Single-cell transcriptomics reveals cell-type-specific diversification in human heart failure

Nature Cardiovascular Research, Journal Year: 2022, Volume and Issue: 1(3), P. 263 - 280

Published: March 16, 2022

Heart failure represents a major cause of morbidity and mortality worldwide. Single-cell transcriptomics have revolutionized our understanding cell composition associated gene expression. Through integrated analysis single-cell single-nucleus RNA-sequencing data generated from 27 healthy donors 18 individuals with dilated cardiomyopathy, here we define the failing human heart. We identify cell-specific transcriptional signatures age heart reveal emergence disease-associated states. Notably, cardiomyocytes converge toward common states, whereas fibroblasts myeloid cells undergo dramatic diversification. Endothelial pericytes display global shifts without changes in complexity. Collectively, findings provide comprehensive cellular transcriptomic landscape failure, type-specific programs states establish valuable resource for investigation failure.

Language: Английский

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Single-nuclear transcriptomics reveals diversity of proximal tubule cell states in a dynamic response to acute kidney injury

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(27)

Published: June 28, 2021

Significance A single acute kidney injury event increases the risk of progression to chronic disease (CKD). Combining single-nucleus RNA sequencing with genetic tracing injured proximal tubule cells identified a spatially dynamic, evolving response following ischemia–reperfusion injury. Failed repair leads persistence profibrotic, proinflammatory Vcam1 + / Ccl2 cell type exhibiting senescence-associated secretory phenotype and marked transcriptional activation NF-κB AP-1 pathway signatures, but no signs G 2 /M cycle arrest. Insights from this study can inform strategies improve renal prevent CKD progression.

Language: Английский

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Mechanistic Pathogenesis of Endothelial Dysfunction in Diabetic Nephropathy and Retinopathy

Frontiers in Endocrinology, Journal Year: 2022, Volume and Issue: 13

Published: May 25, 2022

Diabetic nephropathy (DN) and diabetic retinopathy (DR) are microvascular complications of diabetes. Microvascular endothelial cells thought to be the major targets hyperglycemic injury. In microvasculature, intracellular hyperglycemia causes damages vascular endothelium, via multiple pathophysiological process consist inflammation, cell crosstalk with podocytes/pericytes exosomes. addition, DN DR diseases development involved in several critical regulators including adhesion molecules (CAMs), growth factor (VEGF) family Notch signal. The present review attempts gain a deeper understanding pathogenesis complexities underlying dysfunction diabetes retinopathy, contributing new mechanistic therapeutic strategies against diabetes-induced dysfunction.

Language: Английский

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How Many Cell Types Are in the Kidney and What Do They Do?

Annual Review of Physiology, Journal Year: 2021, Volume and Issue: 84(1), P. 507 - 531

Published: Nov. 29, 2021

The kidney maintains electrolyte, water, and acid-base balance, eliminates foreign waste compounds, regulates blood pressure, secretes hormones. There are at least 16 different highly specialized epithelial cell types in the mammalian kidney. number of endothelial cells, immune interstitial might even be larger. concerted interplay between is critical for function. Traditionally, cells were defined by their function or microscopical morphological appearance. With advent new single-cell modalities such as transcriptomics, epigenetics, metabolomics, proteomics we entering into a era type definition. This technological revolution provides opportunities to classify understand functions.

Language: Английский

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Comprehensive single-cell transcriptional profiling defines shared and unique epithelial injury responses during kidney fibrosis

Cell Metabolism, Journal Year: 2022, Volume and Issue: 34(12), P. 1977 - 1998.e9

Published: Oct. 19, 2022

Language: Английский

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Ferroptotic stress promotes the accumulation of pro-inflammatory proximal tubular cells in maladaptive renal repair

eLife, Journal Year: 2021, Volume and Issue: 10

Published: July 19, 2021

Overwhelming lipid peroxidation induces ferroptotic stress and ferroptosis, a non-apoptotic form of regulated cell death that has been implicated in maladaptive renal repair mice humans. Using single-cell transcriptomic mouse genetic approaches, we show proximal tubular (PT) cells develop molecularly distinct, pro-inflammatory state following injury. While these inflammatory PT transiently appear after mild injury return to their original without inducing fibrosis, severe they accumulate contribute persistent inflammation. This transient significantly downregulates glutathione metabolism genes, making the vulnerable stress. Genetic induction high leads accumulation cells, enhancing inflammation fibrosis. Our study broadens roles from being trigger include promotion proinflammatory underlie repair.

