scholarly journals Single cell transcriptomics reveal disrupted kidney filter cell-cell interactions after early and selective podocyte injury

2020 ◽  
Author(s):  
Abbe R. Clark ◽  
Jamie Marshall ◽  
Yiming Zhou ◽  
Monica S. Montesinos ◽  
Haiqi Chen ◽  
...  
Keyword(s):  
Single Cell ◽  
Mesangial Cells ◽  
Kidney Diseases ◽  
Kidney Tissue ◽  
Cell Interactions ◽  
Therapeutic Window ◽  
Podocyte Injury ◽  
Matrix Deposition ◽  
Filtration Barrier ◽  
Cell Cell

The health of the kidney filtration barrier requires communication between podocytes, endothelial cells and mesangial cells. Disruption of these cell-cell interactions is thought to contribute to disease progression in chronic kidney diseases (CKD). We recently demonstrated that podocyte ablation via doxycycline-inducible deletion of an essential endogenous molecule, CTCF (iCTCFpod-/-), is sufficient to drive progressive CKD. However, the earliest events connecting podocyte injury to disrupted intercellular communication within the kidney filter remain unclear. Here we performed single-cell RNA sequencing of kidney tissue from iCTCFpod-/- mice after one week of doxycycline induction to generate a map of the earliest transcriptional effects of podocyte injury on cell-cell interactions at single cell resolution. A subset of podocytes showed the earliest signs of injury due to disrupted gene programs for cytoskeletal regulation and mitochondrial function. Surviving podocytes upregulated Col4a5, causing reactive changes in integrin expression in endothelial populations and mesangial cells. Intercellular interaction analysis revealed several receptor-ligand-target gene programs as drivers of endothelial cell injury and abnormal matrix deposition. This analysis reveals the earliest disruptive changes within the kidney filter, pointing to new, actionable targets within a therapeutic window that may allow us to maximize the success of much needed therapeutic interventions for CKD.

scholarly journals Single cell transcriptomics reveal disrupted kidney filter cell-cell interactions after early and selective podocyte injury

2021 ◽  
Author(s):  
Abbe R. Clark ◽  
Jamie Marshall ◽  
Yiming Zhou ◽  
Monica S. Montesinos ◽  
Haiqi Chen ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Interactions ◽  
Podocyte Injury ◽  
Filter Cell ◽  
Cell Cell

Abstract 3391: Dissecting intratumoral cell-cell interactions in myeloid reprogramming by single cell RNA-seq

2019 ◽  
Author(s):  
Qianqian Song ◽  
Gregory A. Hawkins ◽  
Leonard Wudel ◽  
Ping-Chieh Chou ◽  
Elizabeth Forbes ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Interactions ◽  
Rna Seq ◽  
Cell Cell

scholarly journals Identifying signaling genes in spatial single-cell expression data

2020 ◽  
Author(s):  
Dongshunyi Li ◽  
Jun Ding ◽  
Ziv Bar-Joseph
Keyword(s):  
Single Cell ◽  
Cell Interactions ◽  
Excitatory Neuron ◽  
Expression Data ◽  
Mixture Of Experts ◽  
Prediction Of Response ◽  
Technological Advances ◽  
A Cell ◽  
Cell Expression ◽  
Cell Cell

Abstract Motivation Recent technological advances enable the profiling of spatial single-cell expression data. Such data present a unique opportunity to study cell–cell interactions and the signaling genes that mediate them. However, most current methods for the analysis of these data focus on unsupervised descriptive modeling, making it hard to identify key signaling genes and quantitatively assess their impact. Results We developed a Mixture of Experts for Spatial Signaling genes Identification (MESSI) method to identify active signaling genes within and between cells. The mixture of experts strategy enables MESSI to subdivide cells into subtypes. MESSI relies on multi-task learning using information from neighboring cells to improve the prediction of response genes within a cell. Applying the methods to three spatial single-cell expression datasets, we show that MESSI accurately predicts the levels of response genes, improving upon prior methods and provides useful biological insights about key signaling genes and subtypes of excitatory neuron cells. Availability and implementation MESSI is available at: https://github.com/doraadong/MESSI

WT1-interacting protein and ZO-1 translocate into podocyte nuclei after puromycin aminonucleoside treatment

2005 ◽  
Vol 289 (2) ◽  
pp. F431-F441 ◽  
Author(s):  
Maribel Rico ◽  
Amitava Mukherjee ◽  
Martha Konieczkowski ◽  
Leslie A. Bruggeman ◽  
R. Tyler Miller ◽  
...  
Keyword(s):  
Adherens Junctions ◽  
Slit Diaphragm ◽  
Cell Junctions ◽  
Puromycin Aminonucleoside ◽  
Glomerular Diseases ◽  
Podocyte Injury ◽  
Interacting Protein ◽  
Filtration Barrier ◽  
Cell Cell

