scholarly journals Spatial Transcriptional Mapping of the Human Nephrogenic Program

2020 ◽  
Author(s):  
Nils O. Lindström ◽  
Rachel Sealfon ◽  
Xi Chen ◽  
Riana Parvez ◽  
Andrew Ransick ◽  
...  
Keyword(s):  
Gene Networks ◽  
Kidney Development ◽  
Three Dimensional ◽  
Human Kidney ◽  
Cell Types ◽  
Disease Genes ◽  
Network Mining ◽  
Spatially Resolved ◽  
Nephron Progenitors ◽  
Nephron Progenitor

SummaryCongenital abnormalities of the kidney and urinary tract are amongst the most common birth defects affecting 3% of newborns. The human kidney develops over a 30-week period in which a nephron progenitor pool gives rise to around a million nephrons. To establish a framework for human nephrogenesis, we spatially resolved a stereotypical process by which equipotent nephron progenitors generate a nephron anlagen, then applied data-driven approaches to construct three-dimensional protein maps on anatomical models of the nephrogenic program. Single cell RNA sequencing identified novel progenitor states which were spatially mapped to the nephron anatomy enabling the generation of functional gene-networks predicting interactions within and between nephron cell-types. Network mining identified known developmental disease genes and predicts new targets of interest. The spatially resolved nephrogenic program made available through the Human Nephrogenesis Atlas (https://sckidney.flatironinstitute.org/) will facilitate an understanding of kidney development and disease, and enhance efforts to generate new kidney structures.

scholarly journals Notch Signaling in Kidney Development, Maintenance, and Disease

Biomolecules ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 692 ◽  
Author(s):  
Malini Mukherjee ◽  
Eric Fogarty ◽  
Madhusudhana Janga ◽  
Kameswaran Surendran
Keyword(s):  
Epithelial Cell ◽  
Notch Signaling ◽  
Kidney Development ◽  
Kidney Diseases ◽  
Human Kidney ◽  
Cell Types ◽  
Multiple Roles ◽  
Collecting Ducts ◽  
Kidney Epithelial Cell ◽  
Nephron Progenitor

Kidney development involves formation of nephrons intricately aligned with the vasculature and connected to a branched network of collecting ducts. Notch signaling plays multiple roles during kidney development involving the formation of nephrons composed of diverse epithelial cell types arranged into tubular segments, all the while maintaining a nephron progenitor niche. Here, we review the roles of Notch signaling identified from rodent kidney development and injury studies, while discussing human kidney diseases associated with aberrant Notch signaling. We also review Notch signaling requirement in maintenance of mature kidney epithelial cell states and speculate that Notch activity regulation mediates certain renal physiologic adaptations.

scholarly journals Small non-coding RNA expression in developing mouse nephron progenitor cells

2018 ◽  
Author(s):  
Yu Leng Phua ◽  
Andrew Clugston ◽  
Kevin Hong Chen ◽  
Dennis Kostka ◽  
Jacqueline Ho
Keyword(s):  
Molecular Mechanisms ◽  
Kidney Development ◽  
Regulation Of Gene Expression ◽  
Cell Types ◽  
Mirna Expression Profile ◽  
Public Resource ◽  
Nephron Progenitors ◽  
Non Coding Rna ◽  
Health And Disease ◽  
Nephron Progenitor

AbstractMicroRNAs (miRNAs) are small non-coding RNAs that are essential for the regulation of gene expression and play critical roles in human health and disease. Here we present comprehensive miRNA profiling data for mouse nephron progenitors, which give rise to most of the cell-types of the nephron, the functional units of the kidney. We describe a miRNA expression profile for nephron progenitors, with 162 miRNAs differentially expressed in nephron progenitors when compared to whole kidney. We also annotated 52, and experimentally validated 4 novel miRNAs, which are expressed in developing kidney. Our data is available as a public resource, so that it can be integrated into future studies and analyzed in the context of other functional and epigenomic data in kidney development. Specifically, it will be useful in the effort to shed light on molecular mechanisms underlying processes essential for normal kidney development, such as nephron progenitor specification, self-renewal and differentiation.

scholarly journals Single-cell RNA sequencing reveals differential cell cycle activity in key cell populations during nephrogenesis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Abha S. Bais ◽  
Débora M. Cerqueira ◽  
Andrew Clugston ◽  
Andrew J. Bodnar ◽  
Jacqueline Ho ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Single Cell ◽  
Molecular Mechanisms ◽  
Kidney Development ◽  
Collecting Duct ◽  
Cell Types ◽  
Nephron Progenitors ◽  
Developing Kidney ◽  
Distal Tubules ◽  
Cycle Regulation

