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Dixon D, Sattar H, Moros N, Kesireddy SR, Ahsan H, Lakkimsetti M, Fatima M, Doshi D, Sadhu K, Junaid Hassan M. Unveiling the Influence of AI Predictive Analytics on Patient Outcomes: A Comprehensive Narrative Review. Cureus 2024; 16:e59954. [PMID: 38854327 PMCID: PMC11161909 DOI: 10.7759/cureus.59954] [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] [Accepted: 05/08/2024] [Indexed: 06/11/2024] Open
Abstract
This comprehensive literature review explores the transformative impact of artificial intelligence (AI) predictive analytics on healthcare, particularly in improving patient outcomes regarding disease progression, treatment response, and recovery rates. AI, encompassing capabilities such as learning, problem-solving, and decision-making, is leveraged to predict disease progression, optimize treatment plans, and enhance recovery rates through the analysis of vast datasets, including electronic health records (EHRs), imaging, and genetic data. The utilization of machine learning (ML) and deep learning (DL) techniques in predictive analytics enables personalized medicine by facilitating the early detection of conditions, precision in drug discovery, and the tailoring of treatment to individual patient profiles. Ethical considerations, including data privacy, bias, and accountability, emerge as vital in the responsible implementation of AI in healthcare. The findings underscore the potential of AI predictive analytics in revolutionizing clinical decision-making and healthcare delivery, emphasizing the necessity of ethical guidelines and continuous model validation to ensure its safe and effective use in augmenting human judgment in medical practice.
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Affiliation(s)
- Diny Dixon
- Medicine, Jubilee Mission Medical College and Research Institute, Thrissur, IND
| | - Hina Sattar
- Medicine, Dow University of Health Sciences, Karachi, PAK
| | - Natalia Moros
- Medicine, Pontifical Javeriana University Medical School, Bogotá, COL
| | | | - Huma Ahsan
- Medicine, Jinnah Postgraduate Medical Centre, Karachi, PAK
| | | | - Madiha Fatima
- Medicine, Fatima Jinnah Medical University, Lahore, PAK
| | - Dhruvi Doshi
- Medicine, Gujarat Cancer Society Medical College, Hospital & Research Centre, Ahmedabad, IND
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2
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Benincasa G, Strozziero MG, Di Pastena MA, Criscuolo C, Cetani G, Trama U, Napoli C. Epigenetic challenges on the horizon of chimeric antigen receptor-T. Cytotherapy 2024; 26:411-412. [PMID: 38466261 DOI: 10.1016/j.jcyt.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 03/12/2024]
Affiliation(s)
- Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli," Naples, Italy.
| | | | - Maria Assunta Di Pastena
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Department of Internal Medicine and Specialistics, University of Campania "Luigi Vanvitelli," Naples, Italy
| | - Clelia Criscuolo
- Division of Hematology, Hospital of Aversa (ASLCE), Aversa, Italy
| | - Giusy Cetani
- Division of Hematology, Antonio Cardarelli Hospital, Naples, Italy
| | - Ugo Trama
- Regional Pharmaceutical Unit, Campania Region, Naples, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli," Naples, Italy; U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Department of Internal Medicine and Specialistics, University of Campania "Luigi Vanvitelli," Naples, Italy
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3
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Ghaffari S, Saleh M, Akbari B, Ramezani F, Mirzaei HR. Applications of single-cell omics for chimeric antigen receptor T cell therapy. Immunology 2024; 171:339-364. [PMID: 38009707 DOI: 10.1111/imm.13720] [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: 07/02/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
Chimeric antigen receptor (CAR) T cell therapy is a promising cancer treatment modality. The breakthroughs in CAR T cell therapy were, in part, possible with the help of cell analysis methods, such as single-cell analysis. Bulk analyses have provided invaluable information regarding the complex molecular dynamics of CAR T cells, but their results are an average of thousands of signals in CAR T or tumour cells. Since cancer is a heterogeneous disease where each minute detail of a subclone could change the outcome of the treatment, single-cell analysis could prove to be a powerful instrument in deciphering the secrets of tumour microenvironment for cancer immunotherapy. With the recent studies in all aspects of adoptive cell therapy making use of single-cell analysis, a comprehensive review of the recent preclinical and clinical findings in CAR T cell therapy was needed. Here, we categorized and summarized the key points of the studies in which single-cell analysis provided insights into the genomics, epigenomics, transcriptomics and proteomics as well as their respective multi-omics of CAR T cell therapy.
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Affiliation(s)
- Sasan Ghaffari
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Mahshid Saleh
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, Madison, Wisconsin, USA
| | - Behnia Akbari
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Faezeh Ramezani
- Department of Medical Biotechnology, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medical Laboratory Sciences, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hamid Reza Mirzaei
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Molecular Imaging and Therapy Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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4
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Strzelec A, Helbig G. Are we ready for personalized CAR-T therapy? Eur J Haematol 2024; 112:174-183. [PMID: 37431655 DOI: 10.1111/ejh.14039] [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: 05/30/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/12/2023]
Abstract
The future of chimeric antigen receptor T (CAR-T) therapy remains unclear. New studies are constantly being published confirming the efficacy and favorable safety profile of its innovative enhancements. Currently approved CAR-T drugs are manufactured exclusively for a specific patient from the recipient's own cells. This does not close the door to further modifications with subsequent personalization and better adaptation to the individual needs. Bringing such a drug to market would involve raising the already high costs, so it is necessary to lower the existing ones. On the other hand, so-called universal CAR-T are also getting closer to the patient's bed, but its implementation may struggle with multiple challenges, including development of graft-versus-host disease (GvHD) and alloimmunity. However, that off-the-shelf therapy could prove useful as a quick solution for patients in very poor condition or excluded from current therapy due to manufacturing limitations. The introduction of currently tested solutions may undoubtedly change the current paradigm of treatment.
