scholarly journals Deciphering cell lineage specification during male sex determination with single-cell RNA sequencing

2017 ◽  
Author(s):  
Isabelle Stévant ◽  
Yasmine Neirjinck ◽  
Christelle Borel ◽  
Jessica Escoffier ◽  
Lee B. Smith ◽  
...  
Keyword(s):  
Sex Determination ◽  
Single Cell ◽  
Progenitor Cells ◽  
Rna Sequencing ◽  
Cell Fate ◽  
Time Course ◽  
Cell Lineage ◽  
Lineage Specification ◽  
Cell Fate Decisions ◽  
Single Cell Rna Sequencing

SummaryThe gonad is a unique biological system for studying cell fate decisions. However, major questions remain regarding the identity of somatic progenitor cells and the transcriptional events driving cell differentiation. Using time course single cell RNA sequencing on XY mouse gonads during sex determination, we identified a single population of somatic progenitor cells prior sex determination. A subset of these progenitors differentiate into Sertoli cells, a process characterized by a highly dynamic genetic program consisting of sequential waves of gene expression. Another subset of multipotent cells maintains their progenitor state but undergo significant transcriptional changes that restrict their competence towards a steroidogenic fate required for the differentiation of fetal Leydig cells. These results question the dogma of the existence of two distinct somatic cell lineages at the onset of sex determination and propose a new model of lineage specification from a unique progenitor cell population.

scholarly journals Deciphering Cell Lineage Specification during Male Sex Determination with Single-Cell RNA Sequencing

Cell Reports ◽  
2018 ◽  
Vol 22 (6) ◽  
pp. 1589-1599 ◽  
Author(s):  
Isabelle Stévant ◽  
Yasmine Neirijnck ◽  
Christelle Borel ◽  
Jessica Escoffier ◽  
Lee B. Smith ◽  
...  
Keyword(s):  
Sex Determination ◽  
Single Cell ◽  
Rna Sequencing ◽  
Cell Lineage ◽  
Lineage Specification ◽  
Single Cell Rna Sequencing ◽  
Male Sex

scholarly journals Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

2019 ◽  
Author(s):  
Anna SE Cuomo ◽  
Daniel D Seaton ◽  
Davis J McCarthy ◽  
Iker Martinez ◽  
Marc Jan Bonder ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Cell Fate ◽  
Cell Biology ◽  
Population Variation ◽  
Ips Cell ◽  
Cell Fate Decisions ◽  
Common Genetic Variants ◽  
Single Cell Rna Sequencing

AbstractRecent developments in stem cell biology have enabled the study of cell fate decisions in early human development that are impossible to study in vivo. However, understanding how development varies across individuals and, in particular, the influence of common genetic variants during this process has not been characterised. Here, we exploit human iPS cell lines from 125 donors, a pooled experimental design, and single-cell RNA-sequencing to study population variation of endoderm differentiation. We identify molecular markers that are predictive of differentiation efficiency, and utilise heterogeneity in the genetic background across individuals to map hundreds of expression quantitative trait loci that influence expression dynamically during differentiation and across cellular contexts.

Using Single-Cell and Spatial Transcriptomes to Understand Stem Cell Lineage Specification During Early Embryo Development

2020 ◽  
Vol 21 (1) ◽  
pp. 163-181
Author(s):  
Guangdun Peng ◽  
Guizhong Cui ◽  
Jincan Ke ◽  
Naihe Jing
Keyword(s):  
Stem Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
Cell Fate ◽  
Cell Lineage ◽  
Stem Cell Differentiation ◽  
Early Embryo ◽  
Stem Cell Lineage ◽  
Single Cell Rna Sequencing ◽  
Cell Organization

Embryonic development and stem cell differentiation provide a paradigm to understand the molecular regulation of coordinated cell fate determination and the architecture of tissue patterning. Emerging technologies such as single-cell RNA sequencing and spatial transcriptomics are opening new avenues to dissect cell organization, the divergence of morphological and molecular properties, and lineage allocation. Rapid advances in experimental and computational tools have enabled researchers to make many discoveries and revisit old hypotheses. In this review, we describe the use of single-cell RNA sequencing in studies of molecular trajectories and gene regulation networks for stem cell lineages, while highlighting the integratedexperimental and computational analysis of single-cell and spatial transcriptomes in the molecular annotation of tissue lineages and development during postimplantation gastrulation.