Podocyte differentiation is required for normal glomerular filtration barrier function and is regulated by the transcription factor WT1. We identified WT1-interacting protein (WTIP) and hypothesized that it functions as both a scaffold for slit diaphragm proteins and a corepressor of WT1 transcriptional activity by shuttling from cell-cell junctions to the nucleus after injury. Endogenous WTIP colocalizes with zonula occludens-1 (ZO-1) in cultured mouse podocyte adherens junctions. To model podocyte injury in vitro, we incubated differentiated podocytes with puromycin aminonucleoside (PAN; 100 μg/ml) for 24 h, which disassembled cell-cell contacts, rearranged actin cytoskeleton, and caused process retraction. Podocyte synaptopodin expression diminished after PAN treatment, consistent with podocyte dedifferentiation in some human glomerular diseases. To assess podocyte function, we measured albumin flux across differentiated podocytes cultured on collagen-coated Transwell filters. Albumin transit across PAN-treated cells increased to levels observed with undifferentiated podocytes. Consistent with our hypothesis, WTIP, as well as ZO-1, translocated from podocyte adherens junctions to nuclei in PAN-treated cells. Because WTIP is a transcriptional corepressor for WT1, we examined the effect of PAN on expression of retinoblastoma binding protein Rbbp7 (also known as RbAp46), a WT1 target gene expressed in S-shaped bodies during nephrogenesis. Rbbp7 expression in PAN-treated podocytes was reduced compared with untreated cells. In conclusion, WTIP translocates from cell-cell junctions to the nucleus in PAN-treated podocytes. We suggest that WTIP monitors slit diaphragm protein assembly and shuttles into the nucleus after podocyte injury, translating changes in slit diaphragm structure into altered gene expression and a less differentiated phenotype.

scholarly journals Microporous scaffolds drive assembly and maturation of progenitors into β-cell clusters

2019 ◽  
Author(s):  
Richard L. Youngblood ◽  
Joshua P. Sampson ◽  
Kimberly R. Lebioda ◽  
Graham Spicer ◽  
Lonnie D. Shea
Keyword(s):  
Basement Membrane ◽  
Suspension Cultures ◽  
Cell Interactions ◽  
Cell Maturation ◽  
Β Cells ◽  
Β Cell ◽  
Cell Clusters ◽  
Matrix Deposition ◽  
Cell Cell

AbstractHuman pluripotent stem cells (hPSCs) represent a promising cell source for the development of β-cells for use in therapies for type 1 diabetes. Current culture approaches provide the signals to drive differentiation towards β-cells, with the cells spontaneously assembling into clusters. Herein, we adapted the current culture systems to cells seeded on microporous biomaterials, with the hypothesis that the pores can guide the assembly into β-cell clusters of defined size that can enhance maturation. The microporous scaffold culture allows hPSC-derived pancreatic progenitors to form clusters at a consistent size as cells undergo differentiation to immature β-cells. By modulating the scaffold pore sizes, we observed 250-425 µm pore size scaffolds significantly enhance insulin expression and key β-cell maturation markers compared to suspension cultures. Furthermore, when compared to suspension cultures, the scaffold culture showed increased insulin secretion in response to glucose stimulus indicating the development of functional β-cells. In addition, scaffolds facilitated cell-cell interactions enabled by the scaffold design and cell-mediated matrix deposition of extracellular matrix (ECM) proteins associated with the basement membrane of islet cells. We further investigated the influence of ECM on cell development by incorporating an ECM matrix on the scaffold prior to cell seeding; however, their presence did not further enhance maturation. These results suggest the microporous scaffold culture facilitates 3D cluster formation, supports cell-cell interactions, and provides a matrix similar to a basement membrane to drive in vitro hPSC-derived β-cell maturation and demonstrates the feasibility of these scaffolds as a biomanufacturing platform.

scholarly journals Spatial analysis of ligand-receptor interactions in skin cancer at genome-wide and single-cell resolution

2020 ◽  
Author(s):  
M Tran ◽  
S Yoon ◽  
ST Min ◽  
S Andersen ◽  
K Devitt ◽  
...  
Keyword(s):  
Cell Carcinoma ◽  
Single Cell ◽  
Molecular Mechanisms ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Cell Interactions ◽  
Genome Wide ◽  
Receptor Interactions ◽  
Cell Cell

AbstractThe ability to study cancer-immune cell communication across the whole tumor section without tissue dissociation is important to understand molecular mechanisms of cancer immunotherapy and drug targets. Current experimental methods such as immunohistochemistry allow researchers to investigate a small number of cells or a limited number of ligand-receptor pairs at tissue scale with limited cellular resolution. In this work, we developed a powerful experimental and analytical pipeline that allows for the genome-wide discovery and targeted validation of cellular communication. By profiling thousands of genes, spatial transcriptomic and single-cell RNA sequencing data show genes that are possibly involved in interactions. The expression of the candidate genes could be visualized by single-molecule in situ hybridization and droplet digital PCR. We developed a computational pipeline called STRISH that enables us to quantitatively model cell-cell interactions by automatically scanning for local expression of RNAscope data to recapitulate an interaction landscape across the whole tissue. Furthermore, we showed the strong correlation of microscopic RNAscope imaging data analyzed by STRISH with the gene expression values measured by droplet digital PCR. We validated the unique ability of this approach to discover new cell-cell interactions in situ through analysis of two types of cancer, basal cell carcinoma and squamous cell carcinoma. We expect that the approach described here will help to discover and validate ligand receptor interactions in different biological contexts such as immune-cancer cell interactions within a tumor.

