Giotto: a toolbox for integrative analysis and visualization of spatial expression data

Genome biology, Journal Year: 2021, Volume and Issue: 22(1)

Published: March 8, 2021

Abstract Spatial transcriptomic and proteomic technologies have provided new opportunities to investigate cells in their native microenvironment. Here we present Giotto, a comprehensive open-source toolbox for spatial data analysis visualization. The module provides end-to-end by implementing wide range of algorithms characterizing tissue composition, expression patterns, cellular interactions. Furthermore, single-cell RNAseq can be integrated cell-type enrichment analysis. visualization allows users interactively visualize outputs imaging features. To demonstrate its general applicability, apply Giotto datasets encompassing diverse platforms.

Language: Английский

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Acute kidney injury in critically ill patients with COVID-19

Intensive Care Medicine, Journal Year: 2020, Volume and Issue: 46(7), P. 1339 - 1348

Published: June 12, 2020

Language: Английский

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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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Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: April 15, 2021

Abstract Determining the epigenetic program that generates unique cell types in kidney is critical for understanding cell-type heterogeneity during tissue homeostasis and injury response. Here, we profile open chromatin gene expression developing adult mouse kidneys at single resolution. We show reliance of on distal regulatory elements (enhancers). reveal key type-specific transcription factors major gene-regulatory circuits cells. Dynamic changes nephron progenitor differentiation demonstrates podocyte commitment occurs early associated with sustained Foxl1 expression. Renal tubule cells follow a more complex differentiation, where Hfn4a proximal Tfap2b fate. Mapping nucleotide variants human disease implicates types, developmental stages, genes, mechanisms. The multi-omics atlas reveals remodeling events dynamics development.

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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Multi-omics integration in the age of million single-cell data

Nature Reviews Nephrology, Journal Year: 2021, Volume and Issue: 17(11), P. 710 - 724

Published: Aug. 20, 2021

Language: Английский

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Spatial charting of single-cell transcriptomes in tissues

Nature Biotechnology, Journal Year: 2022, Volume and Issue: 40(8), P. 1190 - 1199

Published: March 21, 2022

Language: Английский

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A Comprehensive Map of mRNAs and Their Isoforms across All 14 Renal Tubule Segments of Mouse

Journal of the American Society of Nephrology, Journal Year: 2021, Volume and Issue: 32(4), P. 897 - 912

Published: March 4, 2021

The repertoire of protein expression along the renal tubule depends both on regulation transcription and alternative splicing that can generate multiple proteins from a single gene.A full-length, small-sample RNA-seq protocol profiled transcriptomes for all 14 segments microdissected mouse kidneys.This study identified >34,000 transcripts, including 3709 were expressed in segment-specific manner. All data are provided as an online resource (https://esbl.nhlbi.nih.gov/MRECA/Nephron/). Many genes unique patterns solute carriers, factors, or G protein-coupled receptors account function. Mapping distribution transcripts associated with Wnk-SPAK-PKA signaling, renin-angiotensin-aldosterone cystic diseases kidney illustrated applications resource. method allowed full-length mapping reads, which facilitated comprehensive, unbiased characterization exon usage tubule, known isoforms Cldn10, Kcnj1 (ROMK), Slc12a1 (NKCC2), Wnk1, Stk39 (SPAK), Slc14a2 (UT-A urea transporter). It also many novel distribution. These included variants altered structure (Slc9a8, Khk, Tsc22d1, Scoc), may affect untranslated, regulatory regions (Pth1r, Pkar1a, Dab2).Full-length, sequencing gene-expression tubule. data, resource, include quantitative qualitative differences transcripts. Identification prove critical to understanding physiology pathophysiology.

Language: Английский

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Single-Cell Profiling of AKI in a Murine Model Reveals Novel Transcriptional Signatures, Profibrotic Phenotype, and Epithelial-to-Stromal Crosstalk

Journal of the American Society of Nephrology, Journal Year: 2020, Volume and Issue: 31(12), P. 2793 - 2814

Published: Oct. 28, 2020

Significance Statement Because current management of the rapid renal-function decline in AKI is merely supportive, deeper understanding AKI-perturbed molecular pathways needed to identify targets with potential lead improved treatment. In a murine model, authors used single-cell RNA sequencing, single-molecule situ hybridization, and protein expression analyses create first comprehensive renal cell type–specific transcriptional profiles for multiple stages. Their findings revealed marked nephrogenic signature surprising mixed-identity cells (expressing markers different types) injured tubules. Moreover, identified pathologic epithelial-to-stromal crosstalk several novel genes not previously implicated AKI, demonstrated that older onset age exacerbates outcome. This work provides rich resource examining genetics AKI. Background Current potentially fatal disorder can also initiate or exacerbate CKD, supportive. Therefore, perturbed Methods We performed sequencing (scRNA-seq) clinically relevant unilateral ischemia-reperfusion model at days 1, 2, 4, 7, 11, 14 after onset. Using real-time quantitative PCR, immunofluorescence, Western blotting, both chromogenic hybridizations, we validated signatures experiments. Results Our show time course changing gene patterns stages all types. observed elevated crucial injury response factors—including kidney molecule-1 (Kim1), lipocalin 2 (Lcn2), keratin 8 (Krt8)—and ( Ahnak , Sh3bgrl3 Col18a1 ) examined pathologies. induced proximal tubule dedifferentiation, pronounced represented by Sox4 Cd24a . caused formation “mixed-identity cells” are normally seen only during early development. The tubules acquired proinflammatory profibrotic phenotype; moreover, dramatically modified ligand-receptor crosstalk, interactions. Advancing was associated maladaptive fibrosis. Conclusions scRNA-seq, comprehensive, cell-specific provide valuable results fully define AKI-associated dedifferentiation programs, genes, younger mice, highlight injury.

Language: Английский

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Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16high Cells In Vivo

Cell Metabolism, Journal Year: 2020, Volume and Issue: 32(5), P. 814 - 828.e6

Published: Sept. 18, 2020

Language: Английский

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