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Karmaus PWF. Application of Single Cell Methods in Immunometabolism and Immunotoxicology. CURRENT OPINION IN TOXICOLOGY 2024; 39:100488. [PMID: 39091379 PMCID: PMC11290472 DOI: 10.1016/j.cotox.2024.100488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Recent developments of novel single-cell analysis techniques have rapidly advanced the fields of immunotoxicology and immunometabolism. Single-cell analyses enable the characterization of immune cells, unraveling heterogeneity, and population dynamics in response to cellular perturbations, including toxicant insults and changes in cellular metabolism. This review provides an overview of current technologies and recent discoveries, illustrating an emerging role of single-cell analyses in the field of immunotoxicology and immunometabolism. Various single-cell techniques, including flow cytometry, mass cytometry, multiplexed imaging, and sequencing, together with their applications to studying immunotoxicology and immunometabolism are discussed. This review emphasizes the potential for single-cell analyses to revolutionize our understanding of immune cell heterogeneity, uncover novel cellular therapeutic targets, and pave the way for novel mechanistic insights.
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Affiliation(s)
- Peer W F Karmaus
- National Institute of Environmental Health Sciences, US
- Institute for Integrative Toxicology, Michigan State University, US
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2
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Kundu P, Beura S, Mondal S, Das AK, Ghosh A. Machine learning for the advancement of genome-scale metabolic modeling. Biotechnol Adv 2024; 74:108400. [PMID: 38944218 DOI: 10.1016/j.biotechadv.2024.108400] [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: 10/25/2023] [Revised: 05/13/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024]
Abstract
Constraint-based modeling (CBM) has evolved as the core systems biology tool to map the interrelations between genotype, phenotype, and external environment. The recent advancement of high-throughput experimental approaches and multi-omics strategies has generated a plethora of new and precise information from wide-ranging biological domains. On the other hand, the continuously growing field of machine learning (ML) and its specialized branch of deep learning (DL) provide essential computational architectures for decoding complex and heterogeneous biological data. In recent years, both multi-omics and ML have assisted in the escalation of CBM. Condition-specific omics data, such as transcriptomics and proteomics, helped contextualize the model prediction while analyzing a particular phenotypic signature. At the same time, the advanced ML tools have eased the model reconstruction and analysis to increase the accuracy and prediction power. However, the development of these multi-disciplinary methodological frameworks mainly occurs independently, which limits the concatenation of biological knowledge from different domains. Hence, we have reviewed the potential of integrating multi-disciplinary tools and strategies from various fields, such as synthetic biology, CBM, omics, and ML, to explore the biochemical phenomenon beyond the conventional biological dogma. How the integrative knowledge of these intersected domains has improved bioengineering and biomedical applications has also been highlighted. We categorically explained the conventional genome-scale metabolic model (GEM) reconstruction tools and their improvement strategies through ML paradigms. Further, the crucial role of ML and DL in omics data restructuring for GEM development has also been briefly discussed. Finally, the case-study-based assessment of the state-of-the-art method for improving biomedical and metabolic engineering strategies has been elaborated. Therefore, this review demonstrates how integrating experimental and in silico strategies can help map the ever-expanding knowledge of biological systems driven by condition-specific cellular information. This multiview approach will elevate the application of ML-based CBM in the biomedical and bioengineering fields for the betterment of society and the environment.
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Affiliation(s)
- Pritam Kundu
- School School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Satyajit Beura
- Department of Bioscience and Biotechnology, Indian Institute of Technology, Kharagpur, West Bengal 721302, India
| | - Suman Mondal
- P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Amit Kumar Das
- Department of Bioscience and Biotechnology, Indian Institute of Technology, Kharagpur, West Bengal 721302, India
| | - Amit Ghosh
- School School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India; P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
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3
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Jiang X, Baig AH, Palazzo G, Del Pizzo R, Bortecen T, Groessl S, Zaal EA, Amaya Ramirez CC, Kowar A, Aviles-Huerta D, Berkers CR, Palm W, Tschaharganeh D, Krijgsveld J, Loayza-Puch F. P53-dependent hypusination of eIF5A affects mitochondrial translation and senescence immune surveillance. Nat Commun 2024; 15:7458. [PMID: 39198484 PMCID: PMC11358140 DOI: 10.1038/s41467-024-51901-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: 07/03/2023] [Accepted: 08/19/2024] [Indexed: 09/01/2024] Open
Abstract
Cellular senescence is characterized by a permanent growth arrest and is associated with tissue aging and cancer. Senescent cells secrete a number of different cytokines referred to as the senescence-associated secretory phenotype (SASP), which impacts the surrounding tissue and immune response. Here, we find that senescent cells exhibit higher rates of protein synthesis compared to proliferating cells and identify eIF5A as a crucial regulator of this process. Polyamine metabolism and hypusination of eIF5A play a pivotal role in sustaining elevated levels of protein synthesis in senescent cells. Mechanistically, we identify a p53-dependent program in senescent cells that maintains hypusination levels of eIF5A. Finally, we demonstrate that functional eIF5A is required for synthesizing mitochondrial ribosomal proteins and monitoring the immune clearance of premalignant senescent cells in vivo. Our findings establish an important role of protein synthesis during cellular senescence and suggest a link between eIF5A, polyamine metabolism, and senescence immune surveillance.
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Affiliation(s)
- Xiangli Jiang
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany, Heidelberg, Germany
- Department of Thoracic Oncology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Ali Hyder Baig
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany, Heidelberg, Germany
| | - Giuliana Palazzo
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Rossella Del Pizzo
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Toman Bortecen
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
- Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sven Groessl
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
- Division of Cell Signaling and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Esther A Zaal
- Division of Cell Biology, Metabolism and Cancer, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, CL, Utrecht, The Netherlands
| | - Cinthia Claudia Amaya Ramirez
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany, Heidelberg, Germany
| | - Alexander Kowar
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Daniela Aviles-Huerta
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Celia R Berkers
- Division of Cell Biology, Metabolism and Cancer, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, CL, Utrecht, The Netherlands
| | - Wilhelm Palm
- Division of Cell Signaling and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Darjus Tschaharganeh
- Cell Plasticity and Epigenetic Remodeling, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Jeroen Krijgsveld
- Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Fabricio Loayza-Puch
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany, Heidelberg, Germany.
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Brown EM, Nguyen PNU, Xavier RJ. Emerging biochemical, microbial and immunological evidence in the search for why HLA-B ∗27 confers risk for spondyloarthritis. Cell Chem Biol 2024:S2451-9456(24)00314-3. [PMID: 39168118 DOI: 10.1016/j.chembiol.2024.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/25/2024] [Accepted: 07/22/2024] [Indexed: 08/23/2024]
Abstract
The strong association of the human leukocyte antigen B∗27 alleles (HLA-B∗27) with spondyloarthritis and related rheumatic conditions has long fascinated researchers, yet the precise mechanisms underlying its pathogenicity remain elusive. Here, we review how interplay between the microbiome, the immune system, and the enigmatic HLA-B∗27 could trigger spondyloarthritis, with a focus on whether HLA-B∗27 presents an arthritogenic peptide. We propose mechanisms by which the unique biochemical characteristics of the HLA-B∗27 protein structure, particularly its peptide binding groove, could dictate its propensity to induce pathological T cell responses. We further provide new insights into how TRBV9+ CD8+ T cells are implicated in the disease process, as well as how the immunometabolism of T cells modulates tissue-specific inflammatory responses in spondyloarthritis. Finally, we present testable models and suggest approaches to this problem in future studies given recent advances in computational biology, chemical biology, structural biology, and small-molecule therapeutics.
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Affiliation(s)
- Eric M Brown
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | | | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.
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McCain JSP, Britten GL, Hackett SR, Follows MJ, Li GW. Microbial reaction rate estimation using proteins and proteomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.13.607198. [PMID: 39185172 PMCID: PMC11343155 DOI: 10.1101/2024.08.13.607198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Microbes transform their environments using diverse enzymatic reactions. However, it remains challenging to measure microbial reaction rates in natural environments. Despite advances in global quantification of enzyme abundances, the individual relationships between enzyme abundances and their reaction rates have not been systematically examined. Using matched proteomic and reaction rate data from microbial cultures, we show that enzyme abundance is often insufficient to predict its corresponding reaction rate. However, we discovered that global proteomic measurements can be used to make accurate rate predictions of individual reaction rates (median R 2 = 0.78). Accurate rate predictions required only a small number of proteins and they did not need explicit prior mechanistic knowledge or environmental context. These results indicate that proteomes are encoders of cellular reaction rates, potentially enabling proteomic measurements in situ to estimate the rates of microbially mediated reactions in natural systems. Significance One of the most basic phenotypes of a microbe is its set of associated reaction rates, but quantifying these rates in situ remains extremely challenging, especially in natural systems. We used molecular data and statistical models to estimate microbial rates in steady state cultures. We found that many reaction rates are highly predictable using proteomic data, though single proteins are typically not informative for their associated reaction rates. This result suggests that gene expression data from complex microbial communities could be used to estimate in situ reaction rates, providing new clues into the lives and environmental function of microbes.
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Liu S, Gao Y, Feng X, Xu Y, Hu M, Fei H, Zheng H, Huang J, Li T, Zhao C, Sun L. A novel study on CXXC5: unraveling its regulatory mechanisms in hematopoietic stem cell biology through proteomics and gene editing. Genes Genomics 2024:10.1007/s13258-024-01540-8. [PMID: 39150611 DOI: 10.1007/s13258-024-01540-8] [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: 03/05/2024] [Accepted: 06/05/2024] [Indexed: 08/17/2024]
Abstract
BACKGROUND This study investigates the role of CXXC5 in the self-renewal and differentiation of hematopoietic stem cells (HSCs) within the bone marrow microenvironment, utilizing advanced methodologies such as single-cell RNA sequencing (scRNA-seq), CRISPR-Cas9, and proteomic analysis. METHODS We employed flow cytometry to isolate HSCs from bone marrow samples, followed by scRNA-seq analysis using the 10x Genomics platform to examine cell clustering and CXXC5 expression patterns. CRISPR-Cas9 and lentiviral vectors facilitated the knockout and overexpression of CXXC5 in HSCs. The impact on HSCs was assessed through qRT-PCR, Western blot, CCK-8, CFU, and LTC-IC assays, alongside flow cytometry to measure apoptosis and cell proportions. A mouse model was also used to evaluate the effects of CXXC5 manipulation on HSC engraftment and survival rates. RESULTS Our findings highlight the diversity of cell clustering and the significant role of CXXC5 in HSC regulation. Knockout experiments showed reduced proliferation and accelerated differentiation, whereas overexpression led to enhanced proliferation and delayed differentiation. Proteomic analysis identified key biological processes influenced by CXXC5, including cell proliferation, differentiation, and apoptosis. In vivo results demonstrated that CXXC5 silencing impaired HSC engraftment in a bone marrow transplantation model. CONCLUSION CXXC5 is crucial for the regulation of HSC self-renewal and differentiation in the bone marrow microenvironment. Its manipulation presents a novel approach for enhancing HSC function and provides a potential therapeutic target for hematological diseases.
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Affiliation(s)
- Shanshan Liu
- Department of Hematology, The Affiliated Hospital of Qingdao University, No.16, Jiangsu Road, Shinan District, Qingdao, Shandong Province, China
| | - Yan Gao
- Department of Hematology, The Affiliated Hospital of Qingdao University, No.16, Jiangsu Road, Shinan District, Qingdao, Shandong Province, China
| | - Xianqi Feng
- Department of Hematology, The Affiliated Hospital of Qingdao University, No.16, Jiangsu Road, Shinan District, Qingdao, Shandong Province, China
| | - Yujie Xu
- Department of Hematology, The Affiliated Hospital of Qingdao University, No.16, Jiangsu Road, Shinan District, Qingdao, Shandong Province, China
| | - Minghui Hu
- Clinical Lab, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hairong Fei
- Department of Hematology, The Affiliated Hospital of Qingdao University, No.16, Jiangsu Road, Shinan District, Qingdao, Shandong Province, China
| | - Hongying Zheng
- Clinical Lab, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Junxia Huang
- Department of Hematology, The Affiliated Hospital of Qingdao University, No.16, Jiangsu Road, Shinan District, Qingdao, Shandong Province, China
| | - Tianlan Li
- Department of Hematology, The Affiliated Hospital of Qingdao University, No.16, Jiangsu Road, Shinan District, Qingdao, Shandong Province, China
| | - Chunting Zhao
- Department of Hematology, The Affiliated Hospital of Qingdao University, No.16, Jiangsu Road, Shinan District, Qingdao, Shandong Province, China.
| | - Lingjie Sun
- Department of Hematology, The Affiliated Hospital of Qingdao University, No.16, Jiangsu Road, Shinan District, Qingdao, Shandong Province, China.
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Chang S, Wang Z, An T. T-Cell Metabolic Reprogramming in Atherosclerosis. Biomedicines 2024; 12:1844. [PMID: 39200308 PMCID: PMC11352190 DOI: 10.3390/biomedicines12081844] [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: 07/13/2024] [Revised: 08/05/2024] [Accepted: 08/10/2024] [Indexed: 09/02/2024] Open
Abstract
Atherosclerosis is a key pathological basis for cardiovascular diseases, significantly influenced by T-cell-mediated immune responses. T-cells differentiate into various subtypes, such as pro-inflammatory Th1/Th17 and anti-inflammatory Th2/Treg cells. The imbalance between these subtypes is critical for the progression of atherosclerosis (AS). Recent studies indicate that metabolic reprogramming within various microenvironments can shift T-cell differentiation towards pro-inflammatory or anti-inflammatory phenotypes, thus influencing AS progression. This review examines the roles of pro-inflammatory and anti-inflammatory T-cells in atherosclerosis, focusing on how their metabolic reprogramming regulates AS progression and the associated molecular mechanisms of mTOR and AMPK signaling pathways.
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Affiliation(s)
| | | | - Tianhui An
- Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (S.C.); (Z.W.)
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Xu H, Zhang X, Wang X, Li B, Yu H, Quan Y, Jiang Y, You Y, Wang Y, Wen M, Liu J, Wang M, Zhang B, Li Y, Zhang X, Lu Q, Yu CY, Cao X. Cellular spermine targets JAK signaling to restrain cytokine-mediated autoimmunity. Immunity 2024; 57:1796-1811.e8. [PMID: 38908373 DOI: 10.1016/j.immuni.2024.05.025] [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: 04/13/2023] [Revised: 10/06/2023] [Accepted: 05/30/2024] [Indexed: 06/24/2024]
Abstract
Prolonged activation of the type I interferon (IFN-I) pathway leads to autoimmune diseases such as systemic lupus erythematosus (SLE). Metabolic regulation of cytokine signaling is critical for cellular homeostasis. Through metabolomics analyses of IFN-β-activated macrophages and an IFN-stimulated-response-element reporter screening, we identified spermine as a metabolite brake for Janus kinase (JAK) signaling. Spermine directly bound to the FERM and SH2 domains of JAK1 to impair JAK1-cytokine receptor interaction, thus broadly suppressing JAK1 phosphorylation triggered by cytokines IFN-I, IFN-II, interleukin (IL)-2, and IL-6. Peripheral blood mononuclear cells (PBMCs) from individuals with SLE showing decreased spermine concentrations exhibited enhanced IFN-I and lupus gene signatures. Spermine treatment attenuated autoimmune pathogenesis in SLE and psoriasis mice and reduced IFN-I signaling in monocytes from individuals with SLE. We synthesized a spermine derivative (spermine derivative 1 [SD1]) and showed that it had a potent immunosuppressive function. Our findings reveal spermine as a metabolic checkpoint for cellular homeostasis and a potential immunosuppressive molecule for controlling autoimmune disease.