scholarly journals Examining Cell-Cell Interactions in the Kidney Using AFM Single-Cell Force Spectroscopy

2019 ◽  
pp. 189-201 ◽  
Author(s):  
Eleftherios Siamantouras ◽  
Claire E. Hills ◽  
Kuo-Kang Liu ◽  
Paul E. Squires
Keyword(s):  
Single Cell ◽  
Force Spectroscopy ◽  
Cell Interactions ◽  
Cell Force ◽  
Cell Cell

scholarly journals The Updates of Podocyte Lipid Metabolism in Proteinuric Kidney Disease

2021 ◽  
pp. 1-14
Author(s):  
Yu Sun ◽  
Sijia Cui ◽  
Yunfeng Hou ◽  
Fan Yi
Keyword(s):  
Lipid Metabolism ◽  
Kidney Disease ◽  
Lipid Accumulation ◽  
Kidney Diseases ◽  
Early Event ◽  
Podocyte Injury ◽  
Mitochondrial Oxidative Stress ◽  
Filtration Barrier ◽  
Cytoskeleton Remodeling ◽  
And Function

<b><i>Background:</i></b> Podocytes, functionally specialized and terminally differentiated glomerular visceral epithelial cells, are critical for maintaining the structure and function of the glomerular filtration barrier. Podocyte injury is considered as the most important early event contributing to proteinuric kidney diseases such as obesity-related renal disease, diabetic kidney disease, focal segmental glomerulosclerosis, membranous nephropathy, and minimal change disease. Although considerable advances have been made in the understanding of mechanisms that trigger podocyte injury, cell-specific and effective treatments are not clinically available. <b><i>Summary:</i></b> Emerging evidence has indicated that the disorder of podocyte lipid metabolism is closely associated with various proteinuric kidney diseases. Excessive lipid accumulation in podocytes leads to cellular dysfunction which is defined as lipotoxicity, a phenomenon characterized by mitochondrial oxidative stress, actin cytoskeleton remodeling, insulin resistance, and inflammatory response that can eventually result in podocyte hypertrophy, detachment, and death. In this review, we summarize recent advances in the understanding of lipids in podocyte biological function and the regulatory mechanisms leading to podocyte lipid accumulation in proteinuric kidney disease. <b><i>Key Messages:</i></b> Targeting podocyte lipid metabolism may represent a novel therapeutic strategy for patients with proteinuric kidney disease.

scholarly journals Runx2-Twist1 interaction coordinates cranial neural crest guidance of soft palate myogenesis

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Xia Han ◽  
Jifan Feng ◽  
Tingwei Guo ◽  
Yong-Hwee Eddie Loh ◽  
Yuan Yuan ◽  
...  
Keyword(s):  
Neural Crest ◽  
Single Cell ◽  
Soft Palate ◽  
Muscle Development ◽  
Cell Interactions ◽  
Lineage Commitment ◽  
Rna Seq ◽  
Cranial Neural Crest ◽  
Marker Expression ◽  
Cell Cell

Cranial neural crest (CNC) cells give rise to bone, cartilage, tendons, and ligaments of the vertebrate craniofacial musculoskeletal complex, as well as regulate mesoderm-derived craniofacial muscle development through cell-cell interactions. Using the mouse soft palate as a model, we performed an unbiased single-cell RNA-seq analysis to investigate the heterogeneity and lineage commitment of CNC derivatives during craniofacial muscle development. We show that Runx2, a known osteogenic regulator, is expressed in the CNC-derived perimysial and progenitor populations. Loss of Runx2 in CNC-derivatives results in reduced expression of perimysial markers (Aldh1a2 and Hic1) as well as soft palate muscle defects in Osr2-Cre;Runx2fl/fl mice. We further reveal that Runx2 maintains perimysial marker expression through suppressing Twist1, and that myogenesis is restored in Osr2-Cre;Runx2fl/fl;Twist1fl/+ mice. Collectively, our findings highlight the roles of Runx2, Twist1, and their interaction in regulating the fate of CNC-derived cells as they guide craniofacial muscle development through cell-cell interactions.

Immunomodulatory stromal cell interactions in the eye

2020 ◽  
Vol 12 (538) ◽  
pp. eabb5668
Author(s):  
Gerald P. Morris
Keyword(s):  
Single Cell ◽  
Stromal Cell ◽  
Ocular Inflammation ◽  
Cell Interactions ◽  
Single Cell Sequencing ◽  
Cell Cell

Single-cell sequencing of eye stroma reveals cell-cell interactions essential for suppressing ocular inflammation.

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