Developmental trajectory of oligodendrocyte progenitor cells in the human brain revealed by single cell RNA sequencing

Glia ◽  
2020 ◽  
Vol 68 (6) ◽  
pp. 1291-1303 ◽  
Author(s):  
Kelly Perlman ◽  
Charles P. Couturier ◽  
Moein Yaqubi ◽  
Arnaud Tanti ◽  
Qiao‐Ling Cui ◽  
...  
Keyword(s):  
Human Brain ◽  
Single Cell ◽  
Progenitor Cells ◽  
Rna Sequencing ◽  
Developmental Trajectory ◽  
Oligodendrocyte Progenitor Cells ◽  
Oligodendrocyte Progenitor ◽  
Single Cell Rna Sequencing

Abstract 305: Single Cell RNA Sequencing of Adult Cardiac c-kit+ Cells in a Murine Lineage Tracing Model

2015 ◽  
Vol 117 (suppl_1) ◽  
Author(s):  
Bryan D Maliken ◽  
Onur Kanisicak ◽  
Jeffery D Molkentin
Keyword(s):  
Single Cell ◽  
Progenitor Cells ◽  
Rna Sequencing ◽  
Cardiac Injury ◽  
Mesenchymal Cells ◽  
Lineage Tracing ◽  
Tyrosine Kinase Receptor ◽  
Early Differentiation ◽  
Gfp Reporter ◽  
Single Cell Rna Sequencing

A subset of adult cardiac resident cells defined by the stem cell factor tyrosine kinase receptor termed c-kit, are believed to have myogenic potential and are now being delivered via intracoronary infusion to presumably promote cardiac regeneration and improve ventricular function after ischemic cardiac injury. However, recent studies have shown that despite these benefits, c-kit+ progenitor cells in the adult murine heart are more inclined to take on an endothelial rather than cardiomyocyte lineage. To better define the factors involved in early differentiation of these resident cardiac progenitor cells and to distinguish distinct cell subpopulations, we performed single cell RNA sequencing on c-kit+ cells from Kit-Cre lineage traced GFP reporter mice versus total mesenchymal cells from the heart that were CD31- and CD45-. Cells were isolated by cardiac digestion and FACS was performed, positively sorting for the c-kit+ lineage while negatively sorting for CD31 and CD45 to eliminate endothelial and leukocyte progenitor contamination, respectively. Following this isolation, cells were examined to determine GFP reporter status and then submitted for single cell RNA sequencing using the Fluidigm A1 system. Clustering of 654 genes from this data identified 6 distinct subpopulations indicating various stages of early differentiation among CD31- and CD45-negative cardiac interstitial cells. Furthermore, comparison of GFP+ c-kit cells to the total non-GFP mesenchymal cells identified 75 differentially expressed transcripts. These unique gene signatures may help parse the genes that underlie cellular plasticity in the heart and define the best molecular lineages for transdifferentiation into cardiac myocytes.

scholarly journals Basal stem cell fate specification is mediated by SMAD signaling in the developing human lung

2018 ◽  
Author(s):  
Alyssa J. Miller ◽  
Qianhui Yu ◽  
Michael Czerwinski ◽  
Yu-Hwai Tsai ◽  
Renee F. Conway ◽  
...  
Keyword(s):  
Single Cell ◽  
Progenitor Cells ◽  
Cell Fate ◽  
Basal Cell ◽  
Human Lung ◽  
Branching Morphogenesis ◽  
Basal Cells ◽  
Smad Signaling ◽  
Cell Fate Decisions ◽  
Cell Transition

AbstractBasal stem cells (basal cells), located in the bronchi and trachea of the human lung epithelium, play a critical role in normal airway homeostasis and repair, and have been implicated in the development of diseases such as cancer1-4. Additionally, basal-like cells contribute to alveolar regeneration and fibrosis following severe injury5-8. However, the developmental origin of basal cells in humans is unclear. Previous work has shown that specialized progenitor cells exist at the tips of epithelial tubes during lung branching morphogenesis, and in mice, give rise to all alveolar and airway lineages9,10. These ‘bud tip progenitor cells’ have also been described in the developing human lung11-13, but the mechanisms controlling bud tip differentiation into specific cell lineages, including basal cells, are unknown. Here, we interrogated the bud tip-to-basal cell transition using human tissue specimens, bud tip progenitor organoid cultures11, and single-cell transcriptomics. We used single-cell mRNA sequencing (scRNAseq) of developing human lung specimens from 15-21 weeks gestation to identify molecular signatures and cell states in the developing human airway epithelium. We then inferred differentiation trajectories during bud tip-to-airway differentiation, which revealed a previously undescribed transitional cell state (‘hub progenitors’) and implicated SMAD signaling as a regulator of the bud tip-to-basal cell transition. We used bud tip progenitor organoids to show that TGFT1 and BMP4 mediated SMAD signaling robustly induced the transition into functional basal-like cells, and these in vitro-derived basal cells exhibited clonal expansion, self-renewal and multilineage differentiation. This work provides a framework for deducing and validating key regulators of cell fate decisions using single cell transcriptomics and human organoid models. Further, the identification of SMAD signaling as a critical regulator of newly born basal cells in the lung may have implications for regenerative medicine, basal cell development in other organs, and understanding basal cell misregulation in disease.