Language: Английский

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Transition of acute kidney injury to chronic kidney disease: role of metabolic reprogramming

Metabolism, Journal Year: 2022, Volume and Issue: 131, P. 155194 - 155194

Published: March 26, 2022

Language: Английский

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Lineage Tracing and Single-Nucleus Multiomics Reveal Novel Features of Adaptive and Maladaptive Repair after Acute Kidney Injury

Journal of the American Society of Nephrology, Journal Year: 2023, Volume and Issue: 34(4), P. 554 - 571

Published: Jan. 13, 2023

Significance Statement Understanding the mechanisms underlying adaptive and maladaptive renal repair after AKI their long-term consequences is critical to kidney health. The authors used lineage tracing of cycling cells single-nucleus multiomics (profiling transcriptome chromatin accessibility) AKI. They demonstrated that triggers a cell-cycle response in most epithelial nonepithelial cell types. also showed proinflammatory proximal tubule (PTCs) persist until 6 months post-AKI, although they decreased abundance over time, part, through death. Single-nucleus lineage-traced revealed regulatory features repair. These included activation state–specific transcription factors cis-regulatory elements, effects PTCs even repair, weeks injury event. Background proliferative as part an intrinsic cellular program, which can lead restoring structure function, or with persistence injured altered structure. However, molecular understanding these programs limited. Methods To examine transcriptional responses same upon ischemia-reperfusion (IRI), we combined genetic fate mapping ( Ki67 + ) labeled early IRI multiomics—profiling accessibility nucleus—and generated dataset 83,315 nuclei. Results triggered broad cycle preceded by type–specific global changes nephron, collecting vascular systems, stromal immune We observed heterogeneous population throughout segments marked loss from 4 months. Gene expression profiling nuclei highlighted differences between activity elements factors, accompanied corresponding target gene expression. Adaptive was associated reduced genes encoding transmembrane transport proteins essential function. Conclusions Analysis genome organization single-cell resolution using offers new insight into regulation Weeks mild-to-moderate IRI, aberrant epigenetic landscape, exhibit profile following

Language: Английский

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The SOX4/EZH2/SLC7A11 signaling axis mediates ferroptosis in calcium oxalate crystal deposition-induced kidney injury

Journal of Translational Medicine, Journal Year: 2024, Volume and Issue: 22(1)

Published: Jan. 2, 2024

Abstract Epigenetic regulation is reported to play a significant role in the pathogenesis of various kidney diseases, including renal cell carcinoma, acute injury, fibrosis, diabetic nephropathy, and lupus nephritis. However, epigenetic calcium oxalate (CaOx) crystal deposition-induced injury remains unclear. Our study demonstrated that upregulation enhancer zeste homolog 2 (EZH2)-mediated ferroptosis facilitates CaOx-induced injury. CaOx deposition promoted vivo vitro. Usage liproxstatin-1 (Lip-1), inhibitor, mitigated damage. Single-nucleus RNA-sequencing, immunohistochemical western blotting analyses revealed EZH2 was upregulated stone patients, mice, oxalate-stimulated HK-2 cells. Experiments involving knockout, vitro knockdown, GSK-126 (an inhibitor) treatment confirmed protective effects inhibition on ferroptosis. Mechanistically, results RNA-sequencing chromatin immunoprecipitation assays regulates by suppressing solute carrier family 7, member 11 (SLC7A11) expression through trimethylation histone H3 lysine 27 (H3K27me3) modification. Additionally, SOX4 regulated directly modulating expression. Thus, this EZH2/H3K27me3-mediated suppression SLC7A11. Graphical

Language: Английский

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Dephosphorylation of AMP-activated protein kinase exacerbates ischemia/reperfusion-induced acute kidney injury via mitochondrial dysfunction

