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Martins LR, Glimm H, Scholl C. Single-cell RNA sequencing of mouse lower respiratory tract epithelial cells: A meta-analysis. Cells Dev 2023; 174:203847. [PMID: 37146757 DOI: 10.1016/j.cdev.2023.203847] [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: 01/31/2023] [Revised: 04/14/2023] [Accepted: 04/28/2023] [Indexed: 05/07/2023]
Abstract
The respiratory system is a vital component of our body, essential for both oxygen uptake and immune defense. Knowledge of cellular composition and function in different parts of the respiratory tract provides the basis for a better understanding of the pathological processes involved in various diseases such as chronic respiratory diseases and cancer. Single-cell RNA sequencing (scRNA-seq) is a proficient approach for the identification and transcriptional characterization of cellular phenotypes. Although the mouse is an essential tool for the study of lung development, regeneration, and disease, a scRNA-seq mouse atlas of the lung in which all epithelial cell types are included and annotated systematically is lacking. Here, we established a single-cell transcriptome landscape of the mouse lower respiratory tract by performing a meta-analysis of seven different studies in which mouse lungs and trachea were analyzed by droplet and/or plate-based scRNA-seq technologies. We provide information on the best markers for each epithelial cell type, propose surface markers for the isolation of viable cells, harmonized the annotation of cell types, and compare the mouse single-cell transcriptomes with human scRNA-seq data of the lung.
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Affiliation(s)
- Leila R Martins
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany.
| | - Hanno Glimm
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Dresden, Germany
| | - Claudia Scholl
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany.
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Li Y, Liu P, Zhou Y, Maekawa H, Silva JB, Ansari MJ, Boubes K, Alia Y, Deb DK, Thomson BR, Jin J, Quaggin SE. Activation of Angiopoietin-Tie2 Signaling Protects the Kidney from Ischemic Injury by Modulation of Endothelial-Specific Pathways. J Am Soc Nephrol 2023; 34:969-987. [PMID: 36787763 PMCID: PMC10278803 DOI: 10.1681/asn.0000000000000098] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/19/2023] [Indexed: 02/16/2023] Open
Abstract
SIGNIFICANCE STATEMENT Ischemia-reperfusion AKI (IR-AKI) is common and causes significant morbidity. Effective treatments are lacking. However, preclinical studies suggest that inhibition of angiopoietin-Tie2 vascular signaling promotes injury, whereas activation of Tie2 is protective. We show that kidney ischemia leads to increased levels of the endothelial-specific phosphatase vascular endothelial protein tyrosine phosphatase (VE-PTP; PTPRB), which inactivates Tie2. Activation of Tie2 through VE-PTP deletion, or delivery of a novel angiopoietin mimetic (Hepta-ANG1), abrogated IR-AKI in mice. Single-cell RNAseq analysis showed Tie2 activation promotes increased Entpd1 expression, downregulation of FOXO1 target genes in the kidney vasculature, and emergence of a new subpopulation of glomerular endothelial cells. Our data provide a molecular basis and identify a candidate therapeutic to improve endothelial integrity and kidney function after IR-AKI. BACKGROUND Ischemia-reperfusion AKI (IR-AKI) is estimated to affect 2%-7% of all hospitalized patients. The significant morbidity and mortality associated with AKI indicates urgent need for effective treatments. Previous studies have shown activation of the vascular angiopoietin-Tie2 tyrosine kinase signaling pathway abrogates ischemia-reperfusion injury (IRI). We extended previous studies to (1) determine the molecular mechanism(s) underlying kidney injury and protection related to decreased or increased activation of Tie2, respectively, and (2) to test the hypothesis that deletion of the Tie2 inhibitory phosphatase vascular endothelial protein tyrosine phosphatase (VE-PTP) or injection of a new angiopoietin mimetic protects the kidney from IRI by common molecular mechanism(s). METHODS Bilateral IR-AKI was performed in VE-PTP wild-type or knockout mice and in C57BL/6J mice treated with Hepta-ANG1 or vehicle. Histologic, immunostaining, and single-cell RNA sequencing analyses were performed. RESULTS The phosphatase VE-PTP, which negatively regulates the angiopoietin-Tie2 pathway, was upregulated in kidney endothelial cells after IRI, and genetic deletion of VE-PTP in mice protected the kidney from IR-AKI. Injection of Hepta-ANG1 potently activated Tie2 and protected the mouse kidney from IRI. Single-cell RNAseq analysis of kidneys from Hepta-ANG1-treated and vehicle-treated mice identified endothelial-specific gene signatures and emergence of a new glomerular endothelial subpopulation associated with improved kidney function. Overlap was found between endothelial-specific genes upregulated by Hepta-ANG1 treatment and those downregulated in HUVECs with constitutive FOXO1 activation, including Entpd1 / ENTPD1 that modulates purinergic receptor signaling. CONCLUSIONS Our data support a key role of the endothelium in the development of IR-AKI, introduce Hepta-ANG1 as a putative new therapeutic biologic, and report a model to explain how IRI reduces Tie2 signaling and how Tie2 activation protects the kidney. PODCAST This article contains a podcast at https://dts.podtrac.com/redirect.mp3/www.asn-online.org/media/podcast/JASN/2023_05_23_JSN_Ang_EP23_052323.mp3.
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Affiliation(s)
- Yanyang Li
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- The Feinberg Cardiovascular and Renal Research Institute, Chicago, Illinois
| | - Pan Liu
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- The Feinberg Cardiovascular and Renal Research Institute, Chicago, Illinois
| | - Yalu Zhou
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- The Feinberg Cardiovascular and Renal Research Institute, Chicago, Illinois
| | - Hiroshi Maekawa
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - John B. Silva
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Mohammed Javeed Ansari
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Khaled Boubes
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Yazan Alia
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Dilip K. Deb
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | | | - Jing Jin
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- The Feinberg Cardiovascular and Renal Research Institute, Chicago, Illinois
| | - Susan E. Quaggin
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- The Feinberg Cardiovascular and Renal Research Institute, Chicago, Illinois
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Dzanibe S, Wilk AJ, Canny S, Ranganath T, Alinde B, Rubelt F, Huang H, Davis MM, Holmes S, Jaspan HB, Blish CA, Gray CM. Disrupted memory T cell expansion in HIV-exposed uninfected infants is preceded by premature skewing of T cell receptor clonality. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.540713. [PMID: 37292866 PMCID: PMC10245741 DOI: 10.1101/2023.05.19.540713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
While preventing vertical HIV transmission has been very successful, the increasing number of HIV-exposed uninfected infants (iHEU) experience an elevated risk to infections compared to HIV-unexposed and uninfected infants (iHUU). Immune developmental differences between iHEU and iHUU remains poorly understood and here we present a longitudinal multimodal analysis of infant immune ontogeny that highlights the impact of HIV/ARV exposure. Using mass cytometry, we show alterations and differences in the emergence of NK cell populations and T cell memory differentiation between iHEU and iHUU. Specific NK cells observed at birth were also predictive of acellular pertussis and rotavirus vaccine-induced IgG and IgA responses, respectively, at 3 and 9 months of life. T cell receptor Vβ clonotypic diversity was significantly and persistently lower in iHEU preceding the expansion of T cell memory. Our findings show that HIV/ARV exposure disrupts innate and adaptive immunity from birth which may underlie relative vulnerability to infections.
