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Qin S, Xie B, Wang Q, Yang R, Sun J, Hu C, Liu S, Tao Y, Xiao D. New insights into immune cells in cancer immunotherapy: from epigenetic modification, metabolic modulation to cell communication. MedComm (Beijing) 2024; 5:e551. [PMID: 38783893 PMCID: PMC11112485 DOI: 10.1002/mco2.551] [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: 10/16/2023] [Revised: 03/24/2024] [Accepted: 04/02/2024] [Indexed: 05/25/2024] Open
Abstract
Cancer is one of the leading causes of death worldwide, and more effective ways of attacking cancer are being sought. Cancer immunotherapy is a new and effective therapeutic method after surgery, radiotherapy, chemotherapy, and targeted therapy. Cancer immunotherapy aims to kill tumor cells by stimulating or rebuilding the body's immune system, with specific efficiency and high safety. However, only few tumor patients respond to immunotherapy and due to the complex and variable characters of cancer immune escape, the behavior and regulatory mechanisms of immune cells need to be deeply explored from more dimensions. Epigenetic modifications, metabolic modulation, and cell-to-cell communication are key factors in immune cell adaptation and response to the complex tumor microenvironment. They collectively determine the state and function of immune cells through modulating gene expression, changing in energy and nutrient demands. In addition, immune cells engage in complex communication networks with other immune components, which are mediated by exosomes, cytokines, and chemokines, and are pivotal in shaping the tumor progression and therapeutic response. Understanding the interactions and combined effects of such multidimensions mechanisms in immune cell modulation is important for revealing the mechanisms of immunotherapy failure and developing new therapeutic targets and strategies.
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Affiliation(s)
- Sha Qin
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- Department of PathologySchool of Basic Medical ScienceXiangya School of MedicineCentral South UniversityChangshaHunanChina
| | - Bin Xie
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
| | - Qingyi Wang
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- Department of PathologySchool of Basic Medical ScienceXiangya School of MedicineCentral South UniversityChangshaHunanChina
| | - Rui Yang
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- Department of PathologySchool of Basic Medical ScienceXiangya School of MedicineCentral South UniversityChangshaHunanChina
| | - Jingyue Sun
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- Department of PathologySchool of Basic Medical ScienceXiangya School of MedicineCentral South UniversityChangshaHunanChina
| | - Chaotao Hu
- Regenerative Medicine, Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Shuang Liu
- Department of OncologyInstitute of Medical SciencesNational Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangsha, Hunan, China. UniversityChangshaHunanChina
| | - Yongguang Tao
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- NHC Key Laboratory of CarcinogenesisCancer Research Institute and School of Basic MedicineCentral South universityChangshaHunanChina
| | - Desheng Xiao
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- Department of PathologySchool of Basic Medical ScienceXiangya School of MedicineCentral South UniversityChangshaHunanChina
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Hou Q, Wang P, Kong X, Chen J, Yao C, Luo X, Li Y, Jin Z, Wu X. Higher TIGIT+ γδ T CM cells may predict poor prognosis in younger adult patients with non-acute promyelocytic AML. Front Immunol 2024; 15:1321126. [PMID: 38711501 PMCID: PMC11070478 DOI: 10.3389/fimmu.2024.1321126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/19/2024] [Indexed: 05/08/2024] Open
Abstract
Introduction γδ T cells recognize and exert cytotoxicity against tumor cells. They are also considered potential immune cells for immunotherapy. Our previous study revealed that the altered expression of immune checkpoint T-cell immunoreceptor with immunoglobulin and ITIM domain (TIGIT) on γδ T cells may result in immunosuppression and is possibly associated with a poor overall survival in acute myeloid leukemia (AML). However, whether γδ T-cell memory subsets are predominantly involved and whether they have a relationship with clinical outcomes in patients with AML under the age of 65 remain unclear. Methods In this study, we developed a multicolor flow cytometry-based assay to monitor the frequency and distribution of γδ T-cell subsets, including central memory γδ T cells (TCM γδ), effector memory γδ T cells (TEM γδ), and TEM expressing CD45RA (TEMRA γδ), in peripheral blood from 30 young (≤65 years old) patients with newly diagnosed non-acute promyelocytic leukemia (also known as M3) AML (AMLy-DN), 14 young patients with AML in complete remission (AMLy-CR), and 30 healthy individuals (HIs). Results Compared with HIs, patients with AMLy-DN exhibited a significantly higher differentiation of γδ T cells, which was characterized by decreased TCM γδ cells and increased TEMRA γδ cells. A generally higher TIGIT expression was observed in γδ T cells and relative subsets in patients with AMLy-DN, which was partially recovered in patients with AMLy-CR. Furthermore, 17 paired bone marrow from patients with AMLy-DN contained higher percentages of γδ and TIGIT+ γδ T cells and a lower percentage of TCM γδ T cells. Multivariate logistic regression analyses revealed the association of high percentage of TIGIT+ TCM γδ T cells with an increased risk of poor induction chemotherapy response. Conclusions In this study, we investigated the distribution of γδ T cells and their memory subsets in patients with non-M3 AML and suggested TIGIT+ TCM γδ T cells as potential predictive markers of induction chemotherapy response.
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MESH Headings
- Humans
- Receptors, Immunologic/metabolism
- Male
- Female
- Adult
- Middle Aged
- Prognosis
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- Young Adult
- Aged
- Memory T Cells/immunology
- Memory T Cells/metabolism
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/therapy
- Leukemia, Myeloid, Acute/diagnosis
- Immunologic Memory
- Leukemia, Promyelocytic, Acute/immunology
- Leukemia, Promyelocytic, Acute/diagnosis
- Leukemia, Promyelocytic, Acute/mortality
- Immunophenotyping
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Affiliation(s)
- Qi Hou
- Institute of Hematology, Medical Laboratory Center, School of Medicine, Jinan University, Guangzhou, China
| | - Penglin Wang
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China
| | - Xueting Kong
- Institute of Hematology, Medical Laboratory Center, School of Medicine, Jinan University, Guangzhou, China
- Department of Hematology, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, China
| | - Junjie Chen
- Institute of Hematology, Medical Laboratory Center, School of Medicine, Jinan University, Guangzhou, China
| | - Chao Yao
- Institute of Hematology, Medical Laboratory Center, School of Medicine, Jinan University, Guangzhou, China
| | - Xiaodan Luo
- Department of Hematology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yangqiu Li
- Institute of Hematology, Medical Laboratory Center, School of Medicine, Jinan University, Guangzhou, China
- Key Laboratory of Viral Pathogenesis and Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, China
| | - Zhenyi Jin
- Key Laboratory of Viral Pathogenesis and Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, China
- Department of Pathology, School of Medicine, Jinan University, Guangzhou, China
| | - Xiuli Wu
- Institute of Hematology, Medical Laboratory Center, School of Medicine, Jinan University, Guangzhou, China
- Key Laboratory of Viral Pathogenesis and Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, China
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3
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He J, Miao R, Chen Y, Wang H, Liu M. The dual role of regulatory T cells in hepatitis B virus infection and related hepatocellular carcinoma. Immunology 2024; 171:445-463. [PMID: 38093705 DOI: 10.1111/imm.13738] [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: 08/07/2023] [Accepted: 11/27/2023] [Indexed: 03/09/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a major contributor to cancer-related deaths worldwide. Hepatitis B virus (HBV) infection is a major etiologic factor leading to HCC. While there have been significant advancements in controlling HBV replication, achieving a complete cure for HBV-related HCC (HBV-HCC) remains an intricate challenge. HBV persistence is attributed to a myriad of mechanisms, encompassing both innate and adaptive immune responses. Regulatory T cells (Tregs) are pivotal in upholding immune tolerance and modulating excessive immune activation. During HBV infection, Tregs mediate specific T cell suppression, thereby contributing to both persistent infection and the mitigation of liver inflammatory responses. Studies have demonstrated an augmented expression of circulating and intrahepatic Tregs in HBV-HCC, which correlates with impaired CD8+ T cell function. Consequently, Tregs play a dual role in the context of HBV infection and the progression of HBV-HCC. In this comprehensive review, we discuss pertinent studies concerning Tregs in HBV infection, HBV-related cirrhosis and HCC. Furthermore, we summarize Treg responses to antiviral therapy and provide Treg-targeted therapies specific to HBV and HCC.
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Affiliation(s)
- Jinan He
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Rui Miao
- Guangzhou Women and Children Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yao Chen
- Department of Internal Medicine, Northeast Yunnan Regional Central Hospital, Zhaotong, Yunan, China
| | - Han Wang
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Hepato-Biliary-Pancreatic Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mei Liu
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Zhang H, Chen K, Guo K, Tao J, Song L, Ren S, Zhao Y, Teng Z, Qiu W, Wang Z. Multimodal Imaging-Guided Photoimmunotherapy of Pancreatic Cancer by Organosilica Nanomedicine. Adv Healthc Mater 2024; 13:e2302195. [PMID: 37792547 DOI: 10.1002/adhm.202302195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/10/2023] [Indexed: 10/06/2023]
Abstract
Immune checkpoint blockade (ICB) treatments have contributed to substantial clinical progress. However, challenges persist, including inefficient drug delivery and penetration into deep tumor areas, inadequate response to ICB treatments, and potential risk of inflammation due to over-activation of immune cells and uncontrolled release of cytokines following immunotherapy. In response, this study, for the first time, presents a multimodal imaging-guided organosilica nanomedicine (DCCGP) for photoimmunotherapy of pancreatic cancer. The novel DCCGP nanoplatform integrates fluorescence, magnetic resonance, and real-time infrared photothermal imaging, thereby enhancing diagnostic precision and treatment efficacy for pancreatic cancer. In addition, the incorporated copper sulfide nanoparticles (CuS NPs) lead to improved tumor penetration and provide external regulation of immunotherapy via photothermal stimulation. The synergistic immunotherapy effect is realized through the photothermal behavior of CuS NPs, inducing immunogenic cell death and relieving the immunosuppressive tumor microenvironment. Coupling photothermal stimulation with αPD-L1-induced ICB, the platform amplifies the clearance efficiency of tumor cells, achieving an optimized synergistic photoimmunotherapy effect. This study offers a promising strategy for the clinical application of ICB-based combined immunotherapy and presents valuable insights for applications of organosilica in precise tumor immunotherapy and theranostics.
