An atlas of healthy and injured cell states and niches in the human kidney

Nature, Journal Year: 2023, Volume and Issue: 619(7970), P. 585 - 594

Published: July 19, 2023

Abstract Understanding kidney disease relies on defining the complexity of cell types and states, their associated molecular profiles interactions within tissue neighbourhoods 1 . Here we applied multiple single-cell single-nucleus assays (>400,000 nuclei or cells) spatial imaging technologies to a broad spectrum healthy reference kidneys (45 donors) diseased (48 patients). This has provided high-resolution cellular atlas 51 main types, which include rare previously undescribed populations. The multi-omic approach provides detailed transcriptomic profiles, regulatory factors localizations spanning entire kidney. We also define 28 states across nephron segments interstitium that were altered in injury, encompassing cycling, adaptive (successful maladaptive repair), transitioning degenerative states. Molecular signatures permitted localization these injury using transcriptomics, while large-scale 3D analysis (around 1.2 million neighbourhoods) corresponding linkages active immune responses. These analyses defined biological pathways are relevant time-course niches, including underlying epithelial repair predicted with decline function. integrated multimodal human represents comprehensive benchmark neighbourhoods, outcome-associated publicly available interactive visualizations.

Language: Английский

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Kidney fibrosis: from mechanisms to therapeutic medicines

Signal Transduction and Targeted Therapy, Journal Year: 2023, Volume and Issue: 8(1)

Published: March 17, 2023

Abstract Chronic kidney disease (CKD) is estimated to affect 10–14% of global population. Kidney fibrosis, characterized by excessive extracellular matrix deposition leading scarring, a hallmark manifestation in different progressive CKD; However, at present no antifibrotic therapies against CKD exist. fibrosis identified tubule atrophy, interstitial chronic inflammation and fibrogenesis, glomerulosclerosis, vascular rarefaction. Fibrotic niche, where organ initiates, complex interplay between injured parenchyma (like tubular cells) multiple non-parenchymal cell lineages (immune mesenchymal located spatially within scarring areas. Although the mechanisms are complicated due kinds cells involved, with help single-cell technology, many key questions have been explored, such as what kind renal tubules profibrotic, myofibroblasts originate, which immune how communicate each other. In addition, genetics epigenetics deeper that regulate fibrosis. And reversible nature epigenetic changes including DNA methylation, RNA interference, chromatin remodeling, gives an opportunity stop or reverse therapeutic strategies. More marketed (e.g., RAS blockage, SGLT2 inhibitors) developed delay progression recent years. Furthermore, better understanding also favored discover biomarkers fibrotic injury. review, we update advances mechanism summarize novel treatment for CKD.

Language: Английский

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Spatial transcriptomics: Technologies, applications and experimental considerations

Genomics, Journal Year: 2023, Volume and Issue: 115(5), P. 110671 - 110671

Published: June 21, 2023

The diverse cell types of an organ have a highly structured organization to enable their efficient and correct function. To fully appreciate gene functions in given type, one needs understand how much, when where the is expressed. Classic bulk RNA sequencing popular single destroy structural fail provide spatial information. However, location expression or complex tissue provides key clues comprehend neighboring genes cells cross talk, transduce signals work together as team complete job. functional requirement for content has been driving force rapid development transcriptomics technologies past few years. Here, we present overview current with special focus on commercially available currently being commercialized technologies, highlight applications by category discuss experimental considerations first experiment.

