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Zandhuis ND, Guislain A, Popalzij A, Engels S, Popović B, Turner M, Wolkers MC. Regulation of IFN-γ production by ZFP36L2 in T cells is time-dependent. Eur J Immunol 2024; 54:e2451018. [PMID: 38980256 DOI: 10.1002/eji.202451018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/10/2024]
Abstract
CD8+ T cells kill target cells by releasing cytotoxic molecules and proinflammatory cytokines, such as TNF and IFN-γ. The magnitude and duration of cytokine production are defined by posttranscriptional regulation, and critical regulator herein are RNA-binding proteins (RBPs). Although the functional importance of RBPs in regulating cytokine production is established, the kinetics and mode of action through which RBPs control cytokine production are not well understood. Previously, we showed that the RBP ZFP36L2 blocks the translation of preformed cytokine encoding mRNA in quiescent memory T cells. Here, we uncover that ZFP36L2 regulates cytokine production in a time-dependent manner. T cell-specific deletion of ZFP36L2 (CD4-cre) had no effect on T-cell development or cytokine production during early time points (2-6 h) of T-cell activation. In contrast, ZFP36L2 specifically dampened the production of IFN-γ during prolonged T-cell activation (20-48 h). ZFP36L2 deficiency also resulted in increased production of IFN-γ production in tumor-infiltrating T cells that are chronically exposed to antigens. Mechanistically, ZFP36L2 regulates IFN-γ production at late time points of activation by destabilizing Ifng mRNA in an AU-rich element-dependent manner. Together, our results reveal that ZFP36L2 employs different regulatory nodules in effector and memory T cells to regulate cytokine production.
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Affiliation(s)
- Nordin D Zandhuis
- Sanquin Blood Supply Foundation, Department of Research, T cell differentiation Lab, Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Landsteiner Laboratory, Amsterdam, The Netherlands
- Amsterdam Institute for Infection & Immunity, Cancer center Amsterdam, Cancer Immunology, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Aurélie Guislain
- Sanquin Blood Supply Foundation, Department of Research, T cell differentiation Lab, Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Landsteiner Laboratory, Amsterdam, The Netherlands
- Amsterdam Institute for Infection & Immunity, Cancer center Amsterdam, Cancer Immunology, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Abeera Popalzij
- Sanquin Blood Supply Foundation, Department of Research, T cell differentiation Lab, Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Landsteiner Laboratory, Amsterdam, The Netherlands
- Amsterdam Institute for Infection & Immunity, Cancer center Amsterdam, Cancer Immunology, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Sander Engels
- Sanquin Blood Supply Foundation, Department of Research, T cell differentiation Lab, Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Landsteiner Laboratory, Amsterdam, The Netherlands
- Amsterdam Institute for Infection & Immunity, Cancer center Amsterdam, Cancer Immunology, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Branka Popović
- Sanquin Blood Supply Foundation, Department of Research, T cell differentiation Lab, Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Landsteiner Laboratory, Amsterdam, The Netherlands
- Amsterdam Institute for Infection & Immunity, Cancer center Amsterdam, Cancer Immunology, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Martin Turner
- Immunology Programme, The Babraham Institute, Cambridge, UK
| | - Monika C Wolkers
- Sanquin Blood Supply Foundation, Department of Research, T cell differentiation Lab, Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Landsteiner Laboratory, Amsterdam, The Netherlands
- Amsterdam Institute for Infection & Immunity, Cancer center Amsterdam, Cancer Immunology, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
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2
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Li X, Zhu H, Huang BT, Li X, Kim H, Tan H, Zhang Y, Choi I, Peng J, Xu P, Sun J, Yue Z. RAB12-LRRK2 complex suppresses primary ciliogenesis and regulates centrosome homeostasis in astrocytes. Nat Commun 2024; 15:8434. [PMID: 39343966 PMCID: PMC11439917 DOI: 10.1038/s41467-024-52723-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 09/17/2024] [Indexed: 10/01/2024] Open
Abstract
The leucine-rich repeat kinase 2 (LRRK2) phosphorylates a subset of RAB GTPases, and their phosphorylation levels are elevated by Parkinson's disease (PD)-linked mutations of LRRK2. However, the precise function of the LRRK2-regulated RAB GTPase in the brain remains to be elucidated. Here, we identify RAB12 as a robust LRRK2 substrate in the mouse brain through phosphoproteomics profiling and solve the structure of RAB12-LRRK2 protein complex through Cryo-EM analysis. Mechanistically, RAB12 cooperates with LRRK2 to inhibit primary ciliogenesis and regulate centrosome homeostasis in astrocytes through enhancing the phosphorylation of RAB10 and recruiting RILPL1, while the functions of RAB12 require a direct interaction with LRRK2 and LRRK2 activity. Furthermore, the ciliary and centrosome defects caused by the PD-linked LRRK2-G2019S mutation are prevented by Rab12 deletion in astrocytes. Thus, our study reveals a physiological function of the RAB12-LRRK2 complex in regulating ciliogenesis and centrosome homeostasis. The RAB12-LRRK2 structure offers a guidance in the therapeutic development of PD by targeting the RAB12-LRRK2 interaction.
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Affiliation(s)
- Xingjian Li
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Hanwen Zhu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Bik Tzu Huang
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xianting Li
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Heesoo Kim
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yuanxi Zhang
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Insup Choi
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Pingyi Xu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Ji Sun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Zhenyu Yue
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Parkinson's Disease Neurobiology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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3
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Yao Z, Zeng Y, Liu C, Jin H, Wang H, Zhang Y, Ding C, Chen G, Wu D. Focusing on CD8 + T-cell phenotypes: improving solid tumor therapy. J Exp Clin Cancer Res 2024; 43:266. [PMID: 39342365 PMCID: PMC11437975 DOI: 10.1186/s13046-024-03195-5] [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: 07/31/2024] [Accepted: 09/17/2024] [Indexed: 10/01/2024] Open
Abstract
Vigorous CD8+ T cells play a crucial role in recognizing tumor cells and combating solid tumors. How T cells efficiently recognize and target tumor antigens, and how they maintain the activity in the "rejection" of solid tumor microenvironment, are major concerns. Recent advances in understanding of the immunological trajectory and lifespan of CD8+ T cells have provided guidance for the design of more optimal anti-tumor immunotherapy regimens. Here, we review the newly discovered methods to enhance the function of CD8+ T cells against solid tumors, focusing on optimizing T cell receptor (TCR) expression, improving antigen recognition by engineered T cells, enhancing signal transduction of the TCR-CD3 complex, inducing the homing of polyclonal functional T cells to tumors, reversing T cell exhaustion under chronic antigen stimulation, and reprogramming the energy and metabolic pathways of T cells. We also discuss how to participate in the epigenetic changes of CD8+ T cells to regulate two key indicators of anti-tumor responses, namely effectiveness and persistence.
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Affiliation(s)
- Zhouchi Yao
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Laboratory of Structural Immunology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Yayun Zeng
- Department of Histology and Embryology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Cheng Liu
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Laboratory of Structural Immunology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Huimin Jin
- Department of Histology and Embryology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Hong Wang
- Department of Scientific Research, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, 121001, China
| | - Yue Zhang
- Department of Histology and Embryology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| | - Chengming Ding
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Laboratory of Structural Immunology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| | - Guodong Chen
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Laboratory of Structural Immunology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| | - Daichao Wu
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Laboratory of Structural Immunology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
- Department of Histology and Embryology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
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4
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Maliah A, Santana-Magal N, Parikh S, Gordon S, Reshef K, Sade Y, Khateeb A, Richter A, Gutwillig A, Parikh R, Golan T, Krissi M, Na M, Binshtok G, Manich P, Elkoshi N, Grisaru-Tal S, Zemser-Werner V, Brenner R, Vaknine H, Nizri E, Moyal L, Amitay-Laish I, Rosemberg L, Munitz A, Kronfeld-Schor N, Shifrut E, Kobiler O, Madi A, Geiger T, Carmi Y, Levy C. Crosslinking of Ly6a metabolically reprograms CD8 T cells for cancer immunotherapy. Nat Commun 2024; 15:8354. [PMID: 39333093 PMCID: PMC11437002 DOI: 10.1038/s41467-024-52079-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/25/2024] [Indexed: 09/29/2024] Open
Abstract
T cell inhibitory mechanisms prevent autoimmune reactions, while cancer immunotherapy aims to remove these inhibitory signals. Chronic ultraviolet (UV) exposure attenuates autoimmunity through promotion of poorly understood immune-suppressive mechanisms. Here we show that mice with subcutaneous melanoma are not responsive to anti-PD1 immunotherapy following chronic UV irradiation, given prior to tumor injection, due to the suppression of T cell killing ability in skin-draining lymph nodes. Using mass cytometry and single-cell RNA-sequencing analyzes, we discover that skin-specific, UV-induced suppression of T-cells killing activity is mediated by upregulation of a Ly6ahigh T-cell subpopulation. Independently of the UV effect, Ly6ahigh T cells are induced by chronic type-1 interferon in the tumor microenvironment. Treatment with an anti-Ly6a antibody enhances the anti-tumoral cytotoxic activity of T cells and reprograms their mitochondrial metabolism via the Erk/cMyc axis. Treatment with an anti-Ly6a antibody inhibits tumor growth in mice resistant to anti-PD1 therapy. Applying our findings in humans could lead to an immunotherapy treatment for patients with resistance to existing treatments.
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Affiliation(s)
- Avishai Maliah
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nadine Santana-Magal
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shivang Parikh
- The Ragon Institute of Mass General, MIT and Harvard 600/625 Main Street, Cambridge, MA, USA
| | - Sagi Gordon
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Reshef
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yuval Sade
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Aseel Khateeb
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Alon Richter
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amit Gutwillig
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Roma Parikh
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Golan
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Matan Krissi
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Manho Na
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gal Binshtok
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Paulee Manich
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nadav Elkoshi
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sharon Grisaru-Tal
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Ronen Brenner
- Institute of Oncology, E. Wolfson Medical Center, Holon, Israel
| | - Hananya Vaknine
- Institute of Pathology, E. Wolfson Medical Center, Holon, Israel
| | - Eran Nizri
- Peritoneal Surface Malignancies and Melanoma Unit, Department of Surgery A, Tel-Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Lilach Moyal
- Felsenstein Medical Research Center, Tel-Aviv University and the Division of Dermatology, Rabin Medical Center, Petach Tikva, Israel
| | - Iris Amitay-Laish
- Felsenstein Medical Research Center, Tel-Aviv University and the Division of Dermatology, Rabin Medical Center, Petach Tikva, Israel
| | - Luiza Rosemberg
- School of Zoology, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Ariel Munitz
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Eric Shifrut
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Faculty of Life Sciences, School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel
- Dotan Center for Advanced Therapies, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Oren Kobiler
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Asaf Madi
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Geiger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaron Carmi
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Carmit Levy
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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5
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Kavaka V, Mutschler L, de la Rosa Del Val C, Eglseer K, Gómez Martínez AM, Flierl-Hecht A, Ertl-Wagner B, Keeser D, Mortazavi M, Seelos K, Zimmermann H, Haas J, Wildemann B, Kümpfel T, Dornmair K, Korn T, Hohlfeld R, Kerschensteiner M, Gerdes LA, Beltrán E. Twin study identifies early immunological and metabolic dysregulation of CD8 + T cells in multiple sclerosis. Sci Immunol 2024; 9:eadj8094. [PMID: 39331727 DOI: 10.1126/sciimmunol.adj8094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/05/2024] [Indexed: 09/29/2024]
Abstract
Multiple sclerosis (MS) is an inflammatory neurological disease of the central nervous system with a subclinical phase preceding frank neuroinflammation. CD8+ T cells are abundant within MS lesions, but their potential role in disease pathology remains unclear. Using high-throughput single-cell RNA sequencing and single-cell T cell receptor analysis, we compared CD8+ T cell clones from the blood and cerebrospinal fluid (CSF) of monozygotic twin pairs in which the cotwin had either no or subclinical neuroinflammation (SCNI). We identified peripheral MS-associated immunological and metabolic alterations indicative of an enhanced migratory, proinflammatory, and activated CD8+ T cell phenotype, which was also evident in cotwins with SCNI and in an independent validation cohort of people with MS. Together, our in-depth single-cell analysis indicates a disease-driving proinflammatory role of infiltrating CD8+ T cells and identifies potential immunological and metabolic therapeutic targets in both prodromal and definitive stages of the disease.