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Affiliation(s)
- Huifeng Zhang
- Department of Radiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Kun Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Kai Guo
- Department of Radiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
| | - Jun Tao
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, Jiangsu National Synergetic Innovation Centre for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Lina Song
- Department of Radiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Shuai Ren
- Department of Radiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Yatong Zhao
- Department of Radiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Zhaogang Teng
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, Jiangsu National Synergetic Innovation Centre for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Wenli Qiu
- Department of Radiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Zhongqiu Wang
- Department of Radiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
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Gao G, Xue Q, He J, Wu M, Jiang Y, Li Q, Zhang Y, Shi W. Single-cell RNA sequencing in double-hit lymphoma: IMPDH2 induces the progression of lymphoma by activating the PI3K/AKT/mTOR signaling pathway. Int Immunopharmacol 2023; 125:111125. [PMID: 37907047 DOI: 10.1016/j.intimp.2023.111125] [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: 07/15/2023] [Revised: 10/14/2023] [Accepted: 10/20/2023] [Indexed: 11/02/2023]
Abstract
BACKGROUND IMPDH2 is the rate-limiting enzyme of the de novo GTP synthesis pathway and has a key role in tumors; however, the specific mechanism underlying IMPDH2 activity in diffuse large B cell lymphoma (DLBCL) is still undetermined. This study aims to explore the potential mechanism of IMPDH2 in DLBCL, and its possible involvement in double-hit lymphoma (DHL), i.e., cases with translocations involving MYC and BCL2 and/or BCL6. METHODS Using single-cell sequencing and bioinformatics analysis to screen for IMPDH2. Exploring the differential expression of IMPDH2 and its correlation with prognosis through multiplexed immunofluorescence analysis. Using CCK8, EdU, clone formation assay, and animal model to analyze biological behavior changes after inhibiting IMPDH2. Explaining the potential mechanism of IMPDH2 in DLBCL by Western blot and multiplexed immunofluorescence. RESULTS Prognostic risk model was constructed by single-cell sequencing, which identified IMPDH2 as a DHL-related gene. IMPDH2 was highly expressed in cell lines and tissues, associated with poor patient prognosis and an independent prognostic factor. In vitro and in vivo experiments showed that IMPDH2 inhibition significantly inhibited DHL cell proliferation. Flow cytometry showed apoptosis and cycle arrest. Western blot results suggested that c-Myc regulated the activation of PI3K/AKT/mTOR signaling pathway by IMPDH2 to promote tumor development in DHL. Moreover, multiplex immunofluorescence revealed decreased T-cell infiltration within the tumor microenvironment exhibiting concurrent high expression of IMPDH2 and PD-L1. CONCLUSIONS Our results suggest that IMPDH2 functions as a tumor-promoting factor in DHL. This finding is expected to generate novel insights into the pathogenesis of these patients, thereby identifying potential therapeutic targets.
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Affiliation(s)
- Guangcan Gao
- Department of Oncology, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong 226001, Jiangsu, China; Nantong University Medical School, 19, Qixiu Road, Nantong 226001, Jiangsu, China; Department of Clinical Biobank & Institute of Oncology, Nantong University Affiliated Hospital, Nantong 226001, Jiangsu, China
| | - Qingfeng Xue
- Department of Oncology, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong 226001, Jiangsu, China; Nantong University Medical School, 19, Qixiu Road, Nantong 226001, Jiangsu, China; Department of Clinical Biobank & Institute of Oncology, Nantong University Affiliated Hospital, Nantong 226001, Jiangsu, China
| | - Jing He
- Department of Oncology, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong 226001, Jiangsu, China; Nantong University Medical School, 19, Qixiu Road, Nantong 226001, Jiangsu, China; Department of Clinical Biobank & Institute of Oncology, Nantong University Affiliated Hospital, Nantong 226001, Jiangsu, China
| | - Meng Wu
- Department of Oncology, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong 226001, Jiangsu, China
| | - Yongning Jiang
- Department of Oncology, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong 226001, Jiangsu, China; Nantong University Medical School, 19, Qixiu Road, Nantong 226001, Jiangsu, China; Department of Clinical Biobank & Institute of Oncology, Nantong University Affiliated Hospital, Nantong 226001, Jiangsu, China
| | - Quanqing Li
- Department of Oncology, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong 226001, Jiangsu, China; Nantong University Medical School, 19, Qixiu Road, Nantong 226001, Jiangsu, China; Department of Clinical Biobank & Institute of Oncology, Nantong University Affiliated Hospital, Nantong 226001, Jiangsu, China
| | - Yaping Zhang
- Nantong University Medical School, 19, Qixiu Road, Nantong 226001, Jiangsu, China; Department of Clinical Biobank & Institute of Oncology, Nantong University Affiliated Hospital, Nantong 226001, Jiangsu, China; Department of Hematology, Affiliated Hospital of Nantong University, 20, Xisi Road, Nantong 226001, Jiangsu, China.
| | - Wenyu Shi
- Department of Oncology, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong 226001, Jiangsu, China; Nantong University Medical School, 19, Qixiu Road, Nantong 226001, Jiangsu, China; Department of Clinical Biobank & Institute of Oncology, Nantong University Affiliated Hospital, Nantong 226001, Jiangsu, China.
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Onrust-van Schoonhoven A, de Bruijn MJW, Stikker B, Brouwer RWW, Braunstahl GJ, van IJcken WFJ, Graf T, Huylebroeck D, Hendriks RW, Stik G, Stadhouders R. 3D chromatin reprogramming primes human memory T H2 cells for rapid recall and pathogenic dysfunction. Sci Immunol 2023; 8:eadg3917. [PMID: 37418545 DOI: 10.1126/sciimmunol.adg3917] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/13/2023] [Indexed: 07/09/2023]
Abstract
Memory T cells provide long-lasting defense responses through their ability to rapidly reactivate, but how they efficiently "recall" an inflammatory transcriptional program remains unclear. Here, we show that human CD4+ memory T helper 2 (TH2) cells carry a chromatin landscape synergistically reprogrammed at both one-dimensional (1D) and 3D levels to accommodate recall responses, which is absent in naive T cells. In memory TH2 cells, recall genes were epigenetically primed through the maintenance of transcription-permissive chromatin at distal (super)enhancers organized in long-range 3D chromatin hubs. Precise transcriptional control of key recall genes occurred inside dedicated topologically associating domains ("memory TADs"), in which activation-associated promoter-enhancer interactions were preformed and exploited by AP-1 transcription factors to promote rapid transcriptional induction. Resting memory TH2 cells from patients with asthma showed premature activation of primed recall circuits, linking aberrant transcriptional control of recall responses to chronic inflammation. Together, our results implicate stable multiscale reprogramming of chromatin organization as a key mechanism underlying immunological memory and dysfunction in T cells.
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Affiliation(s)
- Anne Onrust-van Schoonhoven
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Marjolein J W de Bruijn
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Bernard Stikker
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Rutger W W Brouwer
- Center for Biomics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Gert-Jan Braunstahl
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Respiratory Medicine, Franciscus Gasthuis and Vlietland, Rotterdam, Netherlands
| | - Wilfred F J van IJcken
- Center for Biomics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Thomas Graf
- Centre for Genomic Regulation (CRG) and Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Grégoire Stik
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
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7
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Singh SP, Parween F, Edara N, Zhang HH, Chen J, Otaizo-Carrasquero F, Cheng D, Oppenheim NA, Ransier A, Zhu W, Shamsaddini A, Gardina PJ, Darko SW, Singh TP, Douek DC, Myers TG, Farber JM. Human CCR6+ Th Cells Show Both an Extended Stable Gradient of Th17 Activity and Imprinted Plasticity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1700-1716. [PMID: 37093875 PMCID: PMC10463241 DOI: 10.4049/jimmunol.2200874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/20/2023] [Indexed: 04/25/2023]
Abstract
Th17 cells have been investigated in mice primarily for their contributions to autoimmune diseases. However, the pathways of differentiation of Th17 and related Th cells (type 17 cells) and the structure of the type 17 memory population in humans are not well understood; such understanding is critical for manipulating these cells in vivo. By exploiting differences in levels of surface CCR6, we found that human type 17 memory cells, including individual T cell clonotypes, form an elongated continuum of type 17 character along which cells can be driven by increasing RORγt. This continuum includes cells preserved within the memory pool with potentials that reflect the early preferential activation of multiple over single lineages. The phenotypes and epigenomes of CCR6+ cells are stable across cell divisions under noninflammatory conditions. Nonetheless, activation in polarizing and nonpolarizing conditions can yield additional functionalities, revealing, respectively, both environmentally induced and imprinted mechanisms that contribute differentially across the type 17 continuum to yield the unusual plasticity ascribed to type 17 cells.
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Affiliation(s)
- Satya P. Singh
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Farhat Parween
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Nithin Edara
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Hongwei H. Zhang
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Jinguo Chen
- Center for Human Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Francisco Otaizo-Carrasquero
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Debby Cheng
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Nicole A. Oppenheim
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Amy Ransier
- Genome Analysis Core, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Wenjun Zhu
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Amirhossein Shamsaddini
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Paul J. Gardina
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Samuel W. Darko
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Tej Pratap Singh
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Daniel C. Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Timothy G. Myers
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Joshua M. Farber
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
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Zhang J, Lei F, Tan H. The development of CD8 T-cell exhaustion heterogeneity and the therapeutic potentials in cancer. Front Immunol 2023; 14:1166128. [PMID: 37275913 PMCID: PMC10232978 DOI: 10.3389/fimmu.2023.1166128] [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: 02/14/2023] [Accepted: 04/25/2023] [Indexed: 06/07/2023] Open
Abstract
CD8+ T cells are essential lymphocytes with cytotoxic properties for antitumor immunotherapy. However, during chronic infection or tumorigenesis, these cells often become dysfunctional with a gradually depleted ability to release cytokines and the exhibition of reduced cytotoxicity, the state referred to as "T-cell exhaustion" (Tex). This unique state was characterized by the increasing expression of inhibitory checkpoint receptors, and interventions targeting immune checkpoint blockades (ICBs) have been considered as a promising strategy to stimulate T-cell killing. Recent investigations have demonstrated that exhausted T cells not only display functional, metabolic, transcriptional, and epigenetic differences but also comprise a heterogeneous group of cells. In this review, we summarize the current findings on dynamic differentiation process during Tex heterogeneity development in cancer and chronic infection. We discuss how the responses to immunotherapy are determined by these distinct subsets and highlight prospective approaches for improving the efficacy of ICB therapy for cancer by leveraging the heterogeneity of T cells.
