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Qiu Y, Xie E, Xu H, Cheng H, Li G. One-carbon metabolism shapes T cell immunity in cancer. Trends Endocrinol Metab 2024:S1043-2760(24)00160-7. [PMID: 38925992 DOI: 10.1016/j.tem.2024.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024]
Abstract
One-carbon metabolism (1CM), comprising folate metabolism and methionine metabolism, serves as an important mechanism for cellular energy provision and the production of vital signaling molecules, including single-carbon moieties. Its regulation is instrumental in sustaining the proliferation of cancer cells and facilitating metastasis; in addition, recent research has shed light on its impact on the efficacy of T cell-mediated immunotherapy. In this review, we consolidate current insights into how 1CM affects T cell activation, differentiation, and functionality. Furthermore, we delve into the strategies for modulating 1CM in both T cells and tumor cells to enhance the efficacy of adoptively transferred T cells, overcome metabolic challenges in the tumor microenvironment (TME), and maximize the benefits of T cell-mediated immunotherapy.
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Affiliation(s)
- Yajing Qiu
- National Key Laboratory of Immunity and Inflammation, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, Jiangsu, China; Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, Jiangsu, China
| | - Ermei Xie
- National Key Laboratory of Immunity and Inflammation, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, Jiangsu, China; Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, Jiangsu, China
| | - Haipeng Xu
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fujian, 350011, China
| | - Hongcheng Cheng
- National Key Laboratory of Immunity and Inflammation, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, Jiangsu, China; Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, Jiangsu, China.
| | - Guideng Li
- National Key Laboratory of Immunity and Inflammation, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, Jiangsu, China; Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, Jiangsu, China.
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3
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Revach OY, Cicerchia AM, Shorer O, Petrova B, Anderson S, Park J, Chen L, Mehta A, Wright SJ, McNamee N, Tal-Mason A, Cattaneo G, Tiwari P, Xie H, Sweere JM, Cheng LC, Sigal N, Enrico E, Miljkovic M, Evans SA, Nguyen N, Whidden ME, Srinivasan R, Spitzer MH, Sun Y, Sharova T, Lawless AR, Michaud WA, Rasmussen MQ, Fang J, Palin CA, Chen F, Wang X, Ferrone CR, Lawrence DP, Sullivan RJ, Liu D, Sachdeva UM, Sen DR, Flaherty KT, Manguso RT, Bod L, Kellis M, Boland GM, Yizhak K, Yang J, Kanarek N, Sade-Feldman M, Hacohen N, Jenkins RW. Disrupting CD38-driven T cell dysfunction restores sensitivity to cancer immunotherapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.579184. [PMID: 38405985 PMCID: PMC10888727 DOI: 10.1101/2024.02.12.579184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
A central problem in cancer immunotherapy with immune checkpoint blockade (ICB) is the development of resistance, which affects 50% of patients with metastatic melanoma1,2. T cell exhaustion, resulting from chronic antigen exposure in the tumour microenvironment, is a major driver of ICB resistance3. Here, we show that CD38, an ecto-enzyme involved in nicotinamide adenine dinucleotide (NAD+) catabolism, is highly expressed in exhausted CD8+ T cells in melanoma and is associated with ICB resistance. Tumour-derived CD38hiCD8+ T cells are dysfunctional, characterised by impaired proliferative capacity, effector function, and dysregulated mitochondrial bioenergetics. Genetic and pharmacological blockade of CD38 in murine and patient-derived organotypic tumour models (MDOTS/PDOTS) enhanced tumour immunity and overcame ICB resistance. Mechanistically, disrupting CD38 activity in T cells restored cellular NAD+ pools, improved mitochondrial function, increased proliferation, augmented effector function, and restored ICB sensitivity. Taken together, these data demonstrate a role for the CD38-NAD+ axis in promoting T cell exhaustion and ICB resistance, and establish the efficacy of CD38 directed therapeutic strategies to overcome ICB resistance using clinically relevant, patient-derived 3D tumour models.