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Affiliation(s)
- Sonwabile Dzanibe
- Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Aaron J. Wilk
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Susan Canny
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA
- Division of Rheumatology, Department of Pediatrics, Seattle Children’s Hospital, Seattle, WA USA
| | - Thanmayi Ranganath
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Berenice Alinde
- Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Florian Rubelt
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Huang Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark M. Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Heather B. Jaspan
- Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Seattle Children’s Research Institute and Department of Paediatrics and Global Health, University of Washington, Seattle, WA
| | - Catherine A. Blish
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA
| | - Clive M. Gray
- Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
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Lemaitre P, Tareen SHK, Pasciuto E, Mascali L, Martirosyan A, Callaerts‐Vegh Z, Poovathingal S, Dooley J, Holt MG, Yshii L, Liston A. Molecular and cognitive signatures of ageing partially restored through synthetic delivery of IL2 to the brain. EMBO Mol Med 2023; 15:e16805. [PMID: 36975362 PMCID: PMC10165365 DOI: 10.15252/emmm.202216805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/29/2023] Open
Abstract
Cognitive decline is a common pathological outcome during aging, with an ill-defined molecular and cellular basis. In recent years, the concept of inflammaging, defined as a low-grade inflammation increasing with age, has emerged. Infiltrating T cells accumulate in the brain with age and may contribute to the amplification of inflammatory cascades and disruptions to the neurogenic niche observed with age. Recently, a small resident population of regulatory T cells has been identified in the brain, and the capacity of IL2-mediated expansion of this population to counter neuroinflammatory disease has been demonstrated. Here, we test a brain-specific IL2 delivery system for the prevention of neurological decline in aging mice. We identify the molecular hallmarks of aging in the brain glial compartments and identify partial restoration of this signature through IL2 treatment. At a behavioral level, brain IL2 delivery prevented the age-induced defect in spatial learning, without improving the general decline in motor skill or arousal. These results identify immune modulation as a potential path to preserving cognitive function for healthy aging.
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Affiliation(s)
- Pierre Lemaitre
- VIB Center for Brain and Disease ResearchLeuvenBelgium
- Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | | | - Emanuela Pasciuto
- VIB Center for Brain and Disease ResearchLeuvenBelgium
- Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Loriana Mascali
- VIB Center for Brain and Disease ResearchLeuvenBelgium
- Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Araks Martirosyan
- VIB Center for Brain and Disease ResearchLeuvenBelgium
- Department of NeurosciencesKU LeuvenLeuvenBelgium
| | | | | | - James Dooley
- Immunology ProgrammeThe Babraham InstituteBabrahamUK
- Department of PathologyThe University of CambridgeCambridgeUK
| | - Matthew G Holt
- VIB Center for Brain and Disease ResearchLeuvenBelgium
- Department of NeurosciencesKU LeuvenLeuvenBelgium
- Instituto de Investigaçāo e Inovaçāo em Saúde (i3S)University of PortoPortoPortugal
| | - Lidia Yshii
- VIB Center for Brain and Disease ResearchLeuvenBelgium
- Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
- Department of NeurosciencesKU LeuvenLeuvenBelgium
| | - Adrian Liston
- VIB Center for Brain and Disease ResearchLeuvenBelgium
- Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
- Immunology ProgrammeThe Babraham InstituteBabrahamUK
- Department of PathologyThe University of CambridgeCambridgeUK
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105
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Amoni M, Vermoortele D, Ekhteraei-Tousi S, Doñate Puertas R, Gilbert G, Youness M, Thienpont B, Willems R, Roderick HL, Claus P, Sipido KR. Heterogeneity of Repolarization and Cell-Cell Variability of Cardiomyocyte Remodeling Within the Myocardial Infarction Border Zone Contribute to Arrhythmia Susceptibility. Circ Arrhythm Electrophysiol 2023; 16:e011677. [PMID: 37128895 PMCID: PMC10187631 DOI: 10.1161/circep.122.011677] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 04/07/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND After myocardial infarction, the infarct border zone (BZ) is the dominant source of life-threatening arrhythmias, where fibrosis and abnormal repolarization create a substrate for reentry. We examined whether repolarization abnormalities are heterogeneous within the BZ in vivo and could be related to heterogeneous cardiomyocyte remodeling. METHODS Myocardial infarction was induced in domestic pigs by 120-minute ischemia followed by reperfusion. After 1 month, remodeling was assessed by magnetic resonance imaging, and electroanatomical mapping was performed to determine the spatial distribution of activation-recovery intervals. Cardiomyocytes were isolated and tissue samples collected from the BZ and remote regions. Optical recording allowed assessment of action potential duration (di-8-ANEPPS, stimulation at 1 Hz, 37 °C) of large cardiomyocyte populations while gene expression in cardiomyocytes was determined by single nuclear RNA sequencing. RESULTS In vivo, activation-recovery intervals in the BZ tended to be longer than in remote with increased spatial heterogeneity evidenced by a greater local SD (3.5±1.3 ms versus remote: 2.0±0.5 ms, P=0.036, npigs=5). Increased activation-recovery interval heterogeneity correlated with enhanced arrhythmia susceptibility. Cellular population studies (ncells=635-862 cells per region) demonstrated greater heterogeneity of action potential duration in the BZ (SD, 105.9±17.0 ms versus remote: 73.9±8.6 ms; P=0.001; npigs=6), which correlated with heterogeneity of activation-recovery interval in vivo. Cell-cell gene expression heterogeneity in the BZ was evidenced by increased Euclidean distances between nuclei of the BZ (12.1 [9.2-15.0] versus 10.6 [7.5-11.6] in remote; P<0.0001). Differentially expressed genes characterizing BZ cardiomyocyte remodeling included hypertrophy-related and ion channel-related genes with high cell-cell variability of expression. These gene expression changes were driven by stress-responsive TFs (transcription factors). In addition, heterogeneity of left ventricular wall thickness was greater in the BZ than in remote. CONCLUSIONS Heterogeneous cardiomyocyte remodeling in the BZ is driven by uniquely altered gene expression, related to heterogeneity in the local microenvironment, and translates to heterogeneous repolarization and arrhythmia vulnerability in vivo.