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Affiliation(s)
- Junfeng Zhang
- Department of Basic Research, Guangzhou Laboratory, Guangzhou, China
| | - Feifei Lei
- Lab of Liver Disease, Department of Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Huabing Tan
- Lab of Liver Disease, Department of Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China
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9
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Robinson EL, Ameri P, Delrue L, Vanderheyden M, Bartunek J, Altieri P, Heymans S, Heggermont WA. Differential expression of epigenetic modifiers in early and late cardiotoxic heart failure reveals DNA methylation as a key regulator of cardiotoxicity. Front Cardiovasc Med 2023; 10:884174. [PMID: 36970338 PMCID: PMC10034031 DOI: 10.3389/fcvm.2023.884174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 02/20/2023] [Indexed: 03/11/2023] Open
Abstract
BackgroundAnthracycline-induced cardiotoxicity is a well-known serious clinical entity. However, detailed mechanistic insights on how short-term administration leads to late and long-lasting cardiotoxicity, are still largely undiscovered. We hypothesize that chemotherapy provokes a memory effect at the level of epigenomic DNA modifications which subsequently lead to cardiotoxicity even years after cessation of chemotherapy.MethodsWe explored the temporal evolution of epigenetic modifiers in early and late cardiotoxicity due to anthracyclines by means of RNA-sequencing of human endomyocardial left ventricular biopsies and mass spectrometry of genomic DNA. Based on these findings, validation of differentially regulated genes was obtained by performing RT-qPCR. Finally, a proof-of-concept in vitro mechanistic study was performed to dissect some of the mechanistic aspects of epigenetic memory in anthracycline-induced cardiotoxicity.ResultsCorrelation of gene expression between late and early onset cardiotoxicity revealed an R2 value of 0.98, demonstrating a total of 369 differentially expressed genes (DEGs, FDR < 0.05). of which 72% (n = 266) were upregulated, and 28% of genes, (n = 103) downregulated in later as compared to earlier onset cardiotoxicity. Gene ontology analysis showed significant enrichment of genes involved in methyl-CpG DNA binding, chromatin remodeling and regulation of transcription and positive regulation of apoptosis. Differential mRNA expression of genes involved in DNA methylation metabolism were confirmed by RT-qPCR in endomyocardial biopsies. In a larger biopsy cohort, it was shown that Tet2 was more abundantly expressed in cardiotoxicity biopsies vs. control biopsies and vs. non-ischemic cardiomyopathy patients. Moreover, an in vitro study was performed: following short-term doxorubicin treatment, H9c2 cells were cultured and passaged once they reached a confluency of 70%–80%. When compared to vehicle-only treated cells, in doxorubicin-treated cells, three weeks after short term treatment, Nppa, Nppb, Tet1/2 and other genes involved in active DNA demethylation were markedly upregulated. These alterations coincided with a loss of DNA methylation and a gain in hydroxymethylation, reflecting the epigenetic changes seen in the endomyocardial biopsies.ConclusionsShort-term administration of anthracyclines provokes long-lasting epigenetic modifications in cardiomyocytes both in vivo and in vitro, which explain in part the time lapse between the use of chemotherapy and the development of cardiotoxicity and, eventually, heart failure.
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Affiliation(s)
- Emma L. Robinson
- Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Pietro Ameri
- Department of Internal Medicine, University of Genova, Genova, Italy
- Cardiothoracic and Vascular Department, Ospedale Policlinico San Martino – IRCCS Italian Cardiovascular Network, Genova, Italy
| | - Leen Delrue
- Cardiovascular Research Center Aalst, Onze-Lieve-Vrouw Hospital Aalst, Aalst, Belgium
| | - Marc Vanderheyden
- Cardiovascular Research Center Aalst, Onze-Lieve-Vrouw Hospital Aalst, Aalst, Belgium
| | - Jozef Bartunek
- Cardiovascular Research Center Aalst, Onze-Lieve-Vrouw Hospital Aalst, Aalst, Belgium
| | - Paola Altieri
- Department of Internal Medicine, University of Genova, Genova, Italy
- Cardiothoracic and Vascular Department, Ospedale Policlinico San Martino – IRCCS Italian Cardiovascular Network, Genova, Italy
| | - Stephane Heymans
- Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
| | - Ward A. Heggermont
- Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
- Cardiovascular Research Center Aalst, Onze-Lieve-Vrouw Hospital Aalst, Aalst, Belgium
- Correspondence: Ward A. Heggermont
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G9a/GLP inhibition during ex vivo lymphocyte expansion increases in vivo cytotoxicity of engineered T cells against hepatocellular carcinoma. Nat Commun 2023; 14:563. [PMID: 36732506 PMCID: PMC9894856 DOI: 10.1038/s41467-023-36160-5] [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: 12/09/2021] [Accepted: 01/19/2023] [Indexed: 02/04/2023] Open
Abstract
Engineered T cells transiently expressing tumor-targeting receptors are an attractive form of engineered T cell therapy as they carry no risk of insertional mutagenesis or long-term adverse side-effects. However, multiple rounds of treatment are often required, increasing patient discomfort and cost. To mitigate this, we sought to improve the antitumor activity of transient engineered T cells by screening a panel of small molecules targeting epigenetic regulators for their effect on T cell cytotoxicity. Using a model for engineered T cells targetting hepatocellular carcinoma, we find that short-term inhibition of G9a/GLP increases T cell antitumor activity in in vitro models and an orthotopic mouse model. G9a/GLP inhibition increases granzyme expression without terminal T cell differentiation or exhaustion and results in specific changes in expression of genes and proteins involved in pro-inflammatory pathways, T cell activation and cytotoxicity.
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11
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Singh SP, Parween F, Edara N, Zhang HH, Chen J, Otaizo-Carrasquero F, Cheng D, Oppenheim NA, Ransier A, Zhu W, Shamsaddini A, Gardina PJ, Darko SW, Singh TP, Douek DC, Myers TG, Farber JM. Human CCR6 + Th cells show both an extended stable gradient of Th17 activity and imprinted plasticity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522630. [PMID: 36789418 PMCID: PMC9928045 DOI: 10.1101/2023.01.05.522630] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Th17 cells have been investigated in mice primarily for their contributions to autoimmune diseases. However, the pathways of differentiation of Th17 and related (type 17) cells and the structure of the type 17 memory population in humans are not well understood; such understanding is critical for manipulating these cells in vivo . By exploiting differences in levels of surface CCR6, we found that human type 17 memory cells, including individual T cell clonotypes, form an elongated continuum of type 17 character along which cells can be driven by increasing RORγt. This continuum includes cells preserved within the memory pool with potentials that reflect the early preferential activation of multiple over single lineages. The CCR6 + cells' phenotypes and epigenomes are stable across cell divisions under homeostatic conditions. Nonetheless, activation in polarizing and non-polarizing conditions can yield additional functionalities, revealing, respectively, both environmentally induced and imprinted mechanisms that contribute differentially across the continuum to yield the unusual plasticity ascribed to type 17 cells.
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Affiliation(s)
- Satya P. Singh
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Farhat Parween
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Nithin Edara
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Hongwei H. Zhang
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Jinguo Chen
- Center for Human Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Francisco Otaizo-Carrasquero
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Debby Cheng
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Nicole A. Oppenheim
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Amy Ransier
- Genome Analysis Core, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Wenjun Zhu
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Amirhossein Shamsaddini
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Paul J. Gardina
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Samuel W. Darko
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Tej Pratap Singh
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Daniel C. Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Timothy G. Myers
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Joshua M. Farber
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
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12
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Zhang Z, Butler R, Koestler DC, Bell-Glenn S, Warrier G, Molinaro AM, Christensen BC, Wiencke JK, Kelsey KT, Salas LA. Comparative analysis of the DNA methylation landscape in CD4, CD8, and B memory lineages. Clin Epigenetics 2022; 14:173. [PMID: 36522672 PMCID: PMC9753273 DOI: 10.1186/s13148-022-01399-0] [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: 05/23/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND There is considerable evidence that epigenetic mechanisms and DNA methylation are critical drivers of immune cell lineage differentiation and activation. However, there has been limited coordinated investigation of common epigenetic pathways among cell lineages. Further, it remains unclear if long-lived memory cell subtypes differentiate distinctly by cell lineages. RESULTS We used the Illumina EPIC array to investigate the consistency of DNA methylation in B cell, CD4 T, and CD8 T naïve and memory cells states. In the process of naïve to memory activation across the three lineages, we identify considerable shared epigenetic regulation at the DNA level for immune memory generation. Further, in central to effector memory differentiation, our analyses revealed specific CpG dinucleotides and genes in CD4 T and CD8 T cells with DNA methylation changes. Finally, we identified unique DNA methylation patterns in terminally differentiated effector memory (TEMRA) CD8 T cells compared to other CD8 T memory cell subtypes. CONCLUSIONS Our data suggest that epigenetic alterations are widespread and essential in generating human lymphocyte memory. Unique profiles are involved in methylation changes that accompany memory genesis in the three subtypes of lymphocytes.