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Affiliation(s)
- Vladyslav Kavaka
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Luisa Mutschler
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Clara de la Rosa Del Val
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University of Munich, Martinsried, Germany
- Graduate School of Systemic Neurosciences, Ludwig Maximilian University of Munich, Munich, Germany
| | - Klara Eglseer
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Ana M Gómez Martínez
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Andrea Flierl-Hecht
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University of Munich, Martinsried, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Birgit Ertl-Wagner
- Department of Radiology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
- Department of Medical Imaging, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Keeser
- Department of Psychiatry and Psychotherapy, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Martin Mortazavi
- Department of Radiology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Klaus Seelos
- Institute of Neuroradiology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Hanna Zimmermann
- Institute of Neuroradiology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Jürgen Haas
- Molecular Neuroimmunology Group, Department of Neurology, University of Heidelberg, Heidelberg, Germany
| | - Brigitte Wildemann
- Molecular Neuroimmunology Group, Department of Neurology, University of Heidelberg, Heidelberg, Germany
| | - Tania Kümpfel
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University of Munich, Martinsried, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Klaus Dornmair
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University of Munich, Martinsried, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Thomas Korn
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
- Institute for Experimental Neuroimmunology, Technical University of Munich School of Medicine, Munich, Germany
- Department of Neurology, Technical University of Munich School of Medicine, Munich, Germany
| | - Reinhard Hohlfeld
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University of Munich, Martinsried, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Martin Kerschensteiner
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University of Munich, Martinsried, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Lisa Ann Gerdes
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University of Munich, Martinsried, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Eduardo Beltrán
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University of Munich, Martinsried, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
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6
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Li Y, Xu T, Ma H, Yue D, Lamao Q, Liu Y, Zhou Z, Wei W. Functional profiling of serine, threonine and tyrosine sites. Nat Chem Biol 2024:10.1038/s41589-024-01731-0. [PMID: 39313591 DOI: 10.1038/s41589-024-01731-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 08/14/2024] [Indexed: 09/25/2024]
Abstract
Systematic perturbation of amino acids at endogenous loci provides diverse insights into protein function. Here, we performed a genome-wide screen to globally assess the cell fitness dependency of serine, threonine and tyrosine residues. Using an adenine base editor, we designed a whole-genome library comprising 817,089 single guide RNAs to perturb 584,337 S, T and Y sites. We identified 3,467 functional substitutions affecting cell fitness and 677 of them involving phosphorylation, including numerous phosphorylation-mediated gain-of-function substitutions that regulate phosphorylation levels of itself or downstream factors. Furthermore, our findings highlight that specific substitution types, notably serine to proline, are crucial for maintaining domain structure broadly. Lastly, we demonstrate that 309 enriched hits capable of initiating cell overproliferation might be potential cancer driver mutations. This study represents an extensive functional profiling of S, T and Y residues and provides insights into the distinctive roles of these amino acids in biological mechanisms and tumor progression.
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Affiliation(s)
- Yizhou Li
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Changping Laboratory, Beijing, China
| | - Tao Xu
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Huazheng Ma
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Di Yue
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Qiezhong Lamao
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Changping Laboratory, Beijing, China
| | - Ying Liu
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Changping Laboratory, Beijing, China
| | - Zhuo Zhou
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Wensheng Wei
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Changping Laboratory, Beijing, China.
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7
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Deng Y, Zhou J, Li HB. The physiological and pathological roles of RNA modifications in T cells. Cell Chem Biol 2024; 31:1578-1592. [PMID: 38986618 DOI: 10.1016/j.chembiol.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/20/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024]
Abstract
RNA molecules undergo dynamic chemical modifications in response to various external or cellular stimuli. Some of those modifications have been demonstrated to post-transcriptionally modulate the RNA transcription, localization, stability, translation, and degradation, ultimately tuning the fate decisions and function of mammalian cells, particularly T cells. As a crucial part of adaptive immunity, T cells play fundamental roles in defending against infections and tumor cells. Recent findings have illuminated the importance of RNA modifications in modulating T cell survival, proliferation, differentiation, and functional activities. Therefore, understanding the epi-transcriptomic control of T cell biology enables a potential avenue for manipulating T cell immunity. This review aims to elucidate the physiological and pathological roles of internal RNA modifications in T cell development, differentiation, and functionality drawn from current literature, with the goal of inspiring new insights for future investigations and providing novel prospects for T cell-based immunotherapy.
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Affiliation(s)
- Yu Deng
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jing Zhou
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hua-Bing Li
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Geriatrics, Medical Center on Aging of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Chongqing International Institute for Immunology, Chongqing 401320, China.
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8
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Wu D, Li X, Khan FA, Yuan C, Pandupuspitasari NS, Huang C, Sun F, Guan K. tRNA modifications and tRNA-derived small RNAs: new insights of tRNA in human disease. Cell Biol Toxicol 2024; 40:76. [PMID: 39276283 PMCID: PMC11401796 DOI: 10.1007/s10565-024-09919-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 09/04/2024] [Indexed: 09/16/2024]
Abstract
tRNAs are codon decoders that convert the transcriptome into the proteome. The field of tRNA research is excited by the increasing discovery of specific tRNA modifications that are installed at specific, evolutionarily conserved positions by a set of specialized tRNA-modifying enzymes and the biogenesis of tRNA-derived regulatory fragments (tsRNAs) which exhibit copious activities through multiple mechanisms. Dysregulation of tRNA modification usually has pathological consequences, a phenomenon referred to as "tRNA modopathy". Current evidence suggests that certain tRNA-modifying enzymes and tsRNAs may serve as promising diagnostic biomarkers and therapeutic targets, particularly for chemoresistant cancers. In this review, we discuss the latest discoveries that elucidate the molecular mechanisms underlying the functions of clinically relevant tRNA modifications and tsRNAs, with a focus on malignancies. We also discuss the therapeutic potential of tRNA/tsRNA-based therapies, aiming to provide insights for the development of innovative therapeutic strategies. Further efforts to unravel the complexities inherent in tRNA biology hold the promise of yielding better biomarkers for the diagnosis and prognosis of diseases, thereby advancing the development of precision medicine for health improvement.
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Affiliation(s)
- Di Wu
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Faheem Ahmed Khan
- Research Center for Animal Husbandry, National Research and Innovation Agency, Jakarta Pusat, 10340, Indonesia
| | - Chenyang Yuan
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | | | - Chunjie Huang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China.
| | - Fei Sun
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China.
| | - Kaifeng Guan
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China.
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9
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Zhang H, Felthaus O, Eigenberger A, Klein S, Prantl L. Treg Cell Therapeutic Strategies for Breast Cancer: Holistic to Local Aspects. Cells 2024; 13:1526. [PMID: 39329710 PMCID: PMC11429654 DOI: 10.3390/cells13181526] [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: 07/30/2024] [Revised: 09/06/2024] [Accepted: 09/10/2024] [Indexed: 09/28/2024] Open
Abstract
Regulatory T cells (Tregs) play a key role in maintaining immune homeostasis and preventing autoimmunity through their immunosuppressive function. There have been numerous reports confirming that high levels of Tregs in the tumor microenvironment (TME) are associated with a poor prognosis, highlighting their role in promoting an immunosuppressive environment. In breast cancer (BC), Tregs interact with cancer cells, ultimately leading to the suppression of immune surveillance and promoting tumor progression. This review discusses the dual role of Tregs in breast cancer, and explores the controversies and therapeutic potential associated with targeting these cells. Researchers are investigating various strategies to deplete or inhibit Tregs, such as immune checkpoint inhibitors, cytokine antagonists, and metabolic inhibition. However, the heterogeneity of Tregs and the variable precision of treatments pose significant challenges. Understanding the functional diversity of Tregs and the latest advances in targeted therapies is critical for the development of effective therapies. This review highlights the latest approaches to Tregs for BC treatment that both attenuate Treg-mediated immunosuppression in tumors and maintain immune tolerance, and advocates precise combination therapy strategies to optimize breast cancer outcomes.
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Affiliation(s)
- Hanwen Zhang
- Department of Plastic, Hand and Reconstructive Surgery, University Hospital Regensburg, Franz-Josef-Strauss Allee 11, 93053 Regensburg, Germany (L.P.)
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10
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Sharma A, Vikramdeo KS, Sudan SK, Anand S, Deshmukh SK, Singh AP, Singh S. Cortisol affects macrophage polarization by inducing miR-143/145 cluster to reprogram glucose metabolism and by promoting TCA cycle anaplerosis. J Biol Chem 2024; 300:107753. [PMID: 39260692 DOI: 10.1016/j.jbc.2024.107753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/22/2024] [Accepted: 08/29/2024] [Indexed: 09/13/2024] Open
Abstract
Chronic stress can have adverse consequences on human health by disrupting the hormonal balance in our body. Earlier, we observed elevated levels of cortisol, a primary stress hormone, and some exosomal microRNAs in the serum of patients with breast cancer. Here, we investigated the role of cortisol in microRNA induction and its functional consequences. We found that cortisol induced the expression of miR-143/145 cluster in human monocyte (THP1 and U937)-derived macrophages but not in breast cancer cells. In silico analysis identified glucocorticoid-response element in the upstream CARMN promoter utilized by the miR-143/145 cluster. Enhanced binding of glucocorticoid-receptor (GR) upon cortisol exposure and its regulatory significance was confirmed by chromatin-immunoprecipitation and promoter-reporter assays. Further, cortisol inhibited IFNγ-induced M1 polarization and promoted M2 polarization, and these effects were suppressed by miR-143-3p and miR-145-5p inhibitors pretreatment. Cortisol-treated macrophages exhibited increased oxygen-consumption rate (OCR) to extracellular-acidification rate (ECAR) ratio, and this change was neutralized by functional inhibition of miR-143-3p and miR-145-5p. HK2 and ADPGK were confirmed as the direct targets of miR-143-3p and miR-145-5p, respectively. Interestingly, silencing of HK2 and ADPGK inhibited IFNγ-induced M1 polarization but failed to induce M2 polarization, since it suppressed both ECAR and OCR, while OCR was largely sustained in cortisol-treated M2-polarized macrophages. We found that cortisol treatment sustained OCR by enhancing fatty acid and glutamine metabolism through upregulation of CPT2 and GLS, respectively, to support M2 polarization. Thus, our findings unfold a novel mechanism of immune suppression by cortisol and open avenues for preventive and therapeutic interventions.
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Affiliation(s)
- Amod Sharma
- Cancer Center and Research Institute, University of Mississippi Medical Center, Jackson, Mississippi, USA; Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Kunwar Somesh Vikramdeo
- Cancer Center and Research Institute, University of Mississippi Medical Center, Jackson, Mississippi, USA; Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Sarabjeet Kour Sudan
- Cancer Center and Research Institute, University of Mississippi Medical Center, Jackson, Mississippi, USA; Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Shashi Anand
- Cancer Center and Research Institute, University of Mississippi Medical Center, Jackson, Mississippi, USA; Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Sachin Kumar Deshmukh
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA; Department of Pathology, University of South Alabama, Mobile, Alabama, USA
| | - Ajay Pratap Singh
- Cancer Center and Research Institute, University of Mississippi Medical Center, Jackson, Mississippi, USA; Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Seema Singh
- Cancer Center and Research Institute, University of Mississippi Medical Center, Jackson, Mississippi, USA; Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA.
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11
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Zhang Z, Yang Y, Chen Y, Su J, Du W. Malic enzyme 2 maintains metabolic state and anti-tumor immunity of CD8 + T cells. Mol Cell 2024; 84:3354-3370.e7. [PMID: 39151423 DOI: 10.1016/j.molcel.2024.07.021] [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: 09/19/2023] [Revised: 04/19/2024] [Accepted: 07/23/2024] [Indexed: 08/19/2024]
Abstract
The functional integrity of CD8+ T cells is closely linked to metabolic reprogramming; therefore, understanding the metabolic basis of CD8+ T cell activation and antitumor immunity could provide insights into tumor immunotherapy. Here, we report that ME2 is critical for mouse CD8+ T cell activation and immune response against malignancy. ME2 deficiency suppresses CD8+ T cell activation and anti-tumor immune response in vitro and in vivo. Mechanistically, ME2 depletion blocks the TCA cycle flux, leading to the accumulation of fumarate. Fumarate directly binds to DAPK1 and inhibits its activity by competing with ATP for binding. Notably, pharmacological inhibition of DAPK1 abolishes the anti-tumor function conferred by ME2 to CD8+ T cells. Collectively, these findings demonstrate a role for ME2 in the regulation of CD8+ T cell metabolism and effector functions as well as an unexpected function for fumarate as a metabolic signal in the inhibition of DAPK1.
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Affiliation(s)
- Zhenxi Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Yanting Yang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Yang Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Jingyu Su
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Wenjing Du
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China.
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12
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He M, Zong X, Xu B, Qi W, Huang W, Djekidel MN, Zhang Y, Pagala VR, Li J, Hao X, Guy C, Bai L, Cross R, Li C, Peng J, Feng Y. Dynamic Foxp3-chromatin interaction controls tunable Treg cell function. J Exp Med 2024; 221:e20232068. [PMID: 38935023 PMCID: PMC11211070 DOI: 10.1084/jem.20232068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/11/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Nuclear factor Foxp3 determines regulatory T (Treg) cell fate and function via mechanisms that remain unclear. Here, we investigate the nature of Foxp3-mediated gene regulation in suppressing autoimmunity and antitumor immune response. Contrasting with previous models, we find that Foxp3-chromatin binding is regulated by Treg activation states, tumor microenvironment, and antigen and cytokine stimulations. Proteomics studies uncover dynamic proteins within Foxp3 proximity upon TCR or IL-2 receptor signaling in vitro, reflecting intricate interactions among Foxp3, signal transducers, and chromatin. Pharmacological inhibition and genetic knockdown experiments indicate that NFAT and AP-1 protein Batf are required for enhanced Foxp3-chromatin binding in activated Treg cells and tumor-infiltrating Treg cells to modulate target gene expression. Furthermore, mutations at the Foxp3 DNA-binding domain destabilize the Foxp3-chromatin association. These representative settings delineate context-dependent Foxp3-chromatin interaction, suggesting that Foxp3 associates with chromatin by hijacking DNA-binding proteins resulting from Treg activation or differentiation, which is stabilized by direct Foxp3-DNA binding, to dynamically regulate Treg cell function according to immunological contexts.
