Single-Nucleus RNA Sequencing Identifies New Classes of Proximal Tubular Epithelial Cells in Kidney Fibrosis

2021 ◽  
pp. ASN.2020081143
Author(s):  
Yueh-An Lu ◽  
Chia-Te Liao ◽  
Rachel Raybould ◽  
Bnar Talabani ◽  
Irina Grigorieva ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Renal Fibrosis ◽  
High Performance ◽  
Genome Mapping ◽  
Gene Expression Signature ◽  
Metabolic Reprogramming ◽  
Normal Kidney ◽  
Kidney Fibrosis ◽  
Proximal Tubular ◽  
Single Nucleus

Background: Proximal tubular cells (PTCs) are the most abundant cell type in the kidney. PTCs are central to normal kidney function and to regeneration versus organ fibrosis following injury. This study used single-nucleus RNA sequencing (snRNA-seq) to describe the phenotype of PTCs in renal fibrosis. Methods: Kidneys were harvested from naïve mice and from mice with renal fibrosis induced by chronic aristolochic acid administration. Nuclei were isolated using Nuclei EZ Lysis buffer. Libraries were prepared on the 10X platform and snRNA-seq completed using the Illumina NextSeq 550 System. Genome mapping was carried out with high-performance computing. Results: A total of 23,885 nuclei were analysed. PTCs were found in five abundant clusters, mapping to S1, S1-2, S2, S2-cortical S3, and medullary S3 segments. Additional cell clusters ("new PTC clusters") were at low abundance in normal kidney and in increased number in kidneys undergoing regeneration/fibrosis following injury. These clusters exhibited clear molecular phenotypes, permitting labelling as proliferating, New-PT1, New-PT2, and (present only following injury) New-PT3. Each cluster exhibited a unique gene expression signature, including multiple genes previously associated with renal injury response and fibrosis progression. Comprehensive pathway analyses revealed metabolic reprogramming, enrichment of cellular communication and cell motility, and various immune activations in new PTC clusters. In ligand-receptor analysis, new PTC clusters promoted fibrotic signaling to fibroblasts and inflammatory activation to macrophages. Conclusion: These data identify unrecognized PTC phenotype heterogeneity and reveal novel PTCs associated with kidney fibrosis.

scholarly journals MiR-9-5p protects from kidney fibrosis by metabolic reprogramming

2019 ◽  
Author(s):  
Marta Fierro-Fernández ◽  
Verónica Miguel ◽  
Laura Márquez-Expósito ◽  
Cristina Nuevo-Tapioles ◽  
J. Ignacio Herrero ◽  
...  
Keyword(s):  
Mitochondrial Dysfunction ◽  
Renal Fibrosis ◽  
Transforming Growth Factor ◽  
Metabolic Reprogramming ◽  
Acid Oxidation ◽  
Peroxisome Proliferator ◽  
Metabolic Derangement ◽  
Peroxisome Proliferator Activated Receptor ◽  
Kidney Fibrosis ◽  
Tgf Β1

AbstractMicroRNAs (miRNAs) regulate gene expression post-transcriptionally and control biological processes, including fibrogenesis. Kidney fibrosis remains a clinical challenge and miRNAs may represent a valid therapeutic avenue. We show that miR-9-5p protected from renal fibrosis in the mouse model of unilateral ureteral obstruction (UUO). This was reflected in reduced expression of pro-fibrotic markers, decreased number of infiltrating monocytes/macrophages and diminished tubular epithelial cell injury and transforming growth factor-beta 1 (TGF-β1)-dependent de-differentiation in human kidney proximal tubular (HKC-8) cells. RNA sequencing (RNA-Seq) studies in the UUO model revealed that this protection was mediated by a global shift in the expression profile of genes related to key metabolic pathways, including mitochondrial dysfunction, oxidative phosphorylation (OXPHOS), fatty acid oxidation (FAO) and glycolysis, preventing their UUO-dependent down-regulation. This effect was mirrored by a prevention in the TGF-β1-induced bioenergetics changes in HKC-8 cells. The expression of the FAO-related axis peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1α)-peroxisome proliferator-activated receptor alpha (PPARα) was reduced by UUO, although preserved by the administration of miR-9-5p. We found that in mice null for the mitochondrial master regulator PGC-1α, miR-9-5p was unable to promote a protective effect in the UUO model. We propose that miR-9-5p elicits a protective response to chronic kidney injury and renal fibrosis by inducing reprogramming of the metabolic derangement and mitochondrial dysfunction affecting tubular epithelial cells.

