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Canas JJ, Arregui SW, Zhang S, Knox T, Calvert C, Saxena V, Schwaderer AL, Hains DS. DEFA1A3 DNA gene-dosage regulates the kidney innate immune response during upper urinary tract infection. Life Sci Alliance 2024; 7:e202302462. [PMID: 38580392 PMCID: PMC10997819 DOI: 10.26508/lsa.202302462] [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: 10/27/2023] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/07/2024] Open
Abstract
Antimicrobial peptides (AMPs) are host defense effectors with potent neutralizing and immunomodulatory functions against invasive pathogens. The AMPs α-Defensin 1-3/DEFA1A3 participate in innate immune responses and influence patient outcomes in various diseases. DNA copy-number variations in DEFA1A3 have been associated with severity and outcomes in infectious diseases including urinary tract infections (UTIs). Specifically, children with lower DNA copy numbers were more susceptible to UTIs. The mechanism of action by which α-Defensin 1-3/DEFA1A3 copy-number variations lead to UTI susceptibility remains to be explored. In this study, we use a previously characterized transgenic knock-in of the human DEFA1A3 gene mouse to dissect α-Defensin 1-3 gene dose-dependent antimicrobial and immunomodulatory roles during uropathogenic Escherichia coli (UPEC) UTI. We elucidate the relationship between kidney neutrophil- and collecting duct intercalated cell-derived α-Defensin 1-3/DEFA1A3 expression and UTI. We further describe cooperative effects between α-Defensin 1-3 and other AMPs that potentiate the neutralizing activity against UPEC. Cumulatively, we demonstrate that DEFA1A3 directly protects against UPEC meanwhile impacting pro-inflammatory innate immune responses in a gene dosage-dependent manner.
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Affiliation(s)
- Jorge J Canas
- Division of Pediatric Nephrology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Samuel W Arregui
- Division of Pediatric Nephrology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
- Kidney and Urology Translational Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Shaobo Zhang
- Division of Pediatric Nephrology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
- Kidney and Urology Translational Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Taylor Knox
- Kidney and Urology Translational Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Christi Calvert
- Kidney and Urology Translational Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Vijay Saxena
- Division of Pediatric Nephrology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
- Kidney and Urology Translational Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andrew L Schwaderer
- Division of Pediatric Nephrology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
- Riley Hospital for Children, Indiana University Health, Indianapolis, IN, USA
- Kidney and Urology Translational Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - David S Hains
- Division of Pediatric Nephrology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
- Riley Hospital for Children, Indiana University Health, Indianapolis, IN, USA
- Kidney and Urology Translational Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
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Schwaderer AL, Rajadhyaksha E, Canas J, Saxena V, Hains DS. Intercalated cell function, kidney innate immunity, and urinary tract infections. Pflugers Arch 2024; 476:565-578. [PMID: 38227050 DOI: 10.1007/s00424-024-02905-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 09/28/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024]
Abstract
Intercalated cells (ICs) in the kidney collecting duct have a versatile role in acid-base and electrolyte regulation along with the host immune defense. Located in the terminal kidney tubule segment, ICs are among the first kidney cells to encounter bacteria when bacteria ascend from the bladder into the kidney. ICs have developed several mechanisms to combat bacterial infections of the kidneys. For example, ICs produce antimicrobial peptides (AMPs), which have direct bactericidal activity, and in many cases are upregulated in response to infections. Some AMP genes with IC-specific kidney expression are multiallelic, and having more copies of the gene confers increased resistance to bacterial infections of the kidney and urinary tract. Similarly, studies in human children demonstrate that those with history of UTIs are more likely to have single-nucleotide polymorphisms in IC-expressed AMP genes that impair the AMP's bactericidal activity. In murine models, depleted or impaired ICs result in decreased clearance of bacterial load following transurethral challenge with uropathogenic E. coli. A 2021 study demonstrated that ICs even act as phagocytes and acidify bacteria within phagolysosomes. Several immune signaling pathways have been identified in ICs which may represent future therapeutic targets in managing kidney infections or inflammation. This review's objective is to highlight IC structure and function with an emphasis on current knowledge of IC's diverse innate immune capabilities.
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Affiliation(s)
- Andrew L Schwaderer
- Division of Nephrology, Department of Pediatrics, Indiana University, 699 Riley Hospital Drive, STE 230, Indianapolis, IN, 46202, USA.
| | - Evan Rajadhyaksha
- Division of Nephrology, Department of Pediatrics, Indiana University, 699 Riley Hospital Drive, STE 230, Indianapolis, IN, 46202, USA
| | - Jorge Canas
- Division of Nephrology, Department of Pediatrics, Indiana University, 699 Riley Hospital Drive, STE 230, Indianapolis, IN, 46202, USA
| | - Vijay Saxena
- Division of Nephrology, Department of Pediatrics, Indiana University, 699 Riley Hospital Drive, STE 230, Indianapolis, IN, 46202, USA
| | - David S Hains
- Division of Nephrology, Department of Pediatrics, Indiana University, 699 Riley Hospital Drive, STE 230, Indianapolis, IN, 46202, USA
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Vitzthum H, Meyer-Schwesinger C, Ehmke H. Novel functions of the anion exchanger AE4 (SLC4A9). Pflugers Arch 2024; 476:555-564. [PMID: 38195948 PMCID: PMC11006790 DOI: 10.1007/s00424-023-02899-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/09/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/11/2024]
Abstract
The kidney plays a crucial role in acid-base homeostasis. In the distal nephron, α-intercalated cells contribute to urinary acid (H+) secretion and β-intercalated cells accomplish urinary base (HCO3-) secretion. β-intercalated cells regulate the acid base status through modulation of the apical Cl-/HCO3- exchanger pendrin (SLC26A4) activity. In this review, we summarize and discuss our current knowledge of the physiological role of the renal transporter AE4 (SLC4A9). The AE4, as cation-dependent Cl-/HCO3- exchanger, is exclusively expressed in the basolateral membrane of β-intercalated cells and is essential for the sensing of metabolic acid-base disturbances in mice, but not for renal sodium reabsorption and plasma volume control. Potential intracellular signaling pathways are discussed that might link basolateral acid-base sensing through the AE4 to apical pendrin activity.