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Affiliation(s)
- Or-Yam Revach
- Mass General Cancer Center, Krantz Family Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Angelina M. Cicerchia
- Mass General Cancer Center, Krantz Family Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ofir Shorer
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Boryana Petrova
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Boston Children’s Hospital, Boston, MA, USA
| | - Seth Anderson
- Mass General Cancer Center, Krantz Family Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joshua Park
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lee Chen
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Arnav Mehta
- Mass General Cancer Center, Krantz Family Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Niamh McNamee
- Harvard Medical School, Boston, MA, USA
- Division of Thoracic Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Aya Tal-Mason
- Harvard Medical School, Boston, MA, USA
- Division of Thoracic Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Giulia Cattaneo
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Payal Tiwari
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hongyan Xie
- Mass General Cancer Center, Krantz Family Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | | | | | | | | | | | | | - Matthew H. Spitzer
- Teiko Bio, Salt Lake City, UT, USA
- Department of Otolaryngology-Head and Neck Cancer, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Yi Sun
- Mass General Cancer Center, Krantz Family Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Tatyana Sharova
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Aleigha R. Lawless
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - William A. Michaud
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Martin Q. Rasmussen
- Mass General Cancer Center, Krantz Family Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacy Fang
- Mass General Cancer Center, Krantz Family Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Claire A. Palin
- Mass General Cancer Center, Krantz Family Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Feng Chen
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Xinhui Wang
- Harvard Medical School, Boston, MA, USA
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Cristina R. Ferrone
- Harvard Medical School, Boston, MA, USA
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
- Department of Surgery, Cedars-Sinai Medical Center Los Angeles, CA, USA
| | - Donald P. Lawrence
- Mass General Cancer Center, Krantz Family Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Ryan J. Sullivan
- Mass General Cancer Center, Krantz Family Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - David Liu
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Uma M. Sachdeva
- Harvard Medical School, Boston, MA, USA
- Division of Thoracic Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Debattama R. Sen
- Mass General Cancer Center, Krantz Family Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Keith T. Flaherty
- Mass General Cancer Center, Krantz Family Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Robert T. Manguso
- Mass General Cancer Center, Krantz Family Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lloyd Bod
- Mass General Cancer Center, Krantz Family Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Manolis Kellis
- Department of Pathology, Boston Children’s Hospital, Boston, MA, USA
| | - Genevieve M. Boland
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Keren Yizhak
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Jiekun Yang
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Naama Kanarek
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Boston Children’s Hospital, Boston, MA, USA
| | - Moshe Sade-Feldman
- Mass General Cancer Center, Krantz Family Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nir Hacohen
- Mass General Cancer Center, Krantz Family Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Russell W. Jenkins
- Mass General Cancer Center, Krantz Family Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Soni J, Chattopadhyay P, Mehta P, Mohite R, Tardalkar K, Joshi M, Pandey R. Dynamics of Whole Transcriptome Analysis (WTA) and Surface markers expression (AbSeq) in Immune Cells of COVID-19 Patients and Recovered captured through Single Cell Genomics. Front Med (Lausanne) 2024; 11:1297001. [PMID: 38357647 PMCID: PMC10864604 DOI: 10.3389/fmed.2024.1297001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/15/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction Single-cell multi-omics studies, such as multidimensional transcriptomics (whole transcriptomic analysis, WTA), and surface marker analysis (antibody sequencing, AbSeq), have turned out to be valuable techniques that offer inaccessible possibilities for single-cell profiling of mRNA, lncRNA, and proteins. Methods We used this technique to understand the dynamics of mRNA and protein-level differences in healthy, COVID-19-infected and recovered individuals using peripheral blood mononuclear cells (PBMCs). Our results demonstrate that compared to mRNA expression, protein abundance is a better indicator of the disease state. Results We demonstrate that compared to mRNA expression, protein abundance is a better indicator of the disease state. We observed high levels of cell identity and regulatory markers, CD3E, CD4, CD8A, CD5, CD7, GITR, and KLRB1 in healthy individuals, whereas markers related to cell activation, CD38, CD28, CD69, CD62L, CD14, and CD16 elevated in the SARS-CoV-2 infected patients at both WTA and AbSeq levels. Curiously, in recovered individuals, there was a high expression of cytokine and chemokine receptors (CCR5, CCR7, CCR4, CXCR3, and PTGRD2). We also observed variations in the expression of markers within cell populations under different states. Discussion Furthermore, our study emphasizes the significance of employing an oligo-based method (AbSeq) that can help in diagnosis, prognosis, and protection from disease/s by identifying cell surface markers that are unique to different cell types or states. It also allows simultaneous study of a vast array of markers, surpassing the constraints of techniques like FACS to query the vast repertoire of proteins.