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Affiliation(s)
- Henan Xu
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China; Frontiers Research Center for Cell Responses, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xiao Zhang
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Xin Wang
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Bo Li
- Frontiers Research Center for Cell Responses, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Hang Yu
- Institute of Materia Medical, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Yuan Quan
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yan Jiang
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yuling You
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yan Wang
- Institute of Materia Medical, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Mingyue Wen
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Juan Liu
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Navy Medical University, Shanghai 200433, China
| | - Min Wang
- Department of Rheumatology, Beijing Hospital, Beijing 100730, China
| | - Bo Zhang
- Department of Dermatology, Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Yixian Li
- CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xuan Zhang
- Department of Rheumatology, Beijing Hospital, Beijing 100730, China
| | - Qianjin Lu
- Department of Dermatology, Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Chu-Yi Yu
- CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xuetao Cao
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China; Frontiers Research Center for Cell Responses, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China; National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Navy Medical University, Shanghai 200433, China.
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Hu Y, Feng Z, An G, Lv Z, Wang J, Cui Y, Corrigan CJ, Wang W, Li Q, Ying S. Edwardsiella tarda induces airways inflammation and production of autoantibodies against lung tissues through regulation of the IL-33-ST2 axis. Immunology 2024. [PMID: 39126327 DOI: 10.1111/imm.13848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 07/28/2024] [Indexed: 08/12/2024] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a highly prevalent chronic respiratory disease characterised by irreversible airways obstruction associated with chronic airways inflammation and remodelling, while the pathogenesis and the mechanistic differences between patients remain to be fully elucidated. We previously reported that alarmin cytokine IL-33 may contribute to the production of autoantibodies against respiratory epithelial cells. Here we expand the hypothesis that pulmonary autoimmune responses induced by airway microbiota also contribute to the progression of COPD. We focused on Edwardsiella tarda which we detected uniquely in the induced sputum of patients with acute exacerbations of COPD. Pernasal challenge of the airways of WT mice with supernatants of cultured E. tarda induced marked, elevated expression of IL-33 in the lung tissues. Immunisation of animals with supernatants of cultured E. tarda resulted in significantly elevated airways inflammation, the formation of tertiary lymphatic structures and significantly elevated proportions of T follicular helper T cells in the lung tissue and mediastinal lymph nodes. Interestingly, such challenge also induced production of IgG autoantibodies directed against lung tissue lysate, alveolar epithelial cell proteins and elastin fragment, while putrescine, one of metabolites generated by the bacterium, might play an important role in the autoantibody production. Furthermore, all of these effects were partly but significantly abrogated in mice with deletion of the IL-33 receptor ST2. Collectively, these data support the hypothesis that COPD is progressed at least partly by airways microbiota such as E. tarda initiating autoimmune attack of the airways epithelium mediated at least partly through the IL-33-ST2 axis.
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Affiliation(s)
- Yue Hu
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Zhihong Feng
- Department of Respiratory Medicine, Beijing Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Gao An
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Zhe Lv
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Jingjing Wang
- Department of Laboratory Animal Sciences, Capital Medical University, Beijing, China
| | - Ye Cui
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Chris J Corrigan
- Faculty of Life Sciences & Medicine, School of Immunology & Microbial Sciences, Department of Inflammation Biology, King's College London, London, UK
| | - Wei Wang
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Qin Li
- Department of Laboratory, Yanjing Medical College, Capital Medical University, Beijing, China
| | - Sun Ying
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
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Chu W, Peng W, Lu Y, Liu Y, Li Q, Wang H, Wang L, Zhang B, Liu Z, Han L, Ma H, Yang H, Han C, Lu X. PRMT6 Epigenetically Drives Metabolic Switch from Fatty Acid Oxidation toward Glycolysis and Promotes Osteoclast Differentiation During Osteoporosis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403177. [PMID: 39120025 DOI: 10.1002/advs.202403177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/23/2024] [Indexed: 08/10/2024]
Abstract
Epigenetic regulation of metabolism profoundly influences cell fate commitment. During osteoclast differentiation, the activation of RANK signaling is accompanied by metabolic reprogramming, but the epigenetic mechanisms by which RANK signaling induces this reprogramming remain elusive. By transcriptional sequence and ATAC analysis, this study identifies that activation of RANK signaling upregulates PRMT6 by epigenetic modification, triggering a metabolic switching from fatty acids oxidation toward glycolysis. Conversely, Prmt6 deficiency reverses this shift, markedly reducing HIF-1α-mediated glycolysis and enhancing fatty acid oxidation. Consequently, PRMT6 deficiency or inhibitor impedes osteoclast differentiation and alleviates bone loss in ovariectomized (OVX) mice. At the molecular level, Prmt6 deficiency reduces asymmetric dimethylation of H3R2 at the promoters of genes including Ppard, Acox3, and Cpt1a, enhancing genomic accessibility for fatty acid oxidation. PRMT6 thus emerges as a metabolic checkpoint, mediating metabolic switch from fatty acid oxidation to glycolysis, thereby supporting osteoclastogenesis. Unveiling PRMT6's critical role in epigenetically orchestrating metabolic shifts in osteoclastogenesis offers a promising target for anti-resorptive therapy.
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Affiliation(s)
- Wenxiang Chu
- Department of Orthopaedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Weilin Peng
- Department of Orthopaedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Yingying Lu
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Yishan Liu
- Department of Orthopaedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Qisheng Li
- Department of Orthopaedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Haibin Wang
- Department of Orthopaedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Liang Wang
- Department of Orthopaedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Bangke Zhang
- Department of Orthopaedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Zhixiao Liu
- Histology and Embryology Department and Shanghai Key Laboratory of Cell Engineering, Naval Medical University, Shanghai, 200433, China
| | - Lin Han
- Department of Orthopaedics, Third Affiliated Hospital of Naval Medical University, Shanghai, 201805, China
| | - Hongdao Ma
- Department of Orthopaedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Haisong Yang
- Department of Orthopaedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Chaofeng Han
- Histology and Embryology Department and Shanghai Key Laboratory of Cell Engineering, Naval Medical University, Shanghai, 200433, China
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Naval Medical University, Shanghai, 200433, China
| | - Xuhua Lu
- Department of Orthopaedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
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Thakore PI, Schnell A, Huang L, Zhao M, Hou Y, Christian E, Zaghouani S, Wang C, Singh V, Singaraju A, Krishnan RK, Kozoriz D, Ma S, Sankar V, Notarbartolo S, Buenrostro JD, Sallusto F, Patsopoulos NA, Rozenblatt-Rosen O, Kuchroo VK, Regev A. BACH2 regulates diversification of regulatory and proinflammatory chromatin states in T H17 cells. Nat Immunol 2024; 25:1395-1410. [PMID: 39009838 DOI: 10.1038/s41590-024-01901-1] [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: 05/20/2022] [Accepted: 06/18/2024] [Indexed: 07/17/2024]
Abstract
Interleukin-17 (IL-17)-producing helper T (TH17) cells are heterogenous and consist of nonpathogenic TH17 (npTH17) cells that contribute to tissue homeostasis and pathogenic TH17 (pTH17) cells that mediate tissue inflammation. Here, we characterize regulatory pathways underlying TH17 heterogeneity and discover substantial differences in the chromatin landscape of npTH17 and pTH17 cells both in vitro and in vivo. Compared to other CD4+ T cell subsets, npTH17 cells share accessible chromatin configurations with regulatory T cells, whereas pTH17 cells exhibit features of both npTH17 cells and type 1 helper T (TH1) cells. Integrating single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) and single-cell RNA sequencing (scRNA-seq), we infer self-reinforcing and mutually exclusive regulatory networks controlling different cell states and predicted transcription factors regulating TH17 cell pathogenicity. We validate that BACH2 promotes immunomodulatory npTH17 programs and restrains proinflammatory TH1-like programs in TH17 cells in vitro and in vivo. Furthermore, human genetics implicate BACH2 in multiple sclerosis. Overall, our work identifies regulators of TH17 heterogeneity as potential targets to mitigate autoimmunity.
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Affiliation(s)
- Pratiksha I Thakore
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Alexandra Schnell
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Linglin Huang
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Maryann Zhao
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yu Hou
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Elena Christian
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sarah Zaghouani
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Chao Wang
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Immunology, University of Toronto and Biological Sciences Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Vasundhara Singh
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anvita Singaraju
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Rajesh Kumar Krishnan
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Deneen Kozoriz
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sai Ma
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Venkat Sankar
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samuele Notarbartolo
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, Switzerland
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Infectious Diseases Unit, Milan, Italy
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Federica Sallusto
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Nikolaos A Patsopoulos
- Systems Biology and Computer Science Program, Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham & Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Vijay K Kuchroo
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Genentech, South San Francisco, CA, USA.
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12
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Meng X, Zheng Y, Zhang L, Liu P, Liu Z, He Y. Single-Cell Analyses Reveal the Metabolic Heterogeneity and Plasticity of the Tumor Microenvironment during Head and Neck Squamous Cell Carcinoma Progression. Cancer Res 2024; 84:2468-2483. [PMID: 38718319 DOI: 10.1158/0008-5472.can-23-1344] [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: 05/04/2023] [Revised: 10/31/2023] [Accepted: 04/29/2024] [Indexed: 08/02/2024]
Abstract
Metabolic reprogramming is a hallmark of cancer. In addition to metabolic alterations in the tumor cells, multiple other metabolically active cell types in the tumor microenvironment (TME) contribute to the emergence of a tumor-specific metabolic milieu. Here, we defined the metabolic landscape of the TME during the progression of head and neck squamous cell carcinoma (HNSCC) by performing single-cell RNA sequencing on 26 human patient specimens, including normal tissue, precancerous lesions, early stage cancer, advanced-stage cancer, lymph node metastases, and recurrent tumors. The analysis revealed substantial heterogeneity at the transcriptional, developmental, metabolic, and functional levels in different cell types. SPP1+ macrophages were identified as a protumor and prometastatic macrophage subtype with high fructose and mannose metabolism, which was further substantiated by integrative analysis and validation experiments. An inhibitor of fructose metabolism reduced the proportion of SPP1+ macrophages, reshaped the immunosuppressive TME, and suppressed tumor growth. In conclusion, this work delineated the metabolic landscape of HNSCC at a single-cell resolution and identified fructose metabolism as a key metabolic feature of a protumor macrophage subpopulation. Significance: Fructose and mannose metabolism is a metabolic feature of a protumor and prometastasis macrophage subtype and can be targeted to reprogram macrophages and the microenvironment of head and neck squamous cell carcinoma.
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Affiliation(s)
- Xiaoyan Meng
- Department of Oral Maxillofacial & Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P.R. China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology Shanghai, Shanghai, P.R. China
| | - Yang Zheng
- Department of Oral Maxillofacial & Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P.R. China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology Shanghai, Shanghai, P.R. China
| | - Lingfang Zhang
- Suzhou Lingdian Biotechnology Co., Ltd., Suzhou, P.R. China
| | - Peipei Liu
- Suzhou Lingdian Biotechnology Co., Ltd., Suzhou, P.R. China
| | - Zhonglong Liu
- Department of Oral Maxillofacial & Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P.R. China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology Shanghai, Shanghai, P.R. China
| | - Yue He
- Department of Oral Maxillofacial & Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P.R. China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology Shanghai, Shanghai, P.R. China
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13
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Schibalski RS, Shulha AS, Tsao BP, Palygin O, Ilatovskaya DV. The role of polyamine metabolism in cellular function and physiology. Am J Physiol Cell Physiol 2024; 327:C341-C356. [PMID: 38881422 DOI: 10.1152/ajpcell.00074.2024] [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: 01/31/2024] [Revised: 06/07/2024] [Accepted: 06/07/2024] [Indexed: 06/18/2024]
Abstract
Polyamines are molecules with multiple amino groups that are essential for cellular function. The major polyamines are putrescine, spermidine, spermine, and cadaverine. Polyamines are important for posttranscriptional regulation, autophagy, programmed cell death, proliferation, redox homeostasis, and ion channel function. Their levels are tightly controlled. High levels of polyamines are associated with proliferative pathologies such as cancer, whereas low polyamine levels are observed in aging, and elevated polyamine turnover enhances oxidative stress. Polyamine metabolism is implicated in several pathophysiological processes in the nervous, immune, and cardiovascular systems. Currently, manipulating polyamine levels is under investigation as a potential preventive treatment for several pathologies, including aging, ischemia/reperfusion injury, pulmonary hypertension, and cancer. Although polyamines have been implicated in many intracellular mechanisms, our understanding of these processes remains incomplete and is a topic of ongoing investigation. Here, we discuss the regulation and cellular functions of polyamines, their role in physiology and pathology, and emphasize the current gaps in knowledge and potential future research directions.
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Affiliation(s)
- Ryan S Schibalski
- Department of Physiology, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
| | - Anastasia S Shulha
- Department of Physiology, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
| | - Betty P Tsao
- Division of Rheumatology & Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Oleg Palygin
- Division of Nephrology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Daria V Ilatovskaya
- Department of Physiology, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
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14
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Damara A, Wegner J, Trzeciak ER, Kolb A, Nastaranpour M, Khatri R, Tuettenberg A, Kramer D, Grabbe S, Shahneh F. LL37/self-DNA complexes mediate monocyte reprogramming. Clin Immunol 2024; 265:110287. [PMID: 38909973 DOI: 10.1016/j.clim.2024.110287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/13/2024] [Accepted: 06/15/2024] [Indexed: 06/25/2024]
Abstract
LL37 alone and in complex with self-DNA triggers inflammatory responses in myeloid cells and plays a crucial role in the development of systemic autoimmune diseases, like psoriasis and systemic lupus erythematosus. We demonstrated that LL37/self-DNA complexes induce long-term metabolic and epigenetic changes in monocytes, enhancing their responsiveness to subsequent stimuli. Monocytes trained with LL37/self-DNA complexes and those derived from psoriatic patients exhibited heightened glycolytic and oxidative phosphorylation rates, elevated release of proinflammatory cytokines, and affected naïve CD4+ T cells. Additionally, KDM6A/B, a demethylase of lysine 27 on histone 3, was upregulated in psoriatic monocytes and monocytes treated with LL37/self-DNA complexes. Inhibition of KDM6A/B reversed the trained immune phenotype by reducing proinflammatory cytokine production, metabolic activity, and the induction of IL-17-producing T cells by LL37/self-DNA-treated monocytes. Our findings highlight the role of LL37/self-DNA-induced innate immune memory in psoriasis pathogenesis, uncovering its impact on monocyte and T cell dynamics.
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Affiliation(s)
- Aman Damara
- Department of Dermatology, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Joanna Wegner
- Department of Dermatology, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Emily R Trzeciak
- Department of Dermatology, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Antonia Kolb
- Department of Dermatology, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Mahsa Nastaranpour
- Department of Dermatology, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Rahul Khatri
- Department of Dermatology, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Andrea Tuettenberg
- Department of Dermatology, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany; Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Daniela Kramer
- Department of Dermatology, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany; Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Stephan Grabbe
- Department of Dermatology, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany; Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Fatemeh Shahneh
- Department of Dermatology, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany; Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany.