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Affiliation(s)
- Helga Vitzthum
- Institute of Cellular and Integrative Physiology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Catherine Meyer-Schwesinger
- Institute of Cellular and Integrative Physiology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Heimo Ehmke
- Institute of Cellular and Integrative Physiology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
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4
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Kang MJ, Ioannou S, Lougheide Q, Dittmar M, Hsu Y, Pastor-Soler NM. The study of intercalated cells using ex vivo techniques: primary cell culture, cell lines, kidney slices, and organoids. Am J Physiol Cell Physiol 2024; 326:C229-C251. [PMID: 37899748 DOI: 10.1152/ajpcell.00479.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/27/2022] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 10/31/2023]
Abstract
This review summarizes methods to study kidney intercalated cell (IC) function ex vivo. While important for acid-base homeostasis, IC dysfunction is often not recognized clinically until it becomes severe. The advantage of using ex vivo techniques is that they allow for the differential evaluation of IC function in controlled environments. Although in vitro kidney tubular perfusion is a classical ex vivo technique to study IC, here we concentrate on primary cell cultures, immortalized cell lines, and ex vivo kidney slices. Ex vivo techniques are useful in evaluating IC signaling pathways that allow rapid responses to extracellular changes in pH, CO2, and bicarbonate (HCO3-). However, these methods for IC work can also be challenging, as cell lines that recapitulate IC do not proliferate easily in culture. Moreover, a "pure" IC population in culture does not necessarily replicate its collecting duct (CD) environment, where ICs are surrounded by the more abundant principal cells (PCs). It is reassuring that many findings obtained in ex vivo IC systems signaling have been largely confirmed in vivo. Some of these newly identified signaling pathways reveal that ICs are important for regulating NaCl reabsorption, thus suggesting new frontiers to target antihypertensive treatments. Moreover, recent single-cell characterization studies of kidney epithelial cells revealed a dual developmental origin of IC, as well as the presence of novel CD cell types with certain IC characteristics. These exciting findings present new opportunities for the study of IC ex vivo and will likely rediscover the importance of available tools in this field.NEW & NOTEWORTHY The study of kidney intercalated cells has been limited by current cell culture and kidney tissue isolation techniques. This review is to be used as a reference to select ex vivo techniques to study intercalated cells. We focused on the use of cell lines and kidney slices as potential useful models to study membrane transport proteins. We also review how novel collecting duct organoids may help better elucidate the role of these intriguing cells.
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Affiliation(s)
- Min Ju Kang
- Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine of USC, Los Angeles, California, United States
| | - Silvia Ioannou
- Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine of USC, Los Angeles, California, United States
| | - Quinn Lougheide
- Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine of USC, Los Angeles, California, United States
| | - Michael Dittmar
- Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine of USC, Los Angeles, California, United States
| | - Young Hsu
- Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine of USC, Los Angeles, California, United States
| | - Nuria M Pastor-Soler
- Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine of USC, Los Angeles, California, United States
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Saxena V, Arregui S, Zhang S, Canas J, Qin X, Hains DS, Schwaderer AL. Generation of Atp6v1g3-Cre mice for investigation of intercalated cells and the collecting duct. Am J Physiol Renal Physiol 2023; 325:F770-F778. [PMID: 37823193 PMCID: PMC10881235 DOI: 10.1152/ajprenal.00137.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 05/22/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023] Open
Abstract
Kidney intercalated cells (ICs) maintain acid-base homeostasis and recent studies have demonstrated that they function in the kidney's innate defense. To study kidney innate immune function, ICs have been enriched using vacuolar ATPase (V-ATPase) B1 subunit (Atp6v1b1)-Cre (B1-Cre) mice. Although Atp6v1b1 is considered kidney specific, it is expressed in multiple organ systems, both in mice and humans, raising the possibility of off-target effects when using the Cre-lox system. We have recently shown using single-cell RNA sequencing that the gene that codes for the V-ATPase G3 subunit (mouse gene: Atp6v1g3; human gene: ATP6V1G3; protein abbreviation: G3) mRNA is selectively enriched in human kidney ICs. In this study, we generated Atp6v1g3-Cre (G3-Cre) reporter mice using CRISPR/CAS technology and crossed them with Tdtomatoflox/flox mice. The resultant G3-Cre+Tdt+ progeny was evaluated for kidney specificity in multiple tissues and found to be highly specific to kidney cells with minimal or no expression in other organs evaluated compared with B1-Cre mice. Tdt+ cells were flow sorted and were enriched for IC marker genes on RT-PCR analysis. Next, we crossed these mice to ihCD59 mice to generate an IC depletion mouse model (G3-Cre+ihCD59+/+). ICs were depleted in these mice using intermedilysin, which resulted in lower blood pH, suggestive of a distal renal tubular acidosis phenotype. The G3-Cre mice were healthy, bred normally, and produce regular-sized litter. Thus, this new "IC reporter" mice can be a useful tool to study ICs.NEW & NOTEWORTHY This study details the development, validation, and experimental use of a new mouse model to study the collecting duct and intercalated cells. Kidney intercalated cells are a cell type increasingly recognized to be important in several human diseases including kidney infections, acid-base disorders, and acute kidney injury.
