Single-cell connectomic analysis of adult mammalian lungs DOI Creative Commons
Micha Sam Brickman Raredon, Taylor Adams, Yasir Suhail

et al.

Science Advances, Journal Year: 2019, Volume and Issue: 5(12)

Published: Dec. 5, 2019

Single-cell network analysis demonstrates species-conserved functional roles for pulmonary alveolar cell types.

Language: Английский

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes DOI
Mirjana Efremova,

Miquel Vento-Tormo,

Sarah A. Teichmann

et al.

Nature Protocols, Journal Year: 2020, Volume and Issue: 15(4), P. 1484 - 1506

Published: Feb. 26, 2020

Language: Английский

Citations

2552
Single-cell reconstruction of the early maternal–fetal interface in humans DOI

Roser Vento‐Tormo,

Mirjana Efremova, Rachel A. Botting

et al.

Nature, Journal Year: 2018, Volume and Issue: 563(7731), P. 347 - 353

Published: Nov. 8, 2018

Language: Английский

Citations

1861
Deciphering cell–cell interactions and communication from gene expression DOI Open Access
Erick Armingol, Adam Officer, Olivier Harismendy

et al.

Nature Reviews Genetics, Journal Year: 2020, Volume and Issue: 22(2), P. 71 - 88

Published: Nov. 9, 2020

Language: Английский

Citations

902
Fibroblasts: Origins, definitions, and functions in health and disease DOI Creative Commons
Maksim V. Plikus, Xiaojie Wang, Sarthak Sinha

et al.

Cell, Journal Year: 2021, Volume and Issue: 184(15), P. 3852 - 3872

Published: July 1, 2021

Language: Английский

Citations

655
Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury DOI Creative Commons
Nona Farbehi, Ralph Patrick, Aude Dorison

et al.

eLife, Journal Year: 2019, Volume and Issue: 8

Published: March 26, 2019

Besides cardiomyocytes (CM), the heart contains numerous interstitial cell types which play key roles in repair, regeneration and disease, including fibroblast, vascular immune cells. However, a comprehensive understanding of this interactive community is lacking. We performed single-cell RNA-sequencing total non-CM fraction enriched (Pdgfra-GFP+) fibroblast lineage cells from murine hearts at days 3 7 post-sham or myocardial infarction (MI) surgery. Clustering >30,000 single identified >30 populations representing nine lineages, previously undescribed trajectory present both sham MI leading to uniquely activated state defined part by strong anti-WNT transcriptome signature. also uncovered novel myofibroblast subtypes expressing either pro-fibrotic anti-fibrotic signatures. Our data highlight non-linear dynamics myeloid lineages after cardiac injury, provide an entry point for deeper analysis homeostasis, inflammation, fibrosis, repair regeneration.

Language: Английский

Citations

477
Transcriptional and Cellular Diversity of the Human Heart DOI Open Access
Nathan R. Tucker, Mark Chaffin, Stephen J. Fleming

et al.

Circulation, Journal Year: 2020, Volume and Issue: 142(5), P. 466 - 482

Published: May 14, 2020

The human heart requires a complex ensemble of specialized cell types to perform its essential function. A greater knowledge the intricate cellular milieu is critical increase our understanding cardiac homeostasis and pathology. As recent advances in low-input RNA sequencing have allowed definitions transcriptomes at single-cell resolution scale, we applied these approaches assess transcriptional diversity nonfailing heart.

Language: Английский

Citations

461
ACE-inhibition induces a cardioprotective transcriptional response in the metabolic syndrome heart DOI Creative Commons
Aziza Yakubova, Lieven Thorrez,

Dmitry Svetlichnyy

et al.

Scientific Reports, Journal Year: 2018, Volume and Issue: 8(1)

Published: Oct. 26, 2018

Abstract Cardiovascular disease associated with metabolic syndrome has a high prevalence, but the mechanistic basis of cardiomyopathy remains poorly understood. We characterised cardiac transcriptome in murine (MetS) model (LDLR−/−; ob/ob, DKO) relative to healthy, control heart (C57BL/6, WT) and transcriptional changes induced by ACE-inhibition those hearts. RNA-Seq, differential gene expression transcription factor analysis identified 288 genes differentially expressed between DKO WT hearts implicating 72 pathways. Hallmarks were increased activity integrin-linked kinase signalling, Rho dendritic cell maturation, production nitric oxide reactive oxygen species macrophages, atherosclerosis, LXR-RXR hypertrophy, acute phase response had limited effect on (55 genes, 23 pathways), prominent (1143 104 pathways). In hearts, ACE-I appears counteract some MetS-specific pathways, while also activating cardioprotective mechanisms. conclude that MetS have unique profiles exhibit partially specific ACE-inhibition.

Language: Английский

Citations

401
Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics DOI Creative Commons

Manu P. Kumar,

Jinyan Du,

Georgia Lagoudas

et al.

Cell Reports, Journal Year: 2018, Volume and Issue: 25(6), P. 1458 - 1468.e4

Published: Nov. 1, 2018

Tumor ecosystems are composed of multiple cell types that communicate by ligand-receptor interactions. Targeting interactions (for instance, with immune checkpoint inhibitors) can provide significant benefits for patients. However, our knowledge which occur in a tumor and how these affect outcome is still limited. We present an approach to characterize communication across all microenvironment using single-cell RNA sequencing. apply this identify compare the six syngeneic mouse models. To potentially associated outcome, we regress against phenotypic measurements growth rate. In addition, quantify between T subsets their relation infiltration publicly available human melanoma dataset. Overall, provides tool studying cell-cell interactions, variability tumors, relationship outcome.

Language: Английский

Citations

383
Single-cell reconstruction of the adult human heart during heart failure and recovery reveals the cellular landscape underlying cardiac function DOI
Li Wang, Yu Peng, Bingying Zhou

et al.

Nature Cell Biology, Journal Year: 2020, Volume and Issue: 22(1), P. 108 - 119

Published: Jan. 1, 2020

Language: Английский

Citations

351
Three tissue resident macrophage subsets coexist across organs with conserved origins and life cycles DOI Open Access
Sarah A. Dick, Anthony Wong, Homaira Hamidzada

et al.

Science Immunology, Journal Year: 2022, Volume and Issue: 7(67)

Published: Jan. 7, 2022

Resident macrophages orchestrate homeostatic, inflammatory, and reparative activities. It is appreciated that different tissues instruct specialized macrophage functions. However, individual contain heterogeneous subpopulations, how these subpopulations are related unclear. We asked whether common transcriptional functional elements could reveal an underlying framework across tissues. Using single-cell RNA sequencing random forest modeling, we observed four genes predict three subsets were present in murine heart, liver, lung, kidney, brain. Parabiotic genetic fate mapping studies revealed core markers predicted unique life cycles 17 TLF+ (expressing TIMD4 and/or LYVE1 FOLR2) maintained through self-renewal with minimal monocyte input; CCR2+ (TIMD4−LYVE1−FOLR2−) almost entirely replaced by monocytes, MHC-IIhi (TIMD4−LYVE1−FOLR2−CCR2−), while receiving modest contribution, not continually replaced. Rather, monocyte-derived contributed to the resident population until they reached a defined upper limit after which did outcompete pre-existing macrophages. Developmentally, first emerge yolk sac early fetal organs. Fate mouse human indicated originated from both precursors. Furthermore, most transcriptionally conserved subset between mice humans, despite organ- species-specific differences. Here, define existence of based on cycle properties gene signatures provide starting point understand tissue heterogeneity.

Language: Английский

Citations

341