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Affiliation(s)
- Minghong He
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Xinying Zong
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Wenjie Qi
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Wenjun Huang
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | | | - Yang Zhang
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Vishwajeeth R. Pagala
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jun Li
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Xiaolei Hao
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Clifford Guy
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Lu Bai
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Richard Cross
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Department of Structure Biology and Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Yongqiang Feng
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
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13
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Kaymak I, Watson MJ, Oswald BM, Ma S, Johnson BK, DeCamp LM, Mabvakure BM, Luda KM, Ma EH, Lau K, Fu Z, Muhire B, Kitchen-Goosen SM, Vander Ark A, Dahabieh MS, Samborska B, Vos M, Shen H, Fan ZP, Roddy TP, Kingsbury GA, Sousa CM, Krawczyk CM, Williams KS, Sheldon RD, Kaech SM, Roy DG, Jones RG. ACLY and ACSS2 link nutrient-dependent chromatin accessibility to CD8 T cell effector responses. J Exp Med 2024; 221:e20231820. [PMID: 39150482 PMCID: PMC11329787 DOI: 10.1084/jem.20231820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 04/02/2024] [Accepted: 07/03/2024] [Indexed: 08/17/2024] Open
Abstract
Coordination of cellular metabolism is essential for optimal T cell responses. Here, we identify cytosolic acetyl-CoA production as an essential metabolic node for CD8 T cell function in vivo. We show that CD8 T cell responses to infection depend on acetyl-CoA derived from citrate via the enzyme ATP citrate lyase (ACLY). However, ablation of ACLY triggers an alternative, acetate-dependent pathway for acetyl-CoA production mediated by acyl-CoA synthetase short-chain family member 2 (ACSS2). Mechanistically, acetate fuels both the TCA cycle and cytosolic acetyl-CoA production, impacting T cell effector responses, acetate-dependent histone acetylation, and chromatin accessibility at effector gene loci. When ACLY is functional, ACSS2 is not required, suggesting acetate is not an obligate metabolic substrate for CD8 T cell function. However, loss of ACLY renders CD8 T cells dependent on acetate (via ACSS2) to maintain acetyl-CoA production and effector function. Together, ACLY and ACSS2 coordinate cytosolic acetyl-CoA production in CD8 T cells to maintain chromatin accessibility and T cell effector function.
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Affiliation(s)
- Irem Kaymak
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - McLane J Watson
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Brandon M Oswald
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Shixin Ma
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies , La Jolla, CA, USA
| | - Benjamin K Johnson
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute , Grand Rapids, MI, USA
| | - Lisa M DeCamp
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute , Grand Rapids, MI, USA
| | - Batsirai M Mabvakure
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Katarzyna M Luda
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen , København, Denmark
| | - Eric H Ma
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Kin Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute , Grand Rapids, MI, USA
| | - Zhen Fu
- Bioinformatics and Biostatistics Core, Van Andel Institute , Grand Rapids, MI, USA
| | - Brejnev Muhire
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Susan M Kitchen-Goosen
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute , Grand Rapids, MI, USA
| | - Alexandra Vander Ark
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Michael S Dahabieh
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Bozena Samborska
- Goodman Cancer Institute, Faculty of Medicine, McGill University , Montréal, Canada
| | - Matthew Vos
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute , Grand Rapids, MI, USA
| | - Hui Shen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | | | | | | | | | - Connie M Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute , Grand Rapids, MI, USA
| | - Kelsey S Williams
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute , Grand Rapids, MI, USA
| | - Ryan D Sheldon
- Mass Spectrometry Core Facility, Van Andel Institute , Grand Rapids, MI, USA
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies , La Jolla, CA, USA
| | - Dominic G Roy
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal , Montréal, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Canada
- Institut du Cancer de Montréal , Montréal, Canada
| | - Russell G Jones
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute , Grand Rapids, MI, USA
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14
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Yazicioglu YF, Mitchell RJ, Clarke AJ. Mitochondrial control of lymphocyte homeostasis. Semin Cell Dev Biol 2024; 161-162:42-53. [PMID: 38608498 DOI: 10.1016/j.semcdb.2024.03.002] [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: 11/03/2023] [Revised: 03/11/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024]
Abstract
Mitochondria play a multitude of essential roles within mammalian cells, and understanding how they control immunity is an emerging area of study. Lymphocytes, as integral cellular components of the adaptive immune system, rely on mitochondria for their function, and mitochondria can dynamically instruct their differentiation and activation by undergoing rapid and profound remodelling. Energy homeostasis and ATP production are often considered the primary functions of mitochondria in immune cells; however, their importance extends across a spectrum of other molecular processes, including regulation of redox balance, signalling pathways, and biosynthesis. In this review, we explore the dynamic landscape of mitochondrial homeostasis in T and B cells, and discuss how mitochondrial disorders compromise adaptive immunity.
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15
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Li X, Zhu H, Huang BT, Li X, Kim H, Tan H, Zhang Y, Choi I, Peng J, Xu P, Sun J, Yue Z. RAB12-LRRK2 Complex Suppresses Primary Ciliogenesis and Regulates Centrosome Homeostasis in Astrocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603999. [PMID: 39071328 PMCID: PMC11275936 DOI: 10.1101/2024.07.17.603999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) phosphorylates a subset of RAB GTPases, and the phosphorylation levels are elevated by Parkinson's disease (PD)-linked mutations of LRRK2. However, the precise function of the specific RAB GTPase targeted by LRRK2 signaling in the brain remains to be elucidated. Here, we identify RAB12 as a robust LRRK2 substrate in the mouse brains through phosphoproteomics profiling and solve the structure of RAB12-LRRK2 protein complex through Cryo-EM analysis. Mechanistically, RAB12 cooperates with LRRK2 to inhibit primary ciliogenesis and regulate centrosome homeostasis in astrocytes through enhancing the phosphorylation of RAB10 and recruiting Rab interacting lysosomal protein like 1 (RILPL1), while the functions of RAB12 require a direct interaction with LRRK2 and LRRK2 kinase activity. Furthermore, the ciliary deficits and centrosome alteration caused by the PD-linked LRRK2-G2019S mutation are prevented by the deletion of Rab12 in astrocytes. Thus, our study reveals a physiological function of the RAB12-LRRK2 complex in regulating ciliogenesis and centrosome homeostasis. The RAB12-LRRK2 structure offers a guidance in the therapeutic development of PD by targeting the RAB12-LRRK2 interaction.
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Affiliation(s)
- Xingjian Li
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Hanwen Zhu
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Bik Tzu Huang
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xianting Li
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Heesoo Kim
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Yuanxi Zhang
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Insup Choi
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Pingyi Xu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Ji Sun
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Zhenyu Yue
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Parkinson’s Disease Neurobiology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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16
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Motawi TK, Shaker OG, Amr G, Senousy MA. RNA methylation machinery and m 6A target genes as circulating biomarkers of ulcerative colitis and Crohn's disease: Correlation with disease activity, location, and inflammatory cytokines. Clin Chim Acta 2024; 561:119831. [PMID: 38925436 DOI: 10.1016/j.cca.2024.119831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 06/17/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024]
Abstract
Accurate diagnosis of ulcerative colitis (UC) and Crohn's disease (CD), the main subtypes of inflammatory bowel disease (IBD), has been challenging due to the constraints of the current techniques. N6-methyl adenosine (m6A) regulators have evolved as key players in IBD pathogenesis; however, their relation to its clinical setting is largely unexplored. This study investigated the potential of selected RNA methylation machinery and m6A target genes as serum biomarkers of UC and CD, their predictive and discriminating capabilities, and their correlations with laboratory data, interleukin (IL)-6, interferon-γ, disease activity scores, and pathological features. Fifty UC and 45 CD patients, along with 30 healthy volunteers were enlisted. The mRNA expression levels of the m6A writers methyltransferase-like 3 (METTL3) and Wilms-tumor associated protein (WTAP), and the reader YTH domain family, member 1 (YTHDF1), along with the m6A candidate genes sex determining region Y-box 2 (SOX2), hexokinase 2 (HK2), and ubiquitin-conjugating enzyme E2 L3 (UBE2L3) were upregulated in UC patients, whereas only METTL3, HK2, and UBE2L3 were upregulated in CD patients versus controls. Serum WTAP (AUC = 0.94, 95 %CI = 0.874-1.006) and HK2 (AUC = 0.911, 95 %CI = 0.843-0.980) expression levels showed excellent diagnostic accuracy for UC, METTL3 showed excellent diagnostic accuracy for CD (AUC = 0.91, 95 %CI = 0.828-0.992), meanwhile, WTAP showed excellent discriminative power between the two diseases (AUC = 0.91, 95 %CI = 0.849-0.979). Multivariate logistic analysis unveiled the association of METTL3 and UBE2L3 expression with the risk of CD and UC diagnosis, respectively, controlled by age and sex as confounders. Remarkable correlations were recorded between the gene expression of studied m6A regulators and targets in both diseases. Among UC patients, serum METTL3 and WTAP were correlated with UC extent/type, while WTAP was correlated with IL-6. Among CD patients, serum METTL3 and HK2 were correlated with CD activity index (CDAI) and CD location. In conclusion, m6A regulators and target genes are distinctly expressed in UC and CD clinical samples, correlate with disease activity and extent/location, and could serve as a novel approach to empower the diagnosis and stratification of IBD subtypes.
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Affiliation(s)
- Tarek K Motawi
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt.
| | - Olfat G Shaker
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Ghada Amr
- General Administration of Blood Banks, Ministry of Health and Population, Cairo, Egypt
| | - Mahmoud A Senousy
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt; Department of Biochemistry, Faculty of Pharmacy and Drug Technology, Egyptian Chinese University, Cairo 11786, Egypt
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17
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Levi J, Guglielmetti C, Henrich TJ, Yoon JC, Gokhale PC, Reardon DA, Packiasamy J, Huynh L, Cabrera H, Ruzevich M, Blecha J, Peluso MJ, Huynh TL, An SM, Dornan M, Belanger AP, Nguyen QD, Seo Y, Song H, Chaumeil MM, VanBrocklin HF, Chae HD. [ 18F]F-AraG imaging reveals association between neuroinflammation and brown- and bone marrow adipose tissue. Commun Biol 2024; 7:793. [PMID: 38951146 PMCID: PMC11217368 DOI: 10.1038/s42003-024-06494-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 06/22/2024] [Indexed: 07/03/2024] Open
Abstract
Brown and brown-like adipose tissues have attracted significant attention for their role in metabolism and therapeutic potential in diabetes and obesity. Despite compelling evidence of an interplay between adipocytes and lymphocytes, the involvement of these tissues in immune responses remains largely unexplored. This study explicates a newfound connection between neuroinflammation and brown- and bone marrow adipose tissue. Leveraging the use of [18F]F-AraG, a mitochondrial metabolic tracer capable of tracking activated lymphocytes and adipocytes simultaneously, we demonstrate, in models of glioblastoma and multiple sclerosis, the correlation between intracerebral immune infiltration and changes in brown- and bone marrow adipose tissue. Significantly, we show initial evidence that a neuroinflammation-adipose tissue link may also exist in humans. This study proposes the concept of an intricate immuno-neuro-adipose circuit, and highlights brown- and bone marrow adipose tissue as an intermediary in the communication between the immune and nervous systems. Understanding the interconnectedness within this circuitry may lead to advancements in the treatment and management of various conditions, including cancer, neurodegenerative diseases and metabolic disorders.