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Affiliation(s)
- Vijay Saxena
- Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Samuel Arregui
- Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Shaobo Zhang
- Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Jorge Canas
- Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Xuebin Qin
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, Louisiana, United States
| | - David S Hains
- Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Andrew L Schwaderer
- Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States
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Abstract
Urinary tract infections (UTIs) are among the most common bacterial infections seen in clinical practice. The ascent of UTI-causing pathogens to the kidneys results in pyelonephritis, which can trigger kidney injury, scarring and ultimately impair kidney function. Despite sizable efforts to understand how infections develop or are cleared in the bladder, our appreciation of the mechanisms by which infections develop, progress or are eradicated in the kidney is limited. The identification of virulence factors that are produced by uropathogenic Escherichia coli to promote pyelonephritis have begun to fill this knowledge gap, as have insights into the mechanisms by which kidney tubular epithelial cells oppose uropathogenic E. coli infection to prevent or eradicate UTIs. Emerging data also illustrate how specific cellular immune responses eradicate infection whereas other immune cell populations promote kidney injury. Insights into the mechanisms by which uropathogenic E. coli circumvent host immune defences or antibiotic therapy to cause pyelonephritis is paramount to the development of new prevention and treatment strategies to mitigate pyelonephritis and its associated complications.
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Affiliation(s)
- Laura Schwartz
- The Kidney and Urinary Tract Center, Nationwide Children's Abigail Wexner Research Institute, Columbus, OH, USA.
- The Ohio State University College of Medicine, Columbus, OH, USA.
| | - Juan de Dios Ruiz-Rosado
- The Kidney and Urinary Tract Center, Nationwide Children's Abigail Wexner Research Institute, Columbus, OH, USA
- The Ohio State University College of Medicine, Columbus, OH, USA
| | - Emily Stonebrook
- The Kidney and Urinary Tract Center, Nationwide Children's Abigail Wexner Research Institute, Columbus, OH, USA
- The Ohio State University College of Medicine, Columbus, OH, USA
| | - Brian Becknell
- The Kidney and Urinary Tract Center, Nationwide Children's Abigail Wexner Research Institute, Columbus, OH, USA
- The Ohio State University College of Medicine, Columbus, OH, USA
| | - John David Spencer
- The Kidney and Urinary Tract Center, Nationwide Children's Abigail Wexner Research Institute, Columbus, OH, USA.
- The Ohio State University College of Medicine, Columbus, OH, USA.
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Chelangarimiyandoab F, Mungara P, Batta M, Cordat E. Urinary Tract Infections: Renal Intercalated Cells Protect against Pathogens. J Am Soc Nephrol 2023; 34:1605-1614. [PMID: 37401780 PMCID: PMC10561816 DOI: 10.1681/asn.0000000000000187] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 01/19/2023] [Accepted: 06/22/2023] [Indexed: 07/05/2023] Open
Abstract
Urinary tract infections affect more than 1 in 2 women during their lifetime. Among these, more than 10% of patients carry antibiotic-resistant bacterial strains, highlighting the urgent need to identify alternative treatments. While innate defense mechanisms are well-characterized in the lower urinary tract, it is becoming evident that the collecting duct (CD), the first renal segment encountered by invading uropathogenic bacteria, also contributes to bacterial clearance. However, the role of this segment is beginning to be understood. This review summarizes the current knowledge on CD intercalated cells in urinary tract bacterial clearance. Understanding the innate protective role of the uroepithelium and of the CD offers new opportunities for alternative therapeutic strategies.
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Affiliation(s)
- Forough Chelangarimiyandoab
- Department of Physiology and Membrane Protein Disease Research Group, Faculty of Medicine & Dentistry, College of Health Sciences, University of Alberta, Edmonton, Alberta, Canada
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Abstract
Recent advances in preclinical modeling of urinary tract infections (UTIs) have enabled the identification of key facets of the host response that influence pathogen clearance and tissue damage. Here, we review new insights into the functions of neutrophils, macrophages, and antimicrobial peptides in innate control of uropathogens and in mammalian infection-related tissue injury and repair. We also discuss novel functions for renal epithelial cells in innate antimicrobial defense. In addition, epigenetic modifications during bacterial cystitis have been implicated in bladder remodeling, conveying susceptibility to recurrent UTI. In total, contemporary work in this arena has better defined host processes that shape UTI susceptibility and severity and might inform the development of novel preventive and therapeutic approaches for acute and recurrent UTI.