Kidney International, Journal Year: 2021, Volume and Issue: 101(2), P. 315 - 330

Published: Nov. 11, 2021

Kidney tubular epithelial cells are high energy-consuming that depend mainly on fatty acid oxidation for an energy supply. AMP-activated protein kinase (AMPK) is a key regulator of production in most cells, but the function AMPK acute kidney disease unclear. Here, we found rapid decrease Thr172-AMPKα phosphorylation after ischemia/reperfusion both vivo and vitro models. Mice with cell–specific AMPKα deletion exhibited exacerbated impairment apoptosis ischemia/reperfusion. deficiency was accompanied by accumulation lipid droplets tubules elevation ceramides free levels following injury. Mechanistically, triggered ceramide activated phosphatase PP2A, which dephosphorylated Thr172-AMPKα. Decreased activity repressed serine/threonine ULK1-mediated autophagy impeded clearance dysfunctional mitochondria. Targeting PP2A-AMPK axis allosteric activator C24 restored reduced cell during ischemia/reperfusion-induced injury, antagonizing PP2A dephosphorylation promoting mitophagy process. Thus, our study reveals plays important role protecting against injury Hence, activation could be potential therapeutic strategy treatment. Translational StatementAcute (AKI) significant health issue all over world. We renal (I/R) decreased (FAO) untargeted lipidomics RNA sequencing. developed α conditional knockout mice confirmed critical mitochondrial homeostasis I/R Furthermore, proved activators as well metformin improve through enhancing FAO. Our studies suggest might represent novel treatment AKI subsequent chronic targeting homeostasis. Acute common clinical syndrome characterized loss function. And, affects ~15% adults 25% children hospitalized patients.1Hoste E.A.J. Bagshaw S.M. Bellomo R. et al.Epidemiology critically ill patients: multinational AKI-EPI study.Intensive Care Med. 2015; 41: 1411-1423Crossref PubMed Scopus (1138) Google Scholar,2Ronco C. Kellum J.A. injury.Lancet. 2019; 394: 1949-1964Abstract Full Text PDF (380) Scholar Unfortunately, no definite therapies currently available to prevent or treat established AKI. The one energy-demanding organs human body, especially cells.3Bhargava P. Schnellmann R.G. Mitochondrial energetics kidney.Nat Rev Nephrol. 2017; 13: 629-646Crossref (405) Scholar,4Wang Z.M. Ying Z. Bosy-Westphal A. al.Specific metabolic rates major tissues across adulthood: evaluation mechanistic model resting expenditure.Am J Clin Nutr. 2010; 92: 1369-1377Crossref (233) Fatty acids have been identified fuel adenosine triphosphate (ATP) method.5Forbes J.M. Thorburn D.R. dysfunction diabetic disease.Nat 2018; 14: 291-312Crossref (169) FAO occurs mitochondria involves repeated sequence reactions result conversion acetyl–coenzyme A (CoA). However, damage has proven AKI, including abundance, swelling, disruption cristae.6Zsengellér Z.K. Ellezian L. Brown D. al.Cisplatin nephrotoxicity impaired enzyme activity.J Histochem Cytochem. 2012; 60: 521-529Crossref (82) Scholar, 7Funk Persistent injury.Am Physiol Renal Physiol. 302: 853-864Crossref (148) 8Zhang Q. Raoof M. Chen Y. al.Circulating DAMPs cause inflammatory responses injury.Nature. 464: 104-107Crossref (2297) linked ATP depletion-induced (AKI), lipotoxicity, disease. Injured not only reduce level also source molecules amplify precipitate death, induce inflammation.9Wan J. Kalpage H.A. Vaishnav al.Regulation respiration cytochrome c threonine 58 phosphorylation.Sci Rep. 9: 1-16Crossref (8) Scholar,10Birk A.V. Chao W.M. Bracken al.Targeting cardiolipin c/cardiolipin complex promote electron transport optimize synthesis.Br Pharmacol. 2014; 171: 2017-2028Crossref Structural releases reactive oxygen species (ROS) c, trigger apoptosis, DNA (mtDNA), can serve proinflammatory danger signal.8Zhang (AMPK), sensor cellular status, network.11Herzig S. Shaw R.J. AMPK: guardian metabolism homeostasis.Nat Mol Cell Biol. 19: 121-135Crossref (1134) stresses, particularly those involving depletion AMP elevation.12Lin S.C. Hardie D.G. sensing glucose status.Cell Metab. 