Single-cell analysis identifies the interaction of altered renal tubules with basophils orchestrating kidney fibrosis

[1]  D. Voehringer,et al.  Basophils balance healing after myocardial infarction via IL-4/IL-13. , 2021, The Journal of clinical investigation.

[2]  A. McMahon,et al.  Single-nuclear transcriptomics reveals diversity of proximal tubule cell states in a dynamic response to acute kidney injury , 2021, Proceedings of the National Academy of Sciences.

[3]  Christopher D. Brown,et al.  Transcriptome-wide association analysis identifies DACH1 as a kidney disease risk gene that contributes to fibrosis. , 2021, The Journal of clinical investigation.

[4]  M. Knepper,et al.  Targeted Single-Cell RNA-seq Identifies Minority Cell Types of Kidney Distal Nephron. , 2021, Journal of the American Society of Nephrology : JASN.

[5]  Raphael Gottardo,et al.  Integrated analysis of multimodal single-cell data , 2020, Cell.

[6]  S. Waikar,et al.  Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney , 2020, Nature Communications.

[7]  Mingyao Li,et al.  The Nuclear Receptor ESRRA Protects from Kidney Disease by Coupling Metabolism and Differentiation. , 2020, Cell metabolism.

[8]  J. Goldin,et al.  Tocilizumab in systemic sclerosis: a randomised, double-blind, placebo-controlled, phase 3 trial. , 2020, The Lancet. Respiratory medicine.

[9]  Aimee M Beaulieu,et al.  Basophils prime group 2 innate lymphoid cells for neuropeptide-mediated inhibition , 2020, Nature Immunology.

[10]  M. Massari,et al.  Tocilizumab in patients with severe COVID-19: a retrospective cohort study , 2020, The Lancet Rheumatology.

[11]  C. Hunter,et al.  Loss of IL-27Rα Results in Enhanced Tubulointerstitial Fibrosis Associated with Elevated Th17 Responses , 2020, The Journal of Immunology.

[12]  Tamir Chandra,et al.  Kidney single-cell atlas reveals myeloid heterogeneity in progression and regression of kidney disease , 2020, bioRxiv.

[13]  F. Ginhoux,et al.  Kidney dendritic cells: fundamental biology and functional roles in health and disease , 2020, Nature Reviews Nephrology.

[14]  Haojia Wu,et al.  Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury , 2020, Proceedings of the National Academy of Sciences.

[15]  Ash A. Alizadeh,et al.  Profiling Cell Type Abundance and Expression in Bulk Tissues with CIBERSORTx. , 2020, Methods in molecular biology.

[16]  V. Jha,et al.  A single number for advocacy and communication-worldwide more than 850 million individuals have kidney diseases. , 2019, Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association.

[17]  Fabian J Theis,et al.  Generalizing RNA velocity to transient cell states through dynamical modeling , 2019, Nature Biotechnology.

[18]  Zhuo-wei Hu,et al.  Targeting Degradation of the Transcription Factor C/EBPβ Reduces Lung Fibrosis by Restoring Activity of the Ubiquitin-Editing Enzyme A20 in Macrophages. , 2019, Immunity.

[19]  H. Lan,et al.  Macrophages: versatile players in renal inflammation and fibrosis , 2019, Nature Reviews Nephrology.

[20]  B. Aronow,et al.  Expression Profiling of Fibroblasts in Chronic and Acute Disease Models Reveals Novel Pathways in Kidney Fibrosis. , 2018, Journal of the American Society of Nephrology : JASN.

[21]  Fan Zhang,et al.  Fast, sensitive, and accurate integration of single cell data with Harmony , 2018, bioRxiv.

[22]  I. Amit,et al.  Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting , 2018, Cell.

[23]  Christopher D. Brown,et al.  Renal compartment-specific genetic variation analyses identify new pathways in chronic kidney disease , 2018, Nature Medicine.

[24]  Leslie S. Gewin,et al.  Renal fibrosis: Primacy of the proximal tubule. , 2018, Matrix biology : journal of the International Society for Matrix Biology.

[25]  Erik Sundström,et al.  RNA velocity of single cells , 2018, Nature.

[26]  Zev J. Gartner,et al.  DoubletFinder: Doublet detection in single-cell RNA sequencing data using artificial nearest neighbors , 2018, bioRxiv.

[27]  Mingyao Li,et al.  Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease , 2018, Science.

[28]  Peggy Kirstetter,et al.  Treatment of MCPT8DTR mice with high‐ or low‐dose diphtheria toxin leads to differential depletion of basophils and granulocyte‐macrophage progenitors , 2018, European journal of immunology.

[29]  P. Boor,et al.  PDGF in organ fibrosis. , 2017, Molecular aspects of medicine.

[30]  U. Panzer,et al.  Tissue-Resident Lymphocytes in the Kidney. , 2017, Journal of the American Society of Nephrology : JASN.

[31]  Fabian J Theis,et al.  SCANPY: large-scale single-cell gene expression data analysis , 2018, Genome Biology.