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Affiliation(s)
- Hunter W Kuhn
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Teri N Hreha
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - David A Hunstad
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
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Canela VH, Bowen WS, Ferreira RM, Syed F, Lingeman JE, Sabo AR, Barwinska D, Winfree S, Lake BB, Cheng YH, Gaut JP, Ferkowicz M, LaFavers KA, Zhang K, Coe FL, Worcester E, Jain S, Eadon MT, Williams JC, El-Achkar TM. A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease. Nat Commun 2023; 14:4140. [PMID: 37468493 PMCID: PMC10356953 DOI: 10.1038/s41467-023-38975-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 07/01/2022] [Accepted: 05/24/2023] [Indexed: 07/21/2023] Open
Abstract
Kidney stone disease causes significant morbidity and increases health care utilization. In this work, we decipher the cellular and molecular niche of the human renal papilla in patients with calcium oxalate (CaOx) stone disease and healthy subjects. In addition to identifying cell types important in papillary physiology, we characterize collecting duct cell subtypes and an undifferentiated epithelial cell type that was more prevalent in stone patients. Despite the focal nature of mineral deposition in nephrolithiasis, we uncover a global injury signature characterized by immune activation, oxidative stress and extracellular matrix remodeling. We also identify the association of MMP7 and MMP9 expression with stone disease and mineral deposition, respectively. MMP7 and MMP9 are significantly increased in the urine of patients with CaOx stone disease, and their levels correlate with disease activity. Our results define the spatial molecular landscape and specific pathways contributing to stone-mediated injury in the human papilla and identify associated urinary biomarkers.
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Affiliation(s)
- Victor Hugo Canela
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - William S Bowen
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Ricardo Melo Ferreira
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Farooq Syed
- Center for Diabetes and Metabolic Diseases, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - James E Lingeman
- Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Angela R Sabo
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Daria Barwinska
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Seth Winfree
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Blue B Lake
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Ying-Hua Cheng
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Joseph P Gaut
- Department of Pathology and Immunology, Washington University, St. Louis, MO, USA
| | - Michael Ferkowicz
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kaice A LaFavers
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kun Zhang
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Fredric L Coe
- Department of Medicine, Division of Nephrology, University of Chicago, Chicago, IL, USA
| | - Elaine Worcester
- Department of Medicine, Division of Nephrology, University of Chicago, Chicago, IL, USA
| | - Sanjay Jain
- Department of Medicine, Division of Nephrology, Washington University, St. Louis, MO, USA.
| | - Michael T Eadon
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - James C Williams
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Tarek M El-Achkar
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Medicine, Indianapolis VA Medical Center, Indianapolis, IN, USA.
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Charytonowicz D, Brody R, Sebra R. Interpretable and context-free deconvolution of multi-scale whole transcriptomic data with UniCell deconvolve. Nat Commun 2023; 14:1350. [PMID: 36906603 PMCID: PMC10008582 DOI: 10.1038/s41467-023-36961-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/27/2023] [Indexed: 03/13/2023] Open
Abstract
We introduce UniCell: Deconvolve Base (UCDBase), a pre-trained, interpretable, deep learning model to deconvolve cell type fractions and predict cell identity across Spatial, bulk-RNA-Seq, and scRNA-Seq datasets without contextualized reference data. UCD is trained on 10 million pseudo-mixtures from a fully-integrated scRNA-Seq training database comprising over 28 million annotated single cells spanning 840 unique cell types from 898 studies. We show that our UCDBase and transfer-learning models achieve comparable or superior performance on in-silico mixture deconvolution to existing, reference-based, state-of-the-art methods. Feature attribute analysis uncovers gene signatures associated with cell-type specific inflammatory-fibrotic responses in ischemic kidney injury, discerns cancer subtypes, and accurately deconvolves tumor microenvironments. UCD identifies pathologic changes in cell fractions among bulk-RNA-Seq data for several disease states. Applied to lung cancer scRNA-Seq data, UCD annotates and distinguishes normal from cancerous cells. Overall, UCD enhances transcriptomic data analysis, aiding in assessment of cellular and spatial context.
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Affiliation(s)
- Daniel Charytonowicz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rachel Brody
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Genomics Institute, New York, NY, USA.
- Black Family Stem Cell Institute, New York, NY, USA.
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11
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Taniguchi A, Miyashita K, Fukae S, Tanaka R, Nishida M, Kitayama T, Ouchi Y, Shimbo T, Nakazawa S, Yamanaka K, Imamura R, Tamai K, Nonomura N. Single-cell transcriptome analysis of a rat model of bilateral renal ischemia-reperfusion injury. Biochem Biophys Rep 2023; 33:101433. [PMID: 36798850 PMCID: PMC9926196 DOI: 10.1016/j.bbrep.2023.101433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 02/04/2023] Open
Abstract
Ischemia-reperfusion injury (IRI) causes massive tissue damage. Renal IRI is the most common type of acute renal injury, and the defects caused by it may progress to chronic kidney disease (CKD). Rodent models of renal IRI, with various patterns, have been used to study the treatment of human kidney injury. A rat model of bilateral IRI, in which the bilateral kidney blood vessels are clamped for 60 min, is widely used, inducing both acute and chronic kidney disease. However, the molecular mechanisms underlying the effects of bilateral IRI on kidney cells have not yet been fully elucidated. This study aimed to perform a whole-transcriptome analysis of the IRI kidney using single-cell RNA sequencing. We found renal parenchymal cells, including those from the proximal tubule, the loop of Henle, and distal tubules, to be damaged by IRI. In addition, we observed significant changes in macrophage population. Our study delineated the detailed cellular and molecular changes that occur in the rat model of bilateral IRI. Collectively, our data and analyses provided a foundation for understanding IRI-related kidney diseases in rat models.