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Affiliation(s)
- Jelena Levi
- CellSight Technologies Incorporated, San Francisco, CA, USA.
| | - Caroline Guglielmetti
- Department of Physical Therapy and Rehabilitation Science, University of California San Francisco, San Francisco, CA, USA
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
- Mallinckrodt Institute of Radiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
| | - John C Yoon
- Division of Endocrinology, Department of Internal Medicine, University of California Davis School of Medicine, Davis, CA, USA
| | | | | | | | - Lyna Huynh
- CellSight Technologies Incorporated, San Francisco, CA, USA
| | - Hilda Cabrera
- CellSight Technologies Incorporated, San Francisco, CA, USA
| | | | - Joseph Blecha
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Michael J Peluso
- Division of HIV, ID and Global Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Tony L Huynh
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Sung-Min An
- Division of Endocrinology, Department of Internal Medicine, University of California Davis School of Medicine, Davis, CA, USA
| | - Mark Dornan
- Molecular Cancer Imaging Facility, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anthony P Belanger
- Molecular Cancer Imaging Facility, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Quang-Dé Nguyen
- Lurie Family Imaging Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Youngho Seo
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Hong Song
- Department of Radiology, Stanford University, Palo Alto, CA, USA
| | - Myriam M Chaumeil
- Department of Physical Therapy and Rehabilitation Science, University of California San Francisco, San Francisco, CA, USA
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Henry F VanBrocklin
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Hee-Don Chae
- CellSight Technologies Incorporated, San Francisco, CA, USA
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18
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Gassaway BM, Huttlin EL, Huntsman EM, Yaron-Barir TM, Johnson JL, Kurmi K, Cantley LC, Paulo JA, Ringel AE, Gygi SP, Haigis MC. Profiling Proteins and Phosphorylation Sites During T Cell Activation Using an Integrated Thermal Shift Assay. Mol Cell Proteomics 2024; 23:100801. [PMID: 38880243 PMCID: PMC11298636 DOI: 10.1016/j.mcpro.2024.100801] [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: 11/03/2023] [Revised: 05/24/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024] Open
Abstract
T cell activation is a complex biological process of naive cells maturing into effector cells. Proteomic and phospho-proteomic approaches have provided critical insights into this process, yet it is not always clear how changes in individual proteins or phosphorylation sites have functional significance. Here, we developed the Phosphorylation Integrated Thermal Shift Assay (PITSA) that combines the measurement of protein or phosphorylation site abundance and thermal stability into a single tandem mass tags experiment and apply this method to study T cell activation. We quantified the abundance and thermal stability of over 7500 proteins and 5000 phosphorylation sites and identified significant differences in chromatin-related, TCR signaling, DNA repair, and proliferative phosphoproteins. PITSA may be applied to a wide range of biological contexts to generate hypotheses as to which proteins or phosphorylation sites are functionally regulated in a given system as well as the mechanisms by which this regulation may occur.
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Affiliation(s)
- Brandon M Gassaway
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA; Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Emily M Huntsman
- Meyer Cancer Center and Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Tomer M Yaron-Barir
- Meyer Cancer Center and Department of Medicine, Weill Cornell Medicine, New York, New York, USA; Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Jared L Johnson
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA; Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kiran Kurmi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Lewis C Cantley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA; Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Alison E Ringel
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA; Ragon Institute of Mass General, MIT, and Harvard, Cambridge, Massachusetts, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.
| | - Marcia C Haigis
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.
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19
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Moraly J, Kondo T, Benzaoui M, DuSold J, Talluri S, Pouzolles MC, Chien C, Dardalhon V, Taylor N. Metabolic dialogues: regulators of chimeric antigen receptor T cell function in the tumor microenvironment. Mol Oncol 2024; 18:1695-1718. [PMID: 38922759 PMCID: PMC11223614 DOI: 10.1002/1878-0261.13691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/23/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Tumor-infiltrating lymphocytes (TILs) and chimeric antigen receptor (CAR) T cells have demonstrated remarkable success in the treatment of relapsed/refractory melanoma and hematological malignancies, respectively. These treatments have marked a pivotal shift in cancer management. However, as "living drugs," their effectiveness is dependent on their ability to proliferate and persist in patients. Recent studies indicate that the mechanisms regulating these crucial functions, as well as the T cell's differentiation state, are conditioned by metabolic shifts and the distinct utilization of metabolic pathways. These metabolic shifts, conditioned by nutrient availability as well as cell surface expression of metabolite transporters, are coupled to signaling pathways and the epigenetic landscape of the cell, modulating transcriptional, translational, and post-translational profiles. In this review, we discuss the processes underlying the metabolic remodeling of activated T cells, the impact of a tumor metabolic environment on T cell function, and potential metabolic-based strategies to enhance T cell immunotherapy.
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Affiliation(s)
- Josquin Moraly
- Pediatric Oncology Branch, National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
- Université Sorbonne Paris CitéParisFrance
| | - Taisuke Kondo
- Pediatric Oncology Branch, National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Mehdi Benzaoui
- Pediatric Oncology Branch, National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
- Université de Montpellier, Institut de Génétique Moléculaire de Montpellier, CNRSMontpellierFrance
| | - Justyn DuSold
- Pediatric Oncology Branch, National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Sohan Talluri
- Pediatric Oncology Branch, National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Marie C. Pouzolles
- Pediatric Oncology Branch, National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Christopher Chien
- Pediatric Oncology Branch, National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Valérie Dardalhon
- Université de Montpellier, Institut de Génétique Moléculaire de Montpellier, CNRSMontpellierFrance
| | - Naomi Taylor
- Pediatric Oncology Branch, National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
- Université de Montpellier, Institut de Génétique Moléculaire de Montpellier, CNRSMontpellierFrance
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20
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Walker MA, Li S, Livak KJ, Karaa A, Wu CJ, Mootha VK. T cell activation contributes to purifying selection against the MELAS-associated m.3243A>G pathogenic variant in blood. J Inherit Metab Dis 2024; 47:757-765. [PMID: 38499449 PMCID: PMC11251844 DOI: 10.1002/jimd.12726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/28/2023] [Accepted: 02/20/2024] [Indexed: 03/20/2024]
Abstract
T cells have been shown to maintain a lower percentage (heteroplasmy) of the pathogenic m.3243A>G variant (MT-TL1, associated with maternally inherited diabetes and deafness [MIDD] and mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes [MELAS]). The mechanism(s) underlying this purifying selection, however, remain unknown. Here we report that purified patient memory CD4+ T cells have lower bulk m.3243A>G heteroplasmy compared to naïve CD4+ T cells. In vitro activation of naïve CD4+ m.3243A>G patient T cells results in lower bulk m.3243A>G heteroplasmy after proliferation. Finally, m.3243A>G patient T cell receptor repertoire sequencing reveals relative oligoclonality compared to controls. These data support a role for T cell activation in peripheral, purifying selection against high m.3243A>G heteroplasmy T cells at the level of the cell, in a likely cell-autonomous fashion.
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Affiliation(s)
- Melissa A Walker
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Howard Hughes Medical Institute and the Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Amel Karaa
- Department of Pediatrics, Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Catherine J Wu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and the Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
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21
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Romero-Carramiñana I, Dominguez-Zorita S, Esparza-Moltó PB, Cuezva JM. Ablation of Atp5if1 impairs metabolic reprogramming and proliferation of T lymphocytes and compromises mouse survival. iScience 2024; 27:109863. [PMID: 38799559 PMCID: PMC11126974 DOI: 10.1016/j.isci.2024.109863] [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: 11/30/2023] [Revised: 03/06/2024] [Accepted: 04/27/2024] [Indexed: 05/29/2024] Open
Abstract
T cells experience metabolic reprogramming to an enhanced glycolysis upon activation. Herein, we have investigated whether ATPase Inhibitory Factor 1 (IF1), the physiological inhibitor of mitochondrial ATP synthase, participates in rewiring T cells to a particular metabolic phenotype. We show that the activation of naive CD4+ T lymphocytes both in vitro and in vivo is accompanied by a sharp upregulation of IF1, which is expressed only in Th1 effector cells. T lymphocytes of conditional CD4+-IF1-knockout mice display impaired glucose uptake and flux through glycolysis, reducing the biogenesis of mitochondria and cellular proliferation after activation. Consequently, mice devoid of IF1 in T lymphocytes cannot mount an effective Th1 response against bacterial infection compromising their survival. Overall, we show that the inhibition of a fraction of ATP synthase by IF1 regulates metabolic reprogramming and functionality of T cells, highlighting the essential role of IF1 in adaptive immune responses.
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Affiliation(s)
- Inés Romero-Carramiñana
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) ISCIII, Madrid, Spain
- Instituto de Investigación Hospital 12 de Octubre, Universidad Autónoma de Madrid, Madrid, Spain
| | - Sonia Dominguez-Zorita
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) ISCIII, Madrid, Spain
- Instituto de Investigación Hospital 12 de Octubre, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pau B. Esparza-Moltó
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) ISCIII, Madrid, Spain
- Instituto de Investigación Hospital 12 de Octubre, Universidad Autónoma de Madrid, Madrid, Spain
| | - José M. Cuezva
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) ISCIII, Madrid, Spain
- Instituto de Investigación Hospital 12 de Octubre, Universidad Autónoma de Madrid, Madrid, Spain
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22
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Voltarelli VA, Amano MT, Tobias GC, Borges GS, Oliveira da Paixão A, Pereira MG, Saraiva Câmara NO, Caldeira W, Ribeiro AF, Otterbein LE, Negrão CE, Turner JE, Brum PC, Camargo AA. Moderate-intensity aerobic exercise training improves CD8 + tumor-infiltrating lymphocytes effector function by reducing mitochondrial loss. iScience 2024; 27:110121. [PMID: 38957793 PMCID: PMC11217614 DOI: 10.1016/j.isci.2024.110121] [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: 10/17/2023] [Revised: 02/09/2024] [Accepted: 05/24/2024] [Indexed: 07/04/2024] Open
Abstract
Aerobic exercise training (AET) has emerged as a strategy to reduce cancer mortality, however, the mechanisms explaining AET on tumor development remain unclear. Tumors escape immune detection by generating immunosuppressive microenvironments and impaired T cell function, which is associated with T cell mitochondrial loss. AET improves mitochondrial content and function, thus we tested whether AET would modulate mitochondrial metabolism in tumor-infiltrating lymphocytes (TIL). Balb/c mice were subjected to a treadmill AET protocol prior to CT26 colon carcinoma cells injection and until tumor harvest. Tissue hypoxia, TIL infiltration and effector function, and mitochondrial content, morphology and function were evaluated. AET reduced tumor growth, improved survival, and decreased tumor hypoxia. An increased CD8+ TIL infiltration, IFN-γ and ATP production promoted by AET was correlated with reduced mitochondrial loss in these cells. Collectively, AET decreases tumor growth partially by increasing CD8+ TIL effector function through an improvement in their mitochondrial content and function.
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Affiliation(s)
- Vanessa Azevedo Voltarelli
- Molecular Oncology Center, Sírio-Libanês Hospital, São Paulo, SP, Brazil
- School of Physical Education and Sport, University of São Paulo, São Paulo, SP, Brazil
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Mariane Tami Amano
- Molecular Oncology Center, Sírio-Libanês Hospital, São Paulo, SP, Brazil
| | - Gabriel Cardial Tobias
- School of Physical Education and Sport, University of São Paulo, São Paulo, SP, Brazil
- Department of Pediatrics, Weill Cornell Medical College, New York, NY, USA
| | - Gabriela Silva Borges
- School of Physical Education and Sport, University of São Paulo, São Paulo, SP, Brazil
| | | | - Marcelo Gomes Pereira
- School of Physical Education and Sport, University of São Paulo, São Paulo, SP, Brazil
- Leeds School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Niels Olsen Saraiva Câmara
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Waldir Caldeira
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - Alberto Freitas Ribeiro
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - Leo Edmond Otterbein
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Carlos Eduardo Negrão
- School of Physical Education and Sport, University of São Paulo, São Paulo, SP, Brazil
- Heart Institute, Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - James Edward Turner
- Department for Health, University of Bath, Bath, UK
- School of Sport, Exercise and Rehabilitation Sciences, University of Birmingham, Birmingham, UK
| | - Patricia Chakur Brum
- School of Physical Education and Sport, University of São Paulo, São Paulo, SP, Brazil
- Department of Physiology & Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
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23
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von Hegedus JH, de Jong AJ, Hoekstra AT, Spronsen E, Zhu W, Cabukusta B, Kwekkeboom JC, Heijink M, Bos E, Berkers CR, Giera MA, Toes REM, Ioan-Facsinay A. Oleic acid enhances proliferation and calcium mobilization of CD3/CD28 activated CD4 + T cells through incorporation into membrane lipids. Eur J Immunol 2024:e2350685. [PMID: 38890809 DOI: 10.1002/eji.202350685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 06/20/2024]
Abstract
Unsaturated fatty acids (UFA) are crucial for T-cell effector functions, as they can affect the growth, differentiation, survival, and function of T cells. Nonetheless, the mechanisms by which UFA affects T-cell behavior are ill-defined. Therefore, we analyzed the processing of oleic acid, a prominent UFA abundantly present in blood, adipocytes, and the fat pads surrounding lymph nodes, in CD4+ T cells. We found that exogenous oleic acid increases proliferation and enhances the calcium flux response upon CD3/CD28 activation. By using a variety of techniques, we found that the incorporation of oleic acid into membrane lipids, rather than regulation of cellular metabolism or TCR expression, is essential for its effects on CD4+ T cells. These results provide novel insights into the mechanism through which exogenous oleic acid enhances CD4+ T-cell function.
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Affiliation(s)
- Johannes Hendrick von Hegedus
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Anja J de Jong
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Anna T Hoekstra
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
- Division of Endocrinology, Department of Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric Spronsen
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Wahwah Zhu
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Birol Cabukusta
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Joanneke C Kwekkeboom
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marieke Heijink
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Erik Bos
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Celia R Berkers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Martin A Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rene E M Toes
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Andreea Ioan-Facsinay
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
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24
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Peng J, Zaman M, Yang S, Huang Y, Yarbro J, Wang Z, Liu D, Soliman H, Hemphill A, Harvey S, Pruett-Miller S, Stewart V, Tanwar A, Kalathur R, Grace C, Turk M, Chittori S, Jiao Y, Wu Z, High A, Wang X, Serrano G, Beach T, Yu G, Yang Y, Chen PC. Midkine Attenuates Aβ Fibril Assembly and AmyloidPlaque Formation. RESEARCH SQUARE 2024:rs.3.rs-4361125. [PMID: 38883748 PMCID: PMC11177971 DOI: 10.21203/rs.3.rs-4361125/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Proteomic profiling of Alzheimer's disease (AD) brains has identified numerous understudied proteins, including midkine (MDK), that are highly upregulated and correlated with Aβ since the early disease stage, but their roles in disease progression are not fully understood. Here we present that MDK attenuates Aβ assembly and influences amyloid formation in the 5xFAD amyloidosis mouse model. MDK protein mitigates fibril formation of both Aβ40 and Aβ42 peptides in Thioflavin T fluorescence assay, circular dichroism, negative stain electron microscopy, and NMR analysis. Knockout of Mdkgene in 5xFAD increases amyloid formation and microglial activation. Further comprehensive mass spectrometry-based profiling of whole proteome and aggregated proteome in these mouse models indicates significant accumulation of Aβ and Aβ-correlated proteins, along with microglial components. Thus, our structural and mouse model studies reveal a protective role of MDK in counteracting amyloid pathology in Alzheimer's disease.