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15
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Schnell A. Stem-like T cells in cancer and autoimmunity. Immunol Rev 2024; 325:9-22. [PMID: 38804499 DOI: 10.1111/imr.13356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Stem-like T cells are characterized by their ability to self-renew, survive long-term, and give rise to a heterogeneous pool of effector and memory T cells. Recent advances in single-cell RNA-sequencing (scRNA-seq) and lineage tracing technologies revealed an important role for stem-like T cells in both autoimmunity and cancer. In cancer, stem-like T cells constitute an important arm of the anti-tumor immune response by giving rise to effector T cells that mediate tumor control. In contrast, in autoimmunity stem-like T cells perform an unfavorable role by forming a reservoir of long-lived autoreactive cells that replenish the pathogenic, effector T-cell pool and thereby driving disease pathology. This review provides background on the discovery of stem-like T cells and their function in cancer and autoimmunity. Moreover, the influence of the microbiota and metabolism on the stem-like T-cell pool is summarized. Lastly, the implications of our knowledge about stem-like T cells for clinical treatment strategies for cancer and autoimmunity will be discussed.
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Affiliation(s)
- Alexandra Schnell
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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16
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Gong X, Su L, Huang J, Liu J, Wang Q, Luo X, Yang G, Chi H. An overview of multi-omics technologies in rheumatoid arthritis: applications in biomarker and pathway discovery. Front Immunol 2024; 15:1381272. [PMID: 39139555 PMCID: PMC11319186 DOI: 10.3389/fimmu.2024.1381272] [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: 02/03/2024] [Accepted: 07/12/2024] [Indexed: 08/15/2024] Open
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease with a complex pathological mechanism involving autoimmune response, local inflammation and bone destruction. Metabolic pathways play an important role in immune-related diseases and their immune responses. The pathogenesis of rheumatoid arthritis may be related to its metabolic dysregulation. Moreover, histological techniques, including genomics, transcriptomics, proteomics and metabolomics, provide powerful tools for comprehensive analysis of molecular changes in biological systems. The present study explores the molecular and metabolic mechanisms of RA, emphasizing the central role of metabolic dysregulation in the RA disease process and highlighting the complexity of metabolic pathways, particularly metabolic remodeling in synovial tissues and its association with cytokine-mediated inflammation. This paper reveals the potential of histological techniques in identifying metabolically relevant therapeutic targets in RA; specifically, we summarize the genetic basis of RA and the dysregulated metabolic pathways, and explore their functional significance in the context of immune cell activation and differentiation. This study demonstrates the critical role of histological techniques in decoding the complex metabolic network of RA and discusses the integration of histological data with other types of biological data.
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Affiliation(s)
- Xiangjin Gong
- Department of Sports Rehabilitation, Southwest Medical University, Luzhou, China
| | - Lanqian Su
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Jinbang Huang
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Jie Liu
- Department of Geriatric, Dazhou Central Hospital, Dazhou, China
| | - Qinglai Wang
- Orthopedics and Traumatology Department of TCM, Wenzhou TCM Hospital of Zhejiang Chinese Medical University, Wenzhou, China
| | - Xiufang Luo
- Department of Geriatric, Dazhou Central Hospital, Dazhou, China
| | - Guanhu Yang
- Department of Specialty Medicine, Ohio University, Athens, OH, United States
| | - Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou, China
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17
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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 2024:103583. [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] [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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18
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Liu X, Ren B, Ren J, Gu M, You L, Zhao Y. The significant role of amino acid metabolic reprogramming in cancer. Cell Commun Signal 2024; 22:380. [PMID: 39069612 DOI: 10.1186/s12964-024-01760-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/21/2024] [Indexed: 07/30/2024] Open
Abstract
Amino acid metabolism plays a pivotal role in tumor microenvironment, influencing various aspects of cancer progression. The metabolic reprogramming of amino acids in tumor cells is intricately linked to protein synthesis, nucleotide synthesis, modulation of signaling pathways, regulation of tumor cell metabolism, maintenance of oxidative stress homeostasis, and epigenetic modifications. Furthermore, the dysregulation of amino acid metabolism also impacts tumor microenvironment and tumor immunity. Amino acids can act as signaling molecules that modulate immune cell function and immune tolerance within the tumor microenvironment, reshaping the anti-tumor immune response and promoting immune evasion by cancer cells. Moreover, amino acid metabolism can influence the behavior of stromal cells, such as cancer-associated fibroblasts, regulate ECM remodeling and promote angiogenesis, thereby facilitating tumor growth and metastasis. Understanding the intricate interplay between amino acid metabolism and the tumor microenvironment is of crucial significance. Expanding our knowledge of the multifaceted roles of amino acid metabolism in tumor microenvironment holds significant promise for the development of more effective cancer therapies aimed at disrupting the metabolic dependencies of cancer cells and modulating the tumor microenvironment to enhance anti-tumor immune responses and inhibit tumor progression.
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Affiliation(s)
- Xiaohong Liu
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R, 100023, China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R, China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R, China
| | - Bo Ren
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R, 100023, China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R, China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R, China
| | - Jie Ren
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R, 100023, China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R, China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R, China
| | - Minzhi Gu
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R, 100023, China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R, China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R, China
| | - Lei You
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R, 100023, China.
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R, China.
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R, China.
| | - Yupei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R, 100023, China.
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R, China.
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R, China.
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19
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Zhu Y, Chen X, Zou Y, Su L, Yan X, Zhu X, Hou Y, Liu M, Jiang W, Zou C, Chen X, Xu Z. Ze-Qi-Tang formula inhibits MDSCs glycolysis through the down-regulation of p21/Hif1α/Glut1 signal in psoriatic-like mice. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 130:155544. [PMID: 38810554 DOI: 10.1016/j.phymed.2024.155544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 03/07/2024] [Accepted: 03/17/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND Psoriasis is a chronic immune-mediated inflammatory skin disease that affects the quality of life and mental health of approximately 150 million people worldwide. Ze-Qi-Tang (ZQT) is a classic compound used in China for lung disease; however, its mechanism of action in psoriasis remains unclear. This study aimed to investigate the therapeutic effect of the ZQT formula on psoriasis and explore the underlying molecular mechanisms. METHODS Peripheral blood samples were collected from patients with psoriasis and healthy individuals. Flow cytometry was used to detect changes in the proportions of myeloid-derived suppressor cells (MDSCs) and other immune cells. Psoriasis was induced in mice by the daily application of imiquimod. ZQT was administered separately or in combination with anti-Gr1 antibody to deplete MDSC. The glycolysis levels of the MDSCs were detected using a Seahorse analyzer. The p21/Hif1α/Glut1 pathway was identified and validated by mRNA sequence, RT-qPCR, WB, IF, and the application of p21 inhibitor UC2288. RESULTS The number of MDSCs was significantly increased in patients with psoriasis, with the increased expression of p21, Hif1α, and Glut1 in MDSCs. ZQT significantly alleviated psoriasis-like skin lesions in mice. ZQT formula significantly reduced the number of MDSCs in psoriatic-like mice and enhanced their suppressive capacity for T cells. The efficacy of ZQT in alleviating psoriatic dermatitis is compromised by MDSC depletion. ZQT decreased the expressions of p21, Hif1α, and Glut1-induced glycolysis in MDSCs, thereby inhibiting Th17 cell differentiation. CONCLUSION These suggest that ZQT alleviates IMQ-induced psoriatic dermatitis, by inhibiting p21/Hif1α/Glut1-induced glycolysis in MDSCs.
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Affiliation(s)
- Yangzhuangzhuang Zhu
- Shanghai Key Laboratory of Health Identification and Assessment, School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Rd., Pudong District, Shanghai, 201203, China
| | - Xi Chen
- Department of Traditional Chinese Medicine Dermatology, Shanghai Skin Disease Hospital, 1278 Baode Rd., Jingan District, Shanghai, 200443, China
| | - Yimeng Zou
- Shanghai Key Laboratory of Health Identification and Assessment, School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Rd., Pudong District, Shanghai, 201203, China
| | - Lin Su
- Shanghai Key Laboratory of Health Identification and Assessment, School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Rd., Pudong District, Shanghai, 201203, China
| | - Xuewei Yan
- Experiment Center for Teaching and Learning, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xiaowen Zhu
- Shanghai Key Laboratory of Health Identification and Assessment, School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Rd., Pudong District, Shanghai, 201203, China
| | - Yifei Hou
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Mingxi Liu
- Shanghai Key Laboratory of Health Identification and Assessment, School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Rd., Pudong District, Shanghai, 201203, China
| | - Wencheng Jiang
- Department of Traditional Chinese Medicine Dermatology, Shanghai Skin Disease Hospital, 1278 Baode Rd., Jingan District, Shanghai, 200443, China.
| | - Chunpu Zou
- Shanghai Key Laboratory of Health Identification and Assessment, School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Rd., Pudong District, Shanghai, 201203, China.
| | - Xiao Chen
- Shanghai Key Laboratory of Health Identification and Assessment, School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Rd., Pudong District, Shanghai, 201203, China.
| | - Zihang Xu
- Shanghai Key Laboratory of Health Identification and Assessment, School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Rd., Pudong District, Shanghai, 201203, China.
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20
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Anannya O, Huang W, August A. The kinase ITK controls a Ca 2+-mediated switch that balances T H17 and T reg cell differentiation. Sci Signal 2024; 17:eadh2381. [PMID: 39042726 DOI: 10.1126/scisignal.adh2381] [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: 02/26/2023] [Revised: 11/13/2023] [Accepted: 07/01/2024] [Indexed: 07/25/2024]
Abstract
The balance of proinflammatory T helper type 17 (TH17) and anti-inflammatory T regulatory (Treg) cells is crucial for immune homeostasis in health and disease. The differentiation of naïve CD4+ T cells into TH17 and Treg cells depends on T cell receptor (TCR) signaling mediated, in part, by interleukin-2-inducible T cell kinase (ITK), which stimulates mitogen-activated protein kinases (MAPKs) and Ca2+ signaling. Here, we report that, in the absence of ITK activity, naïve murine CD4+ T cells cultured under TH17-inducing conditions expressed the Treg transcription factor Foxp3 and did not develop into TH17 cells. Furthermore, ITK inhibition in vivo during allergic inflammation increased the Treg:TH17 ratio in the lung. These switched Foxp3+ Treg-like cells had suppressive function, and their transcriptomic profile resembled that of differentiated, induced Treg (iTreg) cells, but their chromatin accessibility profiles were intermediate between TH17 and iTreg cells. Like iTreg cells, switched Foxp3+ Treg-like cells had reductions in the expression of genes involved in mitochondrial oxidative phosphorylation and glycolysis, in the activation of the mechanistic target of rapamycin (mTOR) signaling pathway, and in the abundance of the TH17 pioneer transcription factor BATF. This ITK-dependent switch between TH17 and Treg cells depended on Ca2+ signaling but not on MAPKs. These findings suggest potential strategies for fine-tuning TCR signal strength through ITK to control the balance of TH17 and Treg cells.
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Affiliation(s)
- Orchi Anannya
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Weishan Huang
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Avery August
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
- Cornell Center for Immunology, Cornell University, Ithaca, NY 14853, USA
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853, USA
- Cornell Center for Health Equity, Cornell University, Ithaca, NY 14853, USA
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21
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Hu H, Li H, Li R, Liu P, Liu H. Re-establishing immune tolerance in multiple sclerosis: focusing on novel mechanisms of mesenchymal stem cell regulation of Th17/Treg balance. J Transl Med 2024; 22:663. [PMID: 39010157 PMCID: PMC11251255 DOI: 10.1186/s12967-024-05450-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: 01/23/2024] [Accepted: 06/27/2024] [Indexed: 07/17/2024] Open
Abstract
The T-helper 17 (Th17) cell and regulatory T cell (Treg) axis plays a crucial role in the development of multiple sclerosis (MS), which is regarded as an immune imbalance between pro-inflammatory cytokines and the maintenance of immune tolerance. Mesenchymal stem cell (MSC)-mediated therapies have received increasing attention in MS research. In MS and its animal model experimental autoimmune encephalomyelitis, MSC injection was shown to alter the differentiation of CD4+T cells. This alteration occurred by inducing anergy and reduction in the number of Th17 cells, stimulating the polarization of antigen-specific Treg to reverse the imbalance of the Th17/Treg axis, reducing the inflammatory cascade response and demyelination, and restoring an overall state of immune tolerance. In this review, we summarize the mechanisms by which MSCs regulate the balance between Th17 cells and Tregs, including extracellular vesicles, mitochondrial transfer, metabolic reprogramming, and autophagy. We aimed to identify new targets for MS treatment using cellular therapy by analyzing MSC-mediated Th17-to-Treg polarization.
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Affiliation(s)
- Huiru Hu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Hui Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Ruoyu Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Peidong Liu
- Department of Neurosurgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China.
- Translational Medicine Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, China.
| | - Hongbo Liu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China.
- Translational Medicine Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, China.
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22
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Subudhi I, Konieczny P, Prystupa A, Castillo RL, Sze-Tu E, Xing Y, Rosenblum D, Reznikov I, Sidhu I, Loomis C, Lu CP, Anandasabapathy N, Suárez-Fariñas M, Gudjonsson JE, Tsirigos A, Scher JU, Naik S. Metabolic coordination between skin epithelium and type 17 immunity sustains chronic skin inflammation. Immunity 2024; 57:1665-1680.e7. [PMID: 38772365 PMCID: PMC11236527 DOI: 10.1016/j.immuni.2024.04.022] [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: 06/29/2023] [Revised: 03/11/2024] [Accepted: 04/24/2024] [Indexed: 05/23/2024]
Abstract
Inflammatory epithelial diseases are spurred by the concomitant dysregulation of immune and epithelial cells. How these two dysregulated cellular compartments simultaneously sustain their heightened metabolic demands is unclear. Single-cell and spatial transcriptomics (ST), along with immunofluorescence, revealed that hypoxia-inducible factor 1α (HIF1α), downstream of IL-17 signaling, drove psoriatic epithelial remodeling. Blocking HIF1α in human psoriatic lesions ex vivo impaired glycolysis and phenocopied anti-IL-17 therapy. In a murine model of skin inflammation, epidermal-specific loss of HIF1α or its target gene, glucose transporter 1, ameliorated epidermal, immune, vascular, and neuronal pathology. Mechanistically, glycolysis autonomously fueled epithelial pathology and enhanced lactate production, which augmented the γδ T17 cell response. RORγt-driven genetic deletion or pharmacological inhibition of either lactate-producing enzymes or lactate transporters attenuated epithelial pathology and IL-17A expression in vivo. Our findings identify a metabolic hierarchy between epithelial and immune compartments and the consequent coordination of metabolic processes that sustain inflammatory disease.