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Affiliation(s)
- Ze Zhang
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Rondi Butler
- Department of Epidemiology, Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Devin C Koestler
- Department of Biostatistics and Data Science, University of Kansas Cancer Center, Kansas City, KS, USA
| | - Shelby Bell-Glenn
- Department of Biostatistics and Data Science, University of Kansas Cancer Center, Kansas City, KS, USA
| | - Gayathri Warrier
- Department of Neurosurgery, University of California, San Francisco, San Francisco, CA, USA
| | - Annette M Molinaro
- Department of Neurosurgery, University of California, San Francisco, San Francisco, CA, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - John K Wiencke
- Department of Neurosurgery, University of California, San Francisco, San Francisco, CA, USA
| | - Karl T Kelsey
- Department of Epidemiology, Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
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13
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Akbari B, Hosseini Z, Shahabinejad P, Ghassemi S, Mirzaei HR, O'Connor RS. Metabolic and epigenetic orchestration of (CAR) T cell fate and function. Cancer Lett 2022; 550:215948. [DOI: 10.1016/j.canlet.2022.215948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/20/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022]
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Li F, Liu H, Zhang D, Ma Y, Zhu B. Metabolic plasticity and regulation of T cell exhaustion. Immunology 2022; 167:482-494. [DOI: 10.1111/imm.13575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/06/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Fei Li
- Gansu Provincial Key Laboratory of Evidence‐Based Medicine and Clinical Translation & Lanzhou Center for Tuberculosis Research, Institute of Pathogen Biology, School of Basic Medical Sciences Lanzhou University Lanzhou China
| | - Huiling Liu
- Department of gynecology and obstetrics Gansu Provincial Hospital Lanzhou China
| | - Dan Zhang
- Gansu Provincial Key Laboratory of Evidence‐Based Medicine and Clinical Translation & Lanzhou Center for Tuberculosis Research, Institute of Pathogen Biology, School of Basic Medical Sciences Lanzhou University Lanzhou China
| | - Yanlin Ma
- Gansu Provincial Key Laboratory of Evidence‐Based Medicine and Clinical Translation & Lanzhou Center for Tuberculosis Research, Institute of Pathogen Biology, School of Basic Medical Sciences Lanzhou University Lanzhou China
| | - Bingdong Zhu
- Gansu Provincial Key Laboratory of Evidence‐Based Medicine and Clinical Translation & Lanzhou Center for Tuberculosis Research, Institute of Pathogen Biology, School of Basic Medical Sciences Lanzhou University Lanzhou China
- State Key Laboratory of Veterinary Etiological Biology, School of Veterinary Medicine and Biosafety Lanzhou University Lanzhou China
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15
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DNA Methylome Mapping Identifies Epigenetic Abnormalities in Intestinal Lymphocyte Regulation in Human Necrotizing Enterocolitis. Dig Dis Sci 2022; 67:4434-4443. [PMID: 34846677 DOI: 10.1007/s10620-021-07314-6] [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: 04/13/2021] [Accepted: 11/02/2021] [Indexed: 12/09/2022]
Abstract
BACKGROUND Epigenetic changes occur in response to environmental factors during the pathogenesis of necrotizing enterocolitis (NEC) in animal models, but the DNA methylation signature in human patients with NEC has not been examined. AIM To illustrate the signature and function of DNA methylation in the intestine of human NEC. METHODS DNA methyltransferases (DNMTs) were compared between intestinal tissue with NEC and control. Genome-wide DNA methylation was analyzed by reduced representation bisulfite sequencing (RRBS). The biological functions of the potential methylation regulated genes were analyzed by Gene Ontology. Gene methylation and expression were confirmed by bisulfite genomic sequencing (BGS) and RT-qPCR. RESULTS By screening the expression of DNMTs, we identified a marked reduction in DNMT3A at both the mRNA and protein levels in NEC. Genome-wide variation of DNA methylation was detected in NEC lesions. The CG methylation level in almost all unique regions except CpG islands (CGIs) was lower in NEC compared with control. A total of 287 differentially methylated regions (DMRs) were identified across the whole genome in NEC, 123 of them are located on the CGI in the promoter. The DMR-associated genes were linked to intestinal epithelial permeability, platelet aggregation, and lymphocyte proliferation. Four genes (ZNF335, MPL, RASAL3, and KDM6A) with roles in the regulation of lymphocytes that may predispose the intestine to imbalanced immune processes were further confirmed to be hypermethylated and transcriptionally downregulated. CONCLUSIONS These findings underscore the novel relationship between epigenetic changes and lymphocyte regulation in human NEC, which may have potential diagnostic and therapeutic relevance for NEC.
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Swati, Rishi P, Chadha VD. Understanding the Epigenetic Mechanisms in SARS CoV-2 Infection and Potential Therapeutic Approaches. Virus Res 2022; 318:198853. [PMID: 35777502 PMCID: PMC9236910 DOI: 10.1016/j.virusres.2022.198853] [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: 02/16/2022] [Revised: 06/14/2022] [Accepted: 06/26/2022] [Indexed: 11/29/2022]
Abstract
COVID-19 pandemic caused by the Severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2) has inflicted a global health challenge. Although the overwhelming escalation of mortality seen during the initial phase of the pandemic has reduced, emerging variants of SARS-CoV-2 continue to impact communities worldwide. Several studies have highlighted the association of gene specific epigenetic modifications in host cells with the pathogenesis and severity of the disease. Therefore, alongside the investigations into the virology and pathogenesis of SARS-CoV-2 infection, understanding the epigenetic mechanisms related to the disease is crucial for the rational design of effective targeted therapies. Here, we discuss the interaction of SARS-CoV-2 with the various epigenetic regulators and their subsequent contribution to the risk of disease severity and dysfunctional immune responses. Finally, we also highlight the use of epigenetically targeted drugs for the potential therapeutic interventions capable of eliminating viral infection and/or build effective immunity against it.
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Affiliation(s)
- Swati
- Center for Nuclear Medicine (U.I.E.A.S.T), South Campus, Panjab University, Sector 25, Chandigarh, India-160014.
| | - Praveen Rishi
- Department of Microbiology, South Campus, Panjab University, Sector 25, Chandigarh, India-160014.
| | - Vijayta D Chadha
- Center for Nuclear Medicine (U.I.E.A.S.T), South Campus, Panjab University, Sector 25, Chandigarh, India-160014.
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Li S, Zhu C, Zhou X, Chen L, Bo X, Shen Y, Guan X, Han X, Shan D, Sun L, Chen Y, Xu H, Yue W. Engineering ROS-Responsive Bioscaffolds for Disrupting Myeloid Cell-Driven Immunosuppressive Niche to Enhance PD-L1 Blockade-Based Postablative Immunotherapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104619. [PMID: 35156339 PMCID: PMC9008797 DOI: 10.1002/advs.202104619] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 01/18/2022] [Indexed: 02/06/2023]
Abstract
The existence of inadequate ablation remains an important cause of treatment failure for loco-regional ablation therapies. Here, using a preclinical model, it is reported that inadequate microwave ablation (iMWA) induces immunosuppressive niche predominated by myeloid cells. The gene signature of ablated tumor presented by transcriptome analyses is highly correlated with immune checkpoint blocking (ICB) resistance. Thus, an in situ scaffold with synergistic delivery of IPI549 and anti-programmed death-ligand 1 blocking antibody (aPDL1) for postablative cancer immunotherapy is designed and engineered, in which IPI549 capable of targeting myeloid cells could disrupt the immunosuppressive niche and subsequently improve ICB-mediated antitumor immune response. Based on five mouse cancer models, it is demonstrated that this biomaterial system (aPDL1&IPI549@Gel) could mimic a "hot" tumor-immunity niche to inhibit tumor progression and metastasis, and protect cured mice against tumor rechallenge. This work enables a new standard-of-care paradigm for the immunotherapy of myeloid cells-mediated "cold" tumors after loco-regional inadequate practices.
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Affiliation(s)
- Shaoyue Li
- Department of Medical UltrasoundShanghai Tenth People's HospitalUltrasound Research and Education InstituteSchool of MedicineTongji UniversityShanghai Engineering Research Center of Ultrasound Diagnosis and TreatmentNational Clinical Research Center of Interventional MedicineShanghai200072P. R. China
- Department of In‐patient UltrasoundThe Second Affiliated HospitalHarbin Medical UniversityHarbin150001P. R. China
| | - Chunyan Zhu
- Department of Medical UltrasoundShanghai Tenth People's HospitalUltrasound Research and Education InstituteSchool of MedicineTongji UniversityShanghai Engineering Research Center of Ultrasound Diagnosis and TreatmentNational Clinical Research Center of Interventional MedicineShanghai200072P. R. China
| | - Xianli Zhou
- Department of In‐patient UltrasoundThe Second Affiliated HospitalHarbin Medical UniversityHarbin150001P. R. China
| | - Liang Chen
- Department of GastroenterologyShanghai Tenth People's HospitalTongji University School of MedicineShanghai200072P. R. China
| | - Xiaowan Bo
- Department of Medical UltrasoundShanghai Tenth People's HospitalUltrasound Research and Education InstituteSchool of MedicineTongji UniversityShanghai Engineering Research Center of Ultrasound Diagnosis and TreatmentNational Clinical Research Center of Interventional MedicineShanghai200072P. R. China
| | - Yuting Shen
- Department of Medical UltrasoundShanghai Tenth People's HospitalUltrasound Research and Education InstituteSchool of MedicineTongji UniversityShanghai Engineering Research Center of Ultrasound Diagnosis and TreatmentNational Clinical Research Center of Interventional MedicineShanghai200072P. R. China
| | - Xin Guan
- Department of Medical UltrasoundShanghai Tenth People's HospitalUltrasound Research and Education InstituteSchool of MedicineTongji UniversityShanghai Engineering Research Center of Ultrasound Diagnosis and TreatmentNational Clinical Research Center of Interventional MedicineShanghai200072P. R. China
| | - Xiaoxia Han
- Department of Medical UltrasoundShanghai Tenth People's HospitalUltrasound Research and Education InstituteSchool of MedicineTongji UniversityShanghai Engineering Research Center of Ultrasound Diagnosis and TreatmentNational Clinical Research Center of Interventional MedicineShanghai200072P. R. China
| | - Dandan Shan
- Department of Medical UltrasoundShanghai Tenth People's HospitalUltrasound Research and Education InstituteSchool of MedicineTongji UniversityShanghai Engineering Research Center of Ultrasound Diagnosis and TreatmentNational Clinical Research Center of Interventional MedicineShanghai200072P. R. China
| | - Liping Sun
- Department of Medical UltrasoundShanghai Tenth People's HospitalUltrasound Research and Education InstituteSchool of MedicineTongji UniversityShanghai Engineering Research Center of Ultrasound Diagnosis and TreatmentNational Clinical Research Center of Interventional MedicineShanghai200072P. R. China
| | - Yu Chen
- Department of Medical UltrasoundShanghai Tenth People's HospitalUltrasound Research and Education InstituteSchool of MedicineTongji UniversityShanghai Engineering Research Center of Ultrasound Diagnosis and TreatmentNational Clinical Research Center of Interventional MedicineShanghai200072P. R. China
- Materdicine LabSchool of Life SciencesShanghai UniversityShanghai200444P. R. China
| | - Huixiong Xu
- Department of Medical UltrasoundShanghai Tenth People's HospitalUltrasound Research and Education InstituteSchool of MedicineTongji UniversityShanghai Engineering Research Center of Ultrasound Diagnosis and TreatmentNational Clinical Research Center of Interventional MedicineShanghai200072P. R. China
- Department of UltrasoundZhongshan HospitalFudan UniversityShanghai200032P. R. China
| | - Wenwen Yue
- Department of Medical UltrasoundShanghai Tenth People's HospitalUltrasound Research and Education InstituteSchool of MedicineTongji UniversityShanghai Engineering Research Center of Ultrasound Diagnosis and TreatmentNational Clinical Research Center of Interventional MedicineShanghai200072P. R. China
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Rah B, Rather RA, Bhat GR, Baba AB, Mushtaq I, Farooq M, Yousuf T, Dar SB, Parveen S, Hassan R, Mohammad F, Qassim I, Bhat A, Ali S, Zargar MH, Afroze D. JAK/STAT Signaling: Molecular Targets, Therapeutic Opportunities, and Limitations of Targeted Inhibitions in Solid Malignancies. Front Pharmacol 2022; 13:821344. [PMID: 35401182 PMCID: PMC8987160 DOI: 10.3389/fphar.2022.821344] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/14/2022] [Indexed: 12/24/2022] Open
Abstract
JAK/STAT signaling pathway is one of the important regulatory signaling cascades for the myriad of cellular processes initiated by various types of ligands such as growth factors, hormones, and cytokines. The physiological processes regulated by JAK/STAT signaling are immune regulation, cell proliferation, cell survival, apoptosis and hematopoiesis of myeloid and non-myeloid cells. Dysregulation of JAK/STAT signaling is reported in various immunological disorders, hematological and other solid malignancies through various oncogenic activation mutations in receptors, downstream mediators, and associated transcriptional factors such as STATs. STATs typically have a dual role when explored in the context of cancer. While several members of the STAT family are involved in malignancies, however, a few members which include STAT3 and STAT5 are linked to tumor initiation and progression. Other STAT members such as STAT1 and STAT2 are pivotal for antitumor defense and maintenance of an effective and long-term immune response through evolutionarily conserved programs. The effects of JAK/STAT signaling and the persistent activation of STATs in tumor cell survival; proliferation and invasion have made the JAK/STAT pathway an ideal target for drug development and cancer therapy. Therefore, understanding the intricate JAK/STAT signaling in the pathogenesis of solid malignancies needs extensive research. A better understanding of the functionally redundant roles of JAKs and STATs may provide a rationale for improving existing cancer therapies which have deleterious effects on normal cells and to identifying novel targets for therapeutic intervention in solid malignancies.