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Affiliation(s)
- Ayumu Taniguchi
- Department of Urology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kazuya Miyashita
- StemRIM Inc., 7-7-15, Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
| | - Shota Fukae
- Department of Urology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ryo Tanaka
- Department of Urology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Mami Nishida
- StemRIM Inc., 7-7-15, Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
- Department of Stem Cell Therapy Science, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomomi Kitayama
- StemRIM Inc., 7-7-15, Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
- Department of Stem Cell Therapy Science, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuya Ouchi
- StemRIM Inc., 7-7-15, Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
- Department of Stem Cell Therapy Science, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takashi Shimbo
- Department of Stem Cell Therapy Science, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- StemRIM Institute of Regeneration-Inducing Medicine, Osaka University, 2-8 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Corresponding author. Department of Stem Cell Therapy Science, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Shigeaki Nakazawa
- Department of Urology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kazuaki Yamanaka
- Department of Urology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ryoichi Imamura
- Department of Urology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Katsuto Tamai
- Department of Stem Cell Therapy Science, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Corresponding author.
| | - Norio Nonomura
- Department of Urology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
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12
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Saxena V, Arregui S, Kamocka MM, Hains DS, Schwaderer A. MAP3K7 is an innate immune regulatory gene with increased expression in human and murine kidney intercalated cells following uropathogenic Escherichia coli exposure. J Cell Biochem 2022; 123:1817-1826. [PMID: 35959632 PMCID: PMC9671826 DOI: 10.1002/jcb.30318] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/28/2022] [Accepted: 08/01/2022] [Indexed: 01/09/2023]
Abstract
Understanding the mechanisms responsible for the kidney's defense against ascending uropathogen is critical to devise novel treatment strategies against increasingly antibiotic resistant uropathogen. Growing body of evidence indicate Intercalated cells of the kidney as the key innate immune epithelial cells against uropathogen. The aim of this study was to find orthologous and differentially expressed bacterial defense genes in human versus murine intercalated cells. We simultaneously analyzed 84 antibacterial genes in intercalated cells enriched from mouse and human kidney samples. Intercalated cell "reporter mice" were exposed to saline versus uropathogenic Escherichia coli (UPEC) transurethrally for 1 h in vivo, and intercalated cells were flow sorted. Human kidney intercalated cells were enriched from kidney biopsy using magnetic-activated cell sorting and exposed to UPEC in vitro for 1 h. RT2 antibacterial PCR array was performed. Mitogen-activated protein kinase kinase kinase 7 (MAP3K7) messenger RNA (mRNA) expression increased in intercalated cells of both humans and mice following UPEC exposure. Intercalated cell MAP3K7 protein expression was defined by immunofluorescence and confocal imaging analysis, was consistent with the increased MAP3K7 mRNA expression profiles defined by PCR. The presence of the orthologous innate immune gene MAP3K7/TAK1 suggests that it may be a key regulator of the intercalated cell antibacterial response and demands further investigation of its role in urinary tract infection pathogenesis.
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Affiliation(s)
- Vijay Saxena
- Department of Pediatric NephrologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Samuel Arregui
- Department of Pediatric NephrologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Malgorzata Maria Kamocka
- Department of Medicine, Division of NephrologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - David S. Hains
- Department of Pediatric NephrologyIndiana University School of MedicineIndianapolisIndianaUSA,Department of Pediatrics, Division of NephrologyRiley Hospital for ChildrenIndianapolisIndianaUSA
| | - Andrew Schwaderer
- Department of Pediatric NephrologyIndiana University School of MedicineIndianapolisIndianaUSA,Department of Pediatrics, Division of NephrologyRiley Hospital for ChildrenIndianapolisIndianaUSA
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13
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Canas JJ, Liang D, Saxena V, Hooks J, Arregui SW, Gao H, Liu Y, Kish D, Linn SC, Bdeir K, Cines DB, Fairchild RL, Spencer JD, Schwaderer AL, Hains DS. Human neutrophil peptides 1-3 protect the murine urinary tract from uropathogenic Escherichia coli challenge. Proc Natl Acad Sci U S A 2022; 119:e2206515119. [PMID: 36161923 DOI: 10.1073/pnas.2206515119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antimicrobial peptides (AMPs) are critical to the protection of the urinary tract of humans and other animals from pathogenic microbial invasion. AMPs rapidly destroy pathogens by disrupting microbial membranes and/or augmenting or inhibiting the host immune system through a variety of signaling pathways. We have previously demonstrated that alpha-defensins 1-3 (DEFA1A3) are AMPs expressed in the epithelial cells of the human kidney collecting duct in response to uropathogens. We also demonstrated that DNA copy number variations in the DEFA1A3 locus are associated with UTI and pyelonephritis risk. Because DEFA1A3 is not expressed in mice, we utilized human DEFA1A3 gene transgenic mice (DEFA4/4) to further elucidate the biological relevance of this locus in the murine urinary tract. We demonstrate that the kidney transcriptional and translational expression pattern is similar in humans and the human gene transgenic mouse upon uropathogenic Escherichia coli (UPEC) stimulus in vitro and in vivo. We also demonstrate transgenic human DEFA4/4 gene mice are protected from UTI and pyelonephritis under various UPEC challenges. This study serves as the foundation to start the exploration of manipulating the DEFA1A3 locus and alpha-defensins 1-3 expression as a potential therapeutic target for UTIs and other infectious diseases.