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Affiliation(s)
- Anna Strzelec
- Department of Hematology and Bone Marrow Transplantation, Faculty of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
| | - Grzegorz Helbig
- Department of Hematology and Bone Marrow Transplantation, Faculty of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
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5
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Lee HY, Yang SB, Park MY, Baek GW, Kang HJ. RE: Epigenetic profiling and response to CD19 chimeric antigen receptor T-cell therapy in B-cell malignancies. J Natl Cancer Inst 2023; 115:1231-1233. [PMID: 37594794 DOI: 10.1093/jnci/djad165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023] Open
Affiliation(s)
- Hwan Young Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, Korea
| | - Soo-Bin Yang
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Mi Young Park
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
- Seoul National University Cancer Research Institute, Seoul, Korea
| | - Gyung Won Baek
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
- Seoul National University Cancer Research Institute, Seoul, Korea
| | - Hyoung Jin Kang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
- Seoul National University Cancer Research Institute, Seoul, Korea
- Seoul National University Children's Hospital, Seoul, Korea
- Wide River Institute of Immunology, Hongcheon-gun, Gangwon-do, Korea
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6
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Salz L, Seitz A, Schäfer D, Franzen J, Holzer T, Garcia-Prieto CA, Bürger I, Hardt O, Esteller M, Wagner W. Culture expansion of CAR T cells results in aberrant DNA methylation that is associated with adverse clinical outcome. Leukemia 2023; 37:1868-1878. [PMID: 37452103 PMCID: PMC10457202 DOI: 10.1038/s41375-023-01966-1] [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: 12/20/2022] [Revised: 06/15/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
Chimeric antigen receptor (CAR) T cells provide new perspectives for treatment of hematological malignancies. Manufacturing of these cellular products includes culture expansion procedures, which may affect cellular integrity and therapeutic outcome. In this study, we investigated culture-associated epigenetic changes in CAR T cells and found continuous gain of DNAm, particularly within genes that are relevant for T cell function. Hypermethylation in many genes, such as TCF7, RUNX1, and TOX, was reflected by transcriptional downregulation. 332 CG dinucleotides (CpGs) showed an almost linear gain in methylation with cell culture time, albeit neighboring CpGs were not coherently regulated on the same DNA strands. An epigenetic signature based on 14 of these culture-associated CpGs predicted cell culture time across various culture conditions. Notably, even in CAR T cell products of similar culture time higher DNAm levels at these CpGs were associated with significantly reduced long-term survival post transfusion. Our data demonstrate that cell culture expansion of CAR T cells evokes DNA hypermethylation at specific sites in the genome and the signature may also reflect loss of potential in CAR T cell products. Hence, reduced cultivation periods are beneficial to avoid dysfunctional methylation programs that seem to be associated with worse therapeutic outcome.
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Affiliation(s)
- Lucia Salz
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Alexander Seitz
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
- Miltenyi Biotec B.V. & Co. KG, Bergisch, Gladbach, Germany
| | - Daniel Schäfer
- Miltenyi Biotec B.V. & Co. KG, Bergisch, Gladbach, Germany
| | - Julia Franzen
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Tatjana Holzer
- Miltenyi Biotec B.V. & Co. KG, Bergisch, Gladbach, Germany
| | - Carlos A Garcia-Prieto
- Josep Carreras Leukemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Iris Bürger
- Miltenyi Biotec B.V. & Co. KG, Bergisch, Gladbach, Germany
| | - Olaf Hardt
- Miltenyi Biotec B.V. & Co. KG, Bergisch, Gladbach, Germany
| | - Manel Esteller
- Josep Carreras Leukemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Wolfgang Wagner
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany.
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany.
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7
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Capelli C, Cuofano C, Pavoni C, Frigerio S, Lisini D, Nava S, Quaroni M, Colombo V, Galli F, Bezukladova S, Panina-Bordignon P, Gaipa G, Comoli P, Cossu G, Martino G, Biondi A, Introna M, Golay J. Potency assays and biomarkers for cell-based advanced therapy medicinal products. Front Immunol 2023; 14:1186224. [PMID: 37359560 PMCID: PMC10288881 DOI: 10.3389/fimmu.2023.1186224] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/24/2023] [Indexed: 06/28/2023] Open
Abstract
Advanced Therapy Medicinal Products (ATMPs) based on somatic cells expanded in vitro, with or without genetic modification, is a rapidly growing area of drug development, even more so following the marketing approval of several such products. ATMPs are produced according to Good Manufacturing Practice (GMP) in authorized laboratories. Potency assays are a fundamental aspect of the quality control of the end cell products and ideally could become useful biomarkers of efficacy in vivo. Here we summarize the state of the art with regard to potency assays used for the assessment of the quality of the major ATMPs used clinic settings. We also review the data available on biomarkers that may substitute more complex functional potency tests and predict the efficacy in vivo of these cell-based drugs.
