1
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Jiang T, Liu X, Wang S, Chen Y, Wang Y, Li X, Yao G. Paeoniflorin alleviated experimental Sjögren's syndrome by inhibiting NLRP3 inflammasome activation of submandibular gland cells via activating Nrf2/HO-1 pathway. Free Radic Biol Med 2025; 233:355-364. [PMID: 40158745 DOI: 10.1016/j.freeradbiomed.2025.03.043] [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: 12/18/2024] [Revised: 02/15/2025] [Accepted: 03/27/2025] [Indexed: 04/02/2025]
Abstract
BACKGROUND Total glucosides of white paeony (TGP) has been used for treatment of Sjögren's syndrome (SS) patients. Paeoniflorin (PF) is the main active ingredient of TGP and has antioxidant and anti-inflammatory effects, but its underlying mechanism on SS remains to be explored. Aberrant activation of NLRP3 inflammasome can cause injury of submandibular gland (SG) in SS. However, whether PF regulates NLRP3 inflammasome activation in SS is unknown. OBJECTIVE This study aims to investigate whether PF alleviated SS through suppressing NLRP3 inflammation activation and to explore the mechanism of PF in improving Sjögren-like symptoms in non-obese diabetic (NOD) mice. METHODS The gene expression profiles of the labial gland (LG) between SS patients and non-SS patients were analyzed by bioinformatics. Non-obese diabetic (NOD) mice were selected as SS model. Mice were divided into normal saline group and two different doses of PF-treatment groups (50 and 100 mg/kg). The SS-like symptoms and pathological changes of submandibular gland (SG) were analyzed after 4 weeks of administration. SG cells were treated with or without PF and with or without ML385 (a specific inhibitor of Nrf2) in vitro, and then lipopolysaccharide(LPS) and adenosine triphosphate (ATP) were used to induce NLRP3 inflammasome activation in SG cells. Results NLRP3 was up-regulated in LG of SS patients and SG of SS mice. PF alleviated SS-like symptoms in SS mice. Compared with control group, NLRP3 and caspase-1 in the SG, and serum IL-1β and IL-18 of NOD mice were decreased in PF group. Furthermore, we found that PF inhibited NLRP3 activation via activating the Nrf2/HO-1 pathway in SG cells. In addition, we observed the activation of Nrf2/HO-1 in the SG of mice after PF administration. CONCLUSIONS Our findings suggested that PF inhibited NLRP3 inflammasome activation through regulating the Nrf2/HO-1 axis in SG of SS mice, which might be the underlying mechanism for the therapeutic effects of PF on SS.
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Affiliation(s)
- Tingting Jiang
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210008, China
| | - Xuanqi Liu
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Clinical College of Nanjing Drum Tower Hospital, Nanjing University of Chinese Medicine, Nanjing, 210008, China
| | - Shumin Wang
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Clinical College of Nanjing Drum Tower Hospital, Nanjing University of Chinese Medicine, Nanjing, 210008, China
| | - Yu Chen
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Clinical College of Nanjing Drum Tower Hospital, Nanjing University of Chinese Medicine, Nanjing, 210008, China
| | - Yong Wang
- State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, 210093, China.
| | - Xiaojing Li
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210008, China.
| | - Genhong Yao
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Clinical College of Nanjing Drum Tower Hospital, Nanjing University of Chinese Medicine, Nanjing, 210008, China; State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, 210093, China.