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Affiliation(s)
- Matthew Amoni
- Department of Cardiovascular Sciences, Experimental Cardiology (M.A., S.E.-T., R.D.P., G.G., M.Y., R.W., H.L.R., K.R.S.), KU Leuven, Belgium
- Division of Cardiology, University Hospitals, Leuven, Belgium (M.A., R.W.)
| | - Dylan Vermoortele
- Imaging and Cardiovascular Dynamics, Department of Cardiovascular Sciences (D.V., P.C.), KU Leuven, Belgium
| | - Samaneh Ekhteraei-Tousi
- Department of Cardiovascular Sciences, Experimental Cardiology (M.A., S.E.-T., R.D.P., G.G., M.Y., R.W., H.L.R., K.R.S.), KU Leuven, Belgium
| | - Rosa Doñate Puertas
- Department of Cardiovascular Sciences, Experimental Cardiology (M.A., S.E.-T., R.D.P., G.G., M.Y., R.W., H.L.R., K.R.S.), KU Leuven, Belgium
| | - Guillaume Gilbert
- Department of Cardiovascular Sciences, Experimental Cardiology (M.A., S.E.-T., R.D.P., G.G., M.Y., R.W., H.L.R., K.R.S.), KU Leuven, Belgium
| | - Mohamad Youness
- Department of Cardiovascular Sciences, Experimental Cardiology (M.A., S.E.-T., R.D.P., G.G., M.Y., R.W., H.L.R., K.R.S.), KU Leuven, Belgium
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics (B.T.), KU Leuven, Belgium
| | - Rik Willems
- Department of Cardiovascular Sciences, Experimental Cardiology (M.A., S.E.-T., R.D.P., G.G., M.Y., R.W., H.L.R., K.R.S.), KU Leuven, Belgium
- Division of Cardiology, University Hospitals, Leuven, Belgium (M.A., R.W.)
| | - H. Llewelyn Roderick
- Department of Cardiovascular Sciences, Experimental Cardiology (M.A., S.E.-T., R.D.P., G.G., M.Y., R.W., H.L.R., K.R.S.), KU Leuven, Belgium
| | - Piet Claus
- Imaging and Cardiovascular Dynamics, Department of Cardiovascular Sciences (D.V., P.C.), KU Leuven, Belgium
| | - Karin R. Sipido
- Department of Cardiovascular Sciences, Experimental Cardiology (M.A., S.E.-T., R.D.P., G.G., M.Y., R.W., H.L.R., K.R.S.), KU Leuven, Belgium
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106
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Corrêa RO, Castro PR, Fachi JL, Nirello VD, El-Sahhar S, Imada S, Pereira GV, Pral LP, Araújo NVP, Fernandes MF, Matheus VA, de Souza Felipe J, Dos Santos Pereira Gomes AB, de Oliveira S, de Rezende Rodovalho V, de Oliveira SRM, de Assis HC, Oliveira SC, Dos Santos Martins F, Martens E, Colonna M, Varga-Weisz P, Vinolo MAR. Inulin diet uncovers complex diet-microbiota-immune cell interactions remodeling the gut epithelium. MICROBIOME 2023; 11:90. [PMID: 37101209 PMCID: PMC10131329 DOI: 10.1186/s40168-023-01520-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 03/16/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND The continuous proliferation of intestinal stem cells followed by their tightly regulated differentiation to epithelial cells is essential for the maintenance of the gut epithelial barrier and its functions. How these processes are tuned by diet and gut microbiome is an important, but poorly understood question. Dietary soluble fibers, such as inulin, are known for their ability to impact the gut bacterial community and gut epithelium, and their consumption has been usually associated with health improvement in mice and humans. In this study, we tested the hypothesis that inulin consumption modifies the composition of colonic bacteria and this impacts intestinal stem cells functions, thus affecting the epithelial structure. METHODS Mice were fed with a diet containing 5% of the insoluble fiber cellulose or the same diet enriched with an additional 10% of inulin. Using a combination of histochemistry, host cell transcriptomics, 16S microbiome analysis, germ-free, gnotobiotic, and genetically modified mouse models, we analyzed the impact of inulin intake on the colonic epithelium, intestinal bacteria, and the local immune compartment. RESULTS We show that the consumption of inulin diet alters the colon epithelium by increasing the proliferation of intestinal stem cells, leading to deeper crypts and longer colons. This effect was dependent on the inulin-altered gut microbiota, as no modulations were observed in animals deprived of microbiota, nor in mice fed cellulose-enriched diets. We also describe the pivotal role of γδ T lymphocytes and IL-22 in this microenvironment, as the inulin diet failed to induce epithelium remodeling in mice lacking this T cell population or cytokine, highlighting their importance in the diet-microbiota-epithelium-immune system crosstalk. CONCLUSION This study indicates that the intake of inulin affects the activity of intestinal stem cells and drives a homeostatic remodeling of the colon epithelium, an effect that requires the gut microbiota, γδ T cells, and the presence of IL-22. Our study indicates complex cross kingdom and cross cell type interactions involved in the adaptation of the colon epithelium to the luminal environment in steady state. Video Abstract.
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Affiliation(s)
- Renan Oliveira Corrêa
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil.
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, 02139, USA.
| | - Pollyana Ribeiro Castro
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - José Luís Fachi
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Vinícius Dias Nirello
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Salma El-Sahhar
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Shinya Imada
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, 02139, USA
- Department of Gastroenterological and Transplant Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8551, Japan
| | - Gabriel Vasconcelos Pereira
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
- University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Laís Passariello Pral
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Nathália Vitoria Pereira Araújo
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Mariane Font Fernandes
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Valquíria Aparecida Matheus
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Jaqueline de Souza Felipe
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Arilson Bernardo Dos Santos Pereira Gomes
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Sarah de Oliveira
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Vinícius de Rezende Rodovalho
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Samantha Roberta Machado de Oliveira
- Laboratory of Biotherapeutics Agents, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Helder Carvalho de Assis
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Sergio Costa Oliveira
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, 05508-000, Brazil
| | - Flaviano Dos Santos Martins
- Laboratory of Biotherapeutics Agents, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Eric Martens
- University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Patrick Varga-Weisz
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
- São Paulo Excellence Chair, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil
| | - Marco Aurélio Ramirez Vinolo
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil.
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP, 13083-862, Brazil.
- Experimental Medicine Research Cluster, Campinas, SP, 13083-862, Brazil.
- Obesity and Comorbidities Research Center (OCRC), University of Campinas, Campinas, SP, 13083-864, Brazil.
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Liu Z, Kong X, Long Y, Liu S, Zhang H, Jia J, Cui W, Zhang Z, Song X, Qiu L, Zhai J, Yan Z. Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation. NATURE PLANTS 2023; 9:515-524. [PMID: 37055554 DOI: 10.1038/s41477-023-01387-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 03/03/2023] [Indexed: 06/19/2023]
Abstract
Legumes form symbiosis with rhizobium leading to the development of nitrogen-fixing nodules. By integrating single-nucleus and spatial transcriptomics, we established a cell atlas of soybean nodules and roots. In central infected zones of nodules, we found that uninfected cells specialize into functionally distinct subgroups during nodule development, and revealed a transitional subtype of infected cells with enriched nodulation-related genes. Overall, our results provide a single-cell perspective for understanding rhizobium-legume symbiosis.
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Affiliation(s)
- Zhijian Liu
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xiangying Kong
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanping Long
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Sirui Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Agricultural Science and Engineering, Liaocheng University, Liaocheng, China
| | - Hong Zhang
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jinbu Jia
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wenhui Cui
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
| | - Zunmian Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Agricultural Science and Engineering, Liaocheng University, Liaocheng, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jixian Zhai
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
| | - Zhe Yan
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.