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Affiliation(s)
| | | | - Shu Yang
- St Jude Children's Research Hospital
| | - Ya Huang
- St Jude Children's Research Hospital
| | | | - Zhen Wang
- St Jude Children's Research Hospital
| | | | | | | | | | | | | | | | | | | | | | | | - Yun Jiao
- St Jude Children's Research Hospital
| | | | | | | | | | | | - Gang Yu
- University of Texas Southwestern Medical Center
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25
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Lin L, Ren R, Xiong Q, Zheng C, Yang B, Wang H. Remodeling of T-cell mitochondrial metabolism to treat autoimmune diseases. Autoimmun Rev 2024; 23:103583. [PMID: 39084278 DOI: 10.1016/j.autrev.2024.103583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 08/02/2024]
Abstract
T cells are key drivers of the pathogenesis of autoimmune diseases by producing cytokines, stimulating the generation of autoantibodies, and mediating tissue and cell damage. Distinct mitochondrial metabolic pathways govern the direction of T-cell differentiation and function and rely on specific nutrients and metabolic enzymes. Metabolic substrate uptake and mitochondrial metabolism form the foundational elements for T-cell activation, proliferation, differentiation, and effector function, contributing to the dynamic interplay between immunological signals and mitochondrial metabolism in coordinating adaptive immunity. Perturbations in substrate availability and enzyme activity may impair T-cell immunosuppressive function, fostering autoreactive responses and disrupting immune homeostasis, ultimately contributing to autoimmune disease pathogenesis. A growing body of studies has explored how metabolic processes regulate the function of diverse T-cell subsets in autoimmune diseases such as systemic lupus erythematosus (SLE), multiple sclerosis (MS), autoimmune hepatitis (AIH), inflammatory bowel disease (IBD), and psoriasis. This review describes the coordination of T-cell biology by mitochondrial metabolism, including the electron transport chain (ETC), oxidative phosphorylation, amino acid metabolism, fatty acid metabolism, and one‑carbon metabolism. This study elucidated the intricate crosstalk between mitochondrial metabolic programs, signal transduction pathways, and transcription factors. This review summarizes potential therapeutic targets for T-cell mitochondrial metabolism and signaling in autoimmune diseases, providing insights for future studies.
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Affiliation(s)
- Liyan Lin
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China; Sichuan Clinical Research Center for Laboratory Medicine, Chengdu 610041, China; Laboratory Medicine Research Center of West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ruyu Ren
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China; Sichuan Clinical Research Center for Laboratory Medicine, Chengdu 610041, China; Laboratory Medicine Research Center of West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qiao Xiong
- Department of Infectious Disease, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Chunfu Zheng
- Department of Microbiology, Immunology & Infection Diseases, University of Calgary, Calgary, Alberta, Canada.
| | - Bin Yang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China; Sichuan Clinical Research Center for Laboratory Medicine, Chengdu 610041, China; Laboratory Medicine Research Center of West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Huiqing Wang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, China.
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26
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Correa-Medero LO, Jankowski SE, Hong HS, Armas ND, Vijendra AI, Reynolds MB, Fogo GM, Awad D, Dils AT, Inoki KA, Williams RG, Ye AM, Svezhova N, Gomez-Rivera F, Collins KL, O'Riordan MX, Sanderson TH, Lyssiotis CA, Carty SA. ER-associated degradation adapter Sel1L is required for CD8 + T cell function and memory formation following acute viral infection. Cell Rep 2024; 43:114156. [PMID: 38687642 PMCID: PMC11194752 DOI: 10.1016/j.celrep.2024.114156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/06/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024] Open
Abstract
The maintenance of antigen-specific CD8+ T cells underlies the efficacy of vaccines and immunotherapies. Pathways contributing to CD8+ T cell loss are not completely understood. Uncovering the pathways underlying the limited persistence of CD8+ T cells would be of significant benefit for developing novel strategies of promoting T cell persistence. Here, we demonstrate that murine CD8+ T cells experience endoplasmic reticulum (ER) stress following activation and that the ER-associated degradation (ERAD) adapter Sel1L is induced in activated CD8+ T cells. Sel1L loss limits CD8+ T cell function and memory formation following acute viral infection. Mechanistically, Sel1L is required for optimal bioenergetics and c-Myc expression. Finally, we demonstrate that human CD8+ T cells experience ER stress upon activation and that ER stress is negatively associated with improved T cell functionality in T cell-redirecting therapies. Together, these results demonstrate that ER stress and ERAD are important regulators of T cell function and persistence.
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Affiliation(s)
- Luis O Correa-Medero
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Hanna S Hong
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nicholas D Armas
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Mack B Reynolds
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Garrett M Fogo
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Dominik Awad
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alexander T Dils
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Reid G Williams
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Nadezhda Svezhova
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Kathleen L Collins
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA; Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mary X O'Riordan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas H Sanderson
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Emergency Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shannon A Carty
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
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27
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Kanno T, Konno R, Sato M, Kurabayashi A, Miyako K, Nakajima T, Yokoyama S, Sasamoto S, Asou HK, Ohzeki J, Hasegawa Y, Ikeda K, Kawashima Y, Ohara O, Endo Y. The integration of metabolic and proteomic data uncovers an augmentation of the sphingolipid biosynthesis pathway during T-cell differentiation. Commun Biol 2024; 7:622. [PMID: 38783005 PMCID: PMC11116545 DOI: 10.1038/s42003-024-06339-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Recent studies have highlighted the significance of cellular metabolism in the initiation of clonal expansion and effector differentiation of T cells. Upon exposure to antigens, naïve CD4+ T cells undergo metabolic reprogramming to meet their metabolic requirements. However, only few studies have simultaneously evaluated the changes in protein and metabolite levels during T cell differentiation. Our research seeks to fill the gap by conducting a comprehensive analysis of changes in levels of metabolites, including sugars, amino acids, intermediates of the TCA cycle, fatty acids, and lipids. By integrating metabolomics and proteomics data, we discovered that the quantity and composition of cellular lipids underwent significant changes in different effector Th cell subsets. Especially, we found that the sphingolipid biosynthesis pathway was commonly activated in Th1, Th2, Th17, and iTreg cells and that inhibition of this pathway led to the suppression of Th17 and iTreg cells differentiation. Additionally, we discovered that Th17 and iTreg cells enhance glycosphingolipid metabolism, and inhibition of this pathway also results in the suppression of Th17 and iTreg cell generation. These findings demonstrate that the utility of our combined metabolomics and proteomics analysis in furthering the understanding of metabolic transition during Th cell differentiation.
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Grants
- Jp20H03455 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- Jp18H04665 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- Jp20K21618 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- Jp21K15476 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
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Affiliation(s)
- Toshio Kanno
- Department of Frontier Research and Development, Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Ryo Konno
- Department of Applied Genomics Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Masaru Sato
- Department of Research and Development, Kazusa DNA Research Institutes, Kisarazu, Japan
| | - Atsushi Kurabayashi
- Department of Research and Development, Kazusa DNA Research Institutes, Kisarazu, Japan
| | - Keisuke Miyako
- Department of Applied Genomics Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Takahiro Nakajima
- Department of Frontier Research and Development, Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Satoru Yokoyama
- Department of Frontier Research and Development, Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Shigemi Sasamoto
- Department of Frontier Research and Development, Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Hikari K Asou
- Department of Frontier Research and Development, Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Junichiro Ohzeki
- Department of Frontier Research and Development, Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Yoshinori Hasegawa
- Department of Applied Genomics Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Kazutaka Ikeda
- Department of Applied Genomics Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Osamu Ohara
- Department of Applied Genomics Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Yusuke Endo
- Department of Frontier Research and Development, Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan.
- Department of Omics Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan.
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28
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Xu X, Chen Z, Bartman CR, Xing X, Olszewski K, Rabinowitz JD. One-carbon unit supplementation fuels purine synthesis in tumor-infiltrating T cells and augments checkpoint blockade. Cell Chem Biol 2024; 31:932-943.e8. [PMID: 38759619 DOI: 10.1016/j.chembiol.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/29/2024] [Accepted: 04/17/2024] [Indexed: 05/19/2024]
Abstract
Nucleotides perform important metabolic functions, carrying energy and feeding nucleic acid synthesis. Here, we use isotope tracing-mass spectrometry to quantitate contributions to purine nucleotides from salvage versus de novo synthesis. We further explore the impact of augmenting a key precursor for purine synthesis, one-carbon (1C) units. We show that tumors and tumor-infiltrating T cells (relative to splenic or lymph node T cells) synthesize purines de novo. Shortage of 1C units for T cell purine synthesis is accordingly a potential bottleneck for anti-tumor immunity. Supplementing 1C units by infusing formate drives formate assimilation into purines in tumor-infiltrating T cells. Orally administered methanol functions as a formate pro-drug, with deuteration enabling kinetic control of formate production. Safe doses of methanol raise formate levels and augment anti-PD-1 checkpoint blockade in MC38 tumors, tripling durable regressions. Thus, 1C deficiency can gate antitumor immunity and this metabolic checkpoint can be overcome with pharmacological 1C supplementation.
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Affiliation(s)
- Xincheng Xu
- Department of Chemistry, Princeton University, Princeton, NJ, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ, USA
| | - Zihong Chen
- Department of Chemistry, Princeton University, Princeton, NJ, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ, USA
| | - Caroline R Bartman
- Department of Chemistry, Princeton University, Princeton, NJ, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ, USA
| | - Xi Xing
- Department of Chemistry, Princeton University, Princeton, NJ, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ, USA
| | - Kellen Olszewski
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ, USA.
| | - Joshua D Rabinowitz
- Department of Chemistry, Princeton University, Princeton, NJ, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ, USA.
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29
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Chapman NM, Chi H. Metabolic rewiring and communication in cancer immunity. Cell Chem Biol 2024; 31:862-883. [PMID: 38428418 PMCID: PMC11177544 DOI: 10.1016/j.chembiol.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/29/2024] [Accepted: 02/08/2024] [Indexed: 03/03/2024]
Abstract
The immune system shapes tumor development and progression. Although immunotherapy has transformed cancer treatment, its overall efficacy remains limited, underscoring the need to uncover mechanisms to improve therapeutic effects. Metabolism-associated processes, including intracellular metabolic reprogramming and intercellular metabolic crosstalk, are emerging as instructive signals for anti-tumor immunity. Here, we first summarize the roles of intracellular metabolic pathways in controlling immune cell function in the tumor microenvironment. How intercellular metabolic communication regulates anti-tumor immunity, and the impact of metabolites or nutrients on signaling events, are also discussed. We then describe how targeting metabolic pathways in tumor cells or intratumoral immune cells or via nutrient-based interventions may boost cancer immunotherapies. Finally, we conclude with discussions on profiling and functional perturbation methods of metabolic activity in intratumoral immune cells, and perspectives on future directions. Uncovering the mechanisms for metabolic rewiring and communication in the tumor microenvironment may enable development of novel cancer immunotherapies.
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Affiliation(s)
- Nicole M Chapman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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30
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Chen Y, Gao J, Ma M, Wang K, Liu F, Yang F, Zou X, Cheng Z, Wu D. The potential role of CMC1 as an immunometabolic checkpoint in T cell immunity. Oncoimmunology 2024; 13:2344905. [PMID: 38659649 PMCID: PMC11042068 DOI: 10.1080/2162402x.2024.2344905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
T cell immunity is critical for human defensive immune response. Exploring the key molecules during the process provides new targets for T cell-based immunotherapies. CMC1 is a mitochondrial electron transport chain (ETC) complex IV chaperon protein. By establishing in-vitro cell culture system and Cmc1 gene knock out mice, we evaluated the role of CMC1 in T cell activation and differentiation. The B16-OVA tumor model was used to test the possibility of targeting CMC1 for improving T cell anti-tumor immunity. We identified CMC1 as a positive regulator in CD8+T cells activation and terminal differentiation. Meanwhile, we found that CMC1 increasingly expressed in exhausted T (Tex) cells. Genetic lost of Cmc1 inhibits the development of CD8+T cell exhaustion in mice. Instead, deletion of Cmc1 in T cells prompts cells to differentiate into metabolically and functionally quiescent cells with increased memory-like features and tolerance to cell death upon repetitive or prolonged T cell receptor (TCR) stimulation. Further, the in-vitro mechanistic study revealed that environmental lactate enhances CMC1 expression by inducing USP7, mediated stabilization and de-ubiquitination of CMC1 protein, in which a mechanism we propose here that the lactate-enriched tumor microenvironment (TME) drives CD8+TILs dysfunction through CMC1 regulatory effects on T cells. Taken together, our study unraveled the novel role of CMC1 as a T cell regulator and its possibility to be utilized for anti-tumor immunotherapy.