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Coren L, Zaffryar-Eilot S, Odeh A, Kaganovsky A, Hasson P. Fibroblast diversification is an embryonic process dependent on muscle contraction. Cell Rep 2024; 43:115034. [PMID: 39636726 DOI: 10.1016/j.celrep.2024.115034] [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: 04/09/2024] [Revised: 09/18/2024] [Accepted: 11/14/2024] [Indexed: 12/07/2024] Open
Abstract
Fibroblasts, the most common cell type found in connective tissues, play major roles in development, homeostasis, regeneration, and disease. Although specific fibroblast subpopulations have been associated with different biological processes, the mechanisms and unique activities underlying their diversity have not been thoroughly examined. Here, we set out to dissect the variation in skeletal-muscle-resident fibroblasts (mrFibroblasts) during development. Our results demonstrate that mrFibroblasts diversify following the transition from embryonic to fetal myogenesis prior to birth. We find that mrFibroblasts segregate into two major subpopulations occupying distinct niches, with interstitial fibroblasts residing between the muscle fibers and delineating fibroblasts sheathing the muscle. We further show that these subpopulations entail distinct cellular dynamics and transcriptomes. Notably, we find that mrFibroblast subpopulations exert distinct regulatory roles on myoblast proliferation and differentiation. Finally, we demonstrate that this diversification depends on muscle contraction. Altogether, these findings establish that mrFibroblasts diversify in a spatiotemporal embryonic process into distinct cell types, entailing different characteristics and roles.
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Affiliation(s)
- Lavi Coren
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology, Haifa 31096, Israel
| | - Shelly Zaffryar-Eilot
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology, Haifa 31096, Israel
| | - Anas Odeh
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology, Haifa 31096, Israel
| | - Anna Kaganovsky
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology, Haifa 31096, Israel
| | - Peleg Hasson
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology, Haifa 31096, Israel.
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3
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Song K, Xu H, Shi Y, Zou X, Da LT, Hao J. Investigating TCR-pMHC interactions for TCRs without identified epitopes by constructing a computational pipeline. Int J Biol Macromol 2024; 282:136502. [PMID: 39423970 DOI: 10.1016/j.ijbiomac.2024.136502] [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: 03/15/2024] [Revised: 10/04/2024] [Accepted: 10/09/2024] [Indexed: 10/21/2024]
Abstract
The molecular mechanisms underlying epitope recognition by T cell receptors (TCRs) are critical for activating T cell immune responses and rationally designing TCR-based therapeutics. Single-cell sequencing techniques vastly boost the accumulation of TCR sequences, while the limitation of available TCR-pMHC structures hampers further investigations. In this study, we proposed a computational pipeline that incorporates structural information and single-cell sequencing data to investigate the epitope-recognition mechanisms for TCRs without identified epitopes. By antigen specificity clustering, we mapped the epitope sequences between epitope-known and epitope-unknown TCRs from COVID-19 patients. One reported SARS-CoV-2 epitope, NQKLIANQF (S919-927), was identified for a TCR expressed by 614 T cells (TCR-614). Epitope screening also identified a potential cross-reactive epitope, KLKTLVATA (NSP31790-1798), for a TCR expressed by 204 T cells (TCR-204). By molecular dynamics (MD) simulations, we revealed the detailed epitope-recognition mechanisms for both TCRs. The structural motifs responsible for epitope recognition revealed by the MD simulations are consistent with the sequential features recognized by the sequence-based clustering method. We hope that this strategy could facilitate the discovery and optimization of TCR-based therapeutics.
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Affiliation(s)
- Kaiyuan Song
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Honglin Xu
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yi Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China; Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Xin Zou
- Digital Diagnosis and Treatment Innovation Center for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China; Ninth People's Hospital, Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai Jiao Tong University, School of Medicine, Shanghai 200011, China.