27: 299-313Abstract (417) Once activated, phosphorylates myriad downstream targets ATP-generating catabolic processes inhibit ATP-consuming anabolic processes.13Hardie Schaffer B.E. Brunet energy-sensing pathway multiple inputs outputs.Trends 2016; 26: 190-201Abstract (487) In ischemia-reperfusion (I/R), stress state changes rapidly ischemia period reperfusion period, may change activity. During ischemic phase, decreases because insufficiency, whereas AMP-to-ATP ratio increases, resulting activation.14Mount P.F. Hill R.E. Fraser S.A. al.Acute activates does increase eNOS-Ser1177.Am 2005; 289: F1103-F1115Crossref (61) rarely reported. present study, (FFAs) I/R, remarkable Then, contributed via maintaining using tubular-specific mice. played protective improving quality. Additional details methods Supplementary Methods. C57BL/6J were purchased from Vital River Laboratory Animal Corporation. Tubular-specific AMPKα1/α2 double-knockout (TAKO mice) generated crossing AMPKα1/α2-floxed Cdh16-cre induced mice, described previous article.15Wei Dong Mouse injury: technical notes tricks.Am 303: F1487-F1494Crossref (186) animal provided Primary (RPTCs) isolated according report.16Ding W. Yousefi K. Shehadeh L.A. Isolation, characterization, throughput extracellular flux analysis mouse primary cells.J Vis Exp. 2018: 1-10Google Detailed protocols Lipidomics acyl-CoA performed I-class ultra-high-performance liquid chromatograph coupled quadruple time-of-flight mass spectrometer. information Quantitative data expressed mean ± SEM. Analytical P < 0.05 considered significantly different. Consistent studies,17Tran M.T. Zsengeller Berg A.H. al.PGC1α drives NAD biosynthesis linking oxidative protection.Nature. 531: 528-532Crossref (257) Scholar,18Zager R.A. Johnson A.C.M. Hanson S.Y. triglyercide endotoxic, toxic, injury.Kidney Int. 67: 111-121Abstract (64) Oil Red O staining revealed droplet I/R-induced indicative dysregulation (Figure 1a). serum triglyceride nonestesterified markedly (Supplementary Figure S1A). To better understand mechanism employed elaborate pattern lipidome. Compared sham group, total 225 lipids increased, 97 kidneys 1b). Among these lipids, group featured elevated triglycerides, consistent observed Moreover, acyls (mainly FFAs) sphingolipids ceramides) remarkably increased 1c), demonstrating perturbations sphingolipid metabolism. Notably, variable importance projection score plot differentiated indicated among top 20 1d), attracted interest lipotoxins pathogenesis many types AKI.19Hao C.M. Breyer M.D. Physiologic pathophysiologic roles mediators kidney.Kidney 2007; 71: 1105-1115Abstract (130) Along ceramides, FFA higher long-chain acylcarnitines acyl-CoAs 1e), suggesting defective FA import into And enzymes (carnitine palmitoyltransferase 1a [CPT-1a], dehydrogenase [LCAD], medium-chain [MCAD]; 1f) indicating insufficient FAO.Figure 1Renal results impairs (a) 24-hour post-ischemia 30-minute kidneys. Bar = 50 μm. (b) Heat map differential (variable [VIP] > 1.2, fold [FC] 1.3, 0.05). VIP obtained orthogonal partial least squares discrimination (OPLS-DA) between ion current (TIC) normalization. (c) number each class. (d) I/R. (e) (Cer), (FFAs), acyl-carnitines, acyl-CoAs. (b–e) n 8. (f) Representative immunoblotting proteins. 3. (g) Volcano differentially genes RNA-sequencing (FC 2, P-adjusted 5. (h) Top upregulated downregulated Kyoto Encyclopedia Genes Genomes enrichments (false discovery rate (i) Schematic summary integrative transcriptomics analysis. detected shown, red blue colors indicate upregulation downregulation, respectively. Akt, B; ECM, matrix; MAPK, mitogen-activated kinase; PI3K, phosphatidylinositol-3′-kinase; PPAR, peroxisome proliferator–activated receptor; TG, triglyceride; TNF, tumor necrosis factor. viewing this image, please see online version article at www.kidney-international.org.View Large Image ViewerDownload Hi-res image Download (PPT) examined mechanisms underlying association dysregulated 1060 595 1g). enrichment highly enriched injury-related pathways. metabolism-related pathways downregulated, peroxisome, receptor signaling, 1h). Given perturbed analysis, mapped related gene 1i). Most synthesis altered. involved FAO, Cpt1b, Mcad, oxidase (Acox) accounted acyl-carnitines group. Reverse transcription–polymerase chain reaction immunohistochemistry showed same conclusion S1B–E). Collectively, findings