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14
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Arndt P, Sradnick J, Kroeger H, Holtzhausen S, Kessel F, Gerlach M, Todorov V, Hugo C. A quantitative 3D intravital look at the juxtaglomerular renin-cell-niche reveals an individual intra/extraglomerular feedback system. Front Physiol 2022; 13:980787. [PMID: 36237522 PMCID: PMC9550881 DOI: 10.3389/fphys.2022.980787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
The juxtaglomerular niche occupied by renin cells (RCN) plays an important role in glomerular repair but the precise temporal and spatial interrelations remain unclear. This study proposes the hypothesis of a local intra-extraglomerular regenerative feedback system and establishes a new quantifiable system for RCN responses in individual glomeruli in vivo. A strictly intraglomerular two-photon laser-induced injury model was established. Labeled renin cells (RC) in transgenic renin reporter mice were fate-traced in healthy and injured glomeruli over several days by intravital microscopy and quantified via new three-dimensional image processing algorithms based on ray tracing. RC in healthy glomeruli demonstrated dynamic extraglomerular protrusions. Upon intraglomerular injury the corresponding RCN first increased in volume and then increased in area of dynamic migration up to threefold compared to their RCN. RC started migration reaching the site of injury within 3 hours and acquired a mesangial cell phenotype without losing physical RCN-contact. During intraglomerular repair only the corresponding RCN responded via stimulated neogenesis, a process of de novo differentiation of RC to replenish the RCN. Repeated continuous intravital microscopy provides a state-of-the-art tool to prove and further study the local intraglomerular RCN repair feedback system in individual glomeruli in vivo in a quantifiable manner.
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Affiliation(s)
- Patrick Arndt
- Experimental Nephrology, Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Jan Sradnick
- Experimental Nephrology, Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Hannah Kroeger
- Experimental Nephrology, Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Stefan Holtzhausen
- Institute of Machine Elements and Machine Design, Chair of Virtual Product Development, Dresden University of Technology, Dresden, Germany
| | - Friederike Kessel
- Experimental Nephrology, Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Michael Gerlach
- Core Facility Cellular Imaging, Experimental Center, Faculty of Medicine Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Vladimir Todorov
- Experimental Nephrology, Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Christian Hugo
- Experimental Nephrology, Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
- *Correspondence: Christian Hugo,
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15
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Purkerson JM, Everett CA, Schwartz GJ. Ammonium chloride-induced acidosis exacerbates cystitis and pyelonephritis caused by uropathogenic E. coli. Physiol Rep 2022; 10:e15471. [PMID: 36151614 PMCID: PMC9508385 DOI: 10.14814/phy2.15471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023] Open
Abstract
Acute pyelonephritis caused by uropathogenic E. coli (UPEC) can cause renal scarring and lead to development of chronic kidney disease. Prevention of kidney injury requires an understanding of host factors and/or UPEC adaptive responses that are permissive for UPEC colonization of the urinary tract. Although some studies have suggested urine acidification limits UPEC growth in culture, other studies have described acid-resistance mechanisms (AR) in E. coli such as the CadC/CadBA module that promotes adaptation to acid and nitrosative stress. Herein we confirm and extend our previous study by demonstrating that despite urine acidification, metabolic acidosis induced by dietary ammonium chloride (NH4 Cl-A) exacerbates cystitis and pyelonephritis in innate immune competent (C3H-HeN) mice characterized by: (1) markedly elevated UPEC burden and increased chemokine/cytokine and NOS2 mRNA expression, (2) accumulation of intravesicular debris noninvasively detected by Power Doppler Ultrasound (PDUS), and (3) collecting duct (CD) dysfunction that manifests as a urine concentration defect. Bladder debris and CD dysfunction were due to the inflammatory response, as neither was observed in Tlr4-deficient (C3H-HeJ) mice. The effect of NH4 Cl-A was unrelated to acidosis as dietary administration of hydrochloric acid (HCl-A) yielded a comparable acid-base status yet did not increase UPEC burden. NH4 Cl-A increased polyamines and decreased nitric oxide (NO) metabolites in urine indicating that excess dietary ammonium shifts arginine metabolism toward polyamines at the expense of NO synthesis. Furthermore, despite increased expression of NOS2, NO production post UPEC infection was attenuated in NH4 Cl-A mice compared to controls. Thus, in addition to induction of metabolic acidosis and urine acidification, excess dietary ammonium alters the polyamine:NO balance and thereby compromises NOS2-mediated innate immune defense.
