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Yashchenko A, Bland SJ, Song CJ, Ahmed UKB, Sharp R, Darby IG, Cordova AM, Smith ME, Lever JM, Li Z, Aloria EJ, Khan S, Maryam B, Liu S, Crowley MR, Jones KL, Zenewicz LA, George JF, Mrug M, Crossman DK, Hopp K, Stavrakis S, Humphrey MB, Ginhoux F, Zimmerman KA. Cx3cr1 controls kidney resident macrophage heterogeneity. Front Immunol 2023; 14:1082078. [PMID: 37256130 PMCID: PMC10225589 DOI: 10.3389/fimmu.2023.1082078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 04/25/2023] [Indexed: 06/01/2023] Open
Abstract
Kidney macrophages are comprised of both monocyte-derived and tissue resident populations; however, the heterogeneity of kidney macrophages and factors that regulate their heterogeneity are poorly understood. Herein, we performed single cell RNA sequencing (scRNAseq), fate mapping, and parabiosis to define the cellular heterogeneity of kidney macrophages in healthy mice. Our data indicate that healthy mouse kidneys contain four major subsets of monocytes and two major subsets of kidney resident macrophages (KRM) including a population with enriched Ccr2 expression, suggesting monocyte origin. Surprisingly, fate mapping data using the newly developed Ms4a3Cre Rosa Stopf/f TdT model indicate that less than 50% of Ccr2+ KRM are derived from Ly6chi monocytes. Instead, we find that Ccr2 expression in KRM reflects their spatial distribution as this cell population is almost exclusively found in the kidney cortex. We also identified Cx3cr1 as a gene that governs cortex specific accumulation of Ccr2+ KRM and show that loss of Ccr2+ KRM reduces the severity of cystic kidney disease in a mouse model where cysts are mainly localized to the kidney cortex. Collectively, our data indicate that Cx3cr1 regulates KRM heterogeneity and niche-specific disease progression.
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Affiliation(s)
- Alex Yashchenko
- Department of Internal Medicine, Division of Nephrology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Sarah J. Bland
- Department of Internal Medicine, Division of Nephrology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Cheng J. Song
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ummey Khalecha Bintha Ahmed
- Department of Internal Medicine, Division of Nephrology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Rachel Sharp
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Isabella G. Darby
- Department of Internal Medicine, Division of Nephrology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Audrey M. Cordova
- Department of Internal Medicine, Division of Nephrology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Morgan E. Smith
- Department of Internal Medicine, Division of Nephrology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Jeremie M. Lever
- Department of Medicine, Division of Nephrology, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Surgery, Division of Cardiothoracic Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Zhang Li
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ernald J. Aloria
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Shuja Khan
- Department of Internal Medicine, Division of Nephrology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Bibi Maryam
- Department of Internal Medicine, Division of Nephrology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Shanrun Liu
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Michael R. Crowley
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Kenneth L. Jones
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Lauren A. Zenewicz
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - James F. George
- Department of Surgery, Division of Cardiothoracic Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Michal Mrug
- Department of Medicine, Division of Nephrology, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Veterans Affairs Medical Center, Birmingham, AL, United States
| | - David K. Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Katharina Hopp
- Department of Medicine, Division of Renal Diseases and Hypertension, Polycystic Kidney Disease Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Stavros Stavrakis
- Department of Internal Medicine, Division of Cardiovascular Diseases, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Mary B. Humphrey
- Department of Internal Medicine, Division of Rheumatology, Immunology, and Allergy, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Department of Veterans Affairs Medical Center, Oklahoma City, OK, United States
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Singapore, Singapore
| | - Kurt A. Zimmerman
- Department of Internal Medicine, Division of Nephrology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
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Larabee JL, Doyle DA, Ahmed UKB, Shadid TM, Sharp RR, Jones KL, Kim YM, Li S, Ballard JD. Discovery of Hippo signaling as a regulator of CSPG4 expression and as a therapeutic target for Clostridioides difficile disease. PLoS Pathog 2023; 19:e1011272. [PMID: 36972308 PMCID: PMC10079225 DOI: 10.1371/journal.ppat.1011272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/06/2023] [Accepted: 03/08/2023] [Indexed: 03/29/2023] Open
Abstract
The signaling pathways and networks regulating expression of chondroitin sulfate proteoglycan 4 (CSPG4), a cancer-related protein that serves as a receptor for Clostridiodes difficile TcdB, are poorly defined. In this study, TcdB-resistant/CSPG4-negative HeLa cells were generated by exposure to increasing concentrations of the toxin. The cells that emerged (HeLa R5) lost expression of CSPG4 mRNA and were resistant to binding by TcdB. mRNA expression profiles paired with integrated pathway analysis correlated changes in the Hippo and estrogen signaling pathways with a CSPG4 decrease in HeLa R5 cells. Both signaling pathways altered CSPG4 expression when modulated chemically or through CRISPR-mediated deletion of key transcriptional regulators in the Hippo pathway. Based on the in vitro findings, we predicted and experimentally confirmed that a Hippo pathway inactivating drug (XMU-MP-1) provides protection from C. difficile disease in a mouse model. These results provide insights into key regulators of CSPG4 expression and identify a therapeutic for C. difficile disease.