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Affiliation(s)
- Ipsita Subudhi
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Piotr Konieczny
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA.
| | - Aleksandr Prystupa
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA; Applied Bioinformatics Laboratories, NYU Langone Health, New York, NY 10016, USA
| | - Rochelle L Castillo
- Division of Rheumatology, Department of Medicine, NYU Langone Health, New York, NY 10016, USA; Psoriatic Arthritis Center, NYU Langone Health, New York, NY 10016, USA
| | - Erica Sze-Tu
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Yue Xing
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Daniel Rosenblum
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Ilana Reznikov
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Ikjot Sidhu
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA; Applied Bioinformatics Laboratories, NYU Langone Health, New York, NY 10016, USA
| | - Cynthia Loomis
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Catherine P Lu
- The Hansjörg Wyss Department of Plastic Surgery and Department of Cell Biology, NYU Langone Health, New York, NY 10016, USA
| | | | - Mayte Suárez-Fariñas
- Department of Genetics and Genomic Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Aristotelis Tsirigos
- Applied Bioinformatics Laboratories, NYU Langone Health, New York, NY 10016, USA; Precision Medicine Institute, Department of Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Jose U Scher
- Division of Rheumatology, Department of Medicine, NYU Langone Health, New York, NY 10016, USA; NYU Colton Center for Autoimmunity, Department of Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Shruti Naik
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA; NYU Colton Center for Autoimmunity, Department of Medicine, NYU Langone Health, New York, NY 10016, USA; Ronald O. Perelman Department of Dermatology, Department of Medicine, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA.
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23
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Guimarães GR, Maklouf GR, Teixeira CE, de Oliveira Santos L, Tessarollo NG, de Toledo NE, Serain AF, de Lanna CA, Pretti MA, da Cruz JGV, Falchetti M, Dimas MM, Filgueiras IS, Cabral-Marques O, Ramos RN, de Macedo FC, Rodrigues FR, Bastos NC, da Silva JL, Lummertz da Rocha E, Chaves CBP, de Melo AC, Moraes-Vieira PMM, Mori MA, Boroni M. Single-cell resolution characterization of myeloid-derived cell states with implication in cancer outcome. Nat Commun 2024; 15:5694. [PMID: 38972873 PMCID: PMC11228020 DOI: 10.1038/s41467-024-49916-4] [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: 07/31/2023] [Accepted: 06/19/2024] [Indexed: 07/09/2024] Open
Abstract
Tumor-associated myeloid-derived cells (MDCs) significantly impact cancer prognosis and treatment responses due to their remarkable plasticity and tumorigenic behaviors. Here, we integrate single-cell RNA-sequencing data from different cancer types, identifying 29 MDC subpopulations within the tumor microenvironment. Our analysis reveals abnormally expanded MDC subpopulations across various tumors and distinguishes cell states that have often been grouped together, such as TREM2+ and FOLR2+ subpopulations. Using deconvolution approaches, we identify five subpopulations as independent prognostic markers, including states co-expressing TREM2 and PD-1, and FOLR2 and PDL-2. Additionally, TREM2 alone does not reliably predict cancer prognosis, as other TREM2+ macrophages show varied associations with prognosis depending on local cues. Validation in independent cohorts confirms that FOLR2-expressing macrophages correlate with poor clinical outcomes in ovarian and triple-negative breast cancers. This comprehensive MDC atlas offers valuable insights and a foundation for futher analyses, advancing strategies for treating solid cancers.
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Affiliation(s)
- Gabriela Rapozo Guimarães
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Giovanna Resk Maklouf
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Cristiane Esteves Teixeira
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Leandro de Oliveira Santos
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Nayara Gusmão Tessarollo
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Nayara Evelin de Toledo
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Alessandra Freitas Serain
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Cristóvão Antunes de Lanna
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Marco Antônio Pretti
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Jéssica Gonçalves Vieira da Cruz
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Marcelo Falchetti
- Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Mylla M Dimas
- Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Igor Salerno Filgueiras
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo,(USP), São Paulo, Brazil
| | - Otavio Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo,(USP), São Paulo, Brazil
- Instituto D'Or de Ensino e Pesquisa, São Paulo, Brazil
- Department of Medicine, Division of Molecular Medicine, Laboratory of Medical Investigation 29, School of Medicine, University of São Paulo (USP), São Paulo, Brazil
| | - Rodrigo Nalio Ramos
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo,(USP), São Paulo, Brazil
- Instituto D'Or de Ensino e Pesquisa, São Paulo, Brazil
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Departament of Hematology and Cell Therapy, Hospital das Clínicas HCFMUSP, School of Medicine, University of São Paulo (USP), São Paulo, Brazil
| | | | | | - Nina Carrossini Bastos
- Division of Pathology, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Jesse Lopes da Silva
- Division of Clinical Research and Technological Development, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Edroaldo Lummertz da Rocha
- Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Cláudia Bessa Pereira Chaves
- Division of Clinical Research and Technological Development, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
- Gynecologic Oncology Section, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Andreia Cristina de Melo
- Division of Clinical Research and Technological Development, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Pedro M M Moraes-Vieira
- Laboratory of Immunometabolism, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
- Obesity and Comorbidities Research Center (OCRC), Universidade Estadual de Campinas, Campinas, SP, Brazil
- Experimental Medicine Research Cluster (EMRC), Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marcelo A Mori
- Obesity and Comorbidities Research Center (OCRC), Universidade Estadual de Campinas, Campinas, SP, Brazil
- Experimental Medicine Research Cluster (EMRC), Universidade Estadual de Campinas, Campinas, SP, Brazil
- Laboratory of Aging Biology, Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Mariana Boroni
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil.
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24
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Simpson CE, Ledford JG, Liu G. Application of Metabolomics across the Spectrum of Pulmonary and Critical Care Medicine. Am J Respir Cell Mol Biol 2024; 71:1-9. [PMID: 38547373 PMCID: PMC11225873 DOI: 10.1165/rcmb.2024-0080ps] [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: 02/19/2024] [Accepted: 03/28/2024] [Indexed: 07/02/2024] Open
Abstract
In recent years, metabolomics, the systematic study of small-molecule metabolites in biological samples, has yielded fresh insights into the molecular determinants of pulmonary diseases and critical illness. The purpose of this article is to orient the reader to this emerging field by discussing the fundamental tenets underlying metabolomics research, the tools and techniques that serve as foundational methodologies, and the various statistical approaches to analysis of metabolomics datasets. We present several examples of metabolomics applied to pulmonary and critical care medicine to illustrate the potential of this avenue of research to deepen our understanding of pathophysiology. We conclude by reviewing recent advances in the field and future research directions that stand to further the goal of personalizing medicine to improve patient care.
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Affiliation(s)
- Catherine E. Simpson
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Julie G. Ledford
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona; and
| | - Gang Liu
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama
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25
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Bilous M, Hérault L, Gabriel AA, Teleman M, Gfeller D. Building and analyzing metacells in single-cell genomics data. Mol Syst Biol 2024; 20:744-766. [PMID: 38811801 PMCID: PMC11220014 DOI: 10.1038/s44320-024-00045-6] [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: 02/04/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/31/2024] Open
Abstract
The advent of high-throughput single-cell genomics technologies has fundamentally transformed biological sciences. Currently, millions of cells from complex biological tissues can be phenotypically profiled across multiple modalities. The scaling of computational methods to analyze and visualize such data is a constant challenge, and tools need to be regularly updated, if not redesigned, to cope with ever-growing numbers of cells. Over the last few years, metacells have been introduced to reduce the size and complexity of single-cell genomics data while preserving biologically relevant information and improving interpretability. Here, we review recent studies that capitalize on the concept of metacells-and the many variants in nomenclature that have been used. We further outline how and when metacells should (or should not) be used to analyze single-cell genomics data and what should be considered when analyzing such data at the metacell level. To facilitate the exploration of metacells, we provide a comprehensive tutorial on the construction and analysis of metacells from single-cell RNA-seq data ( https://github.com/GfellerLab/MetacellAnalysisTutorial ) as well as a fully integrated pipeline to rapidly build, visualize and evaluate metacells with different methods ( https://github.com/GfellerLab/MetacellAnalysisToolkit ).
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Affiliation(s)
- Mariia Bilous
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, 1011, Lausanne, Switzerland
- Agora Cancer Research Centre, 1011, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Léonard Hérault
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, 1011, Lausanne, Switzerland
- Agora Cancer Research Centre, 1011, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Aurélie Ag Gabriel
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, 1011, Lausanne, Switzerland
- Agora Cancer Research Centre, 1011, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Matei Teleman
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, 1011, Lausanne, Switzerland
- Agora Cancer Research Centre, 1011, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - David Gfeller
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, 1011, Lausanne, Switzerland.
- Agora Cancer Research Centre, 1011, Lausanne, Switzerland.
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland.
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26
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Verheijen FWM, Tran TNM, Chang J, Broere F, Zaal EA, Berkers CR. Deciphering metabolic crosstalk in context: lessons from inflammatory diseases. Mol Oncol 2024; 18:1759-1776. [PMID: 38275212 PMCID: PMC11223610 DOI: 10.1002/1878-0261.13588] [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: 07/17/2023] [Revised: 11/02/2023] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
Metabolism plays a crucial role in regulating the function of immune cells in both health and disease, with altered metabolism contributing to the pathogenesis of cancer and many inflammatory diseases. The local microenvironment has a profound impact on the metabolism of immune cells. Therefore, immunological and metabolic heterogeneity as well as the spatial organization of cells in tissues should be taken into account when studying immunometabolism. Here, we highlight challenges of investigating metabolic communication. Additionally, we review the capabilities and limitations of current technologies for studying metabolism in inflamed microenvironments, including single-cell omics techniques, flow cytometry-based methods (Met-Flow, single-cell energetic metabolism by profiling translation inhibition (SCENITH)), cytometry by time of flight (CyTOF), cellular indexing of transcriptomes and epitopes by sequencing (CITE-Seq), and mass spectrometry imaging. Considering the importance of metabolism in regulating immune cells in diseased states, we also discuss the applications of metabolomics in clinical research, as well as some hurdles to overcome to implement these techniques in standard clinical practice. Finally, we provide a flowchart to assist scientists in designing effective strategies to unravel immunometabolism in disease-relevant contexts.
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Affiliation(s)
- Fenne W. M. Verheijen
- Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityThe Netherlands
- Division of Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityThe Netherlands
| | - Thi N. M. Tran
- Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityThe Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular ResearchUtrecht UniversityThe Netherlands
| | - Jung‐Chin Chang
- Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityThe Netherlands
| | - Femke Broere
- Division of Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityThe Netherlands
| | - Esther A. Zaal
- Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityThe Netherlands
| | - Celia R. Berkers
- Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityThe Netherlands
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27
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Phua YL, D'Annibale OM, Karunanidhi A, Mohsen AW, Kirmse B, Dobrowolski SF, Vockley J. A multiomics approach reveals evidence for phenylbutyrate as a potential treatment for combined D,L-2- hydroxyglutaric aciduria. Mol Genet Metab 2024; 142:108495. [PMID: 38772223 DOI: 10.1016/j.ymgme.2024.108495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/30/2024] [Accepted: 05/13/2024] [Indexed: 05/23/2024]
Abstract
PURPOSE To identify therapies for combined D, L-2-hydroxyglutaric aciduria (C-2HGA), a rare genetic disorder caused by recessive variants in the SLC25A1 gene. METHODS Patients C-2HGA were identified and diagnosed by whole exome sequencing and biochemical genetic testing. Patient derived fibroblasts were then treated with phenylbutyrate and the functional effects assessed by metabolomics and RNA-sequencing. RESULTS In this study, we demonstrated that C-2HGA patient derived fibroblasts exhibited impaired cellular bioenergetics. Moreover, Fibroblasts form one patient exhibited worsened cellular bioenergetics when supplemented with citrate. We hypothesized that treating patient cells with phenylbutyrate (PB), an FDA approved pharmaceutical drug that conjugates glutamine for renal excretion, would reduce mitochondrial 2-ketoglutarate, thereby leading to improved cellular bioenergetics. Metabolomic and RNA-seq analyses of PB-treated fibroblasts demonstrated a significant decrease in intracellular 2-ketoglutarate, 2-hydroxyglutarate, and in levels of mRNA coding for citrate synthase and isocitrate dehydrogenase. Consistent with the known action of PB, an increased level of phenylacetylglutamine in patient cells was consistent with the drug acting as 2-ketoglutarate sink. CONCLUSION Our pre-clinical studies suggest that citrate supplementation has the possibility exacerbating energy metabolism in this condition. However, improvement in cellular bioenergetics suggests phenylbutyrate might have interventional utility for this rare disease.
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MESH Headings
- Humans
- Phenylbutyrates/pharmacology
- Phenylbutyrates/therapeutic use
- Fibroblasts/metabolism
- Fibroblasts/drug effects
- Glutarates/metabolism
- Ketoglutaric Acids/metabolism
- Energy Metabolism/drug effects
- Energy Metabolism/genetics
- Mitochondria/drug effects
- Mitochondria/metabolism
- Mitochondria/genetics
- Metabolomics
- Exome Sequencing
- Citrate (si)-Synthase/metabolism
- Citrate (si)-Synthase/genetics
- Brain Diseases, Metabolic, Inborn/drug therapy
- Brain Diseases, Metabolic, Inborn/genetics
- Brain Diseases, Metabolic, Inborn/metabolism
- Isocitrate Dehydrogenase/genetics
- Isocitrate Dehydrogenase/metabolism
- Brain Diseases, Metabolic/drug therapy
- Brain Diseases, Metabolic/genetics
- Brain Diseases, Metabolic/metabolism
- Brain Diseases, Metabolic/pathology
- Multiomics
- Mitochondrial Proteins
- Organic Anion Transporters
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Affiliation(s)
- Yu Leng Phua
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Pathology, Clinical Biochemical Genetics Laboratory, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olivia M D'Annibale
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Anuradha Karunanidhi
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Al-Walid Mohsen
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Brian Kirmse
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Steven F Dobrowolski
- Department of Pathology, Clinical Biochemical Genetics Laboratory, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Jerry Vockley
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.
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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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29
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Puniya BL, Verma M, Damiani C, Bakr S, Dräger A. Perspectives on computational modeling of biological systems and the significance of the SysMod community. BIOINFORMATICS ADVANCES 2024; 4:vbae090. [PMID: 38948011 PMCID: PMC11213628 DOI: 10.1093/bioadv/vbae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/12/2024] [Accepted: 06/14/2024] [Indexed: 07/02/2024]
Abstract
Motivation In recent years, applying computational modeling to systems biology has caused a substantial surge in both discovery and practical applications and a significant shift in our understanding of the complexity inherent in biological systems. Results In this perspective article, we briefly overview computational modeling in biology, highlighting recent advancements such as multi-scale modeling due to the omics revolution, single-cell technology, and integration of artificial intelligence and machine learning approaches. We also discuss the primary challenges faced: integration, standardization, model complexity, scalability, and interdisciplinary collaboration. Lastly, we highlight the contribution made by the Computational Modeling of Biological Systems (SysMod) Community of Special Interest (COSI) associated with the International Society of Computational Biology (ISCB) in driving progress within this rapidly evolving field through community engagement (via both in person and virtual meetings, social media interactions), webinars, and conferences. Availability and implementation Additional information about SysMod is available at https://sysmod.info.