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Jie Hao
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
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4
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Chen SY, Kung HC, Espinoza B, Washington I, Chen K, Wang J, Zlomke H, Loycano M, Wang R, Pickup M, Burns WR, Fu J, Hwang WL, Zheng L. Targeting heterogeneous tumor microenvironments in pancreatic cancer mouse models of metastasis by TGF-β depletion. JCI Insight 2024; 9:e182766. [PMID: 39298276 DOI: 10.1172/jci.insight.182766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 09/13/2024] [Indexed: 09/21/2024] Open
Abstract
The dual tumor-suppressive and -promoting functions of TGF-β signaling has made its targeting challenging. We examined the effects of TGF-β depletion by AVID200/BMS-986416 (TGF-β-TRAP), a TGF-β ligand trap, on the tumor microenvironment of pancreatic ductal adenocarcinoma (PDAC) murine models with different organ-specific metastasis. Our study demonstrated that TGF-β-TRAP potentiates the efficacy of anti-programmed cell death 1 (anti-PD-1) in a PDAC orthotopic murine model with liver metastasis tropism, significantly reducing liver metastases. We further demonstrated the heterogeneous response of cytotoxic effector T cells to combination TGF-β-TRAP and anti-PD-1 treatment across several tumor models. Single-nuclear RNA sequencing suggested that TGF-β-TRAP modulates cancer-associated fibroblast (CAF) heterogeneity and suppresses neutrophil degranulation and CD4+ T cell response to neutrophil degranulation. Ligand-receptor analysis indicated that TGF-β-TRAP may modulate the CCL5/CCR5 axis as well as costimulatory and checkpoint signaling from CAFs and myeloid cells. Notably, the most highly expressed ligands of CCR5 shifted from the immunosuppressive CCL5 to CCL7 and CCL8, which may mediate the immune agonist activity of CCR5 following TGF-β-TRAP and anti-PD-1 combination treatment. This study suggested that TGF-β depletion modulates CAF heterogeneity and potentially reprograms CAFs and myeloid cells into antitumor immune agonists in PDAC, supporting the validation of such effects in human specimens.
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Affiliation(s)
- Sophia Y Chen
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center
- Pancreatic Cancer Precision Medicine Center of Excellence Program, and
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Heng-Chung Kung
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center
- Pancreatic Cancer Precision Medicine Center of Excellence Program, and
| | - Birginia Espinoza
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center
- Pancreatic Cancer Precision Medicine Center of Excellence Program, and
| | - India Washington
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center
- Pancreatic Cancer Precision Medicine Center of Excellence Program, and
| | - Kai Chen
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center
- Pancreatic Cancer Precision Medicine Center of Excellence Program, and
| | - Jianxin Wang
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center
- Pancreatic Cancer Precision Medicine Center of Excellence Program, and
| | - Haley Zlomke
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center
- Pancreatic Cancer Precision Medicine Center of Excellence Program, and
| | - Michael Loycano
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center
- Pancreatic Cancer Precision Medicine Center of Excellence Program, and
| | - Rulin Wang
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center
| | | | - William R Burns
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center
- Pancreatic Cancer Precision Medicine Center of Excellence Program, and
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Juan Fu
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center
- Pancreatic Cancer Precision Medicine Center of Excellence Program, and
| | - William L Hwang
- Center for Systems Biology, Department of Radiation Oncology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Lei Zheng
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center
- Pancreatic Cancer Precision Medicine Center of Excellence Program, and
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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5
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Fahlquist-Hagert C, Wittenborn TR, Pedersen MK, Jensen L, Degn SE. T-follicular regulatory cells expand to control germinal center plasma cell output but fail to curb autoreactivity. iScience 2024; 27:110887. [PMID: 39319261 PMCID: PMC11417334 DOI: 10.1016/j.isci.2024.110887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 07/17/2024] [Accepted: 09/03/2024] [Indexed: 09/26/2024] Open
Abstract
Autoantibodies generated in germinal centers (GCs) contribute to the pathogenesis of autoimmune diseases. GCs are controlled by specialized FoxP3+ T-follicular regulatory cells (Tfr), but their role in established autoimmunity is unclear. We generated autoimmune bone marrow chimeras in which Tfr could be specifically ablated by diphtheria toxin. Furthermore, we tracked the clonal persistence and evolution of Tfr populations using Confetti reporters. Ablation of Tfr caused increased early plasma cell output, but longer-term ablation did not increase plasma cell levels beyond those of Tfr-sufficient controls, suggesting that Tfr fail to contain chronic autoreactive GC responses. In agreement, Tfr were robustly induced in early autoreactive GCs but then waned. Moreover, we observed polyclonal Tfr expansion when ablating part of the Tfr subset. Hence, under homeostatic conditions, a polyclonal population of Tfr operates to control autoreactivity by limiting the output of plasma cells from GCs, but in chronic autoimmunity, this mechanism fails.