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Affiliation(s)
- Yuwen Chen
- Jinshan Hospital Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, China
| | - Jie Gao
- Shanghai Key Laboratory of Lung Inflammation and Injury, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Mingyue Ma
- Institute of Metabolism and Regenerative Medicine, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ke Wang
- Jinshan Hospital Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, China
| | - Fangming Liu
- Shanghai Key Laboratory of Lung Inflammation and Injury, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Feiyu Yang
- Center of Emergency and Critical Medicine, Jinshan Hospital of Fudan University, Shanghai, China
| | - Xin Zou
- Jinshan Hospital Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, China
| | - Zhouli Cheng
- Jinshan Hospital Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, China
| | - Duojiao Wu
- Jinshan Hospital Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Lung Inflammation and Injury, Zhongshan Hospital, Fudan University, Shanghai, China
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31
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Yuan Q, Duren Z. Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data. Nat Biotechnol 2024:10.1038/s41587-024-02182-7. [PMID: 38609714 DOI: 10.1038/s41587-024-02182-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/26/2024] [Indexed: 04/14/2024]
Abstract
Existing methods for gene regulatory network (GRN) inference rely on gene expression data alone or on lower resolution bulk data. Despite the recent integration of chromatin accessibility and RNA sequencing data, learning complex mechanisms from limited independent data points still presents a daunting challenge. Here we present LINGER (Lifelong neural network for gene regulation), a machine-learning method to infer GRNs from single-cell paired gene expression and chromatin accessibility data. LINGER incorporates atlas-scale external bulk data across diverse cellular contexts and prior knowledge of transcription factor motifs as a manifold regularization. LINGER achieves a fourfold to sevenfold relative increase in accuracy over existing methods and reveals a complex regulatory landscape of genome-wide association studies, enabling enhanced interpretation of disease-associated variants and genes. Following the GRN inference from reference single-cell multiome data, LINGER enables the estimation of transcription factor activity solely from bulk or single-cell gene expression data, leveraging the abundance of available gene expression data to identify driver regulators from case-control studies.
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Affiliation(s)
- Qiuyue Yuan
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, USA
| | - Zhana Duren
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, USA.
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32
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Bell M, Lange S, Sejdiu BI, Ibanez J, Shi H, Sun X, Meng X, Nguyen P, Sutton M, Wagner J, Kc A, Langfitt D, Patil SL, Tan H, Pandey RV, Li Y, Yuan ZF, Anido AA, Ho M, Sheppard H, Vogel P, Yu J, Peng J, Chi H, Babu MM, Krenciute G, Gottschalk S. Modular chimeric cytokine receptors with leucine zippers enhance the antitumour activity of CAR T cells via JAK/STAT signalling. Nat Biomed Eng 2024; 8:380-396. [PMID: 38036617 DOI: 10.1038/s41551-023-01143-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 10/20/2023] [Indexed: 12/02/2023]
Abstract
The limited availability of cytokines in solid tumours hinders maintenance of the antitumour activity of chimeric antigen receptor (CAR) T cells. Cytokine receptor signalling pathways in CAR T cells can be activated by transgenic expression or injection of cytokines in the tumour, or by engineering the activation of cognate cytokine receptors. However, these strategies are constrained by toxicity arising from the activation of bystander cells, by the suboptimal biodistribution of the cytokines and by downregulation of the cognate receptor. Here we show that replacement of the extracellular domains of heterodimeric cytokine receptors in T cells with two leucine zipper motifs provides optimal Janus kinase/signal transducer and activator of transcription signalling. Such chimeric cytokine receptors, which can be generated for common γ-chain receptors, interleukin-10 and -12 receptors, enabled T cells to survive cytokine starvation without induction of autonomous cell growth, and augmented the effector function of CAR T cells in vitro in the setting of chronic antigen exposure and in human tumour xenografts in mice. As a modular design, leucine zippers can be used to generate constitutively active cytokine receptors in effector immune cells.
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Affiliation(s)
- Matthew Bell
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shannon Lange
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Besian I Sejdiu
- Center of Excellence for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jorge Ibanez
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hao Shi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiang Sun
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiaoxi Meng
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Phuong Nguyen
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Morgan Sutton
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jessica Wagner
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Anil Kc
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Deanna Langfitt
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sagar L Patil
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ram Vinay Pandey
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zuo-Fei Yuan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Alejandro Allo Anido
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mitchell Ho
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Heather Sheppard
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter Vogel
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - M Madan Babu
- Center of Excellence for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Giedre Krenciute
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA.
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33
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Stevens MG, Mason FM, Bullock TNJ. The mitochondrial fission protein DRP1 influences memory CD8+ T cell formation and function. J Leukoc Biol 2024; 115:679-694. [PMID: 38057151 PMCID: PMC10980353 DOI: 10.1093/jleuko/qiad155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/11/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023] Open
Abstract
Pharmacological methods for promoting mitochondrial elongation suggest that effector T cells can be altered to support a memory T cell-like metabolic state. Such mitochondrial elongation approaches may enhance the development of immunological memory. Therefore, we hypothesized that deletion of the mitochondrial fission protein dynamin-related protein 1 (DRP1) would lead to mitochondrial elongation and generate a large memory T cell population, an approach that could be exploited to enhance vaccination protocols. We find that, as expected, while deletion of DRP1 from T cells in dLckCre × Drp1flfl does compromise the magnitude and functionality of primary effector CD8+ T cells, a disproportionately large pool of memory CD8+ T cells does form. In contrast to primary effector CD8+ T cells, DRP1-deficient memory dLckCre × Drp1flfl CD8+ T cells mount a secondary response comparable to control memory T cells with respect to kinetics, magnitude, and effector capabilities. Interestingly, the relative propensity to form memory cells in the absence of DRP1 was associated with neither differentiation toward more memory precursor CD8+ T cells nor decreased cellular death of effector T cells. Instead, the tendency to form memory CD8+ T cells in the absence of DRP1 is associated with decreased T cell receptor expression. Remarkably, in a competitive environment with DRP1-replete CD8+ T cells, the absence of DRP1 from CD8+ T cells compromised the generation of primary, memory, and secondary responses, indicating that approaches targeting DRP1 need to be carefully tailored.
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Affiliation(s)
- Marissa G Stevens
- Department of Pathology, University of Virginia, 415 Lane Road, PO Box 800904, Charlottesville, VA 22908, United States
| | - Frank M Mason
- Department of Medicine, Vanderbilt University Medical Center, 2220 Pierce Avenue, 612 Preston Research Bldg, Nashville, TN 37232, United States
| | - Timothy N J Bullock
- Department of Pathology, University of Virginia, 415 Lane Road, PO Box 800904, Charlottesville, VA 22908, United States
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34
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Turner L, Van Le TN, Cross E, Queriault C, Knight M, Trihemasava K, Davis J, Schaefer P, Nguyen J, Xu J, Goldspiel B, Hall E, Rome K, Scaglione M, Eggert J, Au-Yeung B, Wallace DC, Mesaros C, Baur JA, Bailis W. Single-cell NAD(H) levels predict clonal lymphocyte expansion dynamics. Sci Immunol 2024; 9:eadj7238. [PMID: 38489349 PMCID: PMC11064129 DOI: 10.1126/sciimmunol.adj7238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 02/22/2024] [Indexed: 03/17/2024]
Abstract
Adaptive immunity requires the expansion of high-affinity lymphocytes from a heterogeneous pool. Whereas current models explain this through signal transduction, we hypothesized that antigen affinity tunes discrete metabolic pathways to license clonal lymphocyte dynamics. Here, we identify nicotinamide adenine dinucleotide (NAD) biosynthesis as a biochemical hub for the T cell receptor affinity-dependent metabolome. Through this central anabolic role, we found that NAD biosynthesis governs a quiescence exit checkpoint, thereby pacing proliferation. Normalizing cellular NAD(H) likewise normalizes proliferation across affinities, and enhancing NAD biosynthesis permits the expansion of lower affinity clones. Furthermore, single-cell differences in NAD(H) could predict division potential for both T and B cells, before the first division, unmixing proliferative heterogeneity. We believe that this supports a broader paradigm in which complex signaling networks converge on metabolic pathways to control single-cell behavior.
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Affiliation(s)
- Lucien Turner
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Tran Ngoc Van Le
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Eric Cross
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104
| | - Clemence Queriault
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Montana Knight
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Krittin Trihemasava
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - James Davis
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, 19104
| | - Patrick Schaefer
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Janet Nguyen
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Jimmy Xu
- Center of Excellence in Environmental Toxicology & Department of Systems Pharmacology & Translational Therapeutics, University of Pennsylvania; Philadelphia, PA 19104
| | - Brian Goldspiel
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Elise Hall
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Kelly Rome
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Michael Scaglione
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Joel Eggert
- Division of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University; Atlanta, GA 30322
| | - Byron Au-Yeung
- Division of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University; Atlanta, GA 30322
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
- Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104
| | - Clementina Mesaros
- Center of Excellence in Environmental Toxicology & Department of Systems Pharmacology & Translational Therapeutics, University of Pennsylvania; Philadelphia, PA 19104
| | - Joseph A Baur
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, 19104
| | - Will Bailis
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104
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35
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Raynor JL, Chi H. Nutrients: Signal 4 in T cell immunity. J Exp Med 2024; 221:e20221839. [PMID: 38411744 PMCID: PMC10899091 DOI: 10.1084/jem.20221839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/28/2024] Open
Abstract
T cells are integral in mediating adaptive immunity to infection, autoimmunity, and cancer. Upon immune challenge, T cells exit from a quiescent state, followed by clonal expansion and effector differentiation. These processes are shaped by three established immune signals, namely antigen stimulation (Signal 1), costimulation (Signal 2), and cytokines (Signal 3). Emerging findings reveal that nutrients, including glucose, amino acids, and lipids, are crucial regulators of T cell responses and interplay with Signals 1-3, highlighting nutrients as Signal 4 to license T cell immunity. Here, we first summarize the functional importance of Signal 4 and the underlying mechanisms of nutrient transport, sensing, and signaling in orchestrating T cell activation and quiescence exit. We also discuss the roles of nutrients in programming T cell differentiation and functional fitness and how nutrients can be targeted to improve disease therapy. Understanding how T cells respond to Signal 4 nutrients in microenvironments will provide insights into context-dependent functions of adaptive immunity and therapeutic interventions.
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Affiliation(s)
- Jana L Raynor
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
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Weerakoon H, Mohamed A, Wong Y, Chen J, Senadheera B, Haigh O, Watkins TS, Kazakoff S, Mukhopadhyay P, Mulvenna J, Miles JJ, Hill MM, Lepletier A. Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation. NPJ Syst Biol Appl 2024; 10:21. [PMID: 38418561 PMCID: PMC10901835 DOI: 10.1038/s41540-024-00346-4] [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: 08/03/2023] [Accepted: 01/25/2024] [Indexed: 03/01/2024] Open
Abstract
Engagement of the T cell receptor (TCR) triggers molecular reprogramming leading to the acquisition of specialized effector functions by CD4 helper and CD8 cytotoxic T cells. While transcription factors, chemokines, and cytokines are known drivers in this process, the temporal proteomic and transcriptomic changes that regulate different stages of human primary T cell activation remain to be elucidated. Here, we report an integrative temporal proteomic and transcriptomic analysis of primary human CD4 and CD8 T cells following ex vivo stimulation with anti-CD3/CD28 beads, which revealed major transcriptome-proteome uncoupling. The early activation phase in both CD4 and CD8 T cells was associated with transient downregulation of the mRNA transcripts and protein of the central glucose transport GLUT1. In the proliferation phase, CD4 and CD8 T cells became transcriptionally more divergent while their proteome became more similar. In addition to the kinetics of proteome-transcriptome correlation, this study unveils selective transcriptional and translational metabolic reprogramming governing CD4 and CD8 T cell responses to TCR stimulation. This temporal transcriptome/proteome map of human T cell activation provides a reference map exploitable for future discovery of biomarkers and candidates targeting T cell responses.
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Affiliation(s)
- Harshi Weerakoon
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
- Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Ahmed Mohamed
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Yide Wong
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Jinjin Chen
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | | | - Oscar Haigh
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Thomas S Watkins
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Stephen Kazakoff
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | | | - Jason Mulvenna
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - John J Miles
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Michelle M Hill
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Ailin Lepletier
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia.
- Institute for Glycomics, Griffith Univeristy, Gold Coast, QLD, Australia.
