scholarly journals Single-cell transcriptomics reveals gene expression dynamics of human fetal kidney development

PLoS Biology ◽  
2019 ◽  
Vol 17 (2) ◽  
pp. e3000152 ◽  
Author(s):  
Mazène Hochane ◽  
Patrick R. van den Berg ◽  
Xueying Fan ◽  
Noémie Bérenger-Currias ◽  
Esmée Adegeest ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Kidney Development ◽  
Fetal Kidney ◽  
Gene Expression Dynamics ◽  
Human Fetal Kidney

scholarly journals Dissecting the Global Dynamic Molecular Profiles of Human Fetal Kidney Development by Single-Cell RNA Sequencing

Cell Reports ◽  
2018 ◽  
Vol 24 (13) ◽  
pp. 3554-3567.e3 ◽  
Author(s):  
Ping Wang ◽  
Yidong Chen ◽  
Jun Yong ◽  
Yueli Cui ◽  
Rui Wang ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Kidney Development ◽  
Fetal Kidney ◽  
Global Dynamic ◽  
Single Cell Rna Sequencing ◽  
Molecular Profiles ◽  
Human Fetal Kidney

scholarly journals Dynamics of Cardiac Neutrophil Diversity in Murine Myocardial Infarction

2020 ◽  
Vol 127 (9) ◽  
Author(s):  
Ehsan Vafadarnejad ◽  
Giuseppe Rizzo ◽  
Laura Krampert ◽  
Panagiota Arampatzi ◽  
Anahi-Paula Arias-Loza ◽  
...  
Keyword(s):  
Gene Expression ◽  
Myocardial Infarction ◽  
Bone Marrow ◽  
Single Cell ◽  
Ischemic Heart ◽  
Time Resolved ◽  
Tissue Healing ◽  
Receptor Interactions ◽  
Blood Neutrophils ◽  
Gene Expression Dynamics

Rationale: After myocardial infarction, neutrophils rapidly and massively infiltrate the heart, where they promote both tissue healing and damage. Objective: To characterize the dynamics of circulating and cardiac neutrophil diversity after infarction. Methods and results: We employed single-cell transcriptomics combined with cell surface epitope detection by sequencing to investigate temporal neutrophil diversity in the blood and heart after murine myocardial infarction. At day 1, 3, and 5 after infarction, cardiac Ly6G + (lymphocyte antigen 6G) neutrophils could be delineated into 6 distinct clusters with specific time-dependent patterning and proportions. At day 1, neutrophils were characterized by a gene expression profile proximal to bone marrow neutrophils ( Cd177 , Lcn2 , Fpr1 ), and putative activity of transcriptional regulators involved in hypoxic response ( Hif1a ) and emergency granulopoiesis ( Cebpb ). At 3 and 5 days, 2 major subsets of Siglecf hi (enriched for eg, Icam1 and Tnf ) and Siglecf low ( Slpi, Ifitm1 ) neutrophils were found. Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) analysis in blood and heart revealed that while circulating neutrophils undergo a process of aging characterized by loss of surface CD62L and upregulation of Cxcr4 , heart infiltrating neutrophils acquired a unique SiglecF hi signature. SiglecF hi neutrophils were absent from the bone marrow and spleen, indicating local acquisition of the SiglecF hi signature. Reducing the influx of blood neutrophils by anti-Ly6G treatment increased proportions of cardiac SiglecF hi neutrophils, suggesting accumulation of locally aged neutrophils. Computational analysis of ligand/receptor interactions revealed putative pathways mediating neutrophil to macrophage communication in the myocardium. Finally, SiglecF hi neutrophils were also found in atherosclerotic vessels, revealing that they arise across distinct contexts of cardiovascular inflammation. Conclusions: Altogether, our data provide a time-resolved census of neutrophil diversity and gene expression dynamics in the mouse blood and ischemic heart at the single-cell level, and reveal a process of local tissue specification of neutrophils in the ischemic heart characterized by the acquisition of a SiglecF hi signature.

scholarly journals Single-cell RNA-sequencing reveals thoracolumbar vertebra heterogeneity and rib-genesis in pigs

2021 ◽  
Author(s):  
Jianbo Li ◽  
Ligang Wang ◽  
Dawei Yu ◽  
Junfeng Hao ◽  
Longchao Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Lumbar Vertebra ◽  
Cell Types ◽  
Cell Type ◽  
Specific Expression ◽  
Coupled Process ◽  
Gene Expression Dynamics ◽  
Cell Type Specific ◽  
Thoracolumbar Vertebra