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Affiliation(s)
- Chiara Capelli
- Center of Cellular Therapy "G. Lanzani", ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Carolina Cuofano
- Center of Cellular Therapy "G. Lanzani", ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Chiara Pavoni
- Center of Cellular Therapy "G. Lanzani", ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Simona Frigerio
- Cell Therapy Production Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Daniela Lisini
- Cell Therapy Production Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Sara Nava
- Cell Therapy Production Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Michele Quaroni
- Laboratory of Cell and Gene Therapy Stefano Verri, ASST Monza Ospedale San Gerardo, Monza, Italy
| | - Valentina Colombo
- Laboratory of Cell and Gene Therapy Stefano Verri, ASST Monza Ospedale San Gerardo, Monza, Italy
| | - Francesco Galli
- Division of Cell Matrix Biology & Regenerative Medicine, Faculty of Biology, Medicine and Health (FBMH), University of Manchester, Manchester, United Kingdom
| | - Svetlana Bezukladova
- Università Vita-Salute San Raffaele, Milan, Italy
- IRCCS San Raffaele Hospital, Neuroimmunology Unit, Division of Neuroscience, Milan, Italy
| | - Paola Panina-Bordignon
- Università Vita-Salute San Raffaele, Milan, Italy
- IRCCS San Raffaele Hospital, Neuroimmunology Unit, Division of Neuroscience, Milan, Italy
| | - Giuseppe Gaipa
- Laboratory of Cell and Gene Therapy Stefano Verri, ASST Monza Ospedale San Gerardo, Monza, Italy
| | - Patrizia Comoli
- Pediatric Hematology/Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Giulio Cossu
- Division of Cell Matrix Biology & Regenerative Medicine, Faculty of Biology, Medicine and Health (FBMH), University of Manchester, Manchester, United Kingdom
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Gianvito Martino
- IRCCS San Raffaele Hospital, Neuroimmunology Unit, Division of Neuroscience, Milan, Italy
- Pediatric Hematology/Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Andrea Biondi
- Department of Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Martino Introna
- Center of Cellular Therapy "G. Lanzani", ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Josée Golay
- Center of Cellular Therapy "G. Lanzani", ASST Papa Giovanni XXIII, Bergamo, Italy
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8
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Song S. RE: COVID-19 severity by vaccination status in the NCI COVID-19 and Cancer Patients Study (NCCAPS). J Natl Cancer Inst 2023; 115:766-767. [PMID: 36946282 PMCID: PMC10248831 DOI: 10.1093/jnci/djad045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 03/23/2023] Open
Affiliation(s)
- Shan Song
- Department of Pediatrics, Changxing People’s Hospital of Chongming District, Shanghai, China
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9
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Zhong F, Lin Y, Zhao L, Yang C, Ye Y, Shen Z. Reshaping the tumour immune microenvironment in solid tumours via tumour cell and immune cell DNA methylation: from mechanisms to therapeutics. Br J Cancer 2023:10.1038/s41416-023-02292-0. [PMID: 37117649 DOI: 10.1038/s41416-023-02292-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 04/30/2023] Open
Abstract
In recent years, the tumour microenvironment (TME) of solid tumours has attracted more and more attention from researchers, especially those non-tumour components such as immune cells. Infiltration of various immune cells causes tumour immune microenvironment (TIME) heterogeneity, and results in different therapeutic effects. Accumulating evidence showed that DNA methylation plays a crucial role in remodelling TIME and is associated with the response towards immune checkpoint inhibitors (ICIs). During carcinogenesis, DNA methylation profoundly changes, specifically, there is a global loss of DNA methylation and increased DNA methylation at the promoters of suppressor genes. Immune cell differentiation is disturbed, and exclusion of immune cells from the TME occurs at least in part due to DNA methylation reprogramming. Therefore, pharmaceutical interventions targeting DNA methylation are promising. DNA methyltransferase inhibitors (DNMTis) enhance antitumor immunity by inducing transcription of transposable elements and consequent viral mimicry. DNMTis upregulate the expression of tumour antigens, mediate immune cells recruitment and reactivate exhausted immune cells. In preclinical studies, DNMTis have shown synergistic effect when combined with immunotherapies, suggesting new strategies to treat refractory solid tumours.
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Affiliation(s)
- Fengyun Zhong
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Yilin Lin
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Long Zhao
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Changjiang Yang
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Yingjiang Ye
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Zhanlong Shen
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China.
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China.
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10
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Chen C, Liu X, Chang CY, Wang HY, Wang RF. The Interplay between T Cells and Cancer: The Basis of Immunotherapy. Genes (Basel) 2023; 14:genes14051008. [PMID: 37239368 DOI: 10.3390/genes14051008] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Over the past decade, immunotherapy has emerged as one of the most promising approaches to cancer treatment. The use of immune checkpoint inhibitors has resulted in impressive and durable clinical responses in the treatment of various cancers. Additionally, immunotherapy utilizing chimeric antigen receptor (CAR)-engineered T cells has produced robust responses in blood cancers, and T cell receptor (TCR)-engineered T cells are showing promising results in the treatment of solid cancers. Despite these noteworthy advancements in cancer immunotherapy, numerous challenges remain. Some patient populations are unresponsive to immune checkpoint inhibitor therapy, and CAR T cell therapy has yet to show efficacy against solid cancers. In this review, we first discuss the significant role that T cells play in the body's defense against cancer. We then delve into the mechanisms behind the current challenges facing immunotherapy, starting with T cell exhaustion due to immune checkpoint upregulation and changes in the transcriptional and epigenetic landscapes of dysfunctional T cells. We then discuss cancer-cell-intrinsic characteristics, including molecular alterations in cancer cells and the immunosuppressive nature of the tumor microenvironment (TME), which collectively facilitate tumor cell proliferation, survival, metastasis, and immune evasion. Finally, we examine recent advancements in cancer immunotherapy, with a specific emphasis on T-cell-based treatments.