scholarly journals Involvement of FATP2-mediated tubular lipid metabolic reprogramming in renal fibrogenesis

2020 ◽  
Vol 11 (11) ◽  
Author(s):  
Yuting Chen ◽  
Qi Yan ◽  
Mengyue Lv ◽  
Kaixin Song ◽  
Yue Dai ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Lipid Metabolism ◽  
Growth Factor ◽  
Renal Fibrosis ◽  
Interstitial Fibrosis ◽  
Tissue Growth ◽  
Metabolic Reprogramming ◽  
Kidney Fibrosis

AbstractFollowing a chronic insult, renal tubular epithelial cells (TECs) contribute to the development of kidney fibrosis through dysregulated lipid metabolism that lead to lipid accumulation and lipotoxicity. Intracellular lipid metabolism is tightly controlled by fatty acids (FAs) uptake, oxidation, lipogenesis, and lipolysis. Although it is widely accepted that impaired fatty acids oxidation (FAO) play a crucial role in renal fibrosis progression, other lipid metabolic pathways, especially FAs uptake, has not been investigated in fibrotic kidney. In this study, we aim to explore the potential mechanically role of FAs transporter in the pathogenesis of renal fibrosis. In the present study, the unbiased gene expression studies showed that fatty acid transporter 2 (FATP2) was one of the predominant expressed FAs transport in TECs and its expression was tightly associated with the decline of renal function. Treatment of unilateral ureteral obstruction (UUO) kidneys and TGF-β induced TECs with FATP2 inhibitor (FATP2i) lipofermata restored the FAO activities and alleviated fibrotic responses both in vivo and in vitro. Moreover, the expression of profibrotic cytokines including TGF-β, connective tissue growth factor (CTGF), fibroblast growth factor (FGF), and platelet-derived growth factor subunit B (PDGFB) were all decreased in FATP2i-treated UUO kidneys. Mechanically, FATP2i can effectively attenuate cell apoptosis and endoplasmic reticulum (ER) stress induced by TGF-β treatment in cultured TECs. Taking together, these findings reveal that FATP2 elicits a profibrotic response to renal interstitial fibrosis by inducing lipid metabolic reprogramming including abnormal FAs uptake and defective FAO in TECs.

scholarly journals Sodium-Glucose Co-Transporter 2 Inhibitors Correct Metabolic Maladaptation of Proximal Tubular Epithelial Cells in High-Glucose Conditions

2020 ◽  
Vol 21 (20) ◽  
pp. 7676
Author(s):  
Kohsuke Shirakawa ◽  
Motoaki Sano
Keyword(s):  
Epithelial Cells ◽  
High Glucose ◽  
Renal Fibrosis ◽  
Sglt2 Inhibitors ◽  
Metabolic Reprogramming ◽  
Phase Iii ◽  
Tubular Epithelial Cells ◽  
Proximal Tubular Epithelial Cells ◽  
Proximal Tubular ◽  
Ros Formation