Language: Английский

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SGLT2 inhibitors mitigate kidney tubular metabolic and mTORC1 perturbations in youth-onset type 2 diabetes

Journal of Clinical Investigation, Journal Year: 2023, Volume and Issue: 133(5)

Published: Jan. 13, 2023

The molecular mechanisms of sodium-glucose cotransporter-2 (SGLT2) inhibitors (SGLT2i) remain incompletely understood. Single-cell RNA sequencing and morphometric data were collected from research kidney biopsies donated by young persons with type 2 diabetes (T2D), aged 12 to 21 years, healthy controls (HCs). Participants T2D obese had higher estimated glomerular filtration rates mesangial volumes than HCs. Ten participants been prescribed SGLT2i (T2Di[+]) 6 not (T2Di[-]). Transcriptional profiles showed SGLT2 expression exclusively in the proximal tubular (PT) cluster highest T2Di(-) patients. However, transcriptional alterations treatment seen across nephron segments, particularly distal nephron. was associated suppression transcripts glycolysis, gluconeogenesis, tricarboxylic acid cycle pathways PT, but opposite effect thick ascending limb. Transcripts energy-sensitive mTORC1-signaling pathway returned toward HC levels all segments T2Di(+), consistent a mouse model treated SGLT2i. Decreased phosphorylated S6 protein tubules T2Di(+) patients confirmed changes mTORC1 activity. We propose that benefits kidneys mitigating diabetes-induced metabolic perturbations via signaling tubules.

Language: Английский

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Histone H3K27 methyltransferase EZH2 regulates apoptotic and inflammatory responses in sepsis-induced AKI

Theranostics, Journal Year: 2023, Volume and Issue: 13(6), P. 1860 - 1875

Published: Jan. 1, 2023

Rationale: The role of histone methylation modifications in renal disease, particularly sepsis-induced acute kidney injury (AKI), remains unclear. This study aims to investigate the potential involvement methyltransferase zeste homolog 2 (EZH2) AKI and its impact on apoptosis inflammation. Methods: We first examined expression EZH2 (LPS injection) mice LPS-stimulated tubular epithelial cells. next constructed knockout further confirm effects inflammatory response AKI. And level cells can be reflected by detecting chemokines chemotaxis macrophages. Subsequently, we knocked-down again performed Chromatin Immunoprecipitation sequencing screen out target genes regulated enrichment pathway. Then confirmed gene regulatory pathway vivo vitro experiments. Experimental results were finally using another model (cecal perforation ligation). Results: found that was upregulated silencing could reduce decreasing showed significantly reduced inflammation macrophage infiltration. immunoprecipitation polymerase chain reaction identified Sox9 as a EZH2. enriched promoter Sox9. Silencing resulted significant increase transcriptional activation Wnt/β-catenin signaling reversed or administering inhibitor icg001. It also positively β-catenin downstream pathway-related genes. Finally, 3-deazaneplanocin A alleviated Conclusion: Our indicate protect function relieving inhibition Sox9, activating pathway, attenuating interstitium. These highlight therapeutic value targeting

Language: Английский

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Genetic studies of paired metabolomes reveal enzymatic and transport processes at the interface of plasma and urine

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(6), P. 995 - 1008

Published: June 1, 2023

Abstract The kidneys operate at the interface of plasma and urine by clearing molecular waste products while retaining valuable solutes. Genetic studies paired metabolomes may identify underlying processes. We conducted genome-wide 1,916 metabolites detected 1,299 significant associations. Associations with 40% implicated would have been missed studying alone. urine-specific findings that provide information about metabolite reabsorption in kidney, such as aquaporin (AQP)-7-mediated glycerol transport, different metabolomic footprints kidney-expressed proteins are consistent their localization function, including transporters NaDC3 ( SLC13A3 ) ASBT SLC10A2 ). Shared genetic determinants 7,073 metabolite–disease combinations represent a resource to better understand metabolic diseases revealed connections dipeptidase 1 circulating digestive enzymes hypertension. Extending metabolome beyond yields unique insights into processes body compartments.