AbstractThe kidney is a complex organ composed of more than 30 terminally differentiated cell types that all are required to perform its numerous homeostatic functions. Defects in kidney development are a significant cause of chronic kidney disease in children, which can lead to kidney failure that can only be treated by transplant or dialysis. A better understanding of molecular mechanisms that drive kidney development is important for designing strategies to enhance renal repair and regeneration. In this study, we profiled gene expression in the developing mouse kidney at embryonic day 14.5 at single-cell resolution. Consistent with previous studies, clusters with distinct transcriptional signatures clearly identify major compartments and cell types of the developing kidney. Cell cycle activity distinguishes between the “primed” and “self-renewing” sub-populations of nephron progenitors, with increased expression of the cell cycle-related genes Birc5, Cdca3, Smc2 and Smc4 in “primed” nephron progenitors. In addition, augmented expression of cell cycle related genes Birc5, Cks2, Ccnb1, Ccnd1 and Tuba1a/b was detected in immature distal tubules, suggesting cell cycle regulation may be required for early events of nephron patterning and tubular fusion between the distal nephron and collecting duct epithelia.

scholarly journals Spatial and single-cell transcriptional landscape of human cerebellar development

2020 ◽  
Author(s):  
Kimberly A. Aldinger ◽  
Zach Thomson ◽  
Parthiv Haldipur ◽  
Mei Deng ◽  
Andrew E. Timms ◽  
...  
Keyword(s):  
Single Cell ◽  
Emotional Regulation ◽  
Cell Types ◽  
Molecular Organization ◽  
Cerebellar Development ◽  
Disease Genes ◽  
Spatially Resolved ◽  
Human Cerebellum ◽  
Spatial Composition ◽  
And Function

ABSTRACTCerebellar development and function require precise regulation of molecular and cellular programs to coordinate motor functions and integrate network signals required for cognition and emotional regulation. However, molecular understanding of human cerebellar development is limited. Here, we combined spatially resolved and single-cell transcriptomics to systematically map the molecular, cellular, and spatial composition of early and mid-gestational human cerebellum. This enabled us to transcriptionally profile major cell types and examine the dynamics of gene expression within cell types and lineages across development. The resulting ‘Developmental Cell Atlas of the Human Cerebellum’ demonstrates that the molecular organization of the cerebellar anlage reflects cytoarchitecturally distinct regions and developmentally transient cell types that are insufficiently captured in bulk transcriptional profiles. By mapping disease genes onto cell types, we implicate the dysregulation of specific cerebellar cell types, especially Purkinje cells, in pediatric and adult neurological disorders. These data provide a critical resource for understanding human cerebellar development with implications for the cellular basis of cerebellar diseases.

scholarly journals Von Hippel-Lindau Acts as a Metabolic Switch Controlling Nephron Progenitor Differentiation

2019 ◽  
Vol 30 (7) ◽  
pp. 1192-1205 ◽  
Author(s):  
Kasey Cargill ◽  
Shelby L. Hemker ◽  
Andrew Clugston ◽  
Anjana Murali ◽  
Elina Mukherjee ◽  
...  
Keyword(s):  
Mitochondrial Respiration ◽  
Metabolic Regulation ◽  
Kidney Development ◽  
Developmentally Delayed ◽  
Metabolic Switch ◽  
Von Hippel Lindau ◽  
Conditional Deletion ◽  
Nephron Progenitors ◽  
Ubiquitin Ligase Complex ◽  
Nephron Progenitor

BackgroundNephron progenitors, the cell population that give rise to the functional unit of the kidney, are metabolically active and self-renew under glycolytic conditions. A switch from glycolysis to mitochondrial respiration drives these cells toward differentiation, but the mechanisms that control this switch are poorly defined. Studies have demonstrated that kidney formation is highly dependent on oxygen concentration, which is largely regulated by von Hippel-Lindau (VHL; a protein component of a ubiquitin ligase complex) and hypoxia-inducible factors (a family of transcription factors activated by hypoxia).MethodsTo explore VHL as a regulator defining nephron progenitor self-renewal versus differentiation, we bred Six2-TGCtg mice with VHLlox/lox mice to generate mice with a conditional deletion of VHL from Six2+ nephron progenitors. We used histologic, immunofluorescence, RNA sequencing, and metabolic assays to characterize kidneys from these mice and controls during development and up to postnatal day 21.ResultsBy embryonic day 15.5, kidneys of nephron progenitor cell–specific VHL knockout mice begin to exhibit reduced maturation of nephron progenitors. Compared with controls, VHL knockout kidneys are smaller and developmentally delayed by postnatal day 1, and have about half the number of glomeruli at postnatal day 21. VHL knockout nephron progenitors also exhibit persistent Six2 and Wt1 expression, as well as decreased mitochondrial respiration and prolonged reliance on glycolysis.ConclusionsOur findings identify a novel role for VHL in mediating nephron progenitor differentiation through metabolic regulation, and suggest that VHL is required for normal kidney development.