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Affiliation(s)
- Cecilia Fahlquist-Hagert
- Laboratory for Lymphocyte Biology, Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Thomas Rea Wittenborn
- Laboratory for Lymphocyte Biology, Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Mattias Krogh Pedersen
- Laboratory for Lymphocyte Biology, Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Lisbeth Jensen
- Laboratory for Lymphocyte Biology, Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Søren Egedal Degn
- Laboratory for Lymphocyte Biology, Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
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6
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Ding Q, Wu Y, Triglia ET, Gommerman JL, Subramanian A, Kuchroo VK, Rothstein DM. TIM-4 Identifies Effector B Cells Expressing a RORγt-Driven Proinflammatory Cytokine Module That Promotes Immune Responsiveness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.22.558524. [PMID: 37790513 PMCID: PMC10542535 DOI: 10.1101/2023.09.22.558524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
B cells can express pro-inflammatory cytokines that promote a wide variety of immune responses. Here we show that B cells expressing the phosphatidylserine receptor TIM-4, preferentially express IL-17A, as well as IL-22, IL-6, IL-1β, and GM-CSF - a collection of cytokines reminiscent of pathogenic Th17 cells. Expression of this proinflammatory module requires IL-23R signaling and selective expression of RORγt and IL-17A by TIM-4+ B cells. TIM-4+ B cell-derived-IL-17A not only enhances the severity of experimental autoimmune encephalomyelitis (EAE) and promotes allograft rejection, but also acts in an autocrine manner to prevent their conversion into IL-10-expressing B cells with regulatory function. Thus, IL-17A acts as an inflammatory mediator and also enforces the proinflammatory activity of TIM-4+ B cells. Thus, TIM-4 serves as a broad marker for RORγt+ effector B cells (Beff) and allows further study of the signals regulating Beff differentiation and effector molecule expression.
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Affiliation(s)
- Qing Ding
- Thomas E. Starzl Transplantation Institute; University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yufan Wu
- Klarman Cell Observatory, Broad Institute of MIT and Harvard; Cambridge, MA, USA
| | - Elena Torlai Triglia
- Klarman Cell Observatory, Broad Institute of MIT and Harvard; Cambridge, MA, USA
| | | | - Ayshwarya Subramanian
- Klarman Cell Observatory, Broad Institute of MIT and Harvard; Cambridge, MA, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA, USA
| | - Vijay K. Kuchroo
- Klarman Cell Observatory, Broad Institute of MIT and Harvard; Cambridge, MA, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
| | - David M. Rothstein
- Thomas E. Starzl Transplantation Institute; University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
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7
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Saeki K, Ha D, Chang G, Mori H, Yoshitake R, Wu X, Wang J, Wang YZ, Wang X, Tzeng T, Shim HJ, Neuhausen SL, Chen S. Perimenopausal and Menopausal Mammary Glands In A 4-Vinylcyclohexene Diepoxide Mouse Model. J Mammary Gland Biol Neoplasia 2024; 29:15. [PMID: 39017946 PMCID: PMC11254995 DOI: 10.1007/s10911-024-09569-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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 07/05/2024] [Indexed: 07/18/2024] Open
Abstract
As both perimenopausal and menopausal periods are recognized critical windows of susceptibility for breast carcinogenesis, development of a physiologically relevant model has been warranted. The traditional ovariectomy model causes instant removal of the entire hormonal repertoire produced by the ovary, which does not accurately approximate human natural menopause with gradual transition. Here, we characterized the mammary glands of 4-vinylcyclohexene diepoxide (VCD)-treated animals at different time points, revealing that the model can provide the mammary glands with both perimenopausal and menopausal states. The perimenopausal gland showed moderate regression in ductal structure with no responsiveness to external hormones, while the menopausal gland showed severe regression with hypersensitivity to hormones. Leveraging the findings on the VCD model, effects of a major endocrine disruptor (polybrominated diphenyl ethers, PBDEs) on the mammary gland were examined during and after menopausal transition, with the two exposure modes; low-dose, chronic (environmental) and high-dose, subacute (experimental). All conditions of PBDE exposure did not augment or compromise the macroscopic ductal reorganization resulting from menopausal transition and/or hormonal treatments. Single-cell RNA sequencing revealed that the experimental PBDE exposure during the post-menopausal period caused specific transcriptomic changes in the non-epithelial compartment such as Errfi1 upregulation in fibroblasts. The environmental PBDE exposure resulted in similar transcriptomic changes to a lesser extent. In summary, the VCD mouse model provides both perimenopausal and menopausal windows of susceptibility for the breast cancer research community. PBDEs, including all tested models, may affect the post-menopausal gland including impacts on the non-epithelial compartments.