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108
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Kiaf B, Bode K, Schuster C, Kissler S. Gata3 is detrimental to regulatory T cell function in autoimmune diabetes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.18.533297. [PMID: 36993342 PMCID: PMC10055278 DOI: 10.1101/2023.03.18.533297] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Regulatory T cells (Tregs) protect against autoimmunity. In type 1 diabetes (T1D), Tregs slow the progression of beta cell autoimmunity within pancreatic islets. Increasing the potency or frequency of Tregs can prevent diabetes, as evidenced by studies in the nonobese diabetic (NOD) mouse model for T1D. We report herein that a significant proportion of islets Tregs in NOD mice express Gata3. The expression of Gata3 was correlated with the presence of IL-33, a cytokine known to induce and expand Gata3+ Tregs. Despite significantly increasing the frequency of Tregs in the pancreas, exogenous IL-33 was not protective. Based on these data, we hypothesized that Gata3 is deleterious to Treg function in autoimmune diabetes. To test this notion, we generated NOD mice with a Treg-specific deletion of Gata3. We found that deleting Gata3 in Tregs strongly protected against diabetes. Disease protection was associated with a shift of islet Tregs toward a suppressive CXCR3+Foxp3+ population. Our results suggest that islet Gata3+ Tregs are maladaptive and that this Treg subpopulation compromises the regulation of islet autoimmunity, contributing to diabetes onset.
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Affiliation(s)
- Badr Kiaf
- Section for Immunobiology, Joslin Diabetes Center, Boston, MA 02215
- Department of Medicine, Harvard Medical School, Boston MA 02115
| | - Kevin Bode
- Section for Immunobiology, Joslin Diabetes Center, Boston, MA 02215
- Department of Medicine, Harvard Medical School, Boston MA 02115
| | - Cornelia Schuster
- Section for Immunobiology, Joslin Diabetes Center, Boston, MA 02215
- Department of Medicine, Harvard Medical School, Boston MA 02115
| | - Stephan Kissler
- Section for Immunobiology, Joslin Diabetes Center, Boston, MA 02215
- Department of Medicine, Harvard Medical School, Boston MA 02115
- Diabetes Program, Harvard Stem Cell Institute, Cambridge MA 02138
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109
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Dunlap G, Wagner A, Meednu N, Zhang F, Jonsson AH, Wei K, Sakaue S, Nathan A, Bykerk VP, Donlin LT, Goodman SM, Firestein GS, Boyle DL, Holers VM, Moreland LW, Tabechian D, Pitzalis C, Filer A, Raychaudhuri S, Brenner MB, McDavid A, Rao DA, Anolik JH. Clonal associations of lymphocyte subsets and functional states revealed by single cell antigen receptor profiling of T and B cells in rheumatoid arthritis synovium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.18.533282. [PMID: 36993527 PMCID: PMC10055242 DOI: 10.1101/2023.03.18.533282] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease initiated by antigen-specific T cells and B cells, which promote synovial inflammation through a complex set of interactions with innate immune and stromal cells. To better understand the phenotypes and clonal relationships of synovial T and B cells, we performed single-cell RNA and repertoire sequencing on paired synovial tissue and peripheral blood samples from 12 donors with seropositive RA ranging from early to chronic disease. Paired transcriptomic-repertoire analyses highlighted 3 clonally distinct CD4 T cells populations that were enriched in RA synovium: T peripheral helper (Tph) and T follicular helper (Tfh) cells, CCL5+ T cells, and T regulatory cells (Tregs). Among these cells, Tph cells showed a unique transcriptomic signature of recent T cell receptor (TCR) activation, and clonally expanded Tph cells expressed an elevated transcriptomic effector signature compared to non-expanded Tph cells. CD8 T cells showed higher oligoclonality than CD4 T cells, and the largest CD8 T cell clones in synovium were highly enriched in GZMK+ cells. TCR analyses revealed CD8 T cells with likely viral-reactive TCRs distributed across transcriptomic clusters and definitively identified MAIT cells in synovium, which showed transcriptomic features of TCR activation. Among B cells, non-naive B cells including age-associated B cells (ABC), NR4A1+ activated B cells, and plasma cells, were enriched in synovium and had higher somatic hypermutation rates compared to blood B cells. Synovial B cells demonstrated substantial clonal expansion, with ABC, memory, and activated B cells clonally linked to synovial plasma cells. Together, these results reveal clonal relationships between functionally distinct lymphocyte populations that infiltrate RA synovium.
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Affiliation(s)
- Garrett Dunlap
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School; Boston, MA, USA
| | - Aaron Wagner
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry; Rochester, NY, USA
| | - Nida Meednu
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center; Rochester, NY, USA
| | - Fan Zhang
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School; Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital; Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital; Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, USA
- Division of Rheumatology and the Center for Health Artificial Intelligence, University of Colorado School of Medicine; Aurora, CO, USA
| | - A Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School; Boston, MA, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School; Boston, MA, USA
| | - Saori Sakaue
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School; Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital; Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital; Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, USA
| | - Aparna Nathan
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School; Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital; Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital; Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, USA
| | - Vivian P Bykerk
- Hospital for Special Surgery; New York, NY, USA
- Weill Cornell Medicine; New York, NY, USA
| | - Laura T Donlin
- Hospital for Special Surgery; New York, NY, USA
- Weill Cornell Medicine; New York, NY, USA
| | - Susan M Goodman
- Hospital for Special Surgery; New York, NY, USA
- Weill Cornell Medicine; New York, NY, USA
| | - Gary S Firestein
- Division of Rheumatology, Allergy, and Immunology, University of California, San Diego; La Jolla, CA, USA
| | - David L Boyle
- Division of Rheumatology, Allergy, and Immunology, University of California, San Diego; La Jolla, CA, USA
| | - V Michael Holers
- Division of Rheumatology, University of Colorado School of Medicine; Aurora, CO, USA
| | - Larry W Moreland
- Division of Rheumatology, University of Colorado School of Medicine; Aurora, CO, USA
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Darren Tabechian
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center; Rochester, NY, USA
| | - Costantino Pitzalis
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Queen Mary University of London; London, UK
| | - Andrew Filer
- Rheumatology Research Group, Institute for Inflammation and Ageing, University of Birmingham, NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital; Birmingham, UK
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School; Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital; Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital; Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, USA
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester; Manchester, UK
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School; Boston, MA, USA
| | - Andrew McDavid
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry; Rochester, NY, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School; Boston, MA, USA
| | - Jennifer H Anolik
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center; Rochester, NY, USA
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110
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An integrated single cell and spatial transcriptomic map of human white adipose tissue. Nat Commun 2023; 14:1438. [PMID: 36922516 PMCID: PMC10017705 DOI: 10.1038/s41467-023-36983-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
To date, single-cell studies of human white adipose tissue (WAT) have been based on small cohort sizes and no cellular consensus nomenclature exists. Herein, we performed a comprehensive meta-analysis of publicly available and newly generated single-cell, single-nucleus, and spatial transcriptomic results from human subcutaneous, omental, and perivascular WAT. Our high-resolution map is built on data from ten studies and allowed us to robustly identify >60 subpopulations of adipocytes, fibroblast and adipogenic progenitors, vascular, and immune cells. Using these results, we deconvolved spatial and bulk transcriptomic data from nine additional cohorts to provide spatial and clinical dimensions to the map. This identified cell-cell interactions as well as relationships between specific cell subtypes and insulin resistance, dyslipidemia, adipocyte volume, and lipolysis upon long-term weight changes. Altogether, our meta-map provides a rich resource defining the cellular and microarchitectural landscape of human WAT and describes the associations between specific cell types and metabolic states.