Glucose filtered in the glomerulus is actively reabsorbed by sodium-glucose co-transporter 2 (SGLT2) in proximal tubular epithelial cells (PTEC) and passively returned to the blood via glucose transporter 2 (GLUT2). Healthy PTEC rely primarily on fatty acid beta-oxidation (FAO) for energy. In phase III trials, SGLT2 inhibitors improved outcomes in diabetic kidney disease (DKD). Tubulointerstitial renal fibrosis due to altered metabolic reprogramming of PTEC might be at the root of the pathogenesis of DKD. Here, we investigated the molecular mechanism of SGLT2 inhibitors’ renoprotective effect by examining transcriptional activity of Spp1, which encodes osteopontin, a key mediator of tubulointerstitial renal fibrosis. With primary cultured PTEC from Spp1-enhanced green fluorescent protein knock-in mice, we proved that in high-glucose conditions, increased SGLT2- and GLUT-mediated glucose uptake is causatively involved in aberrant activation of the glycolytic pathway in PTEC, thereby increasing mitochondrial reactive oxygen species (ROS) formation and transcriptional activation of Spp1. FAO activation did not play a direct role in these processes, but elevated expression of a tubular-specific enzyme, myo-inositol oxygenase, was at least partly involved. Notably, canagliflozin blocked overexpression of myo-inositol oxygenase. In conclusion, SGLT2 inhibitors exerted renoprotective effects by inhibiting aberrant glycolytic metabolism and mitochondrial ROS formation in PTEC in high-glucose conditions.

scholarly journals Value of ultrasound elastography in the diagnosis of native kidney fibrosis.

2016 ◽  
Vol 18 (3) ◽  
pp. 362 ◽  
Author(s):  
Ileana Peride ◽  
Daniela Rădulescu ◽  
Andrei Niculae ◽  
Vladimir Ene ◽  
Ovidiu Gabriel Bratu ◽  
...  
Keyword(s):  
Shear Wave ◽  
Hepatic Fibrosis ◽  
Renal Fibrosis ◽  
Kidney Diseases ◽  
Ultrasound Elastography ◽  
Normal Kidney ◽  
Chronic Kidney Diseases ◽  
Kidney Fibrosis ◽  
Native Kidney ◽  
Deep Location

In the last decade, ultrasound elastography, an already widely used technique in the diagnosis of hepatic fibrosis, has raised the attention of nephrologists as a potential valuable noninvasive tool for the diagnosis of renal fibrosis. Due to renal deep location and anatomic complexity, the shear wave techniques are the most appropriate elastography methods for exploring native kidneys. Recent research offers promising results, but further larger studies are required for a better standardization of this method and also for establishing reference values of normal kidney elasticity. This article reviews the studies conducted for exploring the native kidney, highlighting the advantages and limitations of ultrasound elastography for assessing fibrosis development in chronic kidney diseases.

scholarly journals The molecular taxonomy of primate amygdala via single-nucleus RNA-sequencing analysis

2021 ◽  
Author(s):  
Lei Zhang ◽  
Yanyong Cheng ◽  
Shihao Wu ◽  
Yufeng Lu ◽  
Zhenyu Xue ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Molecular Taxonomy ◽  
Sequencing Analysis ◽  
Single Nucleus

Single-nucleus RNA-sequencing of human choriodecidua before and after the onset of labor

Placenta ◽  
2021 ◽  
Vol 112 ◽  
pp. e67
Author(s):  
Léa Chicoisne ◽  
Muriel Andrieu ◽  
Céline Bertholle ◽  
Vaarany Karunanithy ◽  
Brigitte Izac ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Before And After ◽  
Single Nucleus

Fate alteration of bone marrow-derived macrophages ameliorates kidney fibrosis in murine model of unilateral ureteral obstruction

2018 ◽  
Vol 34 (10) ◽  
pp. 1657-1668 ◽  
Author(s):  
Ying Yang ◽  
Xiaojian Feng ◽  
Xinyan Liu ◽  
Ying Wang ◽  
Min Hu ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Ureteral Obstruction ◽  
Renal Fibrosis ◽  
Kidney Diseases ◽  
Unilateral Ureteral Obstruction ◽  
Immunofluorescent Staining ◽  
Enzyme Linked Immunosorbent Assay ◽  
Pathological Feature ◽  
Kidney Fibrosis ◽  
Anti Inflammatory