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Maimaiti A, Aili Y, Turhon M, Kadeer K, Aikelamu P, Wang Z, Niu W, Aisha M, Kasimu M, Wang Y, Wang Z. Modification Patterns of DNA Methylation-Related lncRNAs Regulating Genomic Instability for Improving the Clinical Outcomes and Tumour Microenvironment Characterisation of Lower-Grade Gliomas. Front Mol Biosci 2022; 9:844973. [PMID: 35359593 PMCID: PMC8960387 DOI: 10.3389/fmolb.2022.844973] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/24/2022] [Indexed: 12/16/2022] Open
Abstract
Background: DNA methylation is an important epigenetic modification that affects genomic instability and regulates gene expression. Long non-coding RNAs (lncRNAs) modulate gene expression by interacting with chromosomal modifications or remodelling factors. It is urgently needed to evaluate the effects of DNA methylation-related lncRNAs (DMlncRNAs) on genome instability and further investigate the mechanism of action of DMlncRNAs in mediating the progression of lower-grade gliomas (LGGs) and their impact on the immune microenvironment.Methods: LGG transcriptome data, somatic mutation profiles and clinical features analysed in the present study were obtained from the CGGA, GEO and TCGA databases. Univariate, multivariate Cox and Lasso regression analyses were performed to establish a DMlncRNA signature. The KEGG and GO analyses were performed to screen for pathways and biological functions associated with key genes. The ESTIMATE and CIBERSORT algorithms were used to determine the level of immune cells in LGGs and the immune microenvironment fraction. In addition, DMlncRNAs were assessed using survival analysis, ROC curves, correlation analysis, external validation, independent prognostic analysis, clinical stratification analysis and qRT-PCR.Results: We identified five DMlncRNAs with prognostic value for LGGs and established a prognostic signature using them. The Kaplan–Meier analysis revealed 10-years survival rate of 10.10% [95% confidence interval (CI): 3.27–31.40%] in high-risk patients and 57.28% (95% CI: 43.17–76.00%) in low-risk patients. The hazard ratio (HR) and 95% CI of risk scores were 1.013 and 1.009–1.017 (p < 0.001), respectively, based on the univariate Cox regression analysis and 1.009 and 1.004–1.013 (p < 0.001), respectively, based on the multivariate Cox regression analysis. Therefore, the five-lncRNAs were identified as independent prognostic markers for patients with LGGs. Furthermore, GO and KEGG analyses revealed that these lncRNAs are involved in the prognosis and tumorigenesis of LGGs by regulating cancer pathways and DNA methylation.Conclusion: The findings of the study provide key information regarding the functions of lncRNAs in DNA methylation and reveal that DNA methylation can regulate tumour progression through modulation of the immune microenvironment and genomic instability. The identified prognostic lncRNAs have high potential for clinical grouping of patients with LGGs to ensure effective treatment and management.
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Affiliation(s)
- Aierpati Maimaiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yirizhati Aili
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Mirzat Turhon
- Department of Neurointerventional Surgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Department of Neurointerventional Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Kaheerman Kadeer
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Paziliya Aikelamu
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zhitao Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Weiwei Niu
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Maimaitili Aisha
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Maimaitijiang Kasimu
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yongxin Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Yongxin Wang, ; Zengliang Wang,
| | - Zengliang Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Yongxin Wang, ; Zengliang Wang,
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20
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Abstract
Vaccination affords protection from disease by activating pathogen-specific immune cells and facilitating the development of persistent immunologic memory toward the vaccine-specific pathogen. Current vaccine regimens are often based on the efficiency of the acute immune response, and not necessarily on the generation of memory cells, in part because the mechanisms underlying the development of efficient immune memory remain incompletely understood. This Review describes recent advances in defining memory T cell metabolism and how metabolism of these cells might be altered in patients affected by mitochondrial diseases or metabolic syndrome, who show higher susceptibility to recurrent infections and higher rates of vaccine failure. It discusses how this new understanding could add to the way we think about immunologic memory, vaccine development, and cancer immunotherapy.
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Affiliation(s)
- Mauro Corrado
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Erika L Pearce
- Department of Oncology, The Bloomberg~Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, Maryland, USA
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21
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Dutta A, Venkataganesh H, Love PE. New Insights into Epigenetic Regulation of T Cell Differentiation. Cells 2021; 10:cells10123459. [PMID: 34943965 PMCID: PMC8700096 DOI: 10.3390/cells10123459] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022] Open
Abstract
Immature CD4− CD8− thymocytes progress through several developmental steps in the thymus, ultimately emerging as mature CD4+ (helper) or CD8+ (cytotoxic) T cells. Activation of naïve CD4+ and CD8+ T cells in the presence of specific cytokines results in the induction of transcriptional programs that result in their differentiation into effector or memory cells and in the case of CD4+ T cells, the adoption of distinct T-helper fates. Previous studies have shown that histone modification and DNA methylation play important roles in each of these events. More recently, the roles of specific epigenetic regulators in T cell differentiation have been clarified. The identification of the epigenetic modifications and modifiers that control mature T cell differentiation and specification has also provided further insights into how dysregulation of these processes can lead to cancer or autoimmune diseases. In this review, we summarize recent findings that have provided new insights into epigenetic regulation of T cell differentiation in both mice and humans.
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Affiliation(s)
- Avik Dutta
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (A.D.); (H.V.)
| | - Harini Venkataganesh
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (A.D.); (H.V.)
- Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Paul E. Love
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (A.D.); (H.V.)
- Correspondence:
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22
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Genetic ablation of PRDM1 in antitumor T cells enhances therapeutic efficacy of adoptive immunotherapy. Blood 2021; 139:2156-2172. [PMID: 34861037 DOI: 10.1182/blood.2021012714] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/23/2021] [Indexed: 11/20/2022] Open
Abstract
Adoptive cancer immunotherapy can induce objective clinical efficacy in patients with advanced cancer; however, a sustained response is achieved in a minority of cases. The persistence of infused T cells is an essential determinant of a durable therapeutic response. Antitumor T cells undergo a genome-wide remodeling of the epigenetic architecture upon repeated antigen encounters, which inevitably induces progressive T-cell differentiation and the loss of longevity. In this study, we identified PR domain zinc finger protein 1 (PRDM1) i.e., Blimp-1, as a key epigenetic gene associated with terminal T-cell differentiation. The genetic knockout of PRDM1 by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) supported the maintenance of an early memory phenotype and polyfunctional cytokine secretion in repeatedly stimulated chimeric antigen receptor (CAR)-engineered T cells. PRDM1 disruption promoted the expansion of less differentiated memory CAR-T cells in vivo, which enhanced T-cell persistence and improved therapeutic efficacy in multiple tumor models. Mechanistically, PRDM1-ablated T cells displayed enhanced chromatin accessibility of the genes that regulate memory formation, thereby leading to the acquisition of gene expression profiles representative of early memory T cells. PRDM1 knockout also facilitated maintaining an early memory phenotype and cytokine polyfunctionality in T-cell receptor-engineered T cells as well as tumor-infiltrating lymphocytes. In other words, targeting PRDM1 enabled the generation of superior antitumor T cells, which is potentially applicable to a wide range of adoptive cancer immunotherapies.
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23
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Mueller K, Saha K. Single Cell Technologies to Dissect Heterogenous Immune Cell Therapy Products. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021; 20:100343. [PMID: 34957355 PMCID: PMC8693636 DOI: 10.1016/j.cobme.2021.100343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Single cell tools have dramatically transformed the life sciences; concurrently, autologous and allogeneic immune cell therapies have recently entered the clinic. Here we discuss methods, applications, and considerations for single cell technologies in the context of immune cell manufacturing. Molecular heterogeneity can be profiled at the level of the genome, epigenome, transcriptome, proteome, metabolome, and antigen receptor repertoire, in isolation or in tandem through multi-omic approaches. Such data inform heterogeneity within cell products and can be linked to potency readouts and clinical data, with the ultimate goal of identifying Critical Quality Attributes to predict patient outcomes. Non-destructive approaches hold promise for monitoring cell state and analyzing the impacts of gene edits within engineered products. Destructive omics approaches could be combined with non-destructive technologies to predict therapeutic potency. These technologies are poised to redefine cell manufacturing toward rapid, cost-effective, and high-throughput methods to detect and respond to dynamic cell states.
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Affiliation(s)
- Katherine Mueller
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - Krishanu Saha
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
- Grainger Institute for Engineering, University of Wisconsin-Madison, Madison, Wisconsin
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24
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Arslan E, Schulz J, Rai K. Machine Learning in Epigenomics: Insights into Cancer Biology and Medicine. Biochim Biophys Acta Rev Cancer 2021; 1876:188588. [PMID: 34245839 PMCID: PMC8595561 DOI: 10.1016/j.bbcan.2021.188588] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/29/2021] [Accepted: 07/02/2021] [Indexed: 02/01/2023]
Abstract
The recent deluge of genome-wide technologies for the mapping of the epigenome and resulting data in cancer samples has provided the opportunity for gaining insights into and understanding the roles of epigenetic processes in cancer. However, the complexity, high-dimensionality, sparsity, and noise associated with these data pose challenges for extensive integrative analyses. Machine Learning (ML) algorithms are particularly suited for epigenomic data analyses due to their flexibility and ability to learn underlying hidden structures. We will discuss four overlapping but distinct major categories under ML: dimensionality reduction, unsupervised methods, supervised methods, and deep learning (DL). We review the preferred use cases of these algorithms in analyses of cancer epigenomics data with the hope to provide an overview of how ML approaches can be used to explore fundamental questions on the roles of epigenome in cancer biology and medicine.