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Affiliation(s)
- Jeffrey M. Purkerson
- Pediatric NephrologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
- Strong Children's Research CenterUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - Coralee A. Everett
- Pediatric NephrologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
- Strong Children's Research CenterUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - George J. Schwartz
- Pediatric NephrologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
- Strong Children's Research CenterUniversity of Rochester Medical CenterRochesterNew YorkUSA
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16
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Huang B, Zhang X, Cao Q, Chen J, Lin C, Xiang T, Zeng P. Construction and validation of a prognostic risk model for breast cancer based on protein expression. BMC Med Genomics 2022; 15:148. [PMID: 35787690 PMCID: PMC9252042 DOI: 10.1186/s12920-022-01299-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/23/2022] [Indexed: 11/17/2022] Open
Abstract
Breast cancer (BRCA) is the primary cause of mortality among females globally. The combination of advanced genomic analysis with proteomics characterization to construct a protein prognostic model will help to screen effective biomarkers and find new therapeutic directions. This study obtained proteomics data from The Cancer Proteome Atlas (TCPA) dataset and clinical data from The Cancer Genome Atlas (TCGA) dataset. Kaplan–Meier and Cox regression analyses were used to construct a prognostic risk model, which was consisted of 6 proteins (CASPASE7CLEAVEDD198, NFKBP65-pS536, PCADHERIN, P27, X4EBP1-pT70, and EIF4G). Based on risk curves, survival curves, receiver operating characteristic curves, and independent prognostic analysis, the protein prognostic model could be viewed as an independent factor to accurately predict the survival time of BRCA patients. We further validated that this prognostic model had good predictive performance in the GSE88770 dataset. The expression of 6 proteins was significantly associated with the overall survival of BRCA patients. The 6 proteins and encoding genes were differentially expressed in normal and primary tumor tissues and in different BRCA stages. In addition, we verified the expression of 3 differential proteins by immunohistochemistry and found that CDH3 and EIF4G1 were significantly higher in breast cancer tissues. Functional enrichment analysis indicated that the 6 genes were mainly related to the HIF-1 signaling pathway and the PI3K-AKT signaling pathway. This study suggested that the prognosis-related proteins might serve as new biomarkers for BRCA diagnosis, and that the risk model could be used to predict the prognosis of BRCA patients.
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Affiliation(s)
- Bo Huang
- Department of Gynecology and Obstetrics, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xujun Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qingyi Cao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianing Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chenhong Lin
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tianxin Xiang
- Department of Hospital Infection Control, The First Affiliated Hospital of Nanchang University, 17 Yongwai Road, Donghu District, Nanchang, China
| | - Ping Zeng
- Department of Hospital Infection Control, The First Affiliated Hospital of Nanchang University, 17 Yongwai Road, Donghu District, Nanchang, China.
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17
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Hansen J, Sealfon R, Menon R, Eadon MT, Lake BB, Steck B, Anjani K, Parikh S, Sigdel TK, Zhang G, Velickovic D, Barwinska D, Alexandrov T, Dobi D, Rashmi P, Otto EA, Rivera M, Rose MP, Anderton CR, Shapiro JP, Pamreddy A, Winfree S, Xiong Y, He Y, de Boer IH, Hodgin JB, Barisoni L, Naik AS, Sharma K, Sarwal MM, Zhang K, Himmelfarb J, Rovin B, El-Achkar TM, Laszik Z, He JC, Dagher PC, Valerius MT, Jain S, Satlin LM, Troyanskaya OG, Kretzler M, Iyengar R, Azeloglu EU. A reference tissue atlas for the human kidney. Sci Adv 2022; 8:eabn4965. [PMID: 35675394 PMCID: PMC9176741 DOI: 10.1126/sciadv.abn4965] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/20/2022] [Indexed: 05/08/2023]
Abstract
Kidney Precision Medicine Project (KPMP) is building a spatially specified human kidney tissue atlas in health and disease with single-cell resolution. Here, we describe the construction of an integrated reference map of cells, pathways, and genes using unaffected regions of nephrectomy tissues and undiseased human biopsies from 56 adult subjects. We use single-cell/nucleus transcriptomics, subsegmental laser microdissection transcriptomics and proteomics, near-single-cell proteomics, 3D and CODEX imaging, and spatial metabolomics to hierarchically identify genes, pathways, and cells. Integrated data from these different technologies coherently identify cell types/subtypes within different nephron segments and the interstitium. These profiles describe cell-level functional organization of the kidney following its physiological functions and link cell subtypes to genes, proteins, metabolites, and pathways. They further show that messenger RNA levels along the nephron are congruent with the subsegmental physiological activity. This reference atlas provides a framework for the classification of kidney disease when multiple molecular mechanisms underlie convergent clinical phenotypes.