within causative factor growing body evidence indicates specifically regulates metabolism, biology, homeostasis, biogenesis quality control.20Fullerton Galic Marcinko al.Single sites Acc1 Acc2 regulate insulin-sensitizing effects metformin.Nat 2013; 1649-1654Crossref (499) 21Quirós P.M. Mottis Auwerx Mitonuclear communication stress.Nat 17: 213-226Crossref (364) 22O'Neill H.M. Maarbjerg S.J. Crane J.D. al.AMP-activated β1β2 muscle null reveal essential content uptake exercise.Proc Natl Acad Sci U S 2011; 108: 16092-16097Crossref (304) 23Garcia-Roves Osler M.E. Holmström M.H. Zierath J.R. Gain-of-function R225Q mutation γ3 subunit increases glycolytic skeletal muscle.J Biol Chem. 2008; 283: 35724-35734Abstract (128) Therefore, next dynamic Plasma creatinine urea dramatically 6 24 hours S2A B). Western blot stage, dramatic occurred early 1 hour reperfusion, pSer79–Acetyl-CoA carboxylase (ACC) similar trend 2a b). further investigate D-R utilized simulating I/R.24Tang Han H. Yan al.PINK1-PRKN/PARK2 protect injury.Autophagy. 880-897Crossref (131) Scholar,25Livingston M.J. Wang Zhou al.Clearance damaged effect preconditioning kidneys.Autophagy. 15: 2142-2162Crossref (72) immunoblot extremely 15 minutes repletion, sustained low 2 repletion 2c). determine vitro, RPTCs performed. knocked down AMPKα1 AMPKα2 expression specific small, interfering RNAs 2d). knockdown cleaved caspase-3 2e), silencing sensitized RPTC apoptosis. measured 14C–palmitic (PA) D-R. silence normal condition 2f). there used confirm vivo. A-769662, PF-06409577, C24,26Li Y.Y. Yu L.F. Zhang L.N. al.Novel small-molecule orally exerts beneficial db/db mice.Toxicol Appl 273: 325-334Crossref (45) lowered than control S2C), dose-dependently inhibited S2D). blocked cytoprotective 2g). These TAKO Littermate homozygous animals controls. transcript whole tissue 55% compared S3A). controls 3a). Under conditions, plasma littermates 3b c). After much urea, more severe mRNA marker (kidney molecule-1 [Kim-1] Ngal) 3d e). Hematoxylin eosin demonstrated displayed extensive tubule cortex outer medulla, brush border, formation casts, sloughing lumen 3f g). Immunohistochemistry neutrophil gelatinase-associated lipocalin (NGAL) h). evaluated terminal deoxynucleotidyl transferase–mediated dUTP nick end-labeling (TUNEL) assay immunohistochemistry. TUNEL-positive caspase-3–positive 3f, i, j). Inflammation initiation extension phases Macrophages neutrophils analyzed macrophages kidney. macrophage infiltration S3B–D). cytokines Il1b Il6 S3E). Taken together, epithelial-specific aggravated slices, positive 4a FFAs 4c), Meanwhile, Cpt1a, Lcad S4A–C). LCAD lower d). implied Next, morphology transmission microscopy. As shown 4a, small fragmentation. severely damaged, showing fragmentation, vacuoles matrix, cristae. length shorter 4e). mtDNA copy examine content. had greater reduction 4f). Consistently, suggested caused 4g). Autophagy/mitophagy play vital model.24Tang Scholar,27Kaushal G.P. Shah S.V. Autophagy 89: 779-791Abstract (206) microtubule-associated 1A/1B-light 3 (LC3) granular LC3 TECs kidneys, autophagosomes 4a). quantified autolysosomes (colocation lysosomal-associated membrane [LAMP1]) controls, inhibits autophagic 4h). Quantification mitolysosomes fewer i). results,24Tang fluorescence intensity dihydroethidium (DHE) signal appeared stronger Peroxisome proliferator-activated receptor-γ coactivator 1-α (PGC-1α), master biogenesis, necessary recovery.28Tran Arany Parikh al.PGC-1α promotes recovery systemic inflammation mice.. 121: 4003-4014Google transcription (TFAM) regulated PGC-1α signaling pathway. S4D F, under condition, TFAM confirming cells. All demonstrate β-oxidation mitochondria, leading disrupted agonist lipogenesis liver.29Sun S.-M. Xie Z.-F. Y.-M. al.AMPK hepatic ameliorates dyslipidemia HFHC diet-induced models.Acta Pharmacol Sin. 2021; 42: 585-592Google assessed, indirect control. Both pThr172-AMPKα 5a 5c d) ameliorated 5e f). NGAL g), Ngal Kim-1 S5A treatments resulted caspase-3– 5e, h, S5C–E). rescue Cpt-1α, Lcad, Mcad S5G–I). did show phenotype, different metformin. examined. promoted mtDNA-to–nuclear (nDNA) 6a mito

Language: Английский

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