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Affiliation(s)
- Kohei Saeki
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
- Faculty of Veterinary Medicine, Okayama University of Science, Ehime, Japan
| | - Desiree Ha
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Gregory Chang
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Hitomi Mori
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Ryohei Yoshitake
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Xiwei Wu
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jinhui Wang
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Yuan-Zhong Wang
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Xiaoqiang Wang
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Tony Tzeng
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Hyun Jeong Shim
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Shiuan Chen
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.
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8
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Akama-Garren EH, Yin X, Prestwood TR, Ma M, Utz PJ, Carroll MC. T cell help shapes B cell tolerance. Sci Immunol 2024; 9:eadj7029. [PMID: 38363829 PMCID: PMC11095409 DOI: 10.1126/sciimmunol.adj7029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/29/2023] [Indexed: 02/18/2024]
Abstract
T cell help is a crucial component of the normal humoral immune response, yet whether it promotes or restrains autoreactive B cell responses remains unclear. Here, we observe that autoreactive germinal centers require T cell help for their formation and persistence. Using retrogenic chimeras transduced with candidate TCRs, we demonstrate that a follicular T cell repertoire restricted to a single autoreactive TCR, but not a foreign antigen-specific TCR, is sufficient to initiate autoreactive germinal centers. Follicular T cell specificity influences the breadth of epitope spreading by regulating wild-type B cell entry into autoreactive germinal centers. These results demonstrate that TCR-dependent T cell help can promote loss of B cell tolerance and that epitope spreading is determined by TCR specificity.
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Affiliation(s)
- Elliot H. Akama-Garren
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Xihui Yin
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tyler R. Prestwood
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Minghe Ma
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Paul J. Utz
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael C. Carroll
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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9
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Gupta A, Weinand K, Nathan A, Sakaue S, Zhang MJ, Donlin L, Wei K, Price AL, Amariuta T, Raychaudhuri S. Dynamic regulatory elements in single-cell multimodal data implicate key immune cell states enriched for autoimmune disease heritability. Nat Genet 2023; 55:2200-2210. [PMID: 38036783 PMCID: PMC10787644 DOI: 10.1038/s41588-023-01577-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023]
Abstract
In autoimmune diseases such as rheumatoid arthritis, the immune system attacks the body's own cells. Developing a precise understanding of the cell states where noncoding autoimmune risk variants impart causal mechanisms is critical to developing curative therapies. Here, to identify noncoding regions with accessible chromatin that associate with cell-state-defining gene expression patterns, we leveraged multimodal single-nucleus RNA and assay for transposase-accessible chromatin (ATAC) sequencing data across 28,674 cells from the inflamed synovial tissue of 12 donors. Specifically, we used a multivariate Poisson model to predict peak accessibility from single-nucleus RNA sequencing principal components. For 14 autoimmune diseases, we discovered that cell-state-dependent ('dynamic') chromatin accessibility peaks in immune cell types were enriched for heritability, compared with cell-state-invariant ('cs-invariant') peaks. These dynamic peaks marked regulatory elements associated with T peripheral helper, regulatory T, dendritic and STAT1+CXCL10+ myeloid cell states. We argue that dynamic regulatory elements can help identify precise cell states enriched for disease-critical genetic variation.