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Affiliation(s)
- Bhanwar Lal Puniya
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, United States
| | - Meghna Verma
- Systems Medicine, Clinical Pharmacology and Quantitative Pharmacology, R&D BioPharmaceuticals, AstraZeneca, Gaithersburg, MD 20878, United States
| | - Chiara Damiani
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Shaimaa Bakr
- Department of Medicine, Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, Stanford, CA 94305-5479, United States
| | - Andreas Dräger
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Cluster of Excellence ‘Controlling Microbes to Fight Infections’, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Tübingen 72076, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen 72076, Germany
- Quantitative Biology Center (QBiC), Eberhard Karl University of Tübingen, Tübingen 72076, Germany
- Data Analytics and Bioinformatics, Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale) 06120, Germany
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30
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Zahoor I, Nematullah M, Ahmed ME, Fatma M, Mir S, Ayasolla K, Cerghet M, Palaniyandi S, Ceci V, Carrera G, Buttari F, Centonze D, Mao-Draayer Y, Rattan R, Chiurchiù V, Giri S. Maresin-1 promotes neuroprotection and prevents disease progression in experimental models of multiple sclerosis through metabolic reprogramming and shaping innate and adaptive disease-associated cell types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.25.559216. [PMID: 37808700 PMCID: PMC10557612 DOI: 10.1101/2023.09.25.559216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Multiple sclerosis (MS) is one of the most common inflammatory neurodegenerative diseases in young adults and causes neurological abnormalities and disability. We studied the effect of maresin 1 (MaR1) on the progression of disease in a relapsing-remitting form of experimental allergic encephalomyelitis (RR-EAE). Treatment with MaR1 in RR-EAE accelerated inflammation resolution, protected against neurological deficits, and delayed disease progression by decreasing immune cell infiltration (CD4+IL17+ and CD4+IFNγ+) into the CNS. Furthermore, the administration of MaR1 increased the production of IL-10, predominantly in macrophages and CD4+ cells. However, neutralizing IL-10 with an anti-IL-10 antibody abolished the protective effect of MaR1 on RR-EAE, suggesting that IL-10 plays a role in mediating the protective effect of MaR1 on EAE. Metabolism is rapidly becoming recognized as an important factor influencing the effector function of many immune cells. Using cutting-edge metabolic assays, our study revealed that compared with vehicle treatment, MaR1 treatment effectively restored the metabolic dysregulation observed in CD4+ cells, macrophages, and microglia in the treated group. Furthermore, MaR1 treatment reversed defective efferocytosis in EAE mice, which was potentially facilitated by the induction of metabolic alterations in macrophages and microglia. MaR1 treatment also protected myelin in the EAE group and regulated the metabolism of O4+ oligodendrocytes by restoring metabolic dysregulation through improved mitochondrial function and decreased glycolysis. Overall, in a preclinical MS animal model, MaR1 treatment produced anti-inflammatory and neuroprotective effects. It also triggered metabolic reprogramming in disease-associated cell types, accelerated efferocytosis, and preserved myelination. These data support that MaR1 has potential as a novel treatment agent for MS and other autoimmune diseases.
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Affiliation(s)
- Insha Zahoor
- Department of Neurology, Henry Ford Health, Detroit, MI 48202, USA
| | | | | | - Mena Fatma
- Department of Neurology, Henry Ford Health, Detroit, MI 48202, USA
| | - Sajad Mir
- Department of Neurology, Henry Ford Health, Detroit, MI 48202, USA
| | - Kamesh Ayasolla
- Department of Neurology, Henry Ford Health, Detroit, MI 48202, USA
| | - Mirela Cerghet
- Department of Neurology, Henry Ford Health, Detroit, MI 48202, USA
| | - Suresh Palaniyandi
- Division of Hypertension and Vascular Research, Department of Internal Medicine, Henry Ford Health, Detroit, MI 48202, USA
- Department of Physiology, Wayne State University, Detroit, MI 48201, USA
| | - Veronica Ceci
- Institute of Translational Pharmacology, National Research Council, Rome, 00133, Italy
- Laboratory of Resolution of Neuroinflammation, IRCCS Santa Lucia Foundation, Rome, 00143, Italy
| | - Giulia Carrera
- Laboratory of Resolution of Neuroinflammation, IRCCS Santa Lucia Foundation, Rome, 00143, Italy
| | - Fabio Buttari
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, 00133, Italy
- Unit of Neurology, IRCCS Neuromed, Pozzilli (Is), 86077, Italy
| | - Diego Centonze
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, 00133, Italy
- Unit of Neurology, IRCCS Neuromed, Pozzilli (Is), 86077, Italy
| | - Yang Mao-Draayer
- Michigan Institute for Neurological Disorders, Farmington Hills, MI 48334, USA
| | - Ramandeep Rattan
- Women’s Health Services, Henry Ford Health, Detroit, MI 48202, USA
| | - Valerio Chiurchiù
- Institute of Translational Pharmacology, National Research Council, Rome, 00133, Italy
- Laboratory of Resolution of Neuroinflammation, IRCCS Santa Lucia Foundation, Rome, 00143, Italy
| | - Shailendra Giri
- Department of Neurology, Henry Ford Health, Detroit, MI 48202, USA
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31
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Yang L, Zhu JC, Li SJ, Zeng X, Xue XR, Dai Y, Wei ZF. HSP90β shapes the fate of Th17 cells with the help of glycolysis-controlled methylation modification. Br J Pharmacol 2024. [PMID: 38881036 DOI: 10.1111/bph.16432] [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: 09/07/2023] [Revised: 02/21/2024] [Accepted: 03/21/2024] [Indexed: 06/18/2024] Open
Abstract
BACKGROUND AND PURPOSE Ulcerative colitis (UC) is a refractory inflammatory disease associated with immune dysregulation. Elevated levels of heat shock protein (HSP) 90 in the β but not α subtype were positively associated with disease status in UC patients. This study validated the possibility that pharmacological inhibition or reduction of HSP90β would alleviate colitis, induced by dextran sulfate sodium, in mice and elucidated its mechanisms. EXPERIMENTAL APPROACH Histopathological and biochemical analysis assessed disease severity, and bioinformatics and correlation analysis explained the association between the many immune cells and HSP90β. Flow cytometry was used to analyse the homeostasis and transdifferentiation of Th17 and Treg cells. In vitro inhibition and adoptive transfer assays were used to investigate functions of the phenotypically transformed Th17 cells. Metabolomic analysis, DNA methylation detection and chromatin immunoprecipitation were used to explore these mechanisms. KEY RESULTS The selective pharmacological inhibitor (HSP90βi) and shHSP90β significantly mitigated UC in mice and promoted transformation of Th17 to Treg cell phenotype, via Foxp3 transcription. The phenotypically-transformed Th17 cells by HSP90βi or shHSP90β were able to inhibit lymphocyte proliferation and colitis in mice. HSP90βi and shHSP90β selectively weakened glycolysis by stopping the direct association of HSP90β and GLUT1, the key glucose transporter, to accelerate ubiquitination degradation of GLUT1, and enhance the methylation of Foxp3 CNS2 region. Then, the mediator path was identified as the "lactate-STAT5-TET2" cascade. CONCLUSION AND IMPLICATIONS HSP90β shapes the fate of Th17 cells via glycolysis-controlled methylation modification to affect UC progression, which provides a new therapeutic target for UC.
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Affiliation(s)
- Ling Yang
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jing-Chao Zhu
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Shi-Jia Li
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xi Zeng
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xin-Ru Xue
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yue Dai
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Zhi-Feng Wei
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
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32
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Zakirova NF, Khomich OA, Smirnova OA, Molle J, Duponchel S, Yanvarev DV, Valuev-Elliston VT, Monnier L, Grigorov B, Ivanova ON, Karpenko IL, Golikov MV, Bovet C, Rindlisbacher B, Khomutov AR, Kochetkov SN, Bartosch B, Ivanov AV. Hepatitis C Virus Dysregulates Polyamine and Proline Metabolism and Perturbs the Urea Cycle. Cells 2024; 13:1036. [PMID: 38920664 PMCID: PMC11201506 DOI: 10.3390/cells13121036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/27/2024] Open
Abstract
Hepatitis C virus (HCV) is an oncogenic virus that causes chronic liver disease in more than 80% of patients. During the last decade, efficient direct-acting antivirals were introduced into clinical practice. However, clearance of the virus does not reduce the risk of end-stage liver diseases to the level observed in patients who have never been infected. So, investigation of HCV pathogenesis is still warranted. Virus-induced changes in cell metabolism contribute to the development of HCV-associated liver pathologies. Here, we studied the impact of the virus on the metabolism of polyamines and proline as well as on the urea cycle, which plays a crucial role in liver function. It was found that HCV strongly suppresses the expression of arginase, a key enzyme of the urea cycle, leading to the accumulation of arginine, and up-regulates proline oxidase with a concomitant decrease in proline concentrations. The addition of exogenous proline moderately suppressed viral replication. HCV up-regulated transcription but suppressed protein levels of polyamine-metabolizing enzymes. This resulted in a decrease in polyamine content in infected cells. Finally, compounds targeting polyamine metabolism demonstrated pronounced antiviral activity, pointing to spermine and spermidine as compounds affecting HCV replication. These data expand our understanding of HCV's imprint on cell metabolism.
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Affiliation(s)
- Natalia F. Zakirova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.F.Z.); (O.A.K.); (O.A.S.); (D.V.Y.); (V.T.V.-E.); (O.N.I.); (I.L.K.); (M.V.G.); (A.R.K.); (S.N.K.)
| | - Olga A. Khomich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.F.Z.); (O.A.K.); (O.A.S.); (D.V.Y.); (V.T.V.-E.); (O.N.I.); (I.L.K.); (M.V.G.); (A.R.K.); (S.N.K.)
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69434 Lyon, France; (J.M.); (L.M.); (B.G.); (B.B.)
| | - Olga A. Smirnova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.F.Z.); (O.A.K.); (O.A.S.); (D.V.Y.); (V.T.V.-E.); (O.N.I.); (I.L.K.); (M.V.G.); (A.R.K.); (S.N.K.)
| | - Jennifer Molle
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69434 Lyon, France; (J.M.); (L.M.); (B.G.); (B.B.)
| | - Sarah Duponchel
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69434 Lyon, France; (J.M.); (L.M.); (B.G.); (B.B.)
| | - Dmitry V. Yanvarev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.F.Z.); (O.A.K.); (O.A.S.); (D.V.Y.); (V.T.V.-E.); (O.N.I.); (I.L.K.); (M.V.G.); (A.R.K.); (S.N.K.)
| | - Vladimir T. Valuev-Elliston
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.F.Z.); (O.A.K.); (O.A.S.); (D.V.Y.); (V.T.V.-E.); (O.N.I.); (I.L.K.); (M.V.G.); (A.R.K.); (S.N.K.)
| | - Lea Monnier
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69434 Lyon, France; (J.M.); (L.M.); (B.G.); (B.B.)
| | - Boyan Grigorov
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69434 Lyon, France; (J.M.); (L.M.); (B.G.); (B.B.)
| | - Olga N. Ivanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.F.Z.); (O.A.K.); (O.A.S.); (D.V.Y.); (V.T.V.-E.); (O.N.I.); (I.L.K.); (M.V.G.); (A.R.K.); (S.N.K.)
| | - Inna L. Karpenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.F.Z.); (O.A.K.); (O.A.S.); (D.V.Y.); (V.T.V.-E.); (O.N.I.); (I.L.K.); (M.V.G.); (A.R.K.); (S.N.K.)
| | - Mikhail V. Golikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.F.Z.); (O.A.K.); (O.A.S.); (D.V.Y.); (V.T.V.-E.); (O.N.I.); (I.L.K.); (M.V.G.); (A.R.K.); (S.N.K.)
| | - Cedric Bovet
- University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; (C.B.); (B.R.)
| | - Barbara Rindlisbacher
- University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; (C.B.); (B.R.)
| | - Alex R. Khomutov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.F.Z.); (O.A.K.); (O.A.S.); (D.V.Y.); (V.T.V.-E.); (O.N.I.); (I.L.K.); (M.V.G.); (A.R.K.); (S.N.K.)
| | - Sergey N. Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.F.Z.); (O.A.K.); (O.A.S.); (D.V.Y.); (V.T.V.-E.); (O.N.I.); (I.L.K.); (M.V.G.); (A.R.K.); (S.N.K.)
| | - Birke Bartosch
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69434 Lyon, France; (J.M.); (L.M.); (B.G.); (B.B.)
| | - Alexander V. Ivanov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.F.Z.); (O.A.K.); (O.A.S.); (D.V.Y.); (V.T.V.-E.); (O.N.I.); (I.L.K.); (M.V.G.); (A.R.K.); (S.N.K.)
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Thorp EB, Karlstaedt A. Intersection of Immunology and Metabolism in Myocardial Disease. Circ Res 2024; 134:1824-1840. [PMID: 38843291 DOI: 10.1161/circresaha.124.323660] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/15/2024] [Indexed: 06/12/2024]
Abstract
Immunometabolism is an emerging field at the intersection of immunology and metabolism. Immune cell activation plays a critical role in the pathogenesis of cardiovascular diseases and is integral for regeneration during cardiac injury. We currently possess a limited understanding of the processes governing metabolic interactions between immune cells and cardiomyocytes. The impact of this intercellular crosstalk can manifest as alterations to the steady state flux of metabolites and impact cardiac contractile function. Although much of our knowledge is derived from acute inflammatory response, recent work emphasizes heterogeneity and flexibility in metabolism between cardiomyocytes and immune cells during pathological states, including ischemic, cardiometabolic, and cancer-associated disease. Metabolic adaptation is crucial because it influences immune cell activation, cytokine release, and potential therapeutic vulnerabilities. This review describes current concepts about immunometabolic regulation in the heart, focusing on intercellular crosstalk and intrinsic factors driving cellular regulation. We discuss experimental approaches to measure the cardio-immunologic crosstalk, which are necessary to uncover unknown mechanisms underlying the immune and cardiac interface. Deeper insight into these axes holds promise for therapeutic strategies that optimize cardioimmunology crosstalk for cardiac health.
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Affiliation(s)
- Edward B Thorp
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (E.B.T.)
| | - Anja Karlstaedt
- Department of Cardiology, Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA (A.K.)
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Hua H, Wang Y, Wang X, Wang S, Zhou Y, Liu Y, Liang Z, Ren H, Lu S, Wu S, Jiang Y, Pu Y, Zheng X, Tang C, Shen Z, Li C, Du Y, Deng H. Remodeling ceramide homeostasis promotes functional maturation of human pluripotent stem cell-derived β cells. Cell Stem Cell 2024; 31:850-865.e10. [PMID: 38697109 DOI: 10.1016/j.stem.2024.04.010] [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: 09/10/2023] [Revised: 03/21/2024] [Accepted: 04/12/2024] [Indexed: 05/04/2024]
Abstract
Human pluripotent stem cell-derived β cells (hPSC-β cells) show the potential to restore euglycemia. However, the immature functionality of hPSC-β cells has limited their efficacy in application. Here, by deciphering the continuous maturation process of hPSC-β cells post transplantation via single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq), we show that functional maturation of hPSC-β cells is an orderly multistep process during which cells sequentially undergo metabolic adaption, removal of negative regulators of cell function, and establishment of a more specialized transcriptome and epigenome. Importantly, remodeling lipid metabolism, especially downregulating the metabolic activity of ceramides, the central hub of sphingolipid metabolism, is critical for β cell maturation. Limiting intracellular accumulation of ceramides in hPSC-β cells remarkably enhanced their function, as indicated by improvements in insulin processing and glucose-stimulated insulin secretion. In summary, our findings provide insights into the maturation of human pancreatic β cells and highlight the importance of ceramide homeostasis in function acquisition.