scholarly journals Wnt/β-catenin signaling is required for the development of multiple nephron segments

2018 ◽  
Author(s):  
Patrick Deacon ◽  
Charles W Concodora ◽  
Eunah Chung ◽  
Joo-Seop Park
Keyword(s):  
Kidney Development ◽  
Critical Role ◽  
Proximal Tubules ◽  
Loss Of Function ◽  
Constitutive Activation ◽  
Nephron Segments ◽  
Mesenchymal To Epithelial Transition ◽  
Nephron Progenitors ◽  
Distal Tubules ◽  
Nephron Progenitor

The nephron is composed of distinct segments that perform unique physiological functions to generate urine. Little is known about how multipotent nephron progenitor cells differentiate into different nephron segments. It is well known that Wnt/β-catenin signaling regulates the maintenance and commitment of mesenchymal nephron progenitors during kidney development. However, it is not fully understood how it regulates nephron patterning after nephron progenitors undergo mesenchymal-to-epithelial transition. To address this, we performed β-catenin loss-of-function and gain-of-function studies in epithelial nephron progenitors in the mouse kidney. Consistent with a previous report, the formation of the renal corpuscle was defective in the absence of β-catenin. Interestingly, we found that epithelial nephron progenitors lacking β-catenin were able to form presumptive proximal tubules but that they failed to further develop into differentiated proximal tubules, suggesting that Wnt/β-catenin signaling plays a critical role in proximal tubule development. We also found that epithelial nephron progenitors lacking β-catenin failed to form the distal tubules. Constitutive activation of Wnt/β-catenin signaling blocked the proper formation of all nephron segments, suggesting tight regulation of Wnt/β-catenin signaling during nephron patterning. This work shows that Wnt/β-catenin signaling regulates the patterning of multiple nephron segments along the proximo-distal axis of the mammalian nephron.

Chromatin Remodelers Interact with Eya1 and Six2 to Target Enhancers to Control Nephron Progenitor Cell Maintenance

2021 ◽  
Vol 32 (11) ◽  
pp. 2815-2833
Author(s):  
Jun Li ◽  
Jinshu Xu ◽  
Huihui Jiang ◽  
Ting Zhang ◽  
Aarthi Ramakrishnan ◽  
...  
Keyword(s):  
Progenitor Cell ◽  
Kidney Development ◽  
Regulatory Elements ◽  
Proximal Promoter ◽  
Specific Expression ◽  
Self Renewal ◽  
Content Type ◽  
Nephron Progenitors ◽  
Genome Wide ◽  
Nephron Progenitor

BackgroundEya1 is a critical regulator of nephron progenitor cell specification and interacts with Six2 to promote NPC self-renewal. Haploinsufficiency of these genes causes kidney hypoplasia. However, how the Eya1-centered network operates remains unknown.MethodsWe engineered a 2×HA-3×Flag-Eya1 knock-in mouse line and performed coimmunoprecipitation with anti-HA or -Flag to precipitate the multitagged-Eya1 and its associated proteins. Loss-of-function, transcriptome profiling, and genome-wide binding analyses for Eya1's interacting chromatin-remodeling ATPase Brg1 were carried out. We assayed the activity of the cis-regulatory elements co-occupied by Brg1/Six2 in vivo.ResultsEya1 and Six2 interact with the Brg1-based SWI/SNF complex during kidney development. Knockout of Brg1 results in failure of metanephric mesenchyme formation and depletion of nephron progenitors, which has been linked to loss of Eya1 expression. Transcriptional profiling shows conspicuous downregulation of important regulators for nephrogenesis in Brg1-deficient cells, including Lin28, Pbx1, and Dchs1-Fat4 signaling, but upregulation of podocyte lineage, oncogenic, and cell death–inducing genes, many of which Brg1 targets. Genome-wide binding analysis identifies Brg1 occupancy to a distal enhancer of Eya1 that drives nephron progenitor–specific expression. We demonstrate that Brg1 enrichment to two distal intronic enhancers of Pbx1 and a proximal promoter region of Mycn requires Six2 activity and that these Brg1/Six2-bound enhancers govern nephron progenitor–specific expression in response to Six2 activity.ConclusionsOur results reveal an essential role for Brg1, its downstream pathways, and its interaction with Eya1-Six2 in mediating the fine balance among the self-renewal, differentiation, and survival of nephron progenitors.

scholarly journals Single cell RNA sequencing reveals differential cell cycle activity in key cell populations during nephrogenesis

2020 ◽  
Author(s):  
Abha S. Bais ◽  
Débora M. Cerqueira ◽  
Andrew Clugston ◽  
Jacqueline Ho ◽  
Dennis Kostka
Keyword(s):  
Cell Cycle ◽  
Single Cell ◽  
Molecular Mechanisms ◽  
Kidney Development ◽  
Collecting Duct ◽  
Cell Types ◽  
Ureteric Bud ◽  
Nephron Progenitors ◽  
Developing Kidney ◽  
Distal Tubules