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Affiliation(s)
- Christina Chen
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Xin Liu
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Che-Yu Chang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Helen Y Wang
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Rong-Fu Wang
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Pediatrics, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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11
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Micevic G, Bosenberg MW, Yan Q. The Crossroads of Cancer Epigenetics and Immune Checkpoint Therapy. Clin Cancer Res 2023; 29:1173-1182. [PMID: 36449280 PMCID: PMC10073242 DOI: 10.1158/1078-0432.ccr-22-0784] [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: 08/09/2022] [Revised: 10/10/2022] [Accepted: 11/16/2022] [Indexed: 12/02/2022]
Abstract
Immune checkpoint inhibitors (ICI) have significantly improved treatment outcomes for several types of cancer over the past decade, but significant challenges that limit wider effectiveness of current immunotherapies remain to be addressed. Certain "cold" tumor types, such as pancreatic cancer, exhibit very low response rates to ICI due to intrinsically low immunogenicity. In addition, many patients who initially respond to ICI lack a sustained response due to T-cell exhaustion. Several recent studies show that epigenetic modifiers, such as SETDB1 and LSD1, can play critical roles in regulating both tumor cell-intrinsic immunity and T-cell exhaustion. Here, we review the evidence showing that multiple epigenetic regulators silence the expression of endogenous antigens, and their loss induces viral mimicry responses bolstering the response of "cold" tumors to ICI in preclinical models. Similarly, a previously unappreciated role for epigenetic enzymes is emerging in the establishment and maintenance of stem-like T-cell populations that are critical mediators of response to ICI. Targeting the crossroads of epigenetics and immune checkpoint therapy has tremendous potential to improve antitumor immune responses and herald the next generation of sustained responses in immuno-oncology.
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Affiliation(s)
- Goran Micevic
- Department of Dermatology, Yale School of Medicine, New Haven, CT 06520
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520
| | - Marcus W. Bosenberg
- Department of Dermatology, Yale School of Medicine, New Haven, CT 06520
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520
- Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT 06520
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520
- Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT 06520
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520
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12
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Yang J, Chen Y, Jing Y, Green MR, Han L. Advancing CAR T cell therapy through the use of multidimensional omics data. Nat Rev Clin Oncol 2023; 20:211-228. [PMID: 36721024 DOI: 10.1038/s41571-023-00729-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2023] [Indexed: 02/01/2023]
Abstract
Despite the notable success of chimeric antigen receptor (CAR) T cell therapies in the treatment of certain haematological malignancies, challenges remain in optimizing CAR designs and cell products, improving response rates, extending the durability of remissions, reducing toxicity and broadening the utility of this therapeutic modality to other cancer types. Data from multidimensional omics analyses, including genomics, epigenomics, transcriptomics, T cell receptor-repertoire profiling, proteomics, metabolomics and/or microbiomics, provide unique opportunities to dissect the complex and dynamic multifactorial phenotypes, processes and responses of CAR T cells as well as to discover novel tumour targets and pathways of resistance. In this Review, we summarize the multidimensional cellular and molecular profiling technologies that have been used to advance our mechanistic understanding of CAR T cell therapies. In addition, we discuss current applications and potential strategies leveraging multi-omics data to identify optimal target antigens and other molecular features that could be exploited to enhance the antitumour activity and minimize the toxicity of CAR T cell therapy. Indeed, fully utilizing multi-omics data will provide new insights into the biology of CAR T cell therapy, further accelerate the development of products with improved efficacy and safety profiles, and enable clinicians to better predict and monitor patient responses.
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Affiliation(s)
- Jingwen Yang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Yamei Chen
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Ying Jing
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Michael R Green
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Leng Han
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, USA.
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13
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Wang S, Fu J, Fang X. A novel DNA methylation-related gene signature for the prediction of overall survival and immune characteristics of ovarian cancer patients. J Ovarian Res 2023; 16:62. [PMID: 36978087 PMCID: PMC10053775 DOI: 10.1186/s13048-023-01142-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Ovarian cancer (OC) is one of the most life-threatening cancers affecting women worldwide. Recent studies have shown that the DNA methylation state can be used in the diagnosis, treatment and prognosis prediction of diseases. Meanwhile, it has been reported that the DNA methylation state can affect the function of immune cells. However, whether DNA methylation-related genes can be used for prognosis and immune response prediction in OC remains unclear. METHODS In this study, DNA methylation-related genes in OC were identified by an integrated analysis of DNA methylation and transcriptome data. Prognostic values of the DNA methylation-related genes were investigated through least absolute shrinkage and selection operator (LASSO) and Cox progression analyses. Immune characteristics were investigated by CIBERSORT, correlation analysis and weighted gene co-expression network analysis (WGCNA). RESULTS Twelve prognostic genes (CA2, CD3G, HABP2, KCTD14, PI3, SERPINB5, SLAMF7, SLC9A2, STC2, TBP, TREML2 and TRIM27) were identified and a risk score signature and a nomogram based on prognostic genes and clinicopathological features were constructed for the survival prediction of OC patients in the training and two validation cohorts. Subsequently, the differences in the immune landscape between the high- and low-risk score groups were systematically investigated. CONCLUSIONS Taken together, our study explored a novel efficient risk score signature and a nomogram for the survival prediction of OC patients. In addition, the differences of the immune characteristics between the two risk groups were clarified preliminarily, which will guide the further exploration of synergistic targets to improve the efficacy of immunotherapy in OC patients.
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Affiliation(s)
- Sixue Wang
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Jie Fu
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China.
| | - Xiaoling Fang
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China.
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14
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Alvanou M, Lysandrou M, Christophi P, Psatha N, Spyridonidis A, Papadopoulou A, Yannaki E. Empowering the Potential of CAR-T Cell Immunotherapies by Epigenetic Reprogramming. Cancers (Basel) 2023; 15:cancers15071935. [PMID: 37046597 PMCID: PMC10093039 DOI: 10.3390/cancers15071935] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
T-cell-based, personalized immunotherapy can nowadays be considered the mainstream treatment for certain blood cancers, with a high potential for expanding indications. Chimeric antigen receptor T cells (CAR-Ts), an ex vivo genetically modified T-cell therapy product redirected to target an antigen of interest, have achieved unforeseen successes in patients with B-cell hematologic malignancies. Frequently, however, CAR-T cell therapies fail to provide durable responses while they have met with only limited success in treating solid cancers because unique, unaddressed challenges, including poor persistence, impaired trafficking to the tumor, and site penetration through a hostile microenvironment, impede their efficacy. Increasing evidence suggests that CAR-Ts' in vivo performance is associated with T-cell intrinsic features that may be epigenetically altered or dysregulated. In this review, we focus on the impact of epigenetic regulation on T-cell differentiation, exhaustion, and tumor infiltration and discuss how epigenetic reprogramming may enhance CAR-Ts' memory phenotype, trafficking, and fitness, contributing to the development of a new generation of potent CAR-T immunotherapies.