Thoracolumbar vertebra (TLV) and rib primordium (RP) development is a common evolutionary feature across vertebrates although whole-organism analysis of TLV and RP gene expression dynamics has been lacking. Here we investigated the single-cell transcriptomic landscape of thoracic vertebra (TV), lumbar vertebra (LV), and RP cells from a pig embryo at 27 days post-fertilization (dpf) and identified six cell types with distinct gene-expression signatures. In-depth dissection of the gene-expression dynamics and RNA velocity revealed a coupled process of osteogenesis and angiogenesis during TLV and rib development. Further analysis of cell-type-specific and strand-specific expression uncovered the extremely high levels of HOXA10 3'-UTR sequence specific to osteoblast of LV cells, which may function as anti-HOXA10-antisense by counteracting the HOXA10-antisense effect to determine TLV transition. Thus, this work provides a valuable resource for understanding embryonic osteogenesis and angiogenesis underlying vertebrate TLV and RP development at the cell-type-specific resolution, which serves as a comprehensive view on the transcriptional profile of animal embryo development.

scholarly journals Exploiting variability of single cells to uncover the in vivo hierarchy of miRNA targets

2015 ◽  
Author(s):  
Andrzej Jerzy Rzepiela ◽  
Arnau Vina-Vilaseca ◽  
Jeremie Breda ◽  
Souvik Ghosh ◽  
Afzal P Syed ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Single Cells ◽  
Human Embryonic Kidney Cells ◽  
Mirna Targets ◽  
Wide Range ◽  
Gene Expression Dynamics ◽  
Cell To Cell Variability ◽  
First Time

MiRNAs are post-transcriptional repressors of gene expression that may additionally reduce the cell-to-cell variability in protein expression, induce correlations between target expression levels and provide a layer through which targets can influence each other's expression as 'competing RNAs' (ceRNAs). Here we combined single cell sequencing of human embryonic kidney cells in which the expression of two distinct miRNAs was induced over a wide range, with mathematical modeling, to estimate Michaelis-Menten (KM)-type constants for hundreds of evolutionarily conserved miRNA targets. These parameters, which we inferred here for the first time in the context of the entire network of endogenous miRNA targets, vary over ~2 orders of magnitude. They reveal an in vivo hierarchy of miRNA targets, defined by the concentration of miRNA-Argonaute complexes at which the targets are most sensitively down-regulated. The data further reveals miRNA-induced correlations in target expression at the single cell level, as well as the response of target noise to the miRNA concentration. The approach is generalizable to other miRNAs and post-transcriptional regulators and provides a deeper understanding of gene expression dynamics.

scholarly journals Single cell resolution regulatory landscape of the mouse kidney highlights cellular differentiation programs and renal disease targets

2020 ◽  
Author(s):  
Zhen Miao ◽  
Michael S. Balzer ◽  
Ziyuan Ma ◽  
Hongbo Liu ◽  
Junnan Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Kidney Development ◽  
Developmental Stages ◽  
Major Gene ◽  
Cell Types ◽  
Regulatory Elements ◽  
Open Chromatin ◽  
Cell Type ◽  
Single Nucleotide Variants

AbstractDetermining the epigenetic program that generates unique cell types in the kidney is critical for understanding cell-type heterogeneity during tissue homeostasis and injury response.Here, we profiled open chromatin and gene expression in developing and adult mouse kidneys at single cell resolution. We show critical reliance of gene expression on distal regulatory elements (enhancers). We define key cell type-specific transcription factors and major gene-regulatory circuits for kidney cells. Dynamic chromatin and expression changes during nephron progenitor differentiation demonstrated that podocyte commitment occurs early and is associated with sustained Foxl1 expression. Renal tubule cells followed a more complex differentiation, where Hfn4a was associated with proximal and Tfap2b with distal fate. Mapping single nucleotide variants associated with human kidney disease identified critical cell types, developmental stages, genes, and regulatory mechanisms.We provide a global single cell resolution view of chromatin accessibility of kidney development. The dataset is available via interactive public websites.

scholarly journals FP065THE AVERAGE AREAS OF GLOMERULAR PROFILES IN DIFFERENT CORTICAL ZONES DURING HUMAN FETAL KIDNEY DEVELOPMENT

2015 ◽  
Vol 30 (suppl_3) ◽  
pp. iii86-iii86
Author(s):  
Marija Bjelakovic ◽  
Slobodan Vlajkovic ◽  
Goran Bjelakovic
Keyword(s):  
Kidney Development ◽  
Fetal Kidney ◽  
Human Fetal Kidney

Gene Expression Dynamics During Germline Specification in Mice Identified by Quantitative Single-Cell Gene Expression Profiling1

2006 ◽  
Vol 75 (5) ◽  
pp. 705-716 ◽  
Author(s):  
Yukihiro Yabuta ◽  
Kazuki Kurimoto ◽  
Yasuhide Ohinata ◽  
Yoshiyuki Seki ◽  
Mitinori Saitou
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Cell Gene Expression ◽  
Gene Expression Dynamics ◽  
Cell Gene

scholarly journals Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy

2011 ◽  
Vol 7 (1) ◽  
pp. 80-88 ◽  
Author(s):  
Jonathan W Young ◽  
James C W Locke ◽  
Alphan Altinok ◽  
Nitzan Rosenfeld ◽  
Tigran Bacarian ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Time Lapse ◽  
Time Lapse Microscopy ◽  
Cell Gene Expression ◽  
Gene Expression Dynamics ◽  
Cell Gene
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