ABSTRACTThe kidney is a complex organ composed of more than 30 terminally differentiated cell types that all are required to perform its numerous homeostatic functions. Defects in kidney development are a significant cause of chronic kidney disease in children, which can lead to kidney failure that can only be treated by transplant or dialysis. A better understanding of molecular mechanisms that drive kidney development is important for designing strategies to enhance renal repair and regeneration. In this study, we profiled gene expression in the developing mouse kidney at embryonic day 14.5 at single cell resolution. Consistent with previous studies, clusters with distinct transcriptional signatures clearly identify major compartments and cell types of the developing kidney. Cell cycle activity distinguishes between the “primed” and “self-renewing” sub-populations of nephron progenitors, with increased expression of the cell cycle related genes Birc5, Cdca3, Smc2 and Smc4 in “primed” nephron progenitors. Augmented Birc5 expression was also detected in immature distal tubules and a sub-set of ureteric bud cells, suggesting that Birc5 might be a novel key molecule required for early events of nephron patterning and tubular fusion between the distal nephron and the collecting duct epithelia.

scholarly journals Spatially mapped single-cell chromatin accessibility

2019 ◽  
Author(s):  
Casey A. Thornton ◽  
Ryan M. Mulqueen ◽  
Andrew Nishida ◽  
Kristof A. Torkenczy ◽  
Eve G. Lowenstein ◽  
...  
Keyword(s):  
Single Cell ◽  
Spatial Information ◽  
Three Dimensional ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Artery Occlusion ◽  
Cell Type ◽  
Cell Type Specificity ◽  
Spatially Resolved ◽  
Typical Experiment

AbstractHigh-throughput single-cell epigenomic assays can resolve the heterogeneity of cell types and states in complex tissues, however, spatial orientation within the network of interconnected cells is lost. Here, we present a novel method for highly scalable, spatially resolved, single-cell profiling of chromatin states. We use high-density multiregional sampling to perform single-cell combinatorial indexing on Microbiopsies Assigned to Positions for the Assay for Transposase Accessible Chromatin (sciMAP-ATAC) to produce single-cell data of an equivalent quality to non-spatially resolved single-cell ATAC-seq, where each cell is localized to a three-dimensional position within the tissue. A typical experiment comprises between 96 and 384 spatially mapped tissue positions, each producing 10s to over 100 individual single-cell ATAC-seq profiles, and a typical resolution of 214 cubic microns; with the ability to tune the resolution and cell throughput to suit each target application. We apply sciMAP-ATAC to the adult mouse primary somatosensory cortex, where we profile cortical lamination and demonstrate the ability to analyze data from a single tissue position or compare a single cell type in adjacent positions. We also profile the human primary visual cortex, where we produce spatial trajectories through the cortex. Finally, we characterize the spatially progressive nature of cerebral ischemic infarct in the mouse brain using a model of transient middle cerebral artery occlusion. We leverage the spatial information to identify novel and known transcription factor activities that vary by proximity to the ischemic infarction core with cell type specificity.

scholarly journals Premature differentiation of nephron progenitors and dysregulation of gene pathways critical to kidney development in a model of preterm birth

2021 ◽  
Author(s):  
Aleksandra Cwiek ◽  
Masako Suzuki ◽  
Kimberly deRonde ◽  
Mark Conaway ◽  
Kevin Bennett ◽  
...  
Keyword(s):  
Preterm Birth ◽  
Progenitor Cells ◽  
Kidney Development ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Neonatal Morbidity ◽  
Expression Of Genes ◽  
Nephron Progenitors ◽  
Nephron Progenitor ◽  
Lower Expression

Abstract Preterm birth is a leading cause of neonatal morbidity. Survivors have a greater risk for kidney dysfunction and hypertension. Little is known about the molecular changes that occur in the kidney of individuals born preterm. Here, we demonstrate that mice delivered two days prior to full term gestation undergo premature cessation of nephrogenesis, resulting in a lower glomerular density. Kidneys from preterm and term groups exhibited differences in gene expression profiles at 20- and 27-days post-conception, including significant differences in expression of fat-soluble vitamin-related genes. Kidneys of the preterm mice exhibited decreased proportions of endothelial cells and a lower expression of genes promoting angiogenesis compared to the term group. Kidneys from the preterm mice also had altered nephron progenitor subpopulations, early Six2 depletion, and altered Jag1 expression in the nephrogenic zone, consistent with premature differentiation of nephron progenitor cells. In conclusion, preterm birth alone was sufficient to shorten the duration of nephrogenesis and cause premature differentiation of nephron progenitor cells. These candidate genes and pathways may provide targets to improve kidney health in preterm infants.

Sign in / Sign up

Export Citation Format

Share Document