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Affiliation(s)
- Maria Alvanou
- Hematology Department-Hematopoietic Cell Transplantation Unit, Gene and Cell Therapy Center, George Papanikolaou Hospital, 570 10 Thessaloniki, Greece
- Bone Marrow Transplantation Unit, Institute of Cell Therapy, University of Patras, 265 04 Rio, Greece
| | - Memnon Lysandrou
- Bone Marrow Transplantation Unit, Institute of Cell Therapy, University of Patras, 265 04 Rio, Greece
| | - Panayota Christophi
- Hematology Department-Hematopoietic Cell Transplantation Unit, Gene and Cell Therapy Center, George Papanikolaou Hospital, 570 10 Thessaloniki, Greece
- Bone Marrow Transplantation Unit, Institute of Cell Therapy, University of Patras, 265 04 Rio, Greece
| | - Nikoleta Psatha
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 570 10 Thessaloniki, Greece
| | - Alexandros Spyridonidis
- Bone Marrow Transplantation Unit, Institute of Cell Therapy, University of Patras, 265 04 Rio, Greece
| | - Anastasia Papadopoulou
- Hematology Department-Hematopoietic Cell Transplantation Unit, Gene and Cell Therapy Center, George Papanikolaou Hospital, 570 10 Thessaloniki, Greece
| | - Evangelia Yannaki
- Hematology Department-Hematopoietic Cell Transplantation Unit, Gene and Cell Therapy Center, George Papanikolaou Hospital, 570 10 Thessaloniki, Greece
- Department of Medicine, University of Washington, Seattle, WA 98195-2100, USA
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15
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Costa PMDS, Sales SLA, Pinheiro DP, Pontes LQ, Maranhão SS, Pessoa CDÓ, Furtado GP, Furtado CLM. Epigenetic reprogramming in cancer: From diagnosis to treatment. Front Cell Dev Biol 2023; 11:1116805. [PMID: 36866275 PMCID: PMC9974167 DOI: 10.3389/fcell.2023.1116805] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/01/2023] [Indexed: 02/16/2023] Open
Abstract
Disruption of the epigenetic program of gene expression is a hallmark of cancer that initiates and propagates tumorigenesis. Altered DNA methylation, histone modifications and ncRNAs expression are a feature of cancer cells. The dynamic epigenetic changes during oncogenic transformation are related to tumor heterogeneity, unlimited self-renewal and multi-lineage differentiation. This stem cell-like state or the aberrant reprogramming of cancer stem cells is the major challenge in treatment and drug resistance. Given the reversible nature of epigenetic modifications, the ability to restore the cancer epigenome through the inhibition of the epigenetic modifiers is a promising therapy for cancer treatment, either as a monotherapy or in combination with other anticancer therapies, including immunotherapies. Herein, we highlighted the main epigenetic alterations, their potential as a biomarker for early diagnosis and the epigenetic therapies approved for cancer treatment.
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Affiliation(s)
- Pedro Mikael da Silva Costa
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil,Postgraduation Program in Biotechnology Northeastern Network of Biotechnology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Sarah Leyenne Alves Sales
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil,Postgraduation Program in Pharmacology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | - Larissa Queiroz Pontes
- Oswaldo Cruz Foundation, FIOCRUZ-Ceará, Sector of Biotechnology, Eusebio, Ceará, Brazil,Postgraduation Program in Biotechnology and Natural Resources, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Sarah Sant’Anna Maranhão
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Claudia do Ó. Pessoa
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil,Postgraduation Program in Biotechnology Northeastern Network of Biotechnology, Federal University of Ceará, Fortaleza, Ceará, Brazil,Postgraduation Program in Pharmacology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Gilvan Pessoa Furtado
- Oswaldo Cruz Foundation, FIOCRUZ-Ceará, Sector of Biotechnology, Eusebio, Ceará, Brazil,Postgraduation Program in Biotechnology and Natural Resources, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Cristiana Libardi Miranda Furtado
- Drug Research and Development Center, Postgraduate Program in Translational Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil,Experimental Biology Center, University of Fortaleza, Fortaleza, Ceará, Brazil,*Correspondence: Cristiana Libardi Miranda Furtado,
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16
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Xie J, Luo X, Deng X, Tang Y, Tian W, Cheng H, Zhang J, Zou Y, Guo Z, Xie X. Advances in artificial intelligence to predict cancer immunotherapy efficacy. Front Immunol 2023; 13:1076883. [PMID: 36685496 PMCID: PMC9845588 DOI: 10.3389/fimmu.2022.1076883] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/09/2022] [Indexed: 01/05/2023] Open
Abstract
Tumor immunotherapy, particularly the use of immune checkpoint inhibitors, has yielded impressive clinical benefits. Therefore, it is critical to accurately screen individuals for immunotherapy sensitivity and forecast its efficacy. With the application of artificial intelligence (AI) in the medical field in recent years, an increasing number of studies have indicated that the efficacy of immunotherapy can be better anticipated with the help of AI technology to reach precision medicine. This article focuses on the current prediction models based on information from histopathological slides, imaging-omics, genomics, and proteomics, and reviews their research progress and applications. Furthermore, we also discuss the existing challenges encountered by AI in the field of immunotherapy, as well as the future directions that need to be improved, to provide a point of reference for the early implementation of AI-assisted diagnosis and treatment systems in the future.