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111
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Campbell KA, Colacino JA, Puttabyatappa M, Dou JF, Elkin ER, Hammoud SS, Domino SE, Dolinoy DC, Goodrich JM, Loch-Caruso R, Padmanabhan V, Bakulski KM. Placental cell type deconvolution reveals that cell proportions drive preeclampsia gene expression differences. Commun Biol 2023; 6:264. [PMID: 36914823 PMCID: PMC10011423 DOI: 10.1038/s42003-023-04623-6] [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: 09/09/2021] [Accepted: 02/22/2023] [Indexed: 03/14/2023] Open
Abstract
The placenta mediates adverse pregnancy outcomes, including preeclampsia, which is characterized by gestational hypertension and proteinuria. Placental cell type heterogeneity in preeclampsia is not well-understood and limits mechanistic interpretation of bulk gene expression measures. We generated single-cell RNA-sequencing samples for integration with existing data to create the largest deconvolution reference of 19 fetal and 8 maternal cell types from placental villous tissue (n = 9 biological replicates) at term (n = 40,494 cells). We deconvoluted eight published microarray case-control studies of preeclampsia (n = 173 controls, 157 cases). Preeclampsia was associated with excess extravillous trophoblasts and fewer mesenchymal and Hofbauer cells. Adjustment for cellular composition reduced preeclampsia-associated differentially expressed genes (log2 fold-change cutoff = 0.1, FDR < 0.05) from 1154 to 0, whereas downregulation of mitochondrial biogenesis, aerobic respiration, and ribosome biogenesis were robust to cell type adjustment, suggesting direct changes to these pathways. Cellular composition mediated a substantial proportion of the association between preeclampsia and FLT1 (37.8%, 95% CI [27.5%, 48.8%]), LEP (34.5%, 95% CI [26.0%, 44.9%]), and ENG (34.5%, 95% CI [25.0%, 45.3%]) overexpression. Our findings indicate substantial placental cellular heterogeneity in preeclampsia contributes to previously observed bulk gene expression differences. This deconvolution reference lays the groundwork for cellular heterogeneity-aware investigation into placental dysfunction and adverse birth outcomes.
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Affiliation(s)
- Kyle A Campbell
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Justin A Colacino
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | | | - John F Dou
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Elana R Elkin
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Saher S Hammoud
- Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
- Obstetrics and Gynecology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Steven E Domino
- Obstetrics and Gynecology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jaclyn M Goodrich
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Rita Loch-Caruso
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Vasantha Padmanabhan
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
- Obstetrics and Gynecology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Kelly M Bakulski
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA.
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112
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Anderson AG, Rogers BB, Loupe JM, Rodriguez-Nunez I, Roberts SC, White LM, Brazell JN, Bunney WE, Bunney BG, Watson SJ, Cochran JN, Myers RM, Rizzardi LF. Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer's disease-specific cis-regulatory elements. CELL GENOMICS 2023; 3:100263. [PMID: 36950385 PMCID: PMC10025452 DOI: 10.1016/j.xgen.2023.100263] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/06/2022] [Accepted: 01/12/2023] [Indexed: 02/05/2023]
Abstract
Cell type-specific transcriptional differences between brain tissues from donors with Alzheimer's disease (AD) and unaffected controls have been well documented, but few studies have rigorously interrogated the regulatory mechanisms responsible for these alterations. We performed single nucleus multiomics (snRNA-seq plus snATAC-seq) on 105,332 nuclei isolated from cortical tissues from 7 AD and 8 unaffected donors to identify candidate cis-regulatory elements (CREs) involved in AD-associated transcriptional changes. We detected 319,861 significant correlations, or links, between gene expression and cell type-specific transposase accessible regions enriched for active CREs. Among these, 40,831 were unique to AD tissues. Validation experiments confirmed the activity of many regions, including several candidate regulators of APP expression. We identified ZEB1 and MAFB as candidate transcription factors playing important roles in AD-specific gene regulation in neurons and microglia, respectively. Microglia links were globally enriched for heritability of AD risk and previously identified active regulatory regions.
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Affiliation(s)
| | - Brianne B. Rogers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jacob M. Loupe
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | - Lauren M. White
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - William E. Bunney
- Department of Psychiatry and Human Behavior, College of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Blynn G. Bunney
- Department of Psychiatry and Human Behavior, College of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Stanley J. Watson
- Mental Health Research Institute, University of Michigan, Ann Arbor, MI, USA
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113
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Osborn RM, Leach J, Zanche M, Ashton JM, Chu C, Thakar J, Dewhurst S, Rosenberger S, Pavelka M, Pryhuber GS, Mariani TJ, Anderson CS. Preparation of noninfectious scRNAseq samples from SARS-CoV-2-infected epithelial cells. PLoS One 2023; 18:e0281898. [PMID: 36827401 PMCID: PMC9956660 DOI: 10.1371/journal.pone.0281898] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/03/2023] [Indexed: 02/26/2023] Open
Abstract
Coronavirus disease (COVID-19) is an infectious disease caused by the SARS coronavirus 2 (SARS-CoV-2) virus. Direct assessment, detection, and quantitative analysis using high throughput methods like single-cell RNA sequencing (scRNAseq) is imperative to understanding the host response to SARS-CoV-2. One barrier to studying SARS-CoV-2 in the laboratory setting is the requirement to process virus-infected cell cultures, and potentially infectious materials derived therefrom, under Biosafety Level 3 (BSL-3) containment. However, there are only 190 BSL3 laboratory facilities registered with the U.S. Federal Select Agent Program, as of 2020, and only a subset of these are outfitted with the equipment needed to perform high-throughput molecular assays. Here, we describe a method for preparing non-hazardous RNA samples from SARS-CoV-2 infected cells, that enables scRNAseq analyses to be conducted safely in a BSL2 facility-thereby making molecular assays of SARS-CoV-2 cells accessible to a much larger community of researchers. Briefly, we infected African green monkey kidney epithelial cells (Vero-E6) with SARS-CoV-2 for 96 hours, trypsin-dissociated the cells, and inactivated them with methanol-acetone in a single-cell suspension. Fixed cells were tested for the presence of infectious SARS-CoV-2 virions using the Tissue Culture Infectious Dose Assay (TCID50), and also tested for viability using flow cytometry. We then tested the dissociation and methanol-acetone inactivation method on primary human lung epithelial cells that had been differentiated on an air-liquid interface. Finally, we performed scRNAseq quality control analysis on the resulting cell populations to evaluate the effects of our virus inactivation and sample preparation protocol on the quality of the cDNA produced. We found that methanol-acetone inactivated SARS-CoV-2, fixed the lung epithelial cells, and could be used to obtain noninfectious, high-quality cDNA libraries. This methodology makes investigating SARS-CoV-2, and related high-containment RNA viruses at a single-cell level more accessible to an expanded community of researchers.