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Affiliation(s)
- Emre Arslan
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77030, United States of America
| | - Jonathan Schulz
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77030, United States of America
| | - Kunal Rai
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77030, United States of America.
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25
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Cai Z, Xing R, Liu J, Xing F. Commentary: PIRs Mediate Innate Myeloid Cell Memory to Nonself MHC Molecules. Front Immunol 2021; 12:721344. [PMID: 34804010 PMCID: PMC8600524 DOI: 10.3389/fimmu.2021.721344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 09/22/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Zhenlong Cai
- Department of Immunobiology, Institute of Tissue Transplantation and Immunology, Ministry of Education (MOE) Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou, China
| | - Rui Xing
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jing Liu
- Department of Prosthodontics, Jinan University School of Stomatology, Guangzhou, China
| | - Feiyue Xing
- Department of Immunobiology, Institute of Tissue Transplantation and Immunology, Ministry of Education (MOE) Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou, China
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26
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Corley MJ, Pang APS, Rasmussen TA, Tolstrup M, Søgaard OS, Ndhlovu LC. Candidate host epigenetic marks predictive for HIV reservoir size, responsiveness to latency reversal, and viral rebound. AIDS 2021; 35:2269-2279. [PMID: 34482353 PMCID: PMC8563431 DOI: 10.1097/qad.0000000000003065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
OBJECTIVE This study aimed to identify candidate host epigenetic biomarkers predicting latency reversal agents (LRA) efficacy and HIV-1 rebound kinetics during analytical treatment interruption (ATI). DESIGN Retrospective longitudinal epigenetic profiling study from 13 people with HIV (PWH) on virologically suppressive antiretroviral therapy (ART) that participated in a LRA (HDAC inhibitor) clinical trial (NCT01680094) and a subsequent optional ATI to monitor for viral recrudescence after ART cessation. METHODS Genome-wide DNA methylation (DNAm) in purified CD4+ T cells was measured at single-nucleotide resolution using the Infinium MethylationEPIC array. HIV-1 DNA and RNA measures were previously assessed by PCR-based methods and the association of DNAm levels at regulatory sites of the human genome were examined with reservoir size, responsiveness to LRA, and time to viral rebound following ATI. RESULTS A distinct set of 15 candidate DNAm sites in purified CD4+ T cells at baseline pre-LRA and pre-ATI significantly correlated with time to viral rebound. Eight of these DNAm sites occurred in genes linked to HIV-1 replication dynamics including (SEPSECS, cg19113954), (MALT1, cg15968021), (CPT1C, cg14318858), (CRTAM, cg10977115), (B4GALNT4, cg04663285), (IL10, cg16284789), (TFPI2, cg19645693), and (LIFR, cg26437306); with the remaining sites at intergenic regions containing regulatory elements. Moreover, baseline DNAm states related to total HIV-1 DNA levels and the fold change in unspliced cell-associated HIV RNA following LRA treatment. CONCLUSION Preexisting host epigenetic states may determine HIV-1 rebound kinetics and reservoir maintenance. These findings suggest integrating a suite of DNA methylation markers to improve optimal participant selection and drug regimen in future HIV cure clinical trials.
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Affiliation(s)
- Michael J. Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Alina PS Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Thomas A. Rasmussen
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Martin Tolstrup
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Ole S. Søgaard
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
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27
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DNA Methylation and Immune Memory Response. Cells 2021; 10:cells10112943. [PMID: 34831166 PMCID: PMC8616503 DOI: 10.3390/cells10112943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 12/16/2022] Open
Abstract
The generation of memory is a cardinal feature of the adaptive immune response, involving different factors in a complex process of cellular differentiation. This process is essential for protecting the second encounter with pathogens and is the mechanism by which vaccines work. Epigenetic changes play important roles in the regulation of cell differentiation events. There are three types of epigenetic regulation: DNA methylation, histone modification, and microRNA expression. One of these epigenetic changes, DNA methylation, occurs in cytosine residues, mainly in CpG dinucleotides. This brief review aimed to analyse the literature to verify the involvement of DNA methylation during memory T and B cell development. Several studies have highlighted the importance of the DNA methyltransferases, enzymes that catalyse the methylation of DNA, during memory differentiation, maintenance, and function. The methylation profile within different subsets of naïve activated and memory cells could be an interesting tool to help monitor immune memory response.
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28
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Abstract
Immunological memory and exhaustion are fundamental features of adaptive immunity. Recent advances reveal increasing heterogeneity and diversity among CD8 T-cell subsets, resulting in new subsets to annotate and understand. Here, we review our current knowledge of differentiation and maintenance of memory and exhausted CD8 T cells, including phenotypic classification, developmental paths, transcriptional and epigenetic features, and cell intrinsic and extrinsic factors. Additionally, we use this outline to discuss the nomenclature of effector, memory, and exhausted CD8 T cells. Finally, we discuss how new findings about these cell types may impact the therapeutic efficacy and development of immunotherapies targeting effector, memory, and/or exhausted CD8 T cells in chronic infections and cancer.
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Affiliation(s)
- Yuki Muroyama
- Institute for Immunology
- Department of Systems Pharmacology and Translational Therapeutics
| | - E John Wherry
- Institute for Immunology
- Department of Systems Pharmacology and Translational Therapeutics
- Abramson Cancer Center
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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29
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Gonzalez NM, Zou D, Gu A, Chen W. Schrödinger's T Cells: Molecular Insights Into Stemness and Exhaustion. Front Immunol 2021; 12:725618. [PMID: 34512656 PMCID: PMC8427607 DOI: 10.3389/fimmu.2021.725618] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/11/2021] [Indexed: 01/16/2023] Open
Abstract
T cell stemness and exhaustion coexist as two key contrasting phenomena during chronic antigen stimulation, such as infection, transplant, cancer, and autoimmunity. T cell exhaustion refers to the progressive loss of effector function caused by chronic antigen exposure. Exhausted T (TEX) cells highly express multiple inhibitory receptors and exhibit severe defects in cell proliferation and cytokine production. The term T cell stemness describes the stem cell-like behaviors of T cells, including self-renewal, multipotency, and functional persistence. It is well accepted that naïve and some memory T cell subsets have stem cell-like properties. When investigating the exhaustive differentiation of T cells in chronic infection and cancer, recent studies highlighted the stemness of "precursors of exhausted" T (TPEX) cells prior to their terminal differentiation to TEX cells. Clinically successful checkpoint blockades for cancer treatment appear to invigorate antitumor TPEX cells but not TEX cells. Here we discuss the transcriptional and epigenetic regulations of T cell stemness and exhaustion, with a focus on how systems immunology was and will be utilized to define the molecular basis underlying the transition of TPEX to TEX cells. We suggest a "stepwise model" of T cell stemness and exhaustion, in which loss of stemness and exhaustion progression are gradual multi-step processes. We provide perspectives on the research needed to define T cell stemness and exhaustion in the transplantation setting, in which allogenic T cells are also chronically exposed to alloantigens. A better understanding of T cell stemness and exhaustion will shed light on developing novel strategies for immunotherapies.
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Affiliation(s)
- Nancy M Gonzalez
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute & Institute for Academic Medicine, Houston Methodist Hospital, Houston, TX, United States.,College of Medicine, Texas A&M Health Science Center, College Station, TX, United States
| | - Dawei Zou
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute & Institute for Academic Medicine, Houston Methodist Hospital, Houston, TX, United States
| | - Andy Gu
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute & Institute for Academic Medicine, Houston Methodist Hospital, Houston, TX, United States
| | - Wenhao Chen
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute & Institute for Academic Medicine, Houston Methodist Hospital, Houston, TX, United States.,Department of Surgery, Weill Cornell Medicine, Cornell University, New York, NY, United States
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30
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Fowell DJ, Kim M. The spatio-temporal control of effector T cell migration. Nat Rev Immunol 2021; 21:582-596. [PMID: 33627851 PMCID: PMC9380693 DOI: 10.1038/s41577-021-00507-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2021] [Indexed: 02/08/2023]
Abstract
Effector T cells leave the lymph nodes armed with specialized functional attributes. Their antigenic targets may be located anywhere in the body, posing the ultimate challenge: how to efficiently identify the target tissue, navigate through a complex tissue matrix and, ultimately, locate the immunological insult. Recent advances in real-time in situ imaging of effector T cell migratory behaviour have revealed a great degree of mechanistic plasticity that enables effector T cells to push and squeeze their way through inflamed tissues. This process is shaped by an array of 'stop' and 'go' guidance signals including target antigens, chemokines, integrin ligands and the mechanical cues of the inflamed microenvironment. Effector T cells must sense and interpret these competing signals to correctly position themselves to mediate their effector functions for complete and durable responses in infectious disease and malignancy. Tuning T cell migration therapeutically will require a new understanding of this complex decision-making process.
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Affiliation(s)
- Deborah J. Fowell
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute for Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY.,Department of Microbiology and Immunology, Cornell University, Ithaca, NY
| | - Minsoo Kim
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute for Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY
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31
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Miao YD, Mu LJ, Mi DH. Metabolism-associated genes in occurrence and development of gastrointestinal cancer: Latest progress and future prospect. World J Gastrointest Oncol 2021; 13:758-771. [PMID: 34457185 PMCID: PMC8371517 DOI: 10.4251/wjgo.v13.i8.758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/27/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023] Open
Abstract
Gastrointestinal (GI) cancer remains one of the most prevalent cancers in the world. The occurrence and progression of GI cancer involve multiple events. Metabolic reprogramming is one of the hallmarks of cancer and is intricately related to tumorigenesis. Many metabolic genes are involved in the occurrence and development of GI cancer. Research approaches combining tumor genomics and metabolomics are more likely to provide deeper insights into this field. In this paper, we review the roles of metabolism-associated genes, especially those involved in the regulation pathways, in the occurrence and progression of GI cancer. We provide the latest progress and future prospect into the different molecular mechanisms of metabolism-associated genes involved in the occurrence and development of GI cancer.