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Affiliation(s)
- Jindong Xie
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xiyuan Luo
- School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xinpei Deng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yuhui Tang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Wenwen Tian
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Hui Cheng
- School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Junsheng Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yutian Zou
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China,*Correspondence: Xiaoming Xie, ; Zhixing Guo, ; Yutian Zou,
| | - Zhixing Guo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China,*Correspondence: Xiaoming Xie, ; Zhixing Guo, ; Yutian Zou,
| | - Xiaoming Xie
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China,*Correspondence: Xiaoming Xie, ; Zhixing Guo, ; Yutian Zou,
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17
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Su Y, Yuan C, Shi M. Editorial: Screening and verification of new targets for CAR-T immunotherapy in cancer. Front Immunol 2023; 14:1189773. [PMID: 37114061 PMCID: PMC10126677 DOI: 10.3389/fimmu.2023.1189773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Affiliation(s)
- Yang Su
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Chen Yuan
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
| | - Ming Shi
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou, Jiangsu, China
- *Correspondence: Ming Shi,
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18
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How Genetics and Genomics Advances Are Rewriting Pediatric Cancer Research and Clinical Care. Medicina (B Aires) 2022; 58:medicina58101386. [PMID: 36295546 PMCID: PMC9610804 DOI: 10.3390/medicina58101386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
In the last two decades, thanks to the data that have been obtained from the Human Genome Project and the development of next-generation sequencing (NGS) technologies, research in oncology has produced extremely important results in understanding the genomic landscape of pediatric cancers, which are the main cause of death during childhood. NGS has provided significant advances in medicine by detecting germline and somatic driver variants that determine the development and progression of many types of cancers, allowing a distinction between hereditary and non-hereditary cancers, characterizing resistance mechanisms that are also related to alterations of the epigenetic apparatus, and quantifying the mutational burden of tumor cells. A combined approach of next-generation technologies allows us to investigate the numerous molecular features of the cancer cell and the effects of the environment on it, discovering and following the path of personalized therapy to defeat an "ancient" disease that has had victories and defeats. In this paper, we provide an overview of the results that have been obtained in the last decade from genomic studies that were carried out on pediatric cancer and their contribution to the more accurate and faster diagnosis in the stratification of patients and the development of new precision therapies.
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19
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Ito Y, Kagoya Y. Epigenetic engineering for optimal CAR-T cell therapy. Cancer Sci 2022; 113:3664-3671. [PMID: 36000807 DOI: 10.1111/cas.15541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/28/2022] [Accepted: 08/15/2022] [Indexed: 11/29/2022] Open
Abstract
Recent advancements in cancer immunotherapy, such as chimeric antigen receptor (CAR)-engineered T cell therapy and immune checkpoint therapy (ICT), have significantly improved the clinical outcomes of patients with several types of cancer. To broaden its applicability further and induce durable therapeutic efficacy, it is imperative to understand how antitumor T cells elicit cytotoxic functions, survive as memory T cells, or are impaired in their effector functions (exhausted) at the molecular level. T cell properties are regulated by their gene expression profiles, which are further controlled by epigenetic architectures, such as DNA methylation and histone modifications. Multiple studies have elucidated specific epigenetic genes associated with T-cell phenotypic changes. Conversely, exogenous modification of these key epigenetic factors can significantly alter T cell functions by extensively altering the transcription network, which can be applied in cancer immunotherapy by improving T cell persistence or augmenting effector functions. Since CAR-T cell therapy involves a genetic engineering step during the preparation of the infusion products, it would be a feasible strategy to additionally modulate specific epigenetic genes in CAR-T cells to improve their quality. Here, we review recent studies investigating how individual epigenetic factors play a crucial role in T-cell biology. We further discuss future directions to integrate these findings for optimal cancer immunotherapy.
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Affiliation(s)
- Yusuke Ito
- Division of Immune Response, Aichi Cancer Center Research Institute
| | - Yuki Kagoya
- Division of Immune Response, Aichi Cancer Center Research Institute.,Division of Cellular Oncology, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine
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20
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Berger SC, Fehse B, Akyüz N, Geffken M, Wolschke C, Janson D, Gagelmann N, Luther M, Wichmann D, Frenzel C, Thayssen G, Alegiani A, Badbaran A, Zeschke S, Dierlamm J, Kröger N, Ayuk FA. Molecular monitoring of T-cell kinetics and migration in severe neurotoxicity after real-world CD19-specific chimeric antigen receptor T cell therapy. Haematologica 2022; 108:444-456. [PMID: 35950534 PMCID: PMC9890009 DOI: 10.3324/haematol.2022.281110] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Indexed: 02/03/2023] Open
Abstract
CD19-specific chimeric antigen receptor (CD19-CAR) T-cell therapies mediate durable responses in late-stage B-cell malignancies, but can be complicated by a potentially severe immune effector cell-associated neurotoxicity syndrome (ICANS). Despite broad efforts, the precise mechanisms of ICANS are not entirely known, and resistance to current ICANSdirected therapies (especially corticosteroids) has been observed. Recent data suggest that inflammatory cytokines and/or targeting of cerebral CD19-expressing pericytes can disrupt the blood-brain barrier and facilitate influx of immune cells, including CAR T cells. However, specific tools for CD19-CAR T-cell analysis within often minute samples of cerebrospinal fluid (CSF) are not broadly available. Here, we applied our recently developed digital polymerase chain reaction assays to monitor CD19-CAR T-cell kinetics in CSF and blood in real-world patients with neurotoxicity. Consistently, we observed a CAR T-cell enrichment within CSF in ICANS patients with further progressive accumulation despite intense corticosteroid- containing immuno-chemotherapies in a subset of patients with prolonged and therapy-resistant grade 3-4 neurotoxicity. We used next-generation T-cell receptor-b sequencing to assess the repertoire of treatment-refractory cells. Longitudinal analysis revealed a profound skewing of the T-cell receptor repertoire, which at least partly reflected selective expansion of infused T-cell clones. Interestingly, a major fraction of eventually dominating hyperexpanded T-cell clones were of non-CAR T-cell derivation. These findings hint to a role of therapy-refractory T-cell clones in severe ICANS development and prompt future systematic research to determine if CAR T cells may serve as 'door openers' and to further characterize both CAR-positive and non-CAR T cells to interrogate the transcriptional signature of these possibly pathologic T cells.