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Affiliation(s)
- Huijuan Hua
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yaqi Wang
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China
| | | | - Shusen Wang
- Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, China
| | - Yunlu Zhou
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yinan Liu
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhen Liang
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Huixia Ren
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Sufang Lu
- Hangzhou Reprogenix Bioscience, Hangzhou, China
| | | | - Yong Jiang
- Hangzhou Reprogenix Bioscience, Hangzhou, China
| | - Yue Pu
- Hangzhou Reprogenix Bioscience, Hangzhou, China
| | - Xiang Zheng
- Hangzhou Repugene Technology, Hangzhou, China
| | - Chao Tang
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhongyang Shen
- Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, China
| | - Cheng Li
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China.
| | - Yuanyuan Du
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
| | - Hongkui Deng
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; Changping Laboratory, Beijing, China.
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35
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Gázquez A, García-Serna AM, Hernández-Caselles T, Martín-Orozco E, Cantero-Cano E, Prieto-Sánchez MT, Molina-Ruano MD, Castillo-Lacalle R, Vioque J, Morales E, García-Marcos L, Larqué E. Plasma polyamines during pregnancy and their relationships with maternal allergies and the immune response of the neonates. Pediatr Allergy Immunol 2024; 35:e14167. [PMID: 38860435 DOI: 10.1111/pai.14167] [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: 12/04/2023] [Revised: 04/22/2024] [Accepted: 05/13/2024] [Indexed: 06/12/2024]
Abstract
BACKGROUND Some studies have reported that polyamine levels may influence immune system programming. The aim of this study was to evaluate the polyamine profile during gestation and its associations with maternal allergy and cytokine production in cord blood cells in response to different allergenic stimuli. METHODS Polyamines were determined in plasma of pregnant women (24 weeks, N = 674) and in umbilical cord samples (N = 353 vein and N = 160 artery) from the Mediterranean NELA birth cohort. Immune cell populations were quantified, and the production of cytokines in response to different allergic and mitogenic stimuli was assessed in cord blood. RESULTS Spermidine and spermine were the most prevalent polyamines in maternal, cord venous, and cord arterial plasma. Maternal allergies, especially allergic conjunctivitis, were associated with lower spermine in umbilical cord vein. Higher levels of polyamines were associated with higher lymphocyte number but lower Th2-related cells in cord venous blood. Those subjects with higher levels of circulating polyamines in cord showed lower production of inflammatory cytokines, especially IFN-α, and lower production of Th2-related cytokines, mainly IL-4 and IL-5. The effects of polyamines on Th1-related cytokines production were uncertain. CONCLUSIONS Spermidine and spermine are the predominant polyamines in plasma of pregnant women at mid-pregnancy and also in umbilical cord. Maternal allergic diseases like allergic conjunctivitis are related to lower levels of polyamines in cord vein, which could influence the immune response of the newborn. Cord polyamine content is related to a decreased Th2 response and inflammatory cytokines production, which might be important to reduce an allergenic phenotype in the neonate.
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Affiliation(s)
- Antonio Gázquez
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
- Department of Physiology, University of Murcia, Murcia, Spain
| | - Azahara M García-Serna
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
- Department of Public Health Sciences, University of Murcia, Murcia, Spain
| | - Trinidad Hernández-Caselles
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Medicine, University of Murcia, Murcia, Spain
- Network of Asthma and Adverse and Allergic Reactions (ARADyAL), Madrid, Spain
| | - Elena Martín-Orozco
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Medicine, University of Murcia, Murcia, Spain
- Network of Asthma and Adverse and Allergic Reactions (ARADyAL), Madrid, Spain
| | | | - María T Prieto-Sánchez
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
- Obstetrics & Gynaecology Service, "Virgen de la Arrixaca" University Clinical Hospital, University of Murcia, Murcia, Spain
| | - María D Molina-Ruano
- Obstetrics & Gynaecology Service, "Virgen de la Arrixaca" University Clinical Hospital, University of Murcia, Murcia, Spain
| | - Rafaela Castillo-Lacalle
- Obstetrics & Gynaecology Service, "Virgen de la Arrixaca" University Clinical Hospital, University of Murcia, Murcia, Spain
| | - Jesús Vioque
- Health and Biomedical Research Institute of Alicante (ISABIAL-UMH), Alicante, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Eva Morales
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
- Department of Public Health Sciences, University of Murcia, Murcia, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Luís García-Marcos
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
- Network of Asthma and Adverse and Allergic Reactions (ARADyAL), Madrid, Spain
| | - Elvira Larqué
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
- Department of Physiology, University of Murcia, Murcia, Spain
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Chen H, You R, Guo J, Zhou W, Chew G, Devapragash N, Loh JZ, Gesualdo L, Li Y, Jiang Y, Tan ELS, Chen S, Pontrelli P, Pesce F, Behmoaras J, Zhang A, Petretto E. WWP2 Regulates Renal Fibrosis and the Metabolic Reprogramming of Profibrotic Myofibroblasts. J Am Soc Nephrol 2024; 35:696-718. [PMID: 38502123 PMCID: PMC11164121 DOI: 10.1681/asn.0000000000000328] [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: 10/02/2023] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Key Points WWP2 expression is elevated in the tubulointerstitium of fibrotic kidneys and contributes to CKD pathogenesis and progression. WWP2 uncouples the profibrotic activation and cell proliferation in renal myofibroblasts. WWP2 controls mitochondrial respiration in renal myofibroblasts through the metabolic regulator peroxisome proliferator-activated receptor gamma coactivator 1-alpha. Background Renal fibrosis is a common pathologic end point in CKD that is challenging to reverse, and myofibroblasts are responsible for the accumulation of a fibrillar collagen–rich extracellular matrix. Recent studies have unveiled myofibroblasts' diversity in proliferative and fibrotic characteristics, which are linked to different metabolic states. We previously demonstrated the regulation of extracellular matrix genes and tissue fibrosis by WWP2, a multifunctional E3 ubiquitin–protein ligase. Here, we investigate WWP2 in renal fibrosis and in the metabolic reprograming of myofibroblasts in CKD. Methods We used kidney samples from patients with CKD and WWP2 -null kidney disease mice models and leveraged single-cell RNA sequencing analysis to detail the cell-specific regulation of WWP2 in fibrotic kidneys. Experiments in primary cultured myofibroblasts by bulk-RNA sequencing, chromatin immunoprecipitation sequencing, metabolomics, and cellular metabolism assays were used to study the metabolic regulation of WWP2 and its downstream signaling. Results The tubulointerstitial expression of WWP2 was associated with fibrotic progression in patients with CKD and in murine kidney disease models. WWP2 deficiency promoted myofibroblast proliferation and halted profibrotic activation, reducing the severity of renal fibrosis in vivo . In renal myofibroblasts, WWP2 deficiency increased fatty acid oxidation and activated the pentose phosphate pathway, boosting mitochondrial respiration at the expense of glycolysis. WWP2 suppressed the transcription of peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α), a metabolic mediator of fibrotic response, and pharmacologic inhibition of PGC-1α partially abrogated the protective effects of WWP2 deficiency on myofibroblasts. Conclusions WWP2 regulates the metabolic reprogramming of profibrotic myofibroblasts by a WWP2-PGC-1α axis, and WWP2 deficiency protects against renal fibrosis in CKD.
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Affiliation(s)
- Huimei Chen
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
| | - Ran You
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Guo
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
| | - Wei Zhou
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Gabriel Chew
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
| | - Nithya Devapragash
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
| | - Jui Zhi Loh
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
| | - Loreto Gesualdo
- Nephrology, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari Aldo Moro, Bari, Italy
| | - Yanwei Li
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yuteng Jiang
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Elisabeth Li Sa Tan
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
| | - Shuang Chen
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
- School of Science, Institute for Big Data and Artificial Intelligence in Medicine, China Pharmaceutical University, Nanjing, China
| | - Paola Pontrelli
- Nephrology, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari Aldo Moro, Bari, Italy
| | - Francesco Pesce
- Division of Renal Medicine, Fatebenefratelli Isola Tiberina—Gemelli Isola, Rome, Italy
| | - Jacques Behmoaras
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
- Centre for Inflammatory Disease, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - Aihua Zhang
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Enrico Petretto
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
- School of Science, Institute for Big Data and Artificial Intelligence in Medicine, China Pharmaceutical University, Nanjing, China
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Bader JE, Wolf MM, Lupica-Tondo GL, Madden MZ, Reinfeld BI, Arner EN, Hathaway ES, Steiner KK, Needle GA, Hatem Z, Landis MD, Faneuff EE, Blackman A, Wolf EM, Cottam MA, Ye X, Bates ME, Smart K, Wang W, Pinheiro LV, Christofides A, Smith D, Boussiotis VA, Haake SM, Beckermann KE, Wellen KE, Reinhart-King CA, Serezani CH, Lee CH, Aubrey C, Chen H, Rathmell WK, Hasty AH, Rathmell JC. Obesity induces PD-1 on macrophages to suppress anti-tumour immunity. Nature 2024; 630:968-975. [PMID: 38867043 DOI: 10.1038/s41586-024-07529-3] [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: 11/04/2022] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Obesity is a leading risk factor for progression and metastasis of many cancers1,2, yet can in some cases enhance survival3-5 and responses to immune checkpoint blockade therapies, including anti-PD-1, which targets PD-1 (encoded by PDCD1), an inhibitory receptor expressed on immune cells6-8. Although obesity promotes chronic inflammation, the role of the immune system in the obesity-cancer connection and immunotherapy remains unclear. It has been shown that in addition to T cells, macrophages can express PD-19-12. Here we found that obesity selectively induced PD-1 expression on tumour-associated macrophages (TAMs). Type I inflammatory cytokines and molecules linked to obesity, including interferon-γ, tumour necrosis factor, leptin, insulin and palmitate, induced macrophage PD-1 expression in an mTORC1- and glycolysis-dependent manner. PD-1 then provided negative feedback to TAMs that suppressed glycolysis, phagocytosis and T cell stimulatory potential. Conversely, PD-1 blockade increased the level of macrophage glycolysis, which was essential for PD-1 inhibition to augment TAM expression of CD86 and major histocompatibility complex I and II molecules and ability to activate T cells. Myeloid-specific PD-1 deficiency slowed tumour growth, enhanced TAM glycolysis and antigen-presentation capability, and led to increased CD8+ T cell activity with a reduced level of markers of exhaustion. These findings show that obesity-associated metabolic signalling and inflammatory cues cause TAMs to induce PD-1 expression, which then drives a TAM-specific feedback mechanism that impairs tumour immune surveillance. This may contribute to increased cancer risk yet improved response to PD-1 immunotherapy in obesity.
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Affiliation(s)
- Jackie E Bader
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Melissa M Wolf
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gian Luca Lupica-Tondo
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Matthew Z Madden
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bradley I Reinfeld
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emily N Arner
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emma S Hathaway
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - KayLee K Steiner
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gabriel A Needle
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Zaid Hatem
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Madelyn D Landis
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eden E Faneuff
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Amondrea Blackman
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elysa M Wolf
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Matthew A Cottam
- Department of Surgery, Division of Surgical Oncology and Endocrine Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiang Ye
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Madison E Bates
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Kyra Smart
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Wenjun Wang
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Laura V Pinheiro
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anthos Christofides
- Department of Medicine, Division of Hematology-Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Harvard University, Boston, MA, USA
| | - DuPreez Smith
- Department of Obstetrics and Gynecology, University of Alberta, Edmonton, Alberta, Canada
| | - Vassiliki A Boussiotis
- Department of Medicine, Division of Hematology-Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Scott M Haake
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kathryn E Beckermann
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kathryn E Wellen
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - C Henrique Serezani
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cheng-Han Lee
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Christa Aubrey
- Department of Obstetrics and Gynecology, University of Alberta, Edmonton, Alberta, Canada
| | - Heidi Chen
- Department of Biostatistics, Vanderbilt University, Nashville, TN, USA
| | - W Kimryn Rathmell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alyssa H Hasty
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- US Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Jeffrey C Rathmell
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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Fleetwood AJ, Noonan J, La Gruta N, Kallies A, Murphy AJ. Immunometabolism in atherosclerotic disorders. NATURE CARDIOVASCULAR RESEARCH 2024; 3:637-650. [PMID: 39196223 DOI: 10.1038/s44161-024-00473-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 04/11/2024] [Indexed: 08/29/2024]
Abstract
Cardiovascular diseases (CVDs), including atherosclerosis, myocardial infarction and heart failure, are the leading causes of morbidity and mortality worldwide. Emerging evidence suggests a crucial role for immune cell dysfunction and inflammation in the progression of this complex set of diseases. Recent advances demonstrate that immune cells, tightly linked to CVD pathogenesis, are sensitive to environmental signals and respond by engaging immunometabolic networks that shape their behavior. Inflammatory cues and altered nutrient availability within atherosclerotic plaques or following ischemia synergize to elicit metabolic shifts in immune cells that influence the course of disease pathology. Understanding these metabolic adaptations and how they contribute to cellular dysfunction may reveal novel therapeutic approaches for the treatment of CVD. Here we provide a comprehensive summary of the metabolic reprogramming that occurs in immune cells and their progenitors during CVD, offering insights into the potential therapeutic interventions to mitigate disease progression.
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Affiliation(s)
- Andrew J Fleetwood
- Division of Immunometabolism, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
| | - Jonathan Noonan
- Division of Immunometabolism, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Nicole La Gruta
- Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Axel Kallies
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew J Murphy
- Division of Immunometabolism, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
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Farr E, Dimitrov D, Schmidt C, Turei D, Lobentanzer S, Dugourd A, Saez-Rodriguez J. MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions. Brief Bioinform 2024; 25:bbae347. [PMID: 39038934 PMCID: PMC11262834 DOI: 10.1093/bib/bbae347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/29/2024] [Accepted: 07/08/2024] [Indexed: 07/24/2024] Open
Abstract
From the catalytic breakdown of nutrients to signaling, interactions between metabolites and proteins play an essential role in cellular function. An important case is cell-cell communication, where metabolites, secreted into the microenvironment, initiate signaling cascades by binding to intra- or extracellular receptors of neighboring cells. Protein-protein cell-cell communication interactions are routinely predicted from transcriptomic data. However, inferring metabolite-mediated intercellular signaling remains challenging, partially due to the limited size of intercellular prior knowledge resources focused on metabolites. Here, we leverage knowledge-graph infrastructure to integrate generalistic metabolite-protein with curated metabolite-receptor resources to create MetalinksDB. MetalinksDB is an order of magnitude larger than existing metabolite-receptor resources and can be tailored to specific biological contexts, such as diseases, pathways, or tissue/cellular locations. We demonstrate MetalinksDB's utility in identifying deregulated processes in renal cancer using multi-omics bulk data. Furthermore, we infer metabolite-driven intercellular signaling in acute kidney injury using spatial transcriptomics data. MetalinksDB is a comprehensive and customizable database of intercellular metabolite-protein interactions, accessible via a web interface (https://metalinks.omnipathdb.org/) and programmatically as a knowledge graph (https://github.com/biocypher/metalinks). We anticipate that by enabling diverse analyses tailored to specific biological contexts, MetalinksDB will facilitate the discovery of disease-relevant metabolite-mediated intercellular signaling processes.