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Affiliation(s)
- Jyoti Soni
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Partha Chattopadhyay
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priyanka Mehta
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ramakant Mohite
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Kishore Tardalkar
- Department of Stem Cells & Regenerative Medicine, D. Y. Patil Education Society, Kolhapur, India
| | - Meghnad Joshi
- Department of Stem Cells & Regenerative Medicine, D. Y. Patil Education Society, Kolhapur, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Nguyen T, Wei Y, Nakada Y, Chen JY, Zhou Y, Walcott G, Zhang J. Analysis of cardiac single-cell RNA-sequencing data can be improved by the use of artificial-intelligence-based tools. Sci Rep 2023; 13:6821. [PMID: 37100826 PMCID: PMC10133286 DOI: 10.1038/s41598-023-32293-1] [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: 10/04/2022] [Accepted: 03/25/2023] [Indexed: 04/28/2023] Open
Abstract
Single-cell RNA sequencing (scRNAseq) enables researchers to identify and characterize populations and subpopulations of different cell types in hearts recovering from myocardial infarction (MI) by characterizing the transcriptomes in thousands of individual cells. However, the effectiveness of the currently available tools for processing and interpreting these immense datasets is limited. We incorporated three Artificial Intelligence (AI) techniques into a toolkit for evaluating scRNAseq data: AI Autoencoding separates data from different cell types and subpopulations of cell types (cluster analysis); AI Sparse Modeling identifies genes and signaling mechanisms that are differentially activated between subpopulations (pathway/gene set enrichment analysis), and AI Semisupervised Learning tracks the transformation of cells from one subpopulation into another (trajectory analysis). Autoencoding was often used in data denoising; yet, in our pipeline, Autoencoding was exclusively used for cell embedding and clustering. The performance of our AI scRNAseq toolkit and other highly cited non-AI tools was evaluated with three scRNAseq datasets obtained from the Gene Expression Omnibus database. Autoencoder was the only tool to identify differences between the cardiomyocyte subpopulations found in mice that underwent MI or sham-MI surgery on postnatal day (P) 1. Statistically significant differences between cardiomyocytes from P1-MI mice and mice that underwent MI on P8 were identified for six cell-cycle phases and five signaling pathways when the data were analyzed via Sparse Modeling, compared to just one cell-cycle phase and one pathway when the data were analyzed with non-AI techniques. Only Semisupervised Learning detected trajectories between the predominant cardiomyocyte clusters in hearts collected on P28 from pigs that underwent apical resection (AR) on P1, and on P30 from pigs that underwent AR on P1 and MI on P28. In another dataset, the pig scRNAseq data were collected after the injection of CCND2-overexpression Human-induced Pluripotent Stem Cell-derived cardiomyocytes (CCND2hiPSC) into injured P28 pig heart; only the AI-based technique could demonstrate that the host cardiomyocytes increase proliferating by through the HIPPO/YAP and MAPK signaling pathways. For the cluster, pathway/gene set enrichment, and trajectory analysis of scRNAseq datasets generated from studies of myocardial regeneration in mice and pigs, our AI-based toolkit identified results that non-AI techniques did not discover. These different results were validated and were important in explaining myocardial regeneration.
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Affiliation(s)
- Thanh Nguyen
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Yuhua Wei
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Yuji Nakada
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Jake Y Chen
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Yang Zhou
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Gregory Walcott
- Department of Medicine, Cardiovascular Diseases, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Jianyi Zhang
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, 35233, USA.
- Department of Medicine, Cardiovascular Diseases, University of Alabama at Birmingham, Birmingham, AL, 35233, USA.
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, 1670 University Blvd, Volker Hall G094J, Birmingham, AL, 35233, USA.
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