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Affiliation(s)
| | - Boris Fehse
- Department of Stem Cell Transplantation,Research Department Cell and Gene Therapy
| | | | | | | | | | | | | | | | | | - Guenther Thayssen
- Department of Neurology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Anna Alegiani
- Department of Neurology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany,°Current address: Department of Neurology with Stroke Unit, Asklepios Clinic Altona, Hamburg, Germany
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21
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Song J, Huang F, Chen L, Feng K, Jian F, Huang T, Cai YD. Identification of methylation signatures associated with CAR T cell in B-cell acute lymphoblastic leukemia and non-hodgkin’s lymphoma. Front Oncol 2022; 12:976262. [PMID: 36033519 PMCID: PMC9402909 DOI: 10.3389/fonc.2022.976262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
CD19-targeted CAR T cell immunotherapy has exceptional efficacy for the treatment of B-cell malignancies. B-cell acute lymphocytic leukemia and non-Hodgkin’s lymphoma are two common B-cell malignancies with high recurrence rate and are refractory to cure. Although CAR T-cell immunotherapy overcomes the limitations of conventional treatments for such malignancies, failure of treatment and tumor recurrence remain common. In this study, we searched for important methylation signatures to differentiate CAR-transduced and untransduced T cells from patients with acute lymphoblastic leukemia and non-Hodgkin’s lymphoma. First, we used three feature ranking methods, namely, Monte Carlo feature selection, light gradient boosting machine, and least absolute shrinkage and selection operator, to rank all methylation features in order of their importance. Then, the incremental feature selection method was adopted to construct efficient classifiers and filter the optimal feature subsets. Some important methylated genes, namely, SERPINB6, ANK1, PDCD5, DAPK2, and DNAJB6, were identified. Furthermore, the classification rules for distinguishing different classes were established, which can precisely describe the role of methylation features in the classification. Overall, we applied advanced machine learning approaches to the high-throughput data, investigating the mechanism of CAR T cells to establish the theoretical foundation for modifying CAR T cells.
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Affiliation(s)
- Jiwei Song
- College of Life Science, Changchun Sci-Tech University, Shuangyang, China
| | - FeiMing Huang
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, China
| | - Fangfang Jian
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Tao Huang, ; Yu-Dong Cai,
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- *Correspondence: Tao Huang, ; Yu-Dong Cai,
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22
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Ferrer G, Álvarez-Errico D, Esteller M. Biological and Molecular Factors Predicting Response to Adoptive Cell Therapies in Cancer. J Natl Cancer Inst 2022; 114:930-939. [PMID: 35438170 PMCID: PMC9275759 DOI: 10.1093/jnci/djac088] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/08/2022] [Accepted: 04/12/2022] [Indexed: 11/23/2022] Open
Abstract
Adoptive cell therapy (ACT) constitutes a major breakthrough in cancer management that has expanded in the past years due to impressive results showing durable and even curative responses for some patients with hematological malignancies. ACT leverages antigen specificity and cytotoxic mechanisms of the immune system, particularly relying on the patient’s T lymphocytes to target and eliminate malignant cells. This personalized therapeutic approach exemplifies the success of the joint effort of basic, translational, and clinical researchers that has turned the patient’s immune system into a great ally in the search for a cancer cure. ACTs are constantly improving to reach a maximum beneficial clinical response. Despite being very promising therapeutic options for certain types of cancers, mainly melanoma and hematological malignancies, these individualized treatments still present several shortcomings, including elevated costs, technical challenges, management of adverse side effects, and a limited population of responder patients. Thus, it is crucial to discover and develop reliable and robust biomarkers to specifically and sensitively pinpoint the patients that will benefit the most from ACT as well as those at higher risk of developing potentially serious toxicities. Although unique readouts of infused cell therapy success have not yet been identified, certain characteristics from the adoptive cells, the tumor, and/or the tumor microenvironment have been recognized to predict patients’ outcome on ACT. Here, we comment on the importance of biomarkers to predict ACT chances of success to maximize efficacy of treatments and increase patients’ survival.