[32]  Cheng-xiang Yang,et al.  Interleukin‐33 signaling contributes to renal fibrosis following ischemia reperfusion , 2017, European journal of pharmacology.

[33]  Hannah A. Pliner,et al.  Reversed graph embedding resolves complex single-cell trajectories , 2017, Nature Methods.

[34]  E. Mickler,et al.  IL‐17A deficiency mitigates bleomycin‐induced complement activation during lung fibrosis , 2017, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[35]  J. Aerts,et al.  SCENIC: Single-cell regulatory network inference and clustering , 2017, Nature Methods.

[36]  Ji-Young Kim,et al.  Basophil-derived IL-6 regulates TH17 cell differentiation and CD4 T cell immunity , 2016, Scientific Reports.

[37]  K. Renner,et al.  Basophils Trigger Fibroblast Activation in Cardiac Allograft Fibrosis Development , 2016, American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons.

[38]  Liqun He,et al.  CXCL16 Deficiency Attenuates Renal Injury and Fibrosis in Salt-Sensitive Hypertension , 2016, Scientific Reports.

[39]  E. Christensen,et al.  Megalin and cubilin in proximal tubule protein reabsorption: from experimental models to human disease. , 2016, Kidney international.

[40]  Fabian J. Theis,et al.  destiny: diffusion maps for large-scale single-cell data in R , 2015, Bioinform..

[41]  M. Colonna,et al.  IL-34 mediates acute kidney injury and worsens subsequent chronic kidney disease. , 2015, The Journal of clinical investigation.

[42]  D. Petrović-Djergović,et al.  CXCL10 induces the recruitment of monocyte‐derived macrophages into kidney, which aggravate puromycin aminonucleoside nephrosis , 2015, Clinical and experimental immunology.

[43]  C. Hunter,et al.  IL-6 as a keystone cytokine in health and disease , 2015, Nature Immunology.

[44]  O. Carretero,et al.  Deletion of interleukin-6 prevents cardiac inflammation, fibrosis and dysfunction without affecting blood pressure in angiotensin II-high salt-induced hypertension , 2015, Journal of hypertension.

[45]  Christophe Pellefigues,et al.  Mast cells in renal inflammation and fibrosis: lessons learnt from animal studies. , 2015, Molecular immunology.

[46]  Anuh T. George,et al.  Blockade of IL-6 Trans Signaling Attenuates Pulmonary Fibrosis , 2014, The Journal of Immunology.

[47]  P. Taylor,et al.  Interleukin-6 Signaling Drives Fibrosis in Unresolved Inflammation , 2014, Immunity.

[48]  Rafael Kramann,et al.  Differentiated kidney epithelial cells repair injured proximal tubule , 2013, Proceedings of the National Academy of Sciences.

[49]  D. Voehringer.  Protective and pathological roles of mast cells and basophils , 2013, Nature Reviews Immunology.

[50]  R. Lahaie,et al.  Human basophils interact with memory T cells to augment Th17 responses. , 2012, Blood.

[51]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[52]  S. Haggarty,et al.  PDGFRβ expression and function in fibroblasts derived from pluripotent cells is linked to DNA demethylation , 2012, Journal of Cell Science.

[53]  R. Cervera,et al.  Basophils, IgE, and Autoantibody-Mediated Kidney Disease , 2011, The Journal of Immunology.

[54]  R. Locksley,et al.  Genetic analysis of basophil function in vivo , 2011, Nature Immunology.

[55]  I. Weissman,et al.  Distinguishing mast cell and granulocyte differentiation at the single-cell level. , 2010, Cell stem cell.

[56]  T. Wynn,et al.  Bleomycin and IL-1β–mediated pulmonary fibrosis is IL-17A dependent , 2010, The Journal of experimental medicine.

[57]  K. Meldrum,et al.  IL-18 neutralization ameliorates obstruction-induced epithelial-mesenchymal transition and renal fibrosis. , 2009, Kidney international.

[58]  D. Koller,et al.  The Immunological Genome Project: networks of gene expression in immune cells , 2008, Nature Immunology.

[59]  Y. Talke,et al.  Basophils enhance immunological memory responses , 2008, Nature Immunology.

[60]  Stephen J. Galli,et al.  The development of allergic inflammation , 2008, Nature.

[61]  F Verrecchia,et al.  [Cellular and molecular mechanisms of fibrosis]. , 2006, Annales de pathologie.

[62]  G. Haines,et al.  CXCL16-mediated cell recruitment to rheumatoid arthritis synovial tissue and murine lymph nodes is dependent upon the MAPK pathway. , 2006, Arthritis and rheumatism.

[63]  I. Clark‐Lewis,et al.  The Interleukin-8-related Chemotactic Cytokines GROa , GROB , and GROT Activate Human Neutrophil and Basophil Leukocytes * , 2001 .

[64]  K. Zsebo,et al.  Development of human mast cells from umbilical cord blood cells by recombinant human and murine c-kit ligand. , 1993, Proceedings of the National Academy of Sciences of the United States of America.