaccines, immunotherapies have had a broad and durable impact on cancer therapy and prevention. One classic example of immunotherapy was identified in 1976 with the use of intravesical administration of BCG in patients with bladder cancer; resulting in a 70 % eradication rate and is now standard of care. However, a greater impact from the use of immunotherapy is documented by the prevention of HPV infections that are responsible for 98 % of cervical cancer cases. In 2020, the World Health Organization (WHO) estimated that 341,831 women died from cervical cancer [1]. However, administration of a single dose of a bivalent HPV vaccine was shown to be 97.5 % effective in preventing HPV infections. These vaccines not only prevent cervical squamous cell carcinoma and adenocarcinoma, but also oropharyngeal, anal, vulvar, vaginal, and penile squamous cell carcinomas. The breadth, response and durability of these vaccines can be contrasted with CAR-T-cell therapies, which have significant barriers to their widespread use including logistics, manufacturing limitations, toxicity concerns, financial burden and lasting remissions observed in only 30 to 40 % of responding patients. Another, recent immunotherapy focus are ICIs. ICIs are a class of antibodies that can increase the immune responses against cancer cells in patients. However, ICIs are only effective against tumors with a high mutational burden and are associated with a broad spectrum of toxicities requiring interruption of administration and/or administration corticosteroids; both of which limit immune therapy. In summary, immune therapeutics have a broad impact worldwide, utilizing numerous mechanisms of action and when considered in their totality are more effective against a broader range of tumors than initially considered. These new cancer interventions have tremendous potential notability when multiple mechanisms of immune intervention are combined as well as with standard of care modalities.
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Affiliation(s)
- Kathryn Cole
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Zaid Al-Kadhimi
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - James E Talmadge
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA; Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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50
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Gupta S, Nerli S, Kandy SK, Mersky GL, Sgourakis NG. HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533510. [PMID: 36993660 PMCID: PMC10055217 DOI: 10.1101/2023.03.20.533510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The class I proteins of the major histocompatibility complex (MHC-I) display epitopic peptides derived from endogenous proteins on the cell surface for immune surveillance. Accurate modeling of peptide/HLA (pHLA, the human MHC) structures has been mired by conformational diversity of the central peptide residues, which are critical for recognition by T cell receptors. Here, analysis of X-ray crystal structures within a curated database (HLA3DB) shows that pHLA complexes encompassing multiple HLA allotypes present a discrete set of peptide backbone conformations. Leveraging these representative backbones, we employ a regression model trained on terms of a physically relevant energy function to develop a comparative modeling approach for nonamer peptide/HLA structures named RepPred. Our method outperforms the top pHLA modeling approach by up to 19% in terms of structural accuracy, and consistently predicts blind targets not included in our training set. Insights from our work provide a framework for linking conformational diversity with antigen immunogenicity and receptor cross-reactivity.
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