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Affiliation(s)
- Anika Gupta
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Kathryn Weinand
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martin Jinye Zhang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Laura Donlin
- Weill Cornell Medicine, New York, NY, USA
- Hospital for Special Surgery, New York, NY, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alkes L Price
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Tiffany Amariuta
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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10
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Tiwari R, Sharma R, Rajendran G, Borkowski GS, An SY, Schonfeld M, O’Sullivan J, Schipma MJ, Zhou Y, Courbon G, David V, Quaggin SE, Thorp E, Chandel NS, Kapitsinou PP. Post-ischemic inactivation of HIF prolyl hydroxylases in endothelium promotes maladaptive kidney repair by inducing glycolysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560700. [PMID: 37873349 PMCID: PMC10592920 DOI: 10.1101/2023.10.03.560700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Ischemic acute kidney injury (AKI) is common in hospitalized patients and increases the risk for chronic kidney disease (CKD). Impaired endothelial cell (EC) functions are thought to contribute in AKI to CKD transition, but the underlying mechanisms remain unclear. Here, we identify a critical role for endothelial oxygen sensing prolyl hydroxylase domain (PHD) enzymes 1-3 in regulating post-ischemic kidney repair. In renal endothelium, we observed compartment-specific differences in the expression of the three PHD isoforms in both mice and humans. We found that post-ischemic concurrent inactivation of endothelial PHD1, PHD2, and PHD3 but not PHD2 alone promoted maladaptive kidney repair characterized by exacerbated tissue injury, fibrosis, and inflammation. Single-cell RNA-seq analysis of the post-ischemic endothelial PHD1, PHD2 and PHD3 deficient (PHDTiEC) kidney revealed an endothelial glycolytic transcriptional signature, also observed in human kidneys with severe AKI. This metabolic program was coupled to upregulation of the SLC16A3 gene encoding the lactate exporter monocarboxylate transporter 4 (MCT4). Strikingly, treatment with the MCT4 inhibitor syrosingopine restored adaptive kidney repair in PHDTiEC mice. Mechanistically, MCT4 inhibition suppressed pro-inflammatory EC activation reducing monocyte-endothelial cell interaction. Our findings suggest avenues for halting AKI to CKD transition based on selectively targeting the endothelial hypoxia-driven glycolysis/MCT4 axis.
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Affiliation(s)
- Ratnakar Tiwari
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL
- Division of Nephrology & Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Rajni Sharma
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL
- Division of Nephrology & Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ganeshkumar Rajendran
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS, USA
| | - Gabriella S. Borkowski
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL
- Division of Nephrology & Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Si Young An
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL
- Division of Nephrology & Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Michael Schonfeld
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS, USA
| | - James O’Sullivan
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL
- Division of Nephrology & Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Matthew J. Schipma
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Yalu Zhou
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL
- Division of Nephrology & Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Guillaume Courbon
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL
- Division of Nephrology & Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Valentin David
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL
- Division of Nephrology & Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Susan E. Quaggin
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL
- Division of Nephrology & Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Edward Thorp
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Navdeep S. Chandel
- Robert H. Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Pinelopi P. Kapitsinou
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL
- Division of Nephrology & Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL
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11
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Cantor H. Renegade T cell clones and autoimmune disease. Proc Natl Acad Sci U S A 2023; 120:e2310236120. [PMID: 37467287 PMCID: PMC10401021 DOI: 10.1073/pnas.2310236120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
Affiliation(s)
- Harvey Cantor
- Department of Cancer Immunology, Dana-Farber Cancer Institute and Department of Immunology, Harvard Medical School, Boston, MA02215
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12
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Shen Y, Voigt A, Leng X, Rodriguez AA, Nguyen CQ. A current and future perspective on T cell receptor repertoire profiling. Front Genet 2023; 14:1159109. [PMID: 37408774 PMCID: PMC10319011 DOI: 10.3389/fgene.2023.1159109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023] Open
Abstract
T cell receptors (TCR) play a vital role in the immune system's ability to recognize and respond to foreign antigens, relying on the highly polymorphic rearrangement of TCR genes. The recognition of autologous peptides by adaptive immunity may lead to the development and progression of autoimmune diseases. Understanding the specific TCR involved in this process can provide insights into the autoimmune process. RNA-seq (RNA sequencing) is a valuable tool for studying TCR repertoires by providing a comprehensive and quantitative analysis of the RNA transcripts. With the development of RNA technology, transcriptomic data must provide valuable information to model and predict TCR and antigen interaction and, more importantly, identify or predict neoantigens. This review provides an overview of the application and development of bulk RNA-seq and single-cell (SC) RNA-seq to examine the TCR repertoires. Furthermore, discussed here are bioinformatic tools that can be applied to study the structural biology of peptide/TCR/MHC (major histocompatibility complex) and predict antigenic epitopes using advanced artificial intelligence tools.