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Affiliation(s)
- Gerardo Ferrer
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Catalonia, Spain.,Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Madrid, Spain
| | | | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Madrid, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
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23
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Luginbuehl V, Abraham E, Kovar K, Flaaten R, Müller AMS. Better by design: What to expect from novel CAR-engineered cell therapies? Biotechnol Adv 2022; 58:107917. [PMID: 35149146 DOI: 10.1016/j.biotechadv.2022.107917] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/30/2022] [Accepted: 02/01/2022] [Indexed: 12/15/2022]
Abstract
Chimeric antigen receptor (CAR) technology, and CAR-T cells in particular, have emerged as a new and powerful tool in cancer immunotherapy since demonstrating efficacy against several hematological malignancies. However, despite encouraging clinical results of CAR-T cell therapy products, a significant proportion of patients do not achieve satisfactory responses, or relapse. In addition, CAR-T cell applications to solid tumors is still limited due to the tumor microenvironment and lack of specifically targetable tumor antigens. All current products on the market, as well as most investigational CAR-T cell therapies, are autologous, using the patient's own peripheral blood mononuclear cells as starting material to manufacture a patient-specific batch. Alternative cell sources are, therefore, under investigation (e.g. allogeneic cells from an at least partially human leukocyte antigen (HLA)-matched healthy donor, universal "third-party" cells from a non-HLA-matched donor, cord blood-derived cells, immortalized cell lines or cells differentiated from induced pluripotent stem cells). However, genetic modifications of CAR-engineered cells, bioprocesses used to expand cells, and improved supply chains are still complex and costly. To overcome drawbacks associated with CAR-T technologies, novel CAR designs have been used to genetically engineer cells derived from alpha beta (αβ) T cells, other immune cells such as natural killer (NK) cells, gamma delta (γδ) T cells, macrophages or dendritic cells. This review endeavours to trigger ideas on the next generation of CAR-engineered cell therapies beyond CAR-T cells and, thus, will enable effective, safe and affordable therapies for clinical management of cancer. To achieve this, we present a multidisciplinary overview, addressing a wide range of critical aspects: CAR design, development and manufacturing technologies, pharmacological concepts and clinical applications of CAR-engineered cell therapies. Each of these fields employs a large number of ground-breaking scientific advances, where coordinated and complex process and product development occur at their interfaces.
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Affiliation(s)
- Vera Luginbuehl
- Novartis Oncology, Cell & Gene Therapy, Novartis Pharma Schweiz AG, Rotkreuz, Switzerland.
| | - Eytan Abraham
- Personalized Medicine Lonza Pharma&Biotech, Lonza Ltd., Walkersville, MD, USA
| | | | - Richard Flaaten
- Novartis Oncology, Cell & Gene Therapy, Novartis Norge AS, Oslo, Norway
| | - Antonia M S Müller
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
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24
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Sun F, Yu X, Ju R, Wang Z, Wang Y. Antitumor responses in gastric cancer by targeting B7H3 via chimeric antigen receptor T cells. Cancer Cell Int 2022; 22:50. [PMID: 35101032 PMCID: PMC8802437 DOI: 10.1186/s12935-022-02471-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/16/2022] [Indexed: 12/31/2022] Open
Abstract
Background Gastric cancer (GC) has a poor prognosis and limited therapeutic options. As a new promising cancer therapeutic approach, chimeric antigen receptor (CAR)-T cells represent a potential GC treatment. We investigated the antitumor activity of CAR-T cells target-B7H3 in GC. Methods In our study, expression of B7H3 was examined in GC tissues and explored the tumoricidal potential of B7H3-targeting CAR-T cells in GC. B7H3-directed CAR-T cells with a humanized antigen-recognizing domain was generated. The anti-tumor effects of this CAR-T cell were finally investigated in vitro and in vivo. Results Our results show that B7H3-directed CAR-T cells efficiently killed GC tumor cells. In addition, we found that B7H3 is correlated with tumor cell stemness, and anti-B7H3 CAR-T can simultaneously target stem cell-like GC cells to improve the treatment outcome. Conclusions Our study indicates that B7H3 is an attractive target for GC therapy, and B7H3 has high potential for clinical application. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02471-8.
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Affiliation(s)
- Fengqiang Sun
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, 261000, Shandong, China
| | - Xiaomei Yu
- Department of Obstetrics, Weifang People's Hospital, Weifang, 261000, Shandong, China
| | - Ruixue Ju
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, 261000, Shandong, China
| | - Zhanzhao Wang
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, 261000, Shandong, China
| | - Yuhui Wang
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, 261000, Shandong, China.
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Merkel A, Esteller M. Experimental and Bioinformatic Approaches to Studying DNA Methylation in Cancer. Cancers (Basel) 2022; 14:349. [PMID: 35053511 PMCID: PMC8773752 DOI: 10.3390/cancers14020349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/26/2021] [Accepted: 01/06/2022] [Indexed: 02/04/2023] Open
Abstract
DNA methylation is an essential epigenetic mark. Alterations of normal DNA methylation are a defining feature of cancer. Here, we review experimental and bioinformatic approaches to showcase the breadth and depth of information that this epigenetic mark provides for cancer research. First, we describe classical approaches for interrogating bulk DNA from cell populations as well as more recently developed approaches for single cells and multi-Omics. Second, we focus on the computational analysis from primary data processing to the identification of unique methylation signatures. Additionally, we discuss challenges such as sparse data and cellular heterogeneity.
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Affiliation(s)
- Angelika Merkel
- Bioinformatics Unit, Josep Carreras Leukemia Research Institute (IJC), 08916 Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukemia Research Institute (IJC), 08916 Barcelona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
- Institucio Catalana de Recerca Avançats (ICREA), 08010 Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Catalonia, 08017 Barcelona, Spain
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26
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Simonetta F, Bertoni F. An epigenetic signature in CD19-CAR T cells predicts clinical outcome. Trends Cancer 2022; 8:81-82. [PMID: 34972674 DOI: 10.1016/j.trecan.2021.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 10/19/2022]
Abstract
The potential impact of epigenetic profiles on adoptive T cell immunotherapies is currently unknown. In a recent study in the Journal of the National Cancer Institute, Garcia-Prieto et al. show that specific DNA methylation profiles of CD19-CAR T cells are associated with improved clinical outcome of patients with B cell malignancies.
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Affiliation(s)
- Federico Simonetta
- Division of Hematology, Department of Oncology, Geneva University Hospitals, University of Geneva, Geneva, Switzerland; Translational Research Centre in Onco-Haematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland; Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland.
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