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Affiliation(s)
- Raven M. Osborn
- Translational Biomedical Sciences Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Clinical and Translational Sciences Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Justin Leach
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Michelle Zanche
- Genomics Research Center, Center for Advanced Research Technologies, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - John M. Ashton
- Genomics Research Center, Center for Advanced Research Technologies, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - ChinYi Chu
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Juilee Thakar
- Translational Biomedical Sciences Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Clinical and Translational Sciences Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Biophysics, Structural, and Computational Biology Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Stephen Dewhurst
- Clinical and Translational Sciences Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Sonia Rosenberger
- Department of Environmental Health and Safety, University of Rochester, Rochester, New York, United States of America
- Biosafety Level 3 Facility, Center for Advanced Research Technologies, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Martin Pavelka
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Biosafety Level 3 Facility, Center for Advanced Research Technologies, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Gloria S. Pryhuber
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Thomas J. Mariani
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Christopher S. Anderson
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Division of Neonatology, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
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114
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Yu L, Wang X, Mu Q, Tam SST, Loi DSC, Chan AKY, Poon WS, Ng HK, Chan DTM, Wang J, Wu AR. scONE-seq: A single-cell multi-omics method enables simultaneous dissection of phenotype and genotype heterogeneity from frozen tumors. SCIENCE ADVANCES 2023; 9:eabp8901. [PMID: 36598983 PMCID: PMC9812385 DOI: 10.1126/sciadv.abp8901] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Single-cell multi-omics can provide a unique perspective on tumor cellular heterogeneity. Most previous single-cell whole-genome RNA sequencing (scWGS-RNA-seq) methods demonstrate utility with intact cells from fresh samples. Among them, many are not applicable to frozen samples that cannot produce intact single-cell suspensions. We have developed scONE-seq, a versatile scWGS-RNA-seq method that amplifies single-cell DNA and RNA without separating them from each other and hence is compatible with frozen biobanked samples. We benchmarked scONE-seq against existing methods using fresh and frozen samples to demonstrate its performance in various aspects. We identified a unique transcriptionally normal-like tumor clone by analyzing a 2-year frozen astrocytoma sample, demonstrating that performing single-cell multi-omics interrogation on biobanked tissue by scONE-seq could enable previously unidentified discoveries in tumor biology.
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Affiliation(s)
- Lei Yu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
| | - Xinlei Wang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
| | - Quanhua Mu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
| | - Sindy Sing Ting Tam
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
| | - Danson Shek Chun Loi
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
| | - Aden K. Y. Chan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong S.A.R., China
| | - Wai Sang Poon
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong S.A.R., China
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong S.A.R., China
| | - Danny T. M. Chan
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong S.A.R., China
| | - Jiguang Wang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong S.A.R., China
| | - Angela Ruohao Wu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
- Center for Aging Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
- Corresponding author.
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Hua Y, Wu N, Miao J, Shen M. Single-cell transcriptomic analysis in two patients with rare systemic autoinflammatory diseases treated with anti-TNF therapy. Front Immunol 2023; 14:1091336. [PMID: 36911721 PMCID: PMC9998688 DOI: 10.3389/fimmu.2023.1091336] [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: 11/06/2022] [Accepted: 02/08/2023] [Indexed: 02/26/2023] Open
Abstract
Systemic autoinflammatory diseases (SAIDs) are a group of rare diseases characterized by recurrent or continuous inflammation, typically accompanied by genetic variants. Good responses to anti-TNF therapy were observed in SAIDs patients. However, the mechanisms underlying the disease flare and the response to TNF blocking therapy have not been fully elucidated. Here, single-cell RNA sequencing technology was used to describe the transcriptomic profile of PBMCs and PMNs in two SAID patients both before and after anti-TNF treatment. Interferon responses were involved in the disease flare. After anti-TNF therapy, clinical symptoms were alleviated while TNF and IL-1 were unexpectedly increased, indicating that these inflammatory cytokines are not positively correlated with disease activity. Trajectory analysis showed that inhibition of macrophage differentiation, rather than reduction of the inflammatory cytokines, as the potential mechanism of anti-TNF treatment response in SAIDs.
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Affiliation(s)
- Yichao Hua
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Na Wu
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Junke Miao
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Min Shen
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
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116
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Zhou W, Liu K, Zeng L, He J, Gao X, Gu X, Chen X, Jing Li J, Wang M, Wu D, Cai Z, Claesson-Welsh L, Ju R, Wang J, Zhang F, Chen Y. Targeting VEGF-A/VEGFR2 Y949 Signaling-Mediated Vascular Permeability Alleviates Hypoxic Pulmonary Hypertension. Circulation 2022; 146:1855-1881. [PMID: 36384284 DOI: 10.1161/circulationaha.122.061900] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BACKGROUND Pulmonary hypertension (PH) is associated with increased expression of VEGF-A (vascular endothelial growth factor A) and its receptor, VEGFR2 (vascular endothelial growth factor 2), but whether and how activation of VEGF-A signal participates in the pathogenesis of PH is unclear. METHODS VEGF-A/VEGFR2 signal activation and VEGFR2 Y949-dependent vascular leak were investigated in lung samples from patients with PH and mice exposed to hypoxia. To study their mechanistic roles in hypoxic PH, we examined right ventricle systolic pressure, right ventricular hypertrophy, and pulmonary vasculopathy in mutant mice carrying knock-in of phenylalanine that replaced the tyrosine at residual 949 of VEGFR2 (Vefgr2Y949F) and mice with conditional endothelial deletion of Vegfr2 after chronic hypoxia exposure. RESULTS We show that PH leads to excessive pulmonary vascular leak in both patients and hypoxic mice, and this is because of an overactivated VEGF-A/VEGFR2 Y949 signaling axis. In the context of hypoxic PH, activation of Yes1 and c-Src and subsequent VE-cadherin phosphorylation in endothelial cells are involved in VEGFR2 Y949-induced vascular permeability. Abolishing VEGFR2 Y949 signaling by Vefgr2Y949F point mutation was sufficient to prevent pulmonary vascular permeability and inhibit macrophage infiltration and Rac1 activation in smooth muscle cells under hypoxia exposure, thereby leading to alleviated PH manifestations, including muscularization of distal pulmonary arterioles, elevated right ventricle systolic pressure, and right ventricular hypertrophy. It is important that we found that VEGFR2 Y949 signaling in myeloid cells including macrophages was trivial and dispensable for hypoxia-induced vascular abnormalities and PH. In contrast with selective blockage of VEGFR2 Y949 signaling, disruption of the entire VEGFR2 signaling by conditional endothelial deletion of Vegfr2 promotes the development of PH. CONCLUSIONS Our results support the notion that VEGF-A/VEGFR2 Y949-dependent vascular permeability is an important determinant in the pathogenesis of PH and might serve as an attractive therapeutic target pathway for this disease.