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Affiliation(s)
- Elias Farr
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - Daniel Dimitrov
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
| | - Christina Schmidt
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
| | - Denes Turei
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
| | - Sebastian Lobentanzer
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
| | - Aurelien Dugourd
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
- EMBL European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
- EMBL European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SA, United Kingdom
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40
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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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Ma S, Ming Y, Wu J, Cui G. Cellular metabolism regulates the differentiation and function of T-cell subsets. Cell Mol Immunol 2024; 21:419-435. [PMID: 38565887 PMCID: PMC11061161 DOI: 10.1038/s41423-024-01148-8] [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: 12/28/2023] [Accepted: 02/23/2024] [Indexed: 04/04/2024] Open
Abstract
T cells are an important component of adaptive immunity and protect the host from infectious diseases and cancers. However, uncontrolled T cell immunity may cause autoimmune disorders. In both situations, antigen-specific T cells undergo clonal expansion upon the engagement and activation of antigens. Cellular metabolism is reprogrammed to meet the increase in bioenergetic and biosynthetic demands associated with effector T cell expansion. Metabolites not only serve as building blocks or energy sources to fuel cell growth and expansion but also regulate a broad spectrum of cellular signals that instruct the differentiation of multiple T cell subsets. The realm of immunometabolism research is undergoing swift advancements. Encapsulating all the recent progress within this concise review in not possible. Instead, our objective is to provide a succinct introduction to this swiftly progressing research, concentrating on the metabolic intricacies of three pivotal nutrient classes-lipids, glucose, and amino acids-in T cells. We shed light on recent investigations elucidating the roles of these three groups of metabolites in mediating the metabolic and immune functions of T cells. Moreover, we delve into the prospect of "editing" metabolic pathways within T cells using pharmacological or genetic approaches, with the aim of synergizing this approach with existing immunotherapies and enhancing the efficacy of antitumor and antiinfection immune responses.
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Affiliation(s)
- Sicong Ma
- Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230601, China
| | - Yanan Ming
- Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230601, China
| | - Jingxia Wu
- Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230601, China.
| | - Guoliang Cui
- Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230601, China.
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Okada J, Landgraf A, Xiaoli AM, Liu L, Horton M, Schuster VL, Yang F, Sidoli S, Qiu Y, Kurland IJ, Eliscovich C, Shinoda K, Pessin JE. Spatial hepatocyte plasticity of gluconeogenesis during the metabolic transitions between fed, fasted and starvation states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591168. [PMID: 38746329 PMCID: PMC11092462 DOI: 10.1101/2024.04.29.591168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The liver acts as a master regulator of metabolic homeostasis in part by performing gluconeogenesis. This process is dysregulated in type 2 diabetes, leading to elevated hepatic glucose output. The parenchymal cells of the liver (hepatocytes) are heterogeneous, existing on an axis between the portal triad and the central vein, and perform distinct functions depending on location in the lobule. Here, using single cell analysis of hepatocytes across the liver lobule, we demonstrate that gluconeogenic gene expression ( Pck1 and G6pc ) is relatively low in the fed state and gradually increases first in the periportal hepatocytes during the initial fasting period. As the time of fasting progresses, pericentral hepatocyte gluconeogenic gene expression increases, and following entry into the starvation state, the pericentral hepatocytes show similar gluconeogenic gene expression to the periportal hepatocytes. Similarly, pyruvate-dependent gluconeogenic activity is approximately 10-fold higher in the periportal hepatocytes during the initial fasting state but only 1.5-fold higher in the starvation state. In parallel, starvation suppresses canonical beta-catenin signaling and modulates expression of pericentral and periportal glutamine synthetase and glutaminase, resulting in an enhanced pericentral glutamine-dependent gluconeogenesis. These findings demonstrate that hepatocyte gluconeogenic gene expression and gluconeogenic activity are highly spatially and temporally plastic across the liver lobule, underscoring the critical importance of using well-defined feeding and fasting conditions to define the basis of hepatic insulin resistance and glucose production.
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Abimannan T, Parthibane V, Le SH, Vijaykrishna N, Fox SD, Karim B, Kunduri G, Blankenberg D, Andresson T, Bamba T, Acharya U, Acharya JK. Sphingolipid biosynthesis is essential for metabolic rewiring during T H17 cell differentiation. SCIENCE ADVANCES 2024; 10:eadk1045. [PMID: 38657065 PMCID: PMC11042737 DOI: 10.1126/sciadv.adk1045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 03/22/2024] [Indexed: 04/26/2024]
Abstract
T helper 17 (TH17) cells are implicated in autoimmune diseases, and several metabolic processes are shown to be important for their development and function. In this study, we report an essential role for sphingolipids synthesized through the de novo pathway in TH17 cell development. Deficiency of SPTLC1, a major subunit of serine palmitoyl transferase enzyme complex that catalyzes the first and rate-limiting step of de novo sphingolipid synthesis, impaired glycolysis in differentiating TH17 cells by increasing intracellular reactive oxygen species (ROS) through enhancement of nicotinamide adenine dinucleotide phosphate oxidase 2 activity. Increased ROS leads to impaired activation of mammalian target of rapamycin C1 and reduced expression of hypoxia-inducible factor 1-alpha and c-Myc-induced glycolytic genes. SPTLCI deficiency protected mice from developing experimental autoimmune encephalomyelitis and experimental T cell transfer colitis. Our results thus show a critical role for de novo sphingolipid biosynthetic pathway in shaping adaptive immune responses with implications in autoimmune diseases.
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Affiliation(s)
| | - Velayoudame Parthibane
- Cancer and Developmental Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Si-Hung Le
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Nagampalli Vijaykrishna
- Genomic Medicine Institute and Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Stephen D. Fox
- Mass Spectrometry Group, National Cancer Institute, Frederick, MD, USA
| | - Baktiar Karim
- Molecular Histopathology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Govind Kunduri
- Cancer and Developmental Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Daniel Blankenberg
- Genomic Medicine Institute and Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Takeshi Bamba
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Usha Acharya
- Cancer and Developmental Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Jairaj K. Acharya
- Cancer and Developmental Biology Laboratory, National Cancer Institute, Frederick, MD, USA
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Chi H, Pepper M, Thomas PG. Principles and therapeutic applications of adaptive immunity. Cell 2024; 187:2052-2078. [PMID: 38670065 PMCID: PMC11177542 DOI: 10.1016/j.cell.2024.03.037] [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: 01/02/2024] [Revised: 03/01/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024]
Abstract
Adaptive immunity provides protection against infectious and malignant diseases. These effects are mediated by lymphocytes that sense and respond with targeted precision to perturbations induced by pathogens and tissue damage. Here, we review key principles underlying adaptive immunity orchestrated by distinct T cell and B cell populations and their extensions to disease therapies. We discuss the intracellular and intercellular processes shaping antigen specificity and recognition in immune activation and lymphocyte functions in mediating effector and memory responses. We also describe how lymphocytes balance protective immunity against autoimmunity and immunopathology, including during immune tolerance, response to chronic antigen stimulation, and adaptation to non-lymphoid tissues in coordinating tissue immunity and homeostasis. Finally, we discuss extracellular signals and cell-intrinsic programs underpinning adaptive immunity and conclude by summarizing key advances in vaccination and engineering adaptive immune responses for therapeutic interventions. A deeper understanding of these principles holds promise for uncovering new means to improve human health.
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Affiliation(s)
- Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Marion Pepper
- Department of Immunology, University of Washington, Seattle, WA, USA.
| | - Paul G Thomas
- Department of Host-Microbe Interactions and Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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45
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Chen Y, Gustafsson J, Yang J, Nielsen J, Kerkhoven EJ. Single-cell omics analysis with genome-scale metabolic modeling. Curr Opin Biotechnol 2024; 86:103078. [PMID: 38359604 DOI: 10.1016/j.copbio.2024.103078] [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: 10/02/2023] [Accepted: 01/19/2024] [Indexed: 02/17/2024]
Abstract
Single-cell technologies have been widely used in biological studies and generated a plethora of single-cell data to be interpreted. Due to the inclusion of the priori metabolic network knowledge as well as gene-protein-reaction associations, genome-scale metabolic models (GEMs) have been a powerful tool to integrate and thereby interpret various omics data mostly from bulk samples. Here, we first review two common ways to leverage bulk omics data with GEMs and then discuss advances on integrative analysis of single-cell omics data with GEMs. We end by presenting our views on current challenges and perspectives in this field.
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Affiliation(s)
- Yu Chen
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Johan Gustafsson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden; Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Jingyu Yang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jens Nielsen
- Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; BioInnovation Institute, DK-2200 Copenhagen, Denmark
| | - Eduard J Kerkhoven
- Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technology University of Denmark, DK-2800 Kgs. Lyngby, Denmark; SciLifeLab, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.
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46
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Chang HW, Lee EM, Wang Y, Zhou C, Pruss KM, Henrissat S, Chen RY, Kao C, Hibberd MC, Lynn HM, Webber DM, Crane M, Cheng J, Rodionov DA, Arzamasov AA, Castillo JJ, Couture G, Chen Y, Balcazo NP, Lebrilla CB, Terrapon N, Henrissat B, Ilkayeva O, Muehlbauer MJ, Newgard CB, Mostafa I, Das S, Mahfuz M, Osterman AL, Barratt MJ, Ahmed T, Gordon JI. Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition. Nat Microbiol 2024; 9:922-937. [PMID: 38503977 PMCID: PMC10994852 DOI: 10.1038/s41564-024-01628-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/31/2024] [Indexed: 03/21/2024]
Abstract
Microbiota-directed complementary food (MDCF) formulations have been designed to repair the gut communities of malnourished children. A randomized controlled trial demonstrated that one formulation, MDCF-2, improved weight gain in malnourished Bangladeshi children compared to a more calorically dense standard nutritional intervention. Metagenome-assembled genomes from study participants revealed a correlation between ponderal growth and expression of MDCF-2 glycan utilization pathways by Prevotella copri strains. To test this correlation, here we use gnotobiotic mice colonized with defined consortia of age- and ponderal growth-associated gut bacterial strains, with or without P. copri isolates closely matching the metagenome-assembled genomes. Combining gut metagenomics and metatranscriptomics with host single-nucleus RNA sequencing and gut metabolomic analyses, we identify a key role of P. copri in metabolizing MDCF-2 glycans and uncover its interactions with other microbes including Bifidobacterium infantis. P. copri-containing consortia mediated weight gain and modulated energy metabolism within intestinal epithelial cells. Our results reveal structure-function relationships between MDCF-2 and members of the gut microbiota of malnourished children with potential implications for future therapies.
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Affiliation(s)
- Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Evan M Lee
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Yi Wang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Kali M Pruss
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Robert Y Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Clara Kao
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Hannah M Lynn
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel M Webber
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Marie Crane
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Jiye Cheng
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Aleksandr A Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Juan J Castillo
- Department of Chemistry, University of California, Davis, CA, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA, USA
| | - Ye Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Chemistry, University of California, Davis, CA, USA
| | - Nikita P Balcazo
- Department of Chemistry, University of California, Davis, CA, USA
| | | | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Michael J Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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47
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Sui H, Deng W, Chai Q, Han B, Zhang Y, Wei Z, Li Z, Wang T, Feng J, Yuan M, Tang Q, Xu H. YTE-17 inhibits colonic carcinogenesis by resetting antitumor immune response via Wnt5a/JNK mediated metabolic signaling. J Pharm Anal 2024; 14:100901. [PMID: 38665223 PMCID: PMC11044051 DOI: 10.1016/j.jpha.2023.11.008] [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: 05/09/2023] [Revised: 11/11/2023] [Accepted: 11/16/2023] [Indexed: 04/28/2024] Open
Abstract
The density and composition of lymphocytes infiltrating colon tumors serve as predictive factors for the clinical outcome of colon cancer. Our previous studies highlighted the potent anti-cancer properties of the principal compounds found in Garcinia yunnanensis (YTE-17), attributing these effects to the regulation of multiple signaling pathways. However, knowledge regarding the mechanism and effect of YTE-17 in the prevention of colorectal cancer is limited. In this study, we conducted isobaric tags for relative and absolute quantification (iTRAQ) analysis on intestinal epithelial cells (IECs) exposed YTE-17, both in vitro and invivo, revealing a significant inhibition of the Wnt family member 5a (Wnt5a)/c-Jun N-terminal kinase (JNK) signaling pathway. Subsequently, we elucidated the influence and mechanism of YTE-17 on the tumor microenvironment (TME), specifically focusing on macrophage-mediated T helper 17 (Th17) cell induction in a colitis-associated cancer (CAC) model with Wnt5a deletion. Additionally, we performed the single-cell RNA sequencing (scRNA-seq) on the colonic tissue from the Wnt5a-deleted CAC model to characterize the composition, lineage, and functional status of immune mesenchymal cells during different stages of colorectal cancer (CRC) progression. Remarkably, our findings demonstrate a significant reduction in M2 macrophage polarization and Th17 cell phenotype upon treatment with YTE-17, leading to the restoration of regulatory T (Treg)/Th17 cell balance in azoxymethane (AOM)/dextran sodium sulfate (DSS) model. Furthermore, we also confirmed that YTE-17 effectively inhibited the glycolysis of Th17 cells in both direct and indirect co-culture systems with M2 macrophages. Notably, our study shed light on potential mechanisms linking the non-canonical Wnt5a/JNK signaling pathway and well-established canonical β-catenin oncogenic pathway in vivo. Specifically, we proposed that Wnt5a/JNK signaling activity in IECs promotes the development of cancer stem cells with β-catenin activity within the TME, involving macrophages and T cells. In summary, our study undergoes the potential of YTE-17 as a preventive strategy against CRC development by addressing the imbalance with the immune microenvironment, thereby mitigating the risk of malignancies.