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Affiliation(s)
- Yan-Dong Miao
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Lin-Jie Mu
- The First Affiliated Hospital, Kunming Medical University, Kunming 650000, Yunnan Province, China
| | - Deng-Hai Mi
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, Gansu Province, China
- Dean’s Office, Gansu Academy of Traditional Chinese Medicine, Lanzhou 730000, Gansu Province, China
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32
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Mapping the landscape of chromatin dynamics during naïve CD4+ T-cell activation. Sci Rep 2021; 11:14101. [PMID: 34238961 PMCID: PMC8266878 DOI: 10.1038/s41598-021-93509-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 06/22/2021] [Indexed: 12/23/2022] Open
Abstract
T-cell activation induces context-specific gene expression programs that promote energy generation and biosynthesis, progression through the cell cycle and ultimately cell differentiation. The aim of this study was to apply the omni ATAC-seq method to characterize the landscape of chromatin changes induced by T-cell activation in mature naïve CD4+ T-cells. Using a well-established ex vivo protocol of canonical T-cell receptor signaling, we generated genome-wide chromatin maps of naïve T-cells from pediatric donors in quiescent or recently activated states. We identified thousands of individual chromatin accessibility peaks that are associated with T-cell activation, the majority of which were annotated intronic and intergenic enhancer regions. A core set of 3268 gene promoters underwent chromatin remodeling and concomitant changes in gene expression in response to activation, and were enriched in multiple pathways controlling cell cycle regulation, metabolism, inflammatory response genes and cell survival. Leukemia inhibitory factor (LIF) was among those factors that gained the highest accessibility and expression, in addition to IL2-STAT5 dependent chromatin remodeling in the T-cell activation response. Using publicly available data we found the chromatin response was far more dynamic at 24-h compared with 72-h post-activation. In total 546 associations were reproduced at both time-points with similar strength of evidence and directionality of effect. At the pathways level, the IL2-STAT5, KRAS signalling and UV response pathways were replicable at both time-points, although differentially modulated from 24 to 72 h post-activation.
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33
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Epigenetic Regulation of Cancer Immune Cells. Semin Cancer Biol 2021; 83:377-383. [PMID: 34182142 DOI: 10.1016/j.semcancer.2021.06.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 05/06/2021] [Accepted: 06/23/2021] [Indexed: 12/17/2022]
Abstract
The epigenetic regulation of immune response involves reversible and heritable changes that do not alter the DNA sequence. Though there have been extensive studies accomplished relating to epigenetic changes in cancer cells, recent focus has been shifted on epigenetic-mediated changes in the immune cells including T cells, Macrophages, Natural Killer cells and anti-tumor immune responses. This review compiles the most relevant and recent literature related to the role of epigenetic mechanisms including DNA methylation and histone modifications in immune cells of wide range of cancers. We also include recent research with respect to role of the most relevant transcription factors that epigenetically control the anti-tumor immune response. Finally, a statement of future direction that promises to look forward for strategies to improve immunotherapy in cancer.
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34
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Lelliott EJ, Kong IY, Zethoven M, Ramsbottom KM, Martelotto LG, Meyran D, Jiang Zhu J, Costacurta M, Kirby L, Sandow JJ, Lim L, Dominguez PM, Todorovski I, Haynes NM, Beavis PA, Neeson PJ, Hawkins ED, McArthur GA, Parish IA, Johnstone RW, Oliaro J, Sheppard KE, Kearney CJ, Vervoort SJ. CDK4/6 inhibition promotes anti-tumor immunity through the induction of T cell memory. Cancer Discov 2021; 11:2582-2601. [PMID: 33990344 DOI: 10.1158/2159-8290.cd-20-1554] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 04/05/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022]
Abstract
Pharmacological inhibitors of cyclin dependent kinases 4 and 6 (CDK4/6) are an approved treatment for hormone receptor-positive breast cancer and are currently under evaluation across hundreds of clinical trials for other cancer types. The clinical success of these inhibitors is largely attributed to well-defined tumor-intrinsic cytostatic mechanisms, while their emerging role as immunomodulatory agents is less understood. Using integrated epigenomic, transcriptomic and proteomic analyses, we demonstrated a novel action of CDK4/6 inhibitors in promoting the phenotypic and functional acquisition of immunological T cell memory. Short-term priming with a CDK4/6 inhibitor promoted long-term endogenous anti-tumor T cell immunity in mice, enhanced the persistence and therapeutic efficacy of chimeric antigen receptor (CAR)-T cells, and induced an RB-dependent T cell phenotype supportive of favorable responses to immune checkpoint blockade in melanoma patients. Together, these mechanistic insights significantly broaden the prospective utility of CDK4/6 inhibitors as clinical tools to boost anti-tumor T cell immunity.
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Affiliation(s)
| | - Isabella Y Kong
- Inflammation, Walter and Eliza Hall Institute of Medical Research
| | | | | | | | | | | | | | - Laura Kirby
- Cancer Research, Peter MacCallum Cancer Centre
| | - Jarrod J Sandow
- Advanced Biology and Technology, The Walter and Eliza Hall Institute
| | - Lydia Lim
- Division of Research, Peter MacCallum Cancer Centre
| | | | | | - Nicole M Haynes
- Sir Peter MacCallum Department of Oncology, Peter MacCallum Cancer Centre
| | - Paul A Beavis
- Cancer Immunology Program, Peter MacCallum Cancer Research Centre
| | - Paul J Neeson
- Cancer Immunology Research, Peter MacCallum Cancer Centre
| | - Edwin D Hawkins
- Immunology Division, Walter and Eliza Hall Institute of Medical Research
| | | | - Ian A Parish
- Cancer Immunology Program, Peter MacCallum Cancer Research Centre
| | | | | | | | | | - Stephin J Vervoort
- Gene Regulation Laboratory, Cancer Therapeutics Program, Peter MacCallum Cancer Centre
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35
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Roy RK, Yadav R, Jain A, Tripathi V, Jain M, Singh S, Prakash H. Yin and yang of immunological memory in controlling infections: Overriding self defence mechanisms. Int Rev Immunol 2021; 41:240-252. [PMID: 33872093 DOI: 10.1080/08830185.2021.1912037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Immunological memory is critical for host immunity and decisive for individual to respond exponentially to previously encountered infection. Both T and B cell memory are known to orchestrate immunological memory with their central and effector memory arms contributing in prolonged immunity/defence mechanisms of host. While central memory helps in maintaining prolonged immunity for a particular infection, effector memory helps in keeping local/seasonal infection in control. In addition to this, generation of long-lived plasma cells is pivotal for generating neutralizing antibodies which can enhance recall and B cell memory to control re-infection. In view of this, scaling up memory response is one of the major objectives for the expected outcome of vaccination. In this line, this review deals with the significance of memory cells, molecular pathways of their development, maintenance, epigenetic regulation and negative regulation in various infections. We have also highlighted the significance of both T and B cell memory responses in the vaccination approaches against range of infections which is not fully explored so far.[Box: see text].
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Affiliation(s)
- Roshan Kumar Roy
- Amity Institute of Virology and Immunology, Amity University, Noida, India
| | - Rakhi Yadav
- Amity Institute of Virology and Immunology, Amity University, Noida, India
| | - Aklank Jain
- Department of Zoology, Central University of Punjab, Bathinda, Punjab, India
| | - Vishwas Tripathi
- School of Biotechnology, Gautam Buddha University, Gautam Buddha Nagar, India
| | - Manju Jain
- Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
| | - Sandhya Singh
- Amity Institute of Physiology and Allied Sciences, Amity University, Noida, India
| | - Hridayesh Prakash
- Amity Institute of Virology and Immunology, Amity University, Noida, India
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36
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Brayshaw LL, Martinez-Fleites C, Athanasopoulos T, Southgate T, Jespers L, Herring C. The role of small molecules in cell and gene therapy. RSC Med Chem 2021; 12:330-352. [PMID: 34046619 PMCID: PMC8130622 DOI: 10.1039/d0md00221f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/25/2020] [Indexed: 01/22/2023] Open
Abstract
Cell and gene therapies have achieved impressive results in the treatment of rare genetic diseases using gene corrected stem cells and haematological cancers using chimeric antigen receptor T cells. However, these two fields face significant challenges such as demonstrating long-term efficacy and safety, and achieving cost-effective, scalable manufacturing processes. The use of small molecules is a key approach to overcome these barriers and can benefit cell and gene therapies at multiple stages of their lifecycle. For example, small molecules can be used to optimise viral vector production during manufacturing or used in the clinic to enhance the resistance of T cell therapies to the immunosuppressive tumour microenvironment. Here, we review current uses of small molecules in cell and gene therapy and highlight opportunities for medicinal chemists to further consolidate the success of cell and gene therapies.
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Affiliation(s)
- Lewis L Brayshaw
- Cell & Gene Therapy Discovery Research, Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
| | - Carlos Martinez-Fleites
- Protein Degradation Group, Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
| | - Takis Athanasopoulos
- Cell & Gene Therapy Discovery Research, Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
| | - Thomas Southgate
- Cell & Gene Therapy Discovery Research, Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
| | - Laurent Jespers
- Cell & Gene Therapy Discovery Research, Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
| | - Christopher Herring
- Cell & Gene Therapy Discovery Research, Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
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37
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Clark M, Kroger CJ, Ke Q, Tisch RM. The Role of T Cell Receptor Signaling in the Development of Type 1 Diabetes. Front Immunol 2021; 11:615371. [PMID: 33603744 PMCID: PMC7884625 DOI: 10.3389/fimmu.2020.615371] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/15/2020] [Indexed: 12/15/2022] Open
Abstract
T cell receptor (TCR) signaling influences multiple aspects of CD4+ and CD8+ T cell immunobiology including thymic development, peripheral homeostasis, effector subset differentiation/function, and memory formation. Additional T cell signaling cues triggered by co-stimulatory molecules and cytokines also affect TCR signaling duration, as well as accessory pathways that further shape a T cell response. Type 1 diabetes (T1D) is a T cell-driven autoimmune disease targeting the insulin producing β cells in the pancreas. Evidence indicates that dysregulated TCR signaling events in T1D impact the efficacy of central and peripheral tolerance-inducing mechanisms. In this review, we will discuss how the strength and nature of TCR signaling events influence the development of self-reactive T cells and drive the progression of T1D through effects on T cell gene expression, lineage commitment, and maintenance of pathogenic anti-self T cell effector function.
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Affiliation(s)
- Matthew Clark
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Charles J Kroger
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Qi Ke
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Roland M Tisch
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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38
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Jiang J, Ahuja S. Addressing Patient to Patient Variability for Autologous CAR T Therapies. J Pharm Sci 2021; 110:1871-1876. [PMID: 33340532 DOI: 10.1016/j.xphs.2020.12.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/10/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022]
Abstract
Chimeric Antigen Receptor (CAR) T cell therapy clinical trials have had unprecedented success in the endeavors to cure cancer patients, particularly those having hematological cancers. As researchers learn more about the ways to make CAR T cells more effective to kill tumor cells, equally important will be understanding the differences between T cells from healthy donors and cancer patients and how these differences could affect ex vivo expansion of T cells during CAR T production. This undoubtedly could be a crucial factor in treating solid tumors, where CAR T cells are needed in significantly higher numbers. As the evidence for significant differences between the patients and healthy donors is compelling, an adaptable and robust production process should be designed to allow manufacture of the required CAR T cells for all cancer patients. Improving the fundamental understanding of the cellular metabolism and accompanying epigenetic and phenotypic changes during in vivo and ex vivo expansion of T cells will be just as important. Such discoveries will provide an invaluable tool box from which actionable knowledge could be drawn for designing an adaptable CAR T production process that is able to absorb the patient-to-patient variation.