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Affiliation(s)
- Weibin Zhou
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China (W.Z., J.H., M.W., D.W., J.W., Y.C.).,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China (W.Z., K.L., L.Z., X. Gao, X. Gu, X.C., J.J.L., R.J., F.Z.).,Guangdong Province Key Laboratory of Arrhythmia and Electrophysiology, Guangzhou, China (W.Z., J.H., J.W., Y.C.)
| | - Keli Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China (W.Z., K.L., L.Z., X. Gao, X. Gu, X.C., J.J.L., R.J., F.Z.)
| | - Lei Zeng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China (W.Z., K.L., L.Z., X. Gao, X. Gu, X.C., J.J.L., R.J., F.Z.)
| | - Jiaqi He
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China (W.Z., J.H., M.W., D.W., J.W., Y.C.).,Guangdong Province Key Laboratory of Arrhythmia and Electrophysiology, Guangzhou, China (W.Z., J.H., J.W., Y.C.)
| | - Xinbo Gao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China (W.Z., K.L., L.Z., X. Gao, X. Gu, X.C., J.J.L., R.J., F.Z.)
| | - Xinyu Gu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China (W.Z., K.L., L.Z., X. Gao, X. Gu, X.C., J.J.L., R.J., F.Z.)
| | - Xun Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China (W.Z., K.L., L.Z., X. Gao, X. Gu, X.C., J.J.L., R.J., F.Z.)
| | - Jing Jing Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China (W.Z., K.L., L.Z., X. Gao, X. Gu, X.C., J.J.L., R.J., F.Z.)
| | - Minghui Wang
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China (W.Z., J.H., M.W., D.W., J.W., Y.C.)
| | - Duoguang Wu
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China (W.Z., J.H., M.W., D.W., J.W., Y.C.)
| | - Zhixiong Cai
- Department of Cardiology, Shantou Central Hospital, China (Z.C.)
| | - Lena Claesson-Welsh
- Rudbeck, SciLifeLab and Beijer Laboratories, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden (L.C.-W.)
| | - Rong Ju
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China (W.Z., K.L., L.Z., X. Gao, X. Gu, X.C., J.J.L., R.J., F.Z.)
| | - Jingfeng Wang
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China (W.Z., J.H., M.W., D.W., J.W., Y.C.).,Guangdong Province Key Laboratory of Arrhythmia and Electrophysiology, Guangzhou, China (W.Z., J.H., J.W., Y.C.)
| | - Feng Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China (W.Z., K.L., L.Z., X. Gao, X. Gu, X.C., J.J.L., R.J., F.Z.)
| | - Yangxin Chen
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China (W.Z., J.H., M.W., D.W., J.W., Y.C.).,Guangdong Province Key Laboratory of Arrhythmia and Electrophysiology, Guangzhou, China (W.Z., J.H., J.W., Y.C.)
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117
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Lou B, Zeng L, Gao X, Qian X, Li JJ, Gu X, Liu Z, Liu K, Chen X, Lin X, Zhang F. A single-cell transcriptomic atlas of the human ciliary body. Cell Mol Life Sci 2022; 79:528. [PMID: 36163311 PMCID: PMC9512889 DOI: 10.1007/s00018-022-04559-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 12/02/2022]
Abstract
The ciliary body critically contributes to the ocular physiology with multiple responsibilities in the production of aqueous humor, vision accommodation and intraocular immunity. Comparatively little work, however, has revealed the single-cell molecular taxonomy of the human ciliary body required for studying these functionalities. In this study, we report a comprehensive atlas of the cellular and molecular components of human ciliary body as well as their interactions using single-cell RNA sequencing (scRNAseq). Cluster analysis of the transcriptome of 14,563 individual ciliary cells from the eyes of 3 human donors identified 14 distinct cell types, including the ciliary epithelium, smooth muscle, vascular endothelial cell, immune cell and other stromal cell populations. Cell-type discriminative gene markers were also revealed. Unique gene expression patterns essential for ciliary epithelium-mediated aqueous humor inflow and ciliary smooth muscle contractility were identified. Importantly, we discovered the transitional states that probably contribute to the transition of ciliary macrophage into retina microglia and verified no lymphatics in the ciliary body. Moreover, the utilization of CellPhoneDB allowed us to systemically infer cell–cell interactions among diverse ciliary cells including those that potentially participate in the pathogenesis of glaucoma and uveitis. Altogether, these new findings provide insights into the regulation of intraocular pressure, accommodation reflex and immune homeostasis under physiological and pathological conditions.
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Affiliation(s)
- Bingsheng Lou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Lei Zeng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Xinbo Gao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Xiaobing Qian
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Jing Jing Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Xinyu Gu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Zheng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Keli Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Xun Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Xiaofeng Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-Sen University, Guangzhou, 510060, China.
| | - Feng Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-Sen University, Guangzhou, 510060, China.
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118
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Szymczak F, Alvelos MI, Marín-Cañas S, Castela Â, Demine S, Colli ML, Op de Beeck A, Thomaidou S, Marselli L, Zaldumbide A, Marchetti P, Eizirik DL. Transcription and splicing regulation by NLRC5 shape the interferon response in human pancreatic β cells. SCIENCE ADVANCES 2022; 8:eabn5732. [PMID: 36103539 PMCID: PMC9473574 DOI: 10.1126/sciadv.abn5732] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
IFNα is a key regulator of the dialogue between pancreatic β cells and the immune system in early type 1 diabetes (T1D). IFNα up-regulates HLA class I expression in human β cells, fostering autoantigen presentation to the immune system. We observed by bulk and single-cell RNA sequencing that exposure of human induced pluripotent-derived islet-like cells to IFNα induces expression of HLA class I and of other genes involved in antigen presentation, including the transcriptional activator NLRC5. We next evaluated the global role of NLRC5 in human insulin-producing EndoC-βH1 and human islet cells by RNA sequencing and targeted gene/protein determination. NLRC5 regulates expression of HLA class I, antigen presentation-related genes, and chemokines. NLRC5 also mediates the effects of IFNα on alternative splicing, a generator of β cell neoantigens, suggesting that it is a central player of the effects of IFNα on β cells that contribute to trigger and amplify autoimmunity in T1D.
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Affiliation(s)
- Florian Szymczak
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
| | - Maria Inês Alvelos
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), Brussels, Belgium
| | - Sandra Marín-Cañas
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), Brussels, Belgium
| | - Ângela Castela
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), Brussels, Belgium
| | - Stéphane Demine
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
| | - Maikel Luis Colli
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), Brussels, Belgium
| | - Anne Op de Beeck
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), Brussels, Belgium
| | - Sofia Thomaidou
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, Pisa, Italy
| | - Arnaud Zaldumbide
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, Pisa, Italy
| | - Décio L. Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), Brussels, Belgium
- Welbio, Medical Faculty, Université Libre De Bruxelles (ULB), Brussels, Belgium
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119
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Single-cell RNA and protein profiling of immune cells from the mouse brain and its border tissues. Nat Protoc 2022; 17:2354-2388. [PMID: 35931780 DOI: 10.1038/s41596-022-00716-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 04/20/2022] [Indexed: 12/15/2022]
Abstract
Brain-immune cross-talk and neuroinflammation critically shape brain physiology in health and disease. A detailed understanding of the brain immune landscape is essential for developing new treatments for neurological disorders. Single-cell technologies offer an unbiased assessment of the heterogeneity, dynamics and functions of immune cells. Here we provide a protocol that outlines all the steps involved in performing single-cell multi-omic analysis of the brain immune compartment. This includes a step-by-step description on how to microdissect the border regions of the mouse brain, together with dissociation protocols tailored to each of these tissues. These combine a high yield with minimal dissociation-induced gene expression changes. Next, we outline the steps involved for high-dimensional flow cytometry and droplet-based single-cell RNA sequencing via the 10x Genomics platform, which can be combined with cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) and offers a higher throughput than plate-based methods. Importantly, we detail how to implement CITE-seq with large antibody panels to obtain unbiased protein-expression screening coupled to transcriptome analysis. Finally, we describe the main steps involved in the analysis and interpretation of the data. This optimized workflow allows for a detailed assessment of immune cell heterogeneity and activation in the whole brain or specific border regions, at RNA and protein level. The wet lab workflow can be completed by properly trained researchers (with basic proficiency in cell and molecular biology) and takes between 6 and 11 h, depending on the chosen procedures. The computational analysis requires a background in bioinformatics and programming in R.