scholarly journals Generation, transcriptome profiling, and functional validation of cone-rich human retinal organoids

2019 ◽  
Vol 116 (22) ◽  
pp. 10824-10833 ◽  
Author(s):  
Sangbae Kim ◽  
Albert Lowe ◽  
Rachayata Dharmat ◽  
Seunghoon Lee ◽  
Leah A. Owen ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Cell Fate ◽  
Time Course ◽  
Transcriptome Profiling ◽  
Retinal Cell ◽  
Peripheral Retina ◽  
Functional Validation ◽  
Retinal Progenitor ◽  
Retinal Differentiation

Rod and cone photoreceptors are light-sensing cells in the human retina. Rods are dominant in the peripheral retina, whereas cones are enriched in the macula, which is responsible for central vision and visual acuity. Macular degenerations affect vision the most and are currently incurable. Here we report the generation, transcriptome profiling, and functional validation of cone-rich human retinal organoids differentiated from hESCs using an improved retinal differentiation system. Induced by extracellular matrix, aggregates of hESCs formed single-lumen cysts composed of epithelial cells with anterior neuroectodermal/ectodermal fates, including retinal cell fate. Then, the cysts were en bloc-passaged, attached to culture surface, and grew, forming colonies in which retinal progenitor cell patches were found. Following gentle cell detachment, retinal progenitor cells self-assembled into retinal epithelium—retinal organoid—that differentiated into stratified cone-rich retinal tissue in agitated cultures. Electron microscopy revealed differentiating outer segments of photoreceptor cells. Bulk RNA-sequencing profiling of time-course retinal organoids demonstrated that retinal differentiation in vitro recapitulated in vivo retinogenesis in temporal expression of cell differentiation markers and retinal disease genes, as well as in mRNA alternative splicing. Single-cell RNA-sequencing profiling of 8-mo retinal organoids identified cone and rod cell clusters and confirmed the cone enrichment initially revealed by quantitative microscopy. Notably, cones from retinal organoids and human macula had similar single-cell transcriptomes, and so did rods. Cones in retinal organoids exhibited electrophysiological functions. Collectively, we have established cone-rich retinal organoids and a reference of transcriptomes that are valuable resources for retinal studies.

scholarly journals Combining single-cell RNA-sequencing with a molecular atlas unveils new markers for Caenorhabditis elegans neuron classes

2020 ◽  
Author(s):  
Ramiro Lorenzo ◽  
Michiho Onizuka ◽  
Matthieu Defrance ◽  
Patrick Laurent
Keyword(s):  
Caenorhabditis Elegans ◽  
Single Cell ◽  
Rna Sequencing ◽  
Cell Fate ◽  
Single Neuron ◽  
Genetic Manipulations ◽  
C Elegans ◽  
Single Cell Rna Sequencing ◽  
Normal Differentiation

Abstract Single-cell RNA-sequencing (scRNA-seq) of the Caenorhabditis elegans nervous system offers the unique opportunity to obtain a partial expression profile for each neuron within a known connectome. Building on recent scRNA-seq data and on a molecular atlas describing the expression pattern of ∼800 genes at the single cell resolution, we designed an iterative clustering analysis aiming to match each cell-cluster to the ∼100 anatomically defined neuron classes of C. elegans. This heuristic approach successfully assigned 97 of the 118 neuron classes to a cluster. Sixty two clusters were assigned to a single neuron class and 15 clusters grouped neuron classes sharing close molecular signatures. Pseudotime analysis revealed a maturation process occurring in some neurons (e.g. PDA) during the L2 stage. Based on the molecular profiles of all identified neurons, we predicted cell fate regulators and experimentally validated unc-86 for the normal differentiation of RMG neurons. Furthermore, we observed that different classes of genes functionally diversify sensory neurons, interneurons and motorneurons. Finally, we designed 15 new neuron class-specific promoters validated in vivo. Amongst them, 10 represent the only specific promoter reported to this day, expanding the list of neurons amenable to genetic manipulations.

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