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Affiliation(s)
- Jason L. Larabee
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - D. Annie Doyle
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Ummey Khalecha Bintha Ahmed
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Tyler M. Shadid
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Rachel R. Sharp
- Laboratory for Molecular Biology and Cytometry Research, Harold Hamm Diabetes Center, Oklahoma City, Oklahoma, United States of America
| | - Kenneth L. Jones
- Laboratory for Molecular Biology and Cytometry Research, Harold Hamm Diabetes Center, Oklahoma City, Oklahoma, United States of America
- Department of Cell Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Young Mi Kim
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Shibo Li
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Jimmy D. Ballard
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
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Song CJ, Li Z, Ahmed UKB, Bland SJ, Yashchenko A, Liu S, Aloria EJ, Lever JM, Gonzalez NM, Bickel MA, Giles CB, Georgescu C, Wren JD, Lang ML, Benveniste EN, Harrington LE, Tsiokas L, George JF, Jones KL, Crossman DK, Agarwal A, Mrug M, Yoder BK, Hopp K, Zimmerman KA. A Comprehensive Immune Cell Atlas of Cystic Kidney Disease Reveals the Involvement of Adaptive Immune Cells in Injury-Mediated Cyst Progression in Mice. J Am Soc Nephrol 2022; 33:747-768. [PMID: 35110364 PMCID: PMC8970461 DOI: 10.1681/asn.2021030278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 01/16/2022] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Inducible disruption of cilia-related genes in adult mice results in slowly progressive cystic disease, which can be greatly accelerated by renal injury. METHODS To identify in an unbiased manner modifier cells that may be influencing the differential rate of cyst growth in injured versus non-injured cilia mutant kidneys at a time of similar cyst severity, we generated a single-cell atlas of cystic kidney disease. We conducted RNA-seq on 79,355 cells from control mice and adult-induced conditional Ift88 mice (hereafter referred to as cilia mutant mice) that were harvested approximately 7 months post-induction or 8 weeks post 30-minute unilateral ischemia reperfusion injury. RESULTS Analyses of single-cell RNA-seq data of CD45+ immune cells revealed that adaptive immune cells differed more in cluster composition, cell proportion, and gene expression than cells of myeloid origin when comparing cystic models with one another and with non-cystic controls. Surprisingly, genetic deletion of adaptive immune cells significantly reduced injury-accelerated cystic disease but had no effect on cyst growth in non-injured cilia mutant mice, independent of the rate of cyst growth or underlying genetic mutation. Using NicheNet, we identified a list of candidate cell types and ligands that were enriched in injured cilia mutant mice compared with aged cilia mutant mice and non-cystic controls that may be responsible for the observed dependence on adaptive immune cells during injury-accelerated cystic disease. CONCLUSIONS Collectively, these data highlight the diversity of immune cell involvement in cystic kidney disease.
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Affiliation(s)
- Cheng J. Song
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Zhang Li
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Ummey Khalecha Bintha Ahmed
- Division of Nephrology, Department of Internal Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Sarah J. Bland
- Division of Nephrology, Department of Internal Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Alex Yashchenko
- Division of Nephrology, Department of Internal Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Shanrun Liu
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Ernald J. Aloria
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jeremie M. Lever
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Nancy M. Gonzalez
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Marisa A. Bickel
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Cory B. Giles
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Constantin Georgescu
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Jonathan D. Wren
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Mark L. Lang
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Etty N. Benveniste
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Laurie E. Harrington
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Leo Tsiokas
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - James F. George
- Division of Cardiothoracic Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Kenneth L. Jones
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - David K. Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Anupam Agarwal
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Michal Mrug
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Veterans Affairs Medical Center, Birmingham, Alabama
| | - Bradley K. Yoder
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Katharina Hopp
- Polycystic Kidney Disease Program, Division of Renal Diseases and Hypertension, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Kurt A. Zimmerman
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
- Division of Nephrology, Department of Internal Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
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Ahmed UKB, Ballard JD. Autoinducing peptide-based quorum signaling systems in Clostridioides difficile. Curr Opin Microbiol 2022; 65:81-86. [PMID: 34773906 PMCID: PMC8792308 DOI: 10.1016/j.mib.2021.10.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/20/2021] [Accepted: 10/25/2021] [Indexed: 02/03/2023]
Abstract
The autoinducing peptide-based Agr system in Clostridioides difficile is involved in virulence factor expression, motility, and sporulation. This review highlights several of the recent discoveries regarding C. difficile Agr. Typical Agr systems rely on the combined activities of four proteins involved in peptide expression, peptide processing, peptide sensing, and transcriptional regulation. As emphasized in this review, at least two C. difficile Agr systems (Agr1 and Agr3) lack the set of proteins associated with this regulatory network. In line with this, recent finding indicate Agr1 can function in ways that may not depend on accumulation of extracellular peptide. Also, described are the similarities and differences in Agr systems within the pathogenic Clostridia.
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