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Affiliation(s)
- Yiran Shen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Alexandria Voigt
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Xuebing Leng
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Amy A. Rodriguez
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Cuong Q. Nguyen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, United States
- Center of Orphaned Autoimmune Diseases, University of Florida, Gainesville, FL, United States
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13
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Kaya T, Mattugini N, Liu L, Ji H, Cantuti-Castelvetri L, Wu J, Schifferer M, Groh J, Martini R, Besson-Girard S, Kaji S, Liesz A, Gokce O, Simons M. CD8 + T cells induce interferon-responsive oligodendrocytes and microglia in white matter aging. Nat Neurosci 2022; 25:1446-1457. [PMID: 36280798 PMCID: PMC9630119 DOI: 10.1038/s41593-022-01183-6] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 09/14/2022] [Indexed: 01/13/2023]
Abstract
A hallmark of nervous system aging is a decline of white matter volume and function, but the underlying mechanisms leading to white matter pathology are unknown. In the present study, we found age-related alterations of oligodendrocyte cell state with a reduction in total oligodendrocyte density in aging murine white matter. Using single-cell RNA-sequencing, we identified interferon (IFN)-responsive oligodendrocytes, which localize in proximity to CD8+ T cells in aging white matter. Absence of functional lymphocytes decreased the number of IFN-responsive oligodendrocytes and rescued oligodendrocyte loss, whereas T-cell checkpoint inhibition worsened the aging response. In addition, we identified a subpopulation of lymphocyte-dependent, IFN-responsive microglia in the vicinity of the CD8+ T cells in aging white matter. In summary, we provide evidence that CD8+ T-cell-induced, IFN-responsive oligodendrocytes and microglia are important modifiers of white matter aging.
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Affiliation(s)
- Tuğberk Kaya
- Institute for Stroke and Dementia Research, University Hospital of Munich, Ludwig Maximilian University (LMU) of Munich, Munich, Germany
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
- German Center for Neurodegenerative Diseases, Munich, Germany
- Graduate School of Systemic Neurosciences, LMU Munich, Munich, Germany
| | - Nicola Mattugini
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
- German Center for Neurodegenerative Diseases, Munich, Germany
| | - Lu Liu
- Institute for Stroke and Dementia Research, University Hospital of Munich, Ludwig Maximilian University (LMU) of Munich, Munich, Germany
| | - Hao Ji
- Institute for Stroke and Dementia Research, University Hospital of Munich, Ludwig Maximilian University (LMU) of Munich, Munich, Germany
| | - Ludovico Cantuti-Castelvetri
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
- German Center for Neurodegenerative Diseases, Munich, Germany
| | - Jianping Wu
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
- German Center for Neurodegenerative Diseases, Munich, Germany
- Graduate School of Systemic Neurosciences, LMU Munich, Munich, Germany
| | - Martina Schifferer
- German Center for Neurodegenerative Diseases, Munich, Germany
- Munich Cluster of Systems Neurology, Munich, Germany
| | - Janos Groh
- Department of Neurology, Section of Developmental Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Rudolf Martini
- Department of Neurology, Section of Developmental Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Simon Besson-Girard
- Institute for Stroke and Dementia Research, University Hospital of Munich, Ludwig Maximilian University (LMU) of Munich, Munich, Germany
- Graduate School of Systemic Neurosciences, LMU Munich, Munich, Germany
| | - Seiji Kaji
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
- German Center for Neurodegenerative Diseases, Munich, Germany
| | - Arthur Liesz
- Institute for Stroke and Dementia Research, University Hospital of Munich, Ludwig Maximilian University (LMU) of Munich, Munich, Germany
| | - Ozgun Gokce
- Institute for Stroke and Dementia Research, University Hospital of Munich, Ludwig Maximilian University (LMU) of Munich, Munich, Germany.