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120
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Cell-type-specific cis-eQTLs in eight human brain cell types identify novel risk genes for psychiatric and neurological disorders. Nat Neurosci 2022; 25:1104-1112. [PMID: 35915177 DOI: 10.1038/s41593-022-01128-z] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 06/22/2022] [Indexed: 12/22/2022]
Abstract
To date, most expression quantitative trait loci (eQTL) studies, which investigate how genetic variants contribute to gene expression, have been performed in heterogeneous brain tissues rather than specific cell types. In this study, we performed an eQTL analysis using single-nuclei RNA sequencing from 192 individuals in eight brain cell types derived from the prefrontal cortex, temporal cortex and white matter. We identified 7,607 eGenes, a substantial fraction (46%, 3,537/7,607) of which show cell-type-specific effects, with strongest effects in microglia. Cell-type-level eQTLs affected more constrained genes and had larger effect sizes than tissue-level eQTLs. Integration of brain cell type eQTLs with genome-wide association studies (GWAS) revealed novel relationships between expression and disease risk for neuropsychiatric and neurodegenerative diseases. For most GWAS loci, a single gene co-localized in a single cell type, providing new clues into disease etiology. Our findings demonstrate substantial contrast in genetic regulation of gene expression among brain cell types and reveal potential mechanisms by which disease risk genes influence brain disorders.
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121
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Kuppe C, Ramirez Flores RO, Li Z, Hayat S, Levinson RT, Liao X, Hannani MT, Tanevski J, Wünnemann F, Nagai JS, Halder M, Schumacher D, Menzel S, Schäfer G, Hoeft K, Cheng M, Ziegler S, Zhang X, Peisker F, Kaesler N, Saritas T, Xu Y, Kassner A, Gummert J, Morshuis M, Amrute J, Veltrop RJA, Boor P, Klingel K, Van Laake LW, Vink A, Hoogenboezem RM, Bindels EMJ, Schurgers L, Sattler S, Schapiro D, Schneider RK, Lavine K, Milting H, Costa IG, Saez-Rodriguez J, Kramann R. Spatial multi-omic map of human myocardial infarction. Nature 2022; 608:766-777. [PMID: 35948637 PMCID: PMC9364862 DOI: 10.1038/s41586-022-05060-x] [Citation(s) in RCA: 198] [Impact Index Per Article: 99.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/29/2022] [Indexed: 02/01/2023]
Abstract
Myocardial infarction is a leading cause of death worldwide1. Although advances have been made in acute treatment, an incomplete understanding of remodelling processes has limited the effectiveness of therapies to reduce late-stage mortality2. Here we generate an integrative high-resolution map of human cardiac remodelling after myocardial infarction using single-cell gene expression, chromatin accessibility and spatial transcriptomic profiling of multiple physiological zones at distinct time points in myocardium from patients with myocardial infarction and controls. Multi-modal data integration enabled us to evaluate cardiac cell-type compositions at increased resolution, yielding insights into changes of the cardiac transcriptome and epigenome through the identification of distinct tissue structures of injury, repair and remodelling. We identified and validated disease-specific cardiac cell states of major cell types and analysed them in their spatial context, evaluating their dependency on other cell types. Our data elucidate the molecular principles of human myocardial tissue organization, recapitulating a gradual cardiomyocyte and myeloid continuum following ischaemic injury. In sum, our study provides an integrative molecular map of human myocardial infarction, represents an essential reference for the field and paves the way for advanced mechanistic and therapeutic studies of cardiac disease.
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Affiliation(s)
- Christoph Kuppe
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Ricardo O Ramirez Flores
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
- Informatics for Life, Heidelberg, Germany
| | - Zhijian Li
- Institute for Computational Genomics, RWTH Aachen University, Medical Faculty, Aachen, Germany
- Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
| | - Sikander Hayat
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Rebecca T Levinson
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
- Informatics for Life, Heidelberg, Germany
- Department of General Internal Medicine and Psychosomatics, Heidelberg University Hospital, Heidelberg, Germany
| | - Xian Liao
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Monica T Hannani
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
| | - Jovan Tanevski
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
- Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Florian Wünnemann
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
| | - James S Nagai
- Institute for Computational Genomics, RWTH Aachen University, Medical Faculty, Aachen, Germany
- Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
| | - Maurice Halder
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - David Schumacher
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Sylvia Menzel
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Gideon Schäfer
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Konrad Hoeft
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Mingbo Cheng
- Institute for Computational Genomics, RWTH Aachen University, Medical Faculty, Aachen, Germany
- Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
| | - Susanne Ziegler
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Xiaoting Zhang
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Fabian Peisker
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Nadine Kaesler
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Turgay Saritas
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Yaoxian Xu
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Astrid Kassner
- Erich and Hanna Klessmann Institute for Cardiovascular Research and Development, Clinic for Thoracic and Cardiovascular Surgery, Heart and Diabetes Center NRW, Bad Oeynhausen, Germany
| | - Jan Gummert
- Heart and Diabetes Center, North Rhine-Westphalia, Bad Oeynhausen, Germany
| | - Michiel Morshuis
- Heart and Diabetes Center, North Rhine-Westphalia, Bad Oeynhausen, Germany
| | - Junedh Amrute
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Rogier J A Veltrop
- Institute for Molecular Cardiovascular Research IMCAR, RWTH Aachen University, Medical Faculty, Aachen, Germany
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
| | - Peter Boor
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Medical Faculty, Aachen, Germany
- Department of Pathology, RWTH Aachen University, Aachen, Germany
| | - Karin Klingel
- Cardiopathology, Institute for Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Linda W Van Laake
- Department of Cardiology, Regenerative Medicine Center and Circulatory Health Lab, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Aryan Vink
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Remco M Hoogenboezem
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Eric M J Bindels
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Leon Schurgers
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
| | - Susanne Sattler
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Denis Schapiro
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Rebekka K Schneider
- Institute of Cell and Tumor Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
- Oncode Institute, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Kory Lavine
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Hendrik Milting
- Erich and Hanna Klessmann Institute for Cardiovascular Research and Development, Clinic for Thoracic and Cardiovascular Surgery, Heart and Diabetes Center NRW, Bad Oeynhausen, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, RWTH Aachen University, Medical Faculty, Aachen, Germany
- Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany.
- Informatics for Life, Heidelberg, Germany.
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany.
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Medical Faculty, Aachen, Germany.
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands.
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