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Wilfahrt D, Delgoffe GM. Metabolic waypoints during T cell differentiation. Nat Immunol 2024; 25:206-217. [PMID: 38238609 DOI: 10.1038/s41590-023-01733-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 12/07/2023] [Indexed: 02/03/2024]
Abstract
This Review explores the interplay between T cell activation and cell metabolism and highlights how metabolites serve two pivotal functions in shaping the immune response. Traditionally, T cell activation has been characterized by T cell antigen receptor-major histocompatibility complex interaction (signal 1), co-stimulation (signal 2) and cytokine signaling (signal 3). However, recent research has unveiled the critical role of metabolites in this process. Firstly, metabolites act as signal propagators that aid in the transmission of core activation signals, such as specific lipid species that are crucial at the immune synapse. Secondly, metabolites also function as unique signals that influence immune differentiation pathways, such as amino acid-induced mTORC1 signaling. Metabolites also play a substantial role in epigenetic remodeling, by directly modifying histones, altering gene expression and influencing T cell behavior. This Review discusses how T cells integrate nutrient sensing with activating stimuli to shape their differentiation and sensitivity to metabolites. We underscore the integration of immunological and metabolic inputs in T cell function and suggest that metabolite availability is a fundamental determinant of adaptive immune responses.
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Affiliation(s)
- Drew Wilfahrt
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Greg M Delgoffe
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA.
- Tumor Microenvironment Center and Department of Immunology, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA.
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Alvarez S, Vanasco V, Adán Areán JS, Magnani N, Evelson P. Mitochondrial Mechanisms in Immunity and Inflammatory Conditions: Beyond Energy Management. Antioxid Redox Signal 2024. [PMID: 38062738 DOI: 10.1089/ars.2023.0367] [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] [Indexed: 01/25/2024]
Abstract
Significance: The growing importance of mitochondria in the immune response and inflammation is multifaceted. Unraveling the different mechanisms by which mitochondria have a relevant role in the inflammatory response beyond the energy management of the process is necessary for improving our understanding of the host immune defense and the pathogenesis of various inflammatory diseases and syndromes. Critical Issues: Mitochondria are relevant in the immune response at different levels, including releasing activation molecules, changing its structure and function to accompany the immune response, and serving as a structural base for activating intermediates as NLRP3 inflammasome. In this scientific journey of dissecting mitochondrial mechanisms, new questions and interesting aspects arise, such as the involvement of mitochondrial-derived vesicles in the immune response with the putative role of preventing uncontrolled situations. Recent Advances: Researchers are continuously rethinking the role of mitochondria in acute and chronic inflammation and related disorders. As such, mitochondria have important roles as centrally positioned signaling hubs in regulating inflammatory and immune responses. In this review, we present the current understanding of mitochondrial mechanisms involved, beyond the largely known mitochondrial dysfunction, in the onset and development of inflammatory situations. Future Directions: Mitochondria emerge as an interesting and multifaceted platform for studying and developing pharmaceutical and therapeutic approaches. There are many ongoing studies aimed to describe the effects of specific mitochondrial targeted molecules and treatments to ameliorate the consequences of exacerbated inflammatory components of pathologies and syndromes, resulting in an open area of increasing research interest.
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Affiliation(s)
- Silvia Alvarez
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Fisicoquímica, CABA, Argentina
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Química General e Inorgánica, CABA, Argentina
| | - Virginia Vanasco
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Fisicoquímica, CABA, Argentina
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Química General e Inorgánica, CABA, Argentina
| | - Juan Santiago Adán Areán
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Fisicoquímica, CABA, Argentina
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Química General e Inorgánica, CABA, Argentina
| | - Natalia Magnani
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Química General e Inorgánica, CABA, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Bioquímica y Medicina Molecular (IBIMOL), Buenos Aires, CABA, Argentina
| | - Pablo Evelson
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Química General e Inorgánica, CABA, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Bioquímica y Medicina Molecular (IBIMOL), Buenos Aires, CABA, Argentina
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Hirose M, Sekar P, Eladham MWA, Albataineh MT, Rahmani M, Ibrahim SM. Interaction between mitochondria and microbiota modulating cellular metabolism in inflammatory bowel disease. J Mol Med (Berl) 2023; 101:1513-1526. [PMID: 37819377 PMCID: PMC10698103 DOI: 10.1007/s00109-023-02381-w] [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: 07/24/2023] [Revised: 09/06/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
Inflammatory bowel disease (IBD) is a prototypic complex disease in the gastrointestinal tract that has been increasing in incidence and prevalence in recent decades. Although the precise pathophysiology of IBD remains to be elucidated, a large body of evidence suggests the critical roles of mitochondria and intestinal microbiota in the pathogenesis of IBD. In addition to their contributions to the disease, both mitochondria and gut microbes may interact with each other and modulate disease-causing cell activities. Therefore, we hypothesize that dissecting this unique interaction may help to identify novel pathways involved in IBD, which will further contribute to discovering new therapeutic approaches to the disease. As poorly treated IBD significantly affects the quality of life of patients and is associated with risks and complications, successful treatment is crucial. In this review, we stratify previously reported experimental and clinical observations of the role of mitochondria and intestinal microbiota in IBD. Additionally, we review the intercommunication between mitochondria, and the intestinal microbiome in patients with IBD is reviewed along with the potential mediators for these interactions. We specifically focus on their roles in cellular metabolism in intestinal epithelial cells and immune cells. To this end, we propose a potential therapeutic intervention strategy for IBD.
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Affiliation(s)
- Misa Hirose
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Priyadharshini Sekar
- Sharjah Institute of Medical Research, RIMHS, University of Sharjah, Sharjah, United Arab Emirates
| | | | - Mohammad T Albataineh
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Mohamed Rahmani
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Saleh Mohamed Ibrahim
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates.
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40
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Richard AC, Ma CY, Marioni JC, Griffiths GM. Cytotoxic T lymphocytes require transcription for infiltration but not target cell lysis. EMBO Rep 2023; 24:e57653. [PMID: 37860838 PMCID: PMC10626425 DOI: 10.15252/embr.202357653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023] Open
Abstract
Effector cytotoxic T lymphocytes (CTLs) are critical for ridding the body of infected or cancerous cells. CTL T cell receptor (TCR) ligation not only drives the delivery and release of cytolytic granules but also initiates a new wave of transcription. In order to address whether TCR-induced transcriptomic changes impact the ability of CTLs to kill, we asked which genes are expressed immediately after CTLs encounter targets and how CTL responses change when inhibiting transcription. Our data demonstrate that while expression of cytokines/chemokines and transcriptional machinery depend on transcription, cytotoxic protein expression and cytolytic activity are relatively robust to transcription blockade, with CTLs lysing nearby target cells for several hours after actinomycin D treatment. Monitoring CTL movement among target cells after inhibiting transcription demonstrates an infiltration defect that is not rectified by provision of exogenous cytokine/chemokine gradients, indicating a cell-intrinsic transcriptional requirement for infiltration. Together, our results reveal differential molecular control of CTL functions, separating recruitment and infiltration from cytolysis.
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Affiliation(s)
- Arianne C Richard
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Present address:
Immunology ProgrammeThe Babraham InstituteCambridgeUK
| | - Claire Y Ma
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | - John C Marioni
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)HinxtonUK
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41
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Xu X, Chen Z, Bartman CR, Xing X, Olszewski K, Rabinowitz JD. One-carbon unit supplementation fuels tumor-infiltrating T cells and augments checkpoint blockade. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.01.565193. [PMID: 37961420 PMCID: PMC10635052 DOI: 10.1101/2023.11.01.565193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Nucleotides perform important metabolic functions, carrying energy and feeding nucleic acid synthesis. Here, we use isotope tracing-mass spectrometry to quantitate the contributions to purine nucleotides of salvage versus de novo synthesis. We further explore the impact of augmenting a key precursor for purine synthesis, one-carbon (1C) units. We show that tumors and tumor-infiltrating T cells (relative to splenic T cells) synthesize purines de novo. Purine synthesis requires two 1C units, which come from serine catabolism and circulating formate. Shortage of 1C units is a potential bottleneck for anti-tumor immunity. Elevating circulating formate drives its usage by tumor-infiltrating T cells. Orally administered methanol functions as a formate pro-drug, with deuteration enabling control of formate-production kinetics. In MC38 tumors, safe doses of methanol raise formate levels and augment anti-PD-1 checkpoint blockade, tripling durable regressions. Thus, 1C deficiency can gate antitumor immunity and this metabolic checkpoint can be overcome with pharmacological 1C supplementation.
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Affiliation(s)
- Xincheng Xu
- Department of Chemistry, Princeton University
- Lewis-Sigler Institute for Integrative Genomics, Princeton University
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University
- These authors contributed equally
| | - Zihong Chen
- Department of Chemistry, Princeton University
- Lewis-Sigler Institute for Integrative Genomics, Princeton University
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University
- These authors contributed equally
| | - Caroline R Bartman
- Department of Chemistry, Princeton University
- Lewis-Sigler Institute for Integrative Genomics, Princeton University
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University
| | - Xi Xing
- Department of Chemistry, Princeton University
- Lewis-Sigler Institute for Integrative Genomics, Princeton University
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University
| | - Kellen Olszewski
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University
- These authors contributed equally
| | - Joshua D Rabinowitz
- Department of Chemistry, Princeton University
- Lewis-Sigler Institute for Integrative Genomics, Princeton University
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University
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42
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Li Y, Chen Z, Cui J, Yu J, Niu Y, Ran S, Wang S, Ye W, Xu H, Zhang X, Wu J, Xia J. MTHFD2 ablation in T cells protects against heart transplant rejection by perturbing IRF4/PD-1 pathway through the metabolic-epigenetic nexus. J Heart Lung Transplant 2023; 42:1608-1620. [PMID: 37495036 DOI: 10.1016/j.healun.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 07/10/2023] [Accepted: 07/15/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND One-carbon metabolism supports the activation, proliferation, and function of multiple immune cells. However, researchers have not clearly determined whether and how one-carbon metabolic enzymes contribute to heart transplant rejection. METHODS We investigated the dynamic metabolic adaptation in grafts during heart transplant rejection by conducting transcriptomics, metabolomics and single-cell RNA sequencing studies of cardiac tissue from human and mouse heart transplant recipients. We also assessed the expression of the one-carbon metabolic enzyme methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) in cardiac grafts by immunofluorescence and flow cytometry assays. Then we constructed a murine heart transplant model with T cell-specific Mthfd2 knockout mice, analyzed T cells function by flow cytometry assays and enzyme-linked immunospot assays, and studied the mechanism by Cleavage Under Targets and Tagmentation assays. Finally, we studied the effect of a pharmacological inhibitor of MTHFD2 in humanized skin transplant model. RESULTS We revealed that the one-carbon metabolism enzyme MTHFD2 was a hallmark of alloreactive T cells and was linked to T cell proliferation and function after exposure to alloantigen. And, Mthfd2 ablation prevented murine heart transplant rejection. Mechanistically, we found Mthfd2 ablation affected the interferon regulatory factor 4/programmed death-1 pathway through a metabolic-epigenetic mechanism involving H3K4me3. Furthermore, we found that inhibiting MTHFD2 attenuated human allograft rejection in a humanized skin transplant model. CONCLUSIONS These data show that the one-carbon metabolic enzyme MTHFD2 serves as a metabolic checkpoint of alloreactive T cells and suggest that it may be a potential therapeutic target for heart transplant rejection.
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Affiliation(s)
- Yuan Li
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhang Chen
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jikai Cui
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jizhang Yu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuqing Niu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuan Ran
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Song Wang
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weicong Ye
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Heng Xu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xi Zhang
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Jie Wu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China.
| | - Jiahong Xia
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China.
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43
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Xu Y, Chiang YH, Ho PC, Vannini N. Mitochondria Dictate Function and Fate of HSCs and T Cells. Cancer Immunol Res 2023; 11:1303-1313. [PMID: 37789763 DOI: 10.1158/2326-6066.cir-22-0685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 01/23/2023] [Accepted: 08/16/2023] [Indexed: 10/05/2023]
Abstract
Hematopoietic stem cells (HSC) and T cells are intimately related, lineage-dependent cell populations that are extensively used as therapeutic products for the treatment of hematologic malignancies and certain types of solid tumors. These cellular therapies can be life-saving treatments; however, their efficacies are often limited by factors influencing their activity and cellular properties. Among these factors is mitochondrial metabolism, which influences the function and fate commitment of both HSCs and T cells. Mitochondria, besides being the "cellular powerhouse," provide metabolic intermediates that are used as substrates for epigenetic modifications and chromatin remodeling, thus, driving cell fate decisions during differentiation. Moreover, mitochondrial fitness and mitochondrial quality control mechanisms are closely related to cellular function, and impairment of these mitochondrial properties associates with cellular dysfunction due to factors such as T-cell exhaustion and aging. Here, we give an overview of the role of mitochondria in shaping the behavior of these lineage-related cell populations. Moreover, we discuss the potential of novel mitochondria-targeting strategies for enhancing HSC- and T cell-based cancer immunotherapies and highlight how design and application of such approaches requires consideration of the metabolic similarities and differences between HSCs and T cells. See related article on p. 1302.