- Munich Cluster of Systems Neurology, Munich, Germany.
| | - Mikael Simons
- Institute for Stroke and Dementia Research, University Hospital of Munich, Ludwig Maximilian University (LMU) of Munich, Munich, Germany.
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany.
- German Center for Neurodegenerative Diseases, Munich, Germany.
- Munich Cluster of Systems Neurology, Munich, Germany.
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14
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Akama-Garren EH, Carroll MC. T Cell Help in the Autoreactive Germinal Center. Scand J Immunol 2022; 95:e13192. [PMID: 35587582 DOI: 10.1111/sji.13192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 11/29/2022]
Abstract
The germinal center serves as a site of B cell selection and affinity maturation, critical processes for productive adaptive immunity. In autoimmune disease tolerance is broken in the germinal center reaction, leading to production of autoreactive B cells that may propagate disease. Follicular T cells are crucial regulators of this process, providing signals necessary for B cell survival in the germinal center. Here we review the emerging roles of follicular T cells in the autoreactive germinal center. Recent advances in immunological techniques have allowed study of the gene expression profiles and repertoire of follicular T cells at unprecedented resolution. These studies provide insight into the potential role follicular T cells play in preventing or facilitating germinal center loss of tolerance. Improved understanding of the mechanisms of T cell help in autoreactive germinal centers provides novel therapeutic targets for diseases of germinal center dysfunction.
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Affiliation(s)
- Elliot H Akama-Garren
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
| | - Michael C Carroll
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
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15
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Akama-Garren EH, Carroll MC. Lupus Susceptibility Loci Predispose Mice to Clonal Lymphocytic Responses and Myeloid Expansion. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:2403-2424. [PMID: 35477687 PMCID: PMC9254690 DOI: 10.4049/jimmunol.2200098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/14/2022] [Indexed: 05/17/2023]
Abstract
Lupus susceptibility results from the combined effects of numerous genetic loci, but the contribution of these loci to disease pathogenesis has been difficult to study due to the large cellular heterogeneity of the autoimmune immune response. We performed single-cell RNA, BCR, and TCR sequencing of splenocytes from mice with multiple polymorphic lupus susceptibility loci. We not only observed lymphocyte and myeloid expansion, but we also characterized changes in subset frequencies and gene expression, such as decreased CD8 and marginal zone B cells and increased Fcrl5- and Cd5l-expressing macrophages. Clonotypic analyses revealed expansion of B and CD4 clones, and TCR repertoires from lupus-prone mice were distinguishable by algorithmic specificity prediction and unsupervised machine learning classification. Myeloid differential gene expression, metabolism, and altered ligand-receptor interaction were associated with decreased Ag presentation. This dataset provides novel mechanistic insight into the pathophysiology of a spontaneous model of lupus, highlighting potential therapeutic targets for autoantibody-mediated disease.
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Affiliation(s)
- Elliot H Akama-Garren
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA; and
- Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA
| | - Michael C Carroll
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA; and
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