AbstractBackgroundRenal fibrosis is a key pathological feature and final common pathway leading to end-stage kidney failure in many chronic kidney diseases. Myofibroblast is the master player in renal fibrosis. However, myofibroblasts are heterogeneous. Recent studies show that bone marrow-derived macrophages transform into myofibroblasts by transforming growth factor (TGF)-β-induced macrophage–myofibroblast transition (MMT) in renal fibrosis.MethodsTGF-β signaling was redirected by inhibition of β-catenin/T-cell factor (TCF) to increase β-catenin/Foxo in bone marrow-derived macrophages. A kidney fibrosis model of unilateral ureteral obstruction was performed in EGFP bone marrow chimera mouse. MMT was examined by flow cytometry analysis of GFP+F4/80+α-SMA+ cells from unilateral ureteral obstruction (UUO) kidney, and by immunofluorescent staining of bone marrow-derived macrophages in vitro. Inflammatory and anti-inflammatory cytokines were analysis by enzyme-linked immunosorbent assay.ResultsInhibition of β-catenin/TCF by ICG-001 combined with TGF-β1 treatment increased β-catenin/Foxo1, reduced the MMT and inflammatory cytokine production by bone marrow-derived macrophages, and thereby, reduced kidney fibrosis in the UUO model.ConclusionsOur results demonstrate that diversion of β-catenin from TCF to Foxo1-mediated transcription not only inhibits the β-catenin/TCF-mediated fibrotic effect of TGF-β, but also enhances its anti-inflammatory action, allowing therapeutic use of TGF-β to reduce both inflammation and fibrosis at least partially by changing the fate of bone marrow-derived macrophages.

scholarly journals Single nucleus and in situ RNA sequencing reveals cell topographies in the human pancreas

2020 ◽  
Author(s):  
Luca Tosti ◽  
Yan Hang ◽  
Olivia Debnath ◽  
Sebastian Tiesmeyer ◽  
Timo Trefzer ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Human Pancreas ◽  
Single Nucleus

scholarly journals Single Cell, Single Nucleus and Spatial RNA Sequencing of the Human Liver Identifies Hepatic Stellate Cell and Cholangiocyte Heterogeneity

2021 ◽  
Author(s):  
Tallulah S Andrews ◽  
Jawairia Atif ◽  
Jeff C Liu ◽  
Catia T Perciani ◽  
Xue-Zhong Ma ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Human Liver ◽  
Stellate Cell ◽  
Parenchymal Cell ◽  
Cell Types ◽  
Cell Populations ◽  
Healthy Human ◽  
Single Nucleus

The critical functions of the human liver are coordinated through the interactions of hepatic parenchymal and non-parenchymal cells. Recent advances in single cell transcriptional approaches have enabled an examination of the human liver with unprecedented resolution. However, dissociation related cell perturbation can limit the ability to fully capture the human liver's parenchymal cell fraction, which limits the ability to comprehensively profile this organ. Here, we report the transcriptional landscape of 73,295 cells from the human liver using matched single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq). The addition of snRNA-seq enabled the characterization of interzonal hepatocytes at single-cell resolution, revealed the presence of rare subtypes of hepatic stellate cells previously only seen in disease, and detection of cholangiocyte progenitors that had only been observed during in vitro differentiation experiments. However, T and B lymphocytes and NK cells were only distinguishable using scRNA-seq, highlighting the importance of applying both technologies to obtain a complete map of tissue-resident cell-types. We validated the distinct spatial distribution of the hepatocyte, cholangiocyte and stellate cell populations by an independent spatial transcriptomics dataset and immunohistochemistry. Our study provides a systematic comparison of the transcriptomes captured by scRNA-seq and snRNA-seq and delivers a high-resolution map of the parenchymal cell populations in the healthy human liver.

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