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Affiliation(s)
- Yingxi Xu
- Department of Fundamental Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Yi-Hsuan Chiang
- Department of Fundamental Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Ping-Chih Ho
- Department of Fundamental Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Nicola Vannini
- Department of Fundamental Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
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44
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Zhou L, Wang S, Hu W, Liu X, Xu L, Tong B, Zhang T, Xue Z, Guo Y, Zhao J, Lu L, Fan H, Qian W, Chen J, Chen W, Wang L. T cell proliferation requires ribosomal maturation in nucleolar condensates dependent on DCAF13. J Cell Biol 2023; 222:e202201096. [PMID: 37615668 PMCID: PMC10450623 DOI: 10.1083/jcb.202201096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/16/2023] [Accepted: 07/31/2023] [Indexed: 08/25/2023] Open
Abstract
T cells require rapid proliferation to initiate adaptive immunity to prevent pathogen attacks. The nucleolus, a distinct subnuclear membrane-less compartment for ribosomal biogenesis, is indispensable for cell proliferation. However, specific nucleolar proteins involved in rapid T cell proliferation and their underlying molecular regulatory mechanism remain elusive. Here, we identified an essential nucleolar protein, DCAF13, in T cells and revealed its significant regulation of rapid T cell proliferation. Its depletion drastically impairs T cell proliferation due to severe 18S rRNA maturation failure, consequent abnormal ribosome assembly in nucleoli, and insufficient production of nascent proteins. Mechanistically, we propose that DCAF13 promotes NPM1 phase separation to accelerate pre-RNA enrichment and its endonuclease UTP23 for 18S rRNA maturation during T cell proliferation. Our findings reveal the modulatory effect of nucleolar NPM1/DCAF13 phase separation on ribosomal maturation to ensure rapid T cell proliferation and further pathogen clearance for the first time.
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Affiliation(s)
- Lina Zhou
- Bone Marrow Transplantation Center and Institute of Immunology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Shuai Wang
- Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Hu
- Zhejiang University School of Medicine, Hangzhou, China
- Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoqian Liu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Lingdong Xu
- Laboratory Animal Center, Zhejiang University, Hangzhou, China
| | - Bolu Tong
- Zhejiang University School of Medicine, Hangzhou, China
| | - Tongtong Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The Center for Integrated Oncology and Precision Medicine, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhonghui Xue
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yixin Guo
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Haining, China
| | - Jing Zhao
- Department of Pathology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Linrong Lu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Hengyu Fan
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Wenbin Qian
- Department of Hematology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jian Chen
- Department of General Surgery of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Wei Chen
- Zhejiang University School of Medicine, Hangzhou, China
- Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Lie Wang
- Bone Marrow Transplantation Center and Institute of Immunology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Laboratory Animal Center, Zhejiang University, Hangzhou, China
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45
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Lee H, Jeon JH, Kim ES. Mitochondrial dysfunctions in T cells: focus on inflammatory bowel disease. Front Immunol 2023; 14:1219422. [PMID: 37809060 PMCID: PMC10556505 DOI: 10.3389/fimmu.2023.1219422] [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: 05/09/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
Mitochondria has emerged as a critical ruler of metabolic reprogramming in immune responses and inflammation. In the context of colitogenic T cells and IBD, there has been increasing research interest in the metabolic pathways of glycolysis, pyruvate oxidation, and glutaminolysis. These pathways have been shown to play a crucial role in the metabolic reprogramming of colitogenic T cells, leading to increased inflammatory cytokine production and tissue damage. In addition to metabolic reprogramming, mitochondrial dysfunction has also been implicated in the pathogenesis of IBD. Studies have shown that colitogenic T cells exhibit impaired mitochondrial respiration, elevated levels of mROS, alterations in calcium homeostasis, impaired mitochondrial biogenesis, and aberrant mitochondria-associated membrane formation. Here, we discuss our current knowledge of the metabolic reprogramming and mitochondrial dysfunctions in colitogenic T cells, as well as the potential therapeutic applications for treating IBD with evidence from animal experiments.
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Affiliation(s)
- Hoyul Lee
- Research Institute of Aging and Metabolism, Kyungpook National University, Daegu, Republic of Korea
| | - Jae-Han Jeon
- Research Institute of Aging and Metabolism, Kyungpook National University, Daegu, Republic of Korea
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea
| | - Eun Soo Kim
- Division of Gastroenterology, Department of Internal Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Republic of Korea
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46
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Coleman C, Wang M, Wang E, Micallef C, Shao Z, Vicari JM, Li Y, Yu K, Cai D, Peng J, Haroutunian V, Fullard JF, Bendl J, Zhang B, Roussos P. Multi-omic atlas of the parahippocampal gyrus in Alzheimer's disease. Sci Data 2023; 10:602. [PMID: 37684260 PMCID: PMC10491684 DOI: 10.1038/s41597-023-02507-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia worldwide, with a projection of 151 million cases by 2050. Previous genetic studies have identified three main genes associated with early-onset familial Alzheimer's disease, however this subtype accounts for less than 5% of total cases. Next-generation sequencing has been well established and holds great promise to assist in the development of novel therapeutics as well as biomarkers to prevent or slow the progression of this devastating disease. Here we present a public resource of functional genomic data from the parahippocampal gyrus of 201 postmortem control, mild cognitively impaired (MCI) and AD individuals from the Mount Sinai brain bank, of which whole-genome sequencing (WGS), and bulk RNA sequencing (RNA-seq) were previously published. The genomic data include bulk proteomics and DNA methylation, as well as cell-type-specific RNA-seq and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) data. We have performed extensive preprocessing and quality control, allowing the research community to access and utilize this public resource available on the Synapse platform at https://doi.org/10.7303/syn51180043.2 .
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Affiliation(s)
- Claire Coleman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Erming Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Courtney Micallef
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zhiping Shao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - James M Vicari
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yuxin Li
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kaiwen Yu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Dongming Cai
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA
- Alzheimer Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Vahram Haroutunian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John F Fullard
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jaroslav Bendl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA.
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47
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Escrig-Larena JI, Delgado-Pulido S, Mittelbrunn M. Mitochondria during T cell aging. Semin Immunol 2023; 69:101808. [PMID: 37473558 DOI: 10.1016/j.smim.2023.101808] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/30/2023] [Accepted: 07/10/2023] [Indexed: 07/22/2023]
Abstract
Mitochondrial dysfunction is a hallmark of aging that contributes to inflammaging. It is characterized by alterations of the mitochondrial DNA, reduced respiratory capacity, decreased mitochondrial membrane potential and increased reactive oxygen species production. These primary alterations disrupt other interconnected and important mitochondrial-related processes such as metabolism, mitochondrial dynamics and biogenesis, mitophagy, calcium homeostasis or apoptosis. In this review, we gather the current knowledge about the different mitochondrial processes which are altered during aging, with special focus on their contribution to age-associated T cell dysfunction and inflammaging.
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Affiliation(s)
- Jose Ignacio Escrig-Larena
- Consejo Superior de Investigaciones Científicas (CSIC), Centro de Biología Molcular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Sandra Delgado-Pulido
- Departamento de Biología Molecular, Facultad de Ciencias (UAM), Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - María Mittelbrunn
- Consejo Superior de Investigaciones Científicas (CSIC), Centro de Biología Molcular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid (UAM), Madrid, Spain.
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48
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Salerno F, Howden AJM, Matheson LS, Gizlenci Ö, Screen M, Lingel H, Brunner-Weinzierl MC, Turner M. An integrated proteome and transcriptome of B cell maturation defines poised activation states of transitional and mature B cells. Nat Commun 2023; 14:5116. [PMID: 37612319 PMCID: PMC10447577 DOI: 10.1038/s41467-023-40621-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 08/03/2023] [Indexed: 08/25/2023] Open
Abstract
During B cell maturation, transitional and mature B cells acquire cell-intrinsic features that determine their ability to exit quiescence and mount effective immune responses. Here we use label-free proteomics to quantify the proteome of B cell subsets from the mouse spleen and map the differential expression of environmental sensing, transcription, and translation initiation factors that define cellular identity and function. Cross-examination of the full-length transcriptome and proteome identifies mRNAs related to B cell activation and antibody secretion that are not accompanied by detection of the encoded proteins. In addition, proteomic data further suggests that the translational repressor PDCD4 restrains B cell responses, in particular those from marginal zone B cells, to a T-cell independent antigen. In summary, our molecular characterization of B cell maturation presents a valuable resource to further explore the mechanisms underpinning the specialized functions of B cell subsets, and suggest the presence of 'poised' mRNAs that enable expedited B cell responses.
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Affiliation(s)
- Fiamma Salerno
- Immunology programme, The Babraham Institute, Cambridge, UK.
| | | | | | - Özge Gizlenci
- Immunology programme, The Babraham Institute, Cambridge, UK
| | - Michael Screen
- Immunology programme, The Babraham Institute, Cambridge, UK
| | - Holger Lingel
- Department of Experimental Pediatrics, Otto-von-Guericke-University, Magdeburg, Germany
| | | | - Martin Turner
- Immunology programme, The Babraham Institute, Cambridge, UK.
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49
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Chen L, Zhou M, Li H, Liu D, Liao P, Zong Y, Zhang C, Zou W, Gao J. Mitochondrial heterogeneity in diseases. Signal Transduct Target Ther 2023; 8:311. [PMID: 37607925 PMCID: PMC10444818 DOI: 10.1038/s41392-023-01546-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 02/21/2023] [Accepted: 06/13/2023] [Indexed: 08/24/2023] Open
Abstract
As key organelles involved in cellular metabolism, mitochondria frequently undergo adaptive changes in morphology, components and functions in response to various environmental stresses and cellular demands. Previous studies of mitochondria research have gradually evolved, from focusing on morphological change analysis to systematic multiomics, thereby revealing the mitochondrial variation between cells or within the mitochondrial population within a single cell. The phenomenon of mitochondrial variation features is defined as mitochondrial heterogeneity. Moreover, mitochondrial heterogeneity has been reported to influence a variety of physiological processes, including tissue homeostasis, tissue repair, immunoregulation, and tumor progression. Here, we comprehensively review the mitochondrial heterogeneity in different tissues under pathological states, involving variant features of mitochondrial DNA, RNA, protein and lipid components. Then, the mechanisms that contribute to mitochondrial heterogeneity are also summarized, such as the mutation of the mitochondrial genome and the import of mitochondrial proteins that result in the heterogeneity of mitochondrial DNA and protein components. Additionally, multiple perspectives are investigated to better comprehend the mysteries of mitochondrial heterogeneity between cells. Finally, we summarize the prospective mitochondrial heterogeneity-targeting therapies in terms of alleviating mitochondrial oxidative damage, reducing mitochondrial carbon stress and enhancing mitochondrial biogenesis to relieve various pathological conditions. The possibility of recent technological advances in targeted mitochondrial gene editing is also discussed.
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Affiliation(s)
- Long Chen
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Sciences, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Mengnan Zhou
- Department of Pathogenic Biology, School of Basic Medical Science, China Medical University, Shenyang, 110001, China
| | - Hao Li
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Delin Liu
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Peng Liao
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Yao Zong
- Centre for Orthopaedic Research, Medical School, The University of Western Australia, Nedlands, WA, 6009, Australia
| | - Changqing Zhang
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China.
| | - Weiguo Zou
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Sciences, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
- Institute of Microsurgery on Extremities, and Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China.
| | - Junjie Gao
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China.
- Institute of Microsurgery on Extremities, and Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China.
- Shanghai Sixth People's Hospital Fujian, No. 16, Luoshan Section, Jinguang Road, Luoshan Street, Jinjiang City, Quanzhou, Fujian, China.
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50
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Sun S, Tranchina D, Gresham D. Parallel proteomics and phosphoproteomics defines starvation signal specific processes in cell quiescence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551843. [PMID: 37577636 PMCID: PMC10418281 DOI: 10.1101/2023.08.03.551843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Cells arrest growth and enter a quiescent state upon nutrient deprivation. However, the molecular processes by which cells respond to different starvation signals to regulate exit from the cell division cycle and initiation of quiescence remains poorly understood. To study the role of protein expression and signaling in quiescence we combined temporal profiling of the proteome and phosphoproteome using stable isotope labeling with amino acids in cell culture (SILAC) in Saccharomyces cerevisiae (budding yeast). We find that carbon and phosphorus starvation signals activate quiescence through largely distinct remodeling of the proteome and phosphoproteome. However, increased expression of mitochondrial proteins is associated with quiescence establishment in response to both starvation signals. Deletion of the putative quiescence regulator RIM15, which encodes a serine-threonine kinase, results in reduced survival of cells starved for phosphorus and nitrogen, but not carbon. However, we identified common protein phosphorylation roles for RIM15 in quiescence that are enriched for RNA metabolism and translation. We also find evidence for RIM15-mediated phosphorylation of some targets, including IGO1, prior to starvation consistent with a functional role for RIM15 in proliferative cells. Finally, our results reveal widespread catabolism of amino acids in response to nitrogen starvation, indicating widespread amino acid recycling via salvage pathways in conditions lacking environmental nitrogen. Our study defines an expanded quiescent proteome and phosphoproteome in yeast, and highlights the multiple coordinated molecular processes at the level of protein expression and phosphorylation that are required for quiescence.
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Affiliation(s)
- Siyu Sun
- Center for Genomics and Systems Biology
- Department of Biology, New York University, New York, NY, 10003, USA
| | - Daniel Tranchina
- Department of Biology, New York University, New York, NY, 10003, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY, 10003, USA
| | - David Gresham
- Center for Genomics and Systems Biology
- Department of Biology, New York University, New York, NY, 10003, USA
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