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Affiliation(s)
- Jinlin Jiang
- Cell Culture and Fermentation Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD
| | - Sanjeev Ahuja
- Cell Culture and Fermentation Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD.
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39
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Law JC, Koh WH, Budylowski P, Lin J, Yue F, Abe KT, Rathod B, Girard M, Li Z, Rini JM, Mubareka S, McGeer A, Chan AK, Gingras AC, Watts TH, Ostrowski MA. Systematic Examination of Antigen-Specific Recall T Cell Responses to SARS-CoV-2 versus Influenza Virus Reveals a Distinct Inflammatory Profile. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 206:37-50. [PMID: 33208459 PMCID: PMC7750861 DOI: 10.4049/jimmunol.2001067] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022]
Abstract
There is a pressing need for an in-depth understanding of immunity to SARS-CoV-2. In this study, we investigated human T cell recall responses to fully glycosylated spike trimer, recombinant N protein, as well as to S, N, M, and E peptide pools in the early convalescent phase and compared them with influenza-specific memory responses from the same donors. All subjects showed SARS-CoV-2-specific T cell responses to at least one Ag. Both SARS-CoV-2-specific and influenza-specific CD4+ T cell responses were predominantly of the central memory phenotype; however SARS-CoV-2-specific CD4+ T cells exhibited a lower IFN-γ to TNF ratio compared with influenza-specific memory responses from the same donors, independent of disease severity. SARS-CoV-2-specific T cells were less multifunctional than influenza-specific T cells, particularly in severe cases, potentially suggesting exhaustion. Most SARS-CoV-2-convalescent subjects also produced IFN-γ in response to seasonal OC43 S protein. We observed granzyme B+/IFN-γ+, CD4+, and CD8+ proliferative responses to peptide pools in most individuals, with CD4+ T cell responses predominating over CD8+ T cell responses. Peripheral T follicular helper (pTfh) responses to S or N strongly correlated with serum neutralization assays as well as receptor binding domain-specific IgA; however, the frequency of pTfh responses to SARS-CoV-2 was lower than the frequency of pTfh responses to influenza virus. Overall, T cell responses to SARS-CoV-2 are robust; however, CD4+ Th1 responses predominate over CD8+ T cell responses, have a more inflammatory profile, and have a weaker pTfh response than the response to influenza virus within the same donors, potentially contributing to COVID-19 disease.
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Affiliation(s)
- Jaclyn C Law
- Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Wan Hon Koh
- Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario M5S 3H2, Canada
| | - Patrick Budylowski
- Department of Medicine, University of Toronto, Toronto, Ontario M5S 3H2, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jonah Lin
- Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - FengYun Yue
- Department of Medicine, University of Toronto, Toronto, Ontario M5S 3H2, Canada
| | - Kento T Abe
- Lunenfeld-Tanenbaum Research Institute at Mt. Sinai Hospital, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Bhavisha Rathod
- Lunenfeld-Tanenbaum Research Institute at Mt. Sinai Hospital, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Melanie Girard
- Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Zhijie Li
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - James M Rini
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Samira Mubareka
- Sunnybrook Research Institute, Toronto, Ontario M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Allison McGeer
- Lunenfeld-Tanenbaum Research Institute at Mt. Sinai Hospital, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Adrienne K Chan
- Sunnybrook Research Institute, Toronto, Ontario M4N 3M5, Canada
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, Ontario M5S 3H2, Canada; and
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute at Mt. Sinai Hospital, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Tania H Watts
- Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada;
| | - Mario A Ostrowski
- Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario M5S 3H2, Canada
- Keenan Research Centre for Biomedical Science of St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario M5B 1W8, Canada
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40
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Rezinciuc S, Tian Z, Wu S, Hengel S, Pasa-Tolic L, Smallwood HS. Mapping Influenza-Induced Posttranslational Modifications on Histones from CD8+ T Cells. Viruses 2020; 12:v12121409. [PMID: 33302437 PMCID: PMC7762524 DOI: 10.3390/v12121409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 12/25/2022] Open
Abstract
T cell function is determined by transcriptional networks that are regulated by epigenetic programming via posttranslational modifications (PTMs) to histone proteins and DNA. Bottom-up mass spectrometry (MS) can identify histone PTMs, whereas intact protein analysis by MS can detect species missed by bottom-up approaches. We used a novel approach of online two-dimensional liquid chromatography-tandem MS with high-resolution reversed-phase liquid chromatography (RPLC), alternating electron transfer dissociation (ETD) and collision-induced dissociation (CID) on precursor ions to maximize fragmentation of uniquely modified species. The first online RPLC separation sorted histone families, then RPLC or weak cation exchange hydrophilic interaction liquid chromatography (WCX-HILIC) separated species heavily clad in PTMs. Tentative identifications were assigned by matching proteoform masses to predicted theoretical masses that were verified with tandem MS. We used this innovative approach for histone-intact protein PTM mapping (HiPTMap) to identify and quantify proteoforms purified from CD8 T cells after in vivo influenza infection. Activation significantly altered PTMs following influenza infection, histone maps changed as T cells migrated to the site of infection, and T cells responding to secondary infections had significantly more transcription enhancing modifications. Thus, HiPTMap identified and quantified proteoforms and determined changes in CD8 T cell histone PTMs over the course of infection.
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Affiliation(s)
- Svetlana Rezinciuc
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Zhixin Tian
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Si Wu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Shawna Hengel
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Heather S. Smallwood
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
- Children’s Foundation Research Institute, Memphis, TN 38105, USA
- Correspondence: ; Tel.: +1-(901)-448–3068
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41
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Pak B, Schmitt CE, Oh S, Kim JD, Choi W, Han O, Kim M, Kim MJ, Ham HJ, Kim S, Huh TL, Kim JI, Jin SW. Pax9 is essential for granulopoiesis but dispensable for erythropoiesis in zebrafish. Biochem Biophys Res Commun 2020; 534:359-366. [PMID: 33256983 DOI: 10.1016/j.bbrc.2020.11.077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/17/2020] [Indexed: 11/26/2022]
Abstract
Paired Box (Pax) gene family, a group of transcription regulators have been implicated in diverse physiological processes. However, their role during hematopoiesis which generate a plethora of blood cells remains largely unknown. Using a previously reported single cell transcriptomics data, we analyzed the expression of individual Pax family members in hematopoietic cells in zebrafish. We have identified that Pax9, which is an essential regulator for odontogenesis and palatogenesis, is selectively localized within a single cluster of the hematopoietic lineage. To further analyze the function of Pax9 in hematopoiesis, we generated two independent pax9 knock-out mutants using the CRISPR-Cas9 technique. We found that Pax9 appears to be an essential regulator for granulopoiesis but dispensable for erythropoiesis during development, as lack of pax9 selectively decreased the number of neutrophils with a concomitant decrease in the expression level of neutrophil markers. In addition, embryos, where pax9 was functionally disrupted by injecting morpholinos, failed to increase the number of neutrophils in response to pathogenic bacteria, suggesting that Pax9 is not only essential for developmental granulopoiesis but also emergency granulopoiesis. Due to the inability to initiate emergency granulopoiesis, innate immune responses were severely compromised in pax9 morpholino-mediated embryos, increasing their susceptibility and mortality. Taken together, our data indicate that Pax9 is essential for granulopoiesis and promotes innate immunity in zebrafish larvae.
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Affiliation(s)
- Boryeong Pak
- Cell Logistics Research Center and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Chris E Schmitt
- Yale Cardiovascular Research Center and Section of Cardiovascular Medicine, Dept. of Internal Medicine, Yale University School of Medicine, New Haven, CT, 06511, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Sera Oh
- Cell Logistics Research Center and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Jun-Dae Kim
- Yale Cardiovascular Research Center and Section of Cardiovascular Medicine, Dept. of Internal Medicine, Yale University School of Medicine, New Haven, CT, 06511, USA; Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, TX, USA
| | - Woosoung Choi
- Cell Logistics Research Center and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Orjin Han
- Cell Logistics Research Center and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Minjung Kim
- Cell Logistics Research Center and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Myoung-Jin Kim
- School of Life Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Hyung-Jin Ham
- School of Life Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Shanghyeon Kim
- Cell Logistics Research Center and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Tae-Lin Huh
- School of Life Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Jae-Il Kim
- Cell Logistics Research Center and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Suk-Won Jin
- Cell Logistics Research Center and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea; Yale Cardiovascular Research Center and Section of Cardiovascular Medicine, Dept. of Internal Medicine, Yale University School of Medicine, New Haven, CT, 06511, USA.
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42
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Pan X, Zheng L. Epigenetics in modulating immune functions of stromal and immune cells in the tumor microenvironment. Cell Mol Immunol 2020; 17:940-953. [PMID: 32699350 PMCID: PMC7609272 DOI: 10.1038/s41423-020-0505-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022] Open
Abstract
Epigenetic regulation of gene expression in cancer cells has been extensively studied in recent decades, resulting in the FDA approval of multiple epigenetic agents for treating different cancer types. Recent studies have revealed novel roles of epigenetic dysregulation in altering the phenotypes of immune cells and tumor-associated stromal cells, including fibroblasts and endothelial cells. As a result, epigenetic dysregulation of these cells reshapes the tumor microenvironment (TME), changing it from an antitumor environment to an immunosuppressive environment. Here, we review recent studies demonstrating how specific epigenetic mechanisms drive aspects of stromal and immune cell differentiation with implications for the development of solid tumor therapeutics, focusing on the pancreatic ductal adenocarcinoma (PDA) TME as a representative of solid tumors. Due to their unique ability to reprogram the TME into a more immunopermissive environment, epigenetic agents have great potential for sensitizing cancer immunotherapy to augment the antitumor response, as an immunopermissive TME is a prerequisite for the success of cancer immunotherapy but is often not developed with solid tumors. The idea of combining epigenetic agents with cancer immunotherapy has been tested both in preclinical settings and in multiple clinical trials. In this review, we highlight the basic biological mechanisms underlying the synergy between epigenetic therapy and immunotherapy and discuss current efforts to translate this knowledge into clinical benefits for patients.
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Affiliation(s)
- Xingyi Pan
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Pancreatic Cancer Precision Medicine Center of Excellence Program, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Cellular & Molecular Medicine Graduate Training Program, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lei Zheng
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- The Pancreatic Cancer Precision Medicine Center of Excellence Program, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Cellular & Molecular Medicine Graduate Training Program, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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