Language: Английский

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Cell–cell communication: new insights and clinical implications

Signal Transduction and Targeted Therapy, Journal Year: 2024, Volume and Issue: 9(1)

Published: Aug. 7, 2024

Multicellular organisms are composed of diverse cell types that must coordinate their behaviors through communication. Cell-cell communication (CCC) is essential for growth, development, differentiation, tissue and organ formation, maintenance, physiological regulation. Cells communicate direct contact or at a distance using ligand-receptor interactions. So cellular encompasses two processes: signal conduction generation intercellular transmission signals, transduction reception procession signals. Deciphering networks critical understanding metabolism. First, we comprehensively review the historical milestones in CCC studies, followed by detailed description mechanisms molecule importance main signaling pathways they mediate maintaining biological functions. Then systematically introduce series human diseases caused abnormalities progress clinical applications. Finally, summarize various methods monitoring interactions, including imaging, proximity-based chemical labeling, mechanical force analysis, downstream analysis strategies, single-cell technologies. These aim to illustrate how functions depend on these interactions complexity regulatory regulate crucial processes, homeostasis, immune responses diseases. In addition, this enhances our processes occur after cell-cell binding, highlighting its application discovering new therapeutic targets biomarkers related precision medicine. This collective provides foundation developing targeted drugs personalized treatments.

Language: Английский

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Transcriptomic, epigenomic, and spatial metabolomic cell profiling redefines regional human kidney anatomy

Cell Metabolism, Journal Year: 2024, Volume and Issue: 36(5), P. 1105 - 1125.e10

Published: March 20, 2024

A large-scale multimodal atlas that includes major kidney regions is lacking. Here, we employed simultaneous high-throughput single-cell ATAC/RNA sequencing (SHARE-seq) and spatially resolved metabolomics to profile 54 human samples from distinct anatomical regions. We generated transcriptomes of 446,267 cells chromatin accessibility profiles 401,875 developed a package analyze 408,218 metabolomes. find the same cell type, including thin limb, thick ascending limb loop Henle principal cells, display transcriptomic, accessibility, metabolomic signatures, depending on anatomic location. Surveying metabolism-associated gene revealed non-overlapping metabolic signatures between nephron segments dysregulated lipid metabolism in diseased proximal tubule (PT) cells. Integrating omics with clinical data identified PLEKHA1 as disease marker, its vitro knockdown increased expression PT differentiation, suggesting possible pathogenic roles. This study highlights previously underrepresented cellular heterogeneity underlying anatomy.

Language: Английский

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Metabolism at the crossroads of inflammation and fibrosis in chronic kidney disease

Nature Reviews Nephrology, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 17, 2024

Language: Английский

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Spatial top-down proteomics for the functional characterization of human kidney

Clinical Proteomics, Journal Year: 2025, Volume and Issue: 22(1)

Published: March 5, 2025

The Human Proteome Project has credibly detected nearly 93% of the roughly 20,000 proteins which are predicted by human genome. However, proteome is enigmatic, where alterations in amino acid sequences from polymorphisms and alternative splicing, errors translation, post-translational modifications result a depth estimated at several million unique proteoforms. Recently mass spectrometry been demonstrated landmark efforts mapping proteoform landscape bulk analyses. Herein, we developed an integrated workflow for characterizing proteoforms tissue spatially resolved manner coupling laser capture microdissection, nanoliter-scale sample preparation, imaging. Using healthy kidney sections as case study, focused our analyses on major functional units including glomeruli, tubules, medullary rays. After these isolated were processed with microPOTS (microdroplet processing one-pot trace samples) sensitive top-down proteomics measurement. This provided quantitative database 616 that was further leveraged library imaging near-cellular spatial resolution over entire section. Notably, mitochondrial found to be differentially abundant between glomeruli convoluted contextualization confirming differences identified microPOTS, expanding field-of-view distributions such enhanced abundance truncated form (1-74) ubiquitin within cortical regions. We directly identify reveal their distributions. Of 20 discriminate tubules vast majority tubular origin (8 10) while primarily hemoglobin subunits (9 10). These trends also ion images demonstrating characterization potential reshape discovery-based because ultimate effector cellular functions. Applications this technology have unravel etiology pathophysiology disease states, informing biologically active proteoforms, remodel proteomic chronic acute disorders.

Language: Английский

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