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Affiliation(s)
- Hua Sui
- Medical Experiment Center, Jiading Branch of Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201803, China
- Translational Medicine Research Center for Cancer Prevention and Treatment, Shanghai General Hospital Jiading Branch-School of Pharmacy of Shanghai University of Traditional Chinese Medicine Joint Laboratory, Shanghai, 201803, China
| | - Wanli Deng
- Department of Medical Oncology, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, China
| | - Qiong Chai
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Bing Han
- The Second Clinical Medical College of Henan University of Traditional Chinese Medicine, Zhengzhou, 450000, China
| | - Yuli Zhang
- Translational Medicine Research Center for Cancer Prevention and Treatment, Shanghai General Hospital Jiading Branch-School of Pharmacy of Shanghai University of Traditional Chinese Medicine Joint Laboratory, Shanghai, 201803, China
| | - Zhenzhen Wei
- Medical Experiment Center, Jiading Branch of Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201803, China
- Translational Medicine Research Center for Cancer Prevention and Treatment, Shanghai General Hospital Jiading Branch-School of Pharmacy of Shanghai University of Traditional Chinese Medicine Joint Laboratory, Shanghai, 201803, China
| | - Zan Li
- Medical Experiment Center, Jiading Branch of Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201803, China
- Translational Medicine Research Center for Cancer Prevention and Treatment, Shanghai General Hospital Jiading Branch-School of Pharmacy of Shanghai University of Traditional Chinese Medicine Joint Laboratory, Shanghai, 201803, China
| | - Ting Wang
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jiling Feng
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201620, China
| | - Man Yuan
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Qingfeng Tang
- Medical Experiment Center, Jiading Branch of Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201803, China
| | - Hongxi Xu
- Translational Medicine Research Center for Cancer Prevention and Treatment, Shanghai General Hospital Jiading Branch-School of Pharmacy of Shanghai University of Traditional Chinese Medicine Joint Laboratory, Shanghai, 201803, China
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
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48
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Sun X, Wu J, Zhang X, Xie C, Wei H, Li P, Yang Y, Yuan H, Cai J, Xiao Q, Cheng J, Xu Q. Atlas of Cell Repertoire Within Neointimal Lesions Is Metabolically Altered in Hypertensive Rats. Hypertension 2024; 81:787-800. [PMID: 38240164 DOI: 10.1161/hypertensionaha.123.22057] [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: 09/14/2023] [Accepted: 01/09/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND High blood pressure has been suggested to accelerate vascular injury-induced neointimal formation and progression. However, little is known about the intricate relationships between vascular injury and hypertension in the context of arterial remodeling. METHODS Single-cell RNA-sequencing analysis was used to depict the cell atlas of carotid arteries of Wistar Kyoto rats and spontaneously hypertensive rats with or without balloon injury. RESULTS We found that hypertension significantly aggravated balloon injury-induced arterial stenosis. A total of 36 202 cells from carotid arteries with or without balloon injury were included in single-cell RNA-sequencing analysis. Cell composition analysis showed that vascular injury and hypertension independently induced distinct aortic cell phenotypic alterations including immune cells, endothelial cells (ECs), and smooth muscle cells. Specifically, our data showed that injury and hypertension-induced specific EC phenotypic alterations, and revealed a transition from functional ECs to hypermetabolic, and eventually dysfunctional ECs in hypertensive rats upon balloon injury. Importantly, our data also showed that vascular injury and hypertension-induced different smooth muscle cell phenotypic alterations, characterized by deferential expression of synthetic signatures. Interestingly, pathway analysis showed that dysregulated metabolic pathways were a common feature in monocytes/macrophages, ECs, and smooth muscle cells in response to injury and hypertension. Functionally, we demonstrate that inhibition of mitochondrial respiration significantly ameliorated injury-induced neointimal formation in spontaneously hypertensive rats. CONCLUSIONS This study provides the cell landscape changes of the main aortic cell phenotypic alterations in response to injury and hypertension. Our findings suggest that targeting cellular mitochondrial respiration could be a novel therapeutic for patients with hypertension undergoing vascular angioplasty.
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Affiliation(s)
- Xiaolei Sun
- Department of General Surgery (Vascular Surgery), Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, The Affiliated Hospital of Southwest Medical University, Luzhou, China (X.S., H.W.)
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province (Collaborative Innovation Center for Prevention of Cardiovascular Diseases), Institute of Cardiovascular Research, Public Center of Experimental Technology, Southwest Medical University, Luzhou, China (X.S., X.Z., C.X., P.L., Y.Y., J. Cheng, Q. Xu)
| | - Junru Wu
- Department of Cardiology and Center of Pharmacology, Postdoctoral Station of Clinical Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China (J.W., H.Y., J. Cai)
| | - Xiaolin Zhang
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province (Collaborative Innovation Center for Prevention of Cardiovascular Diseases), Institute of Cardiovascular Research, Public Center of Experimental Technology, Southwest Medical University, Luzhou, China (X.S., X.Z., C.X., P.L., Y.Y., J. Cheng, Q. Xu)
| | - Cheng Xie
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province (Collaborative Innovation Center for Prevention of Cardiovascular Diseases), Institute of Cardiovascular Research, Public Center of Experimental Technology, Southwest Medical University, Luzhou, China (X.S., X.Z., C.X., P.L., Y.Y., J. Cheng, Q. Xu)
| | - Haijun Wei
- Department of General Surgery (Vascular Surgery), Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, The Affiliated Hospital of Southwest Medical University, Luzhou, China (X.S., H.W.)
| | - Pengyun Li
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province (Collaborative Innovation Center for Prevention of Cardiovascular Diseases), Institute of Cardiovascular Research, Public Center of Experimental Technology, Southwest Medical University, Luzhou, China (X.S., X.Z., C.X., P.L., Y.Y., J. Cheng, Q. Xu)
| | - Yan Yang
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province (Collaborative Innovation Center for Prevention of Cardiovascular Diseases), Institute of Cardiovascular Research, Public Center of Experimental Technology, Southwest Medical University, Luzhou, China (X.S., X.Z., C.X., P.L., Y.Y., J. Cheng, Q. Xu)
| | - Hong Yuan
- Department of Cardiology and Center of Pharmacology, Postdoctoral Station of Clinical Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China (J.W., H.Y., J. Cai)
| | - Jingjing Cai
- Department of Cardiology and Center of Pharmacology, Postdoctoral Station of Clinical Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China (J.W., H.Y., J. Cai)
| | - Qingzhong Xiao
- Centre for Clinical Pharmacology and Precision Medicine, William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, United Kingdom (Q. Xiao, Q. Xu)
| | - Jun Cheng
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province (Collaborative Innovation Center for Prevention of Cardiovascular Diseases), Institute of Cardiovascular Research, Public Center of Experimental Technology, Southwest Medical University, Luzhou, China (X.S., X.Z., C.X., P.L., Y.Y., J. Cheng, Q. Xu)
| | - Qingbo Xu
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province (Collaborative Innovation Center for Prevention of Cardiovascular Diseases), Institute of Cardiovascular Research, Public Center of Experimental Technology, Southwest Medical University, Luzhou, China (X.S., X.Z., C.X., P.L., Y.Y., J. Cheng, Q. Xu)
- Centre for Clinical Pharmacology and Precision Medicine, William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, United Kingdom (Q. Xiao, Q. Xu)
- Department of Cardiology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China (Q. Xu)
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Han K, Meadows AM, Rodman MJ, Russo AC, Sharma R, Singh K, Hassanzadeh S, Dagur PK, Huffstutler RD, Krause FN, Griffin JL, Baumer Y, Powell-Wiley TM, Sack MN. Propionate functions as a feeding state-dependent regulatory metabolite to counter proinflammatory signaling linked to nutrient load and obesity. J Leukoc Biol 2024; 115:738-749. [PMID: 38207130 PMCID: PMC10980352 DOI: 10.1093/jleuko/qiae006] [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: 06/14/2023] [Revised: 12/18/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024] Open
Abstract
Generally, fasting and refeeding confer anti- and proinflammatory effects, respectively. In humans, these caloric-load interventions function, in part, via regulation of CD4+ T cell biology. However, mechanisms orchestrating this regulation remain incomplete. We employed integrative bioinformatics of RNA sequencing and high-performance liquid chromatography-mass spectrometry data to measure serum metabolites and gene expression of peripheral blood mononuclear cells isolated from fasting and refeeding in volunteers to identify nutrient-load metabolite-driven immunoregulation. Propionate, a short chain fatty acid (SCFA), and the SCFA-sensing G protein-coupled receptor 43 (ffar2) were coordinately and inversely regulated by fasting and refeeding. Propionate and free fatty acid receptor agonists decreased interferon-γ and interleukin-17 and significantly blunted histone deacetylase activity in CD4+ T cells. Furthermore, propionate blunted nuclear factor κB activity and diminished interleukin-6 release. In parallel, propionate reduced phosphorylation of canonical T helper 1 (TH1) and TH17 regulators, STAT1 and STAT3, respectively. Conversely, knockdown of free fatty acid receptors significantly attenuated the anti-inflammatory role of propionate. Interestingly, propionate recapitulated the blunting of CD4+ TH cell activation in primary cells from obese individuals, extending the role of this metabolite to a disease associated with low-grade inflammation. Together, these data identify a nutrient-load responsive SCFA-G protein-coupled receptor linked pathway to regulate CD4+ TH cell immune responsiveness.
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Affiliation(s)
- Kim Han
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Room 5-3342, Bld 10-CRC, 10 Center Drive, Bethesda, MD 20817, United States
| | - Allison M Meadows
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Room 5-3342, Bld 10-CRC, 10 Center Drive, Bethesda, MD 20817, United States
- Department of Biochemistry, University of Cambridge, Sanger Bld, 80 Tennis Ct Rd, Cambridge CB2 1GA, United Kingdom
| | - Matthew J Rodman
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Room 5-3342, Bld 10-CRC, 10 Center Drive, Bethesda, MD 20817, United States
| | - Anna Chiara Russo
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Room 5-3342, Bld 10-CRC, 10 Center Drive, Bethesda, MD 20817, United States
| | - Rahul Sharma
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Room 5-3342, Bld 10-CRC, 10 Center Drive, Bethesda, MD 20817, United States
| | - Komudi Singh
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Room 5-3342, Bld 10-CRC, 10 Center Drive, Bethesda, MD 20817, United States
| | - Shahin Hassanzadeh
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Room 5-3342, Bld 10-CRC, 10 Center Drive, Bethesda, MD 20817, United States
| | - Pradeep K Dagur
- Flow Cytometry Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, United States
| | - Rebecca D Huffstutler
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, United States
| | - Fynn N Krause
- Department of Biochemistry, University of Cambridge, Sanger Bld, 80 Tennis Ct Rd, Cambridge CB2 1GA, United Kingdom
| | - Julian L Griffin
- Department of Biochemistry, University of Cambridge, Sanger Bld, 80 Tennis Ct Rd, Cambridge CB2 1GA, United Kingdom
- Rowett Institute, School of Medicine, Medical Sciences and Nutrition, Foresterhill Campus, University of Aberdeen, Ashgrove Rd W, Aberdeen AB25 2ZD, United Kingdom
| | - Yvonne Baumer
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, United States
| | - Tiffany M Powell-Wiley
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, United States
| | - Michael N Sack
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Room 5-3342, Bld 10-CRC, 10 Center Drive, Bethesda, MD 20817, United States
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, United States
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50
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Zelante T, Paolicelli G, Fallarino F, Gargaro M, Vascelli G, De Zuani M, Fric J, Laznickova P, Kohoutkova MH, Macchiarulo A, Dolciami D, Pieraccini G, Gaetani L, Scalisi G, Trevisan C, Frossi B, Pucillo C, De Luca A, Nunzi E, Spaccapelo R, Pariano M, Borghi M, Boscaro F, Romoli R, Mancini A, Gentili L, Renga G, Costantini C, Puccetti M, Giovagnoli S, Ricci M, Antonini M, Calabresi P, Puccetti P, Di Filippo M, Romani L. A microbially produced AhR ligand promotes a Tph1-driven tolerogenic program in multiple sclerosis. Sci Rep 2024; 14:6651. [PMID: 38509264 PMCID: PMC10954611 DOI: 10.1038/s41598-024-57400-8] [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: 11/15/2023] [Accepted: 03/18/2024] [Indexed: 03/22/2024] Open
Abstract
Multiple sclerosis is a debilitating autoimmune disease, characterized by chronic inflammation of the central nervous system. While the significance of the gut microbiome on multiple sclerosis pathogenesis is established, the underlining mechanisms are unknown. We found that serum levels of the microbial postbiotic tryptophan metabolite indole-3-carboxaldehyde (3-IAld) inversely correlated with disease duration in multiple sclerosis patients. Much like the host-derived tryptophan derivative L-Kynurenine, 3-IAld would bind and activate the Aryl hydrocarbon Receptor (AhR), which, in turn, controls endogenous tryptophan catabolic pathways. As a result, in peripheral lymph nodes, microbial 3-IAld, affected mast-cell tryptophan metabolism, forcing mast cells to produce serotonin via Tph1. We thus propose a protective role for AhR-mast-cell activation driven by the microbiome, whereby natural metabolites or postbiotics will have a physiological role in immune homeostasis and may act as therapeutic targets in autoimmune diseases.
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Affiliation(s)
- Teresa Zelante
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy.
- Interuniversity Consortium for Biotechnology, (CIB), 34149, Trieste, Italy.
| | - Giuseppe Paolicelli
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
| | - Francesca Fallarino
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
| | - Marco Gargaro
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
| | - Gianluca Vascelli
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
| | - Marco De Zuani
- International Clinical Research Centre, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jan Fric
- International Clinical Research Centre, St. Anne's University Hospital Brno, Brno, Czech Republic
- Institute of Hematology and Blood Transfusion, U Nemocnice 2094/1, 128 20, Prague, Czech Republic
- International Clinical Research Centre, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Petra Laznickova
- International Clinical Research Centre, St. Anne's University Hospital Brno, Brno, Czech Republic
- International Clinical Research Centre, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Marcela Hortova Kohoutkova
- International Clinical Research Centre, St. Anne's University Hospital Brno, Brno, Czech Republic
- International Clinical Research Centre, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Antonio Macchiarulo
- Department of Pharmaceutical Science, University of Perugia, 06132, Perugia, Italy
| | - Daniela Dolciami
- Department of Pharmaceutical Science, University of Perugia, 06132, Perugia, Italy
| | - Giuseppe Pieraccini
- Mass Spectrometry Center (CISM), University of Florence, 50139, Florence, Italy
| | - Lorenzo Gaetani
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
| | - Giulia Scalisi
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
| | - Caterina Trevisan
- Department of Medical and Biological Science, University of Udine, 33100, Udine, Italy
| | - Barbara Frossi
- Department of Medical and Biological Science, University of Udine, 33100, Udine, Italy
| | - Carlo Pucillo
- Department of Medical and Biological Science, University of Udine, 33100, Udine, Italy
| | - Antonella De Luca
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
| | - Emilia Nunzi
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
- Center of Functional Genomics, C.U.R.Ge.F, University of Perugia, 06132, Perugia, Italy
| | - Roberta Spaccapelo
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
- Center of Functional Genomics, C.U.R.Ge.F, University of Perugia, 06132, Perugia, Italy
- Interuniversity Consortium for Biotechnology, (CIB), 34149, Trieste, Italy
| | - Marilena Pariano
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
| | - Monica Borghi
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
| | - Francesca Boscaro
- Mass Spectrometry Center (CISM), University of Florence, 50139, Florence, Italy
| | - Riccardo Romoli
- Mass Spectrometry Center (CISM), University of Florence, 50139, Florence, Italy
| | - Andrea Mancini
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
| | - Lucia Gentili
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
| | - Giorgia Renga
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
| | - Claudio Costantini
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
| | - Matteo Puccetti
- Department of Pharmaceutical Science, University of Perugia, 06132, Perugia, Italy
| | - Stefano Giovagnoli
- Department of Pharmaceutical Science, University of Perugia, 06132, Perugia, Italy
| | - Maurizio Ricci
- Department of Pharmaceutical Science, University of Perugia, 06132, Perugia, Italy
| | - Martina Antonini
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
| | - Paolo Calabresi
- Unità di Neurologia, Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, Rome, Italy
| | - Paolo Puccetti
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
- Center of Functional Genomics, C.U.R.Ge.F, University of Perugia, 06132, Perugia, Italy
| | - Massimiliano Di Filippo
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
| | - Luigina Romani
- Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 1, 06132, Perugia, Italy
- Center of Functional Genomics, C.U.R.Ge.F, University of Perugia, 06132, Perugia, Italy
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