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Affiliation(s)
- Jens Hansen
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rachel Sealfon
- Princeton University, Princeton, NJ, USA
- Flatiron Institute, New York, NY, USA
| | - Rajasree Menon
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | | | - Blue B. Lake
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Becky Steck
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Kavya Anjani
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Samir Parikh
- Ohio State University College of Medicine, Columbus, OH, USA
| | - Tara K. Sigdel
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Guanshi Zhang
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
| | | | - Daria Barwinska
- Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Dejan Dobi
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Priyanka Rashmi
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Edgar A. Otto
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Miguel Rivera
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Michael P. Rose
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Christopher R. Anderton
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - John P. Shapiro
- Ohio State University College of Medicine, Columbus, OH, USA
| | - Annapurna Pamreddy
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
| | - Seth Winfree
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yuguang Xiong
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yongqun He
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Ian H. de Boer
- Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA
| | | | | | - Abhijit S. Naik
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Kumar Sharma
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
| | - Minnie M. Sarwal
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jonathan Himmelfarb
- Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA
| | - Brad Rovin
- Ohio State University College of Medicine, Columbus, OH, USA
| | | | - Zoltan Laszik
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | | | | | - M. Todd Valerius
- Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Sanjay Jain
- Washington University in Saint Louis School of Medicine, St. Louis, MS, USA
| | - Lisa M. Satlin
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olga G. Troyanskaya
- Princeton University, Princeton, NJ, USA
- Flatiron Institute, New York, NY, USA
| | | | - Ravi Iyengar
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Kidney Precision Medicine Project
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Princeton University, Princeton, NJ, USA
- Flatiron Institute, New York, NY, USA
- University of Michigan School of Medicine, Ann Arbor, MI, USA
- Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- University of California San Francisco School of Medicine, San Francisco, CA, USA
- Ohio State University College of Medicine, Columbus, OH, USA
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
- Pacific Northwest National Laboratory, Richland, WA, USA
- European Molecular Biology Laboratory, Heidelberg, Germany
- Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA
- Duke University School of Medicine, Durham, NC, USA
- Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA, USA
- Washington University in Saint Louis School of Medicine, St. Louis, MS, USA
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18
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Abstract
The field of single-cell genomics and spatial technologies is rapidly evolving and has already provided unprecedented insights into complex tissues. Major advances have been made in dissecting the cellular composition and spatiotemporal interactions that mediate developmental processes in the fetal kidney. Single-cell technologies have also provided detailed insights into the heterogeneity of cell types within the healthy adult and shed light on the complex cellular mechanisms that contribute to kidney disease. The in-depth characterization of specific cell types associated with acute kidney injury and glomerular diseases has potential for the development of prognostic biomarkers and new therapeutics. Analyses of pathway activity in clear-cell renal cell carcinoma can predict the sensitivity of tumour cells to specific inhibitors. The identification of the cell of origin of renal cell carcinoma and of new cell types within the tumour microenvironment also has implications for the development of targeted therapeutics. Similarly, single-cell sequencing has provided new insights into the mechanisms underlying kidney fibrosis, specifically our understanding of myofibroblast origins and the contribution of cell crosstalk within the fibrotic niche to disease progression. These and future studies will enable the creation of a map to aid our understanding of the cellular processes and interactions in the developing, healthy and diseased kidney.
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19
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Breton S, Battistone MA. Unexpected Participation of Intercalated Cells in Renal Inflammation and Acute Kidney Injury. Nephron Clin Pract 2022; 146:268-273. [PMID: 34657041 PMCID: PMC9010481 DOI: 10.1159/000519265] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/17/2021] [Indexed: 01/03/2023] Open
Abstract
Epithelial cells constitute the 1st line of defense against pathogens, and their participation in innate immunity is rapidly emerging. In this mini-review, we discuss the noncanonical role of renal intercalated cells (ICs) in pathogen defense and in the initiation of sterile inflammation. This last function has strong implications in the onset of acute kidney injury (AKI), a potentially fatal medical complication that is seen in hospitalized patients. AKI is associated with inflammation, and it is often diagnosed only after the kidneys have suffered significant and often irreversible damage. While examining the regulation of proton secretion by type A ICs (A-ICs), we unexpectedly found high expression of the pro-inflammatory purinergic receptor P2Y14 in these cells. This receptor is located on the apical surface of A-ICs and binds UDP-glucose (UDP-Glc), a danger-associated molecular pattern molecule released from injured cells that is filtered by the glomeruli and is concentrated in the collecting duct lumen. UDP-Glc activates P2Y14 in A-ICs and triggers the production of chemokines that attract pro-inflammatory immune cells into the kidney stroma and aggravate ischemia-induced proximal tubule injury. Inhibition of P2Y14 or deletion of its gene specifically in ICs in a murine model of ischemia-reperfusion injury attenuated these effects. Thus, together with their previously recognized role in pathogen defense, A-ICs are now recognized as sensors and mediators of renal sterile inflammation that participate in the onset of AKI. Blocking the UDP-Glc/P2Y14 pathway in A-ICs provides new insights into the development of novel AKI therapeutics.
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Affiliation(s)
- Sylvie Breton
- Research Center, Centre Hospitalier Universitaire de
Québec, Université Laval, Québec, Québec, Canada, G1V
4G2
| | - Maria Agustina Battistone
- Program in Membrane Biology/Nephrology Division,
Massachusetts General Hospital, Boston, MA 02114 and Harvard Medical School, Boston,
MA 02115, USA
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20
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Abstract
The connecting tubule (CNT) is a unique segment of the nephron connecting the metanephric mesenchyme (MM)-derived distal convoluted tubule (DCT) and ureteric bud (UB)-derived collecting duct (CD). Views on the cellular origin of the CNT in the human kidney are controversial. It was suggested that in mice, the connecting segment arises from the distal compartment of the renal vesicle (RV). However, there are several differences in embryonic development between the mouse and human kidney. The aim of our study was to establish the possible origin of the CNT in the human kidney. We analysed the expression of markers defining distinct cells of the CNT CD in foetal and adult human kidneys by immunohistochemistry. Based on microscopic observation, we suggest that CNT differentiates from the outgrowth of cells of the UB tip, and therefore the CNT is an integral part of the CD system. In the adult kidney, the CNT and CD consist of functionally and morphologically similar cells expressing α- and β-intercalated cell (IC) and principal cell (PC) markers, indicating their common origin.
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Affiliation(s)
- Beatrix Sarkany
- Department of Urology, Medical School, University of Pecs, Pecs, 7621, Hungary
| | - Gyula Kovacs
- Department of Urology, Medical School, University of Pecs, Pecs, 7621, Hungary.
- Medical Faculty, Ruprecht-Karls-University, 69120, Heidelberg, Germany.
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21
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Allison S. Phagocytic properties of intercalated cells. Nat Rev Nephrol 2021; 17:437. [PMID: 33990793 DOI: 10.1038/s41581-021-00441-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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