Single-Cell Transcriptional Heterogeneity Landscapes of Third Heart Field Progenitor Cells

AbstractWhereas the critical roles of innate lymphoid cells (ILCs) in adult are increasingly appreciated, their developmental hierarchy in early human fetus remains largely elusive. In this study, we sorted human hematopoietic stem/progenitor cells, lymphoid progenitors, putative ILC progenitor/precursors and mature ILCs in the fetal hematopoietic, lymphoid and non-lymphoid tissues, from 8 to 12 post-conception weeks, for single-cell RNA-sequencing, followed by computational analysis and functional validation at bulk and single-cell levels. We delineated the early phase of ILC lineage commitment from hematopoietic stem/progenitor cells, which mainly occurred in fetal liver and intestine. We further unveiled interleukin-3 receptor as a surface marker for the lymphoid progenitors in fetal liver with T, B, ILC and myeloid potentials, while IL-3RA– lymphoid progenitors were predominantly B-lineage committed. Notably, we determined the heterogeneity and tissue distribution of each ILC subpopulation, revealing the proliferating characteristics shared by the precursors of each ILC subtype. Additionally, a novel unconventional ILC2 subpopulation (CRTH2– CCR9+ ILC2) was identified in fetal thymus. Taken together, our study illuminates the precise cellular and molecular features underlying the stepwise formation of human fetal ILC hierarchy with remarkable spatiotemporal heterogeneity.

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

Circulation Research ◽

10.1161/res.117.suppl_1.305 ◽

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.

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Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing

Journal of Experimental Medicine ◽

10.1084/jem.20170976 ◽

2017 ◽

Vol 214 (10) ◽

pp. 2875-2887 ◽

Cited By ~ 54

Author(s):

Qin Tang ◽

Sowmya Iyer ◽

Riadh Lobbardi ◽

John C. Moore ◽

Huidong Chen ◽

...

Keyword(s):

Single Cell ◽

Natural Killer ◽

Progenitor Cells ◽

Rna Sequencing ◽

Immune Cell ◽

Interleukin 2 ◽

Kidney Cells ◽

Cell Heterogeneity ◽

Adult Zebrafish ◽

Hematopoietic Stem

Recent advances in single-cell, transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. In this study, we used massively parallel, single-cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow, constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner, our approach was useful in characterizing immune-cell deficiencies within DNA–protein kinase catalytic subunit (prkdc), interleukin-2 receptor γ a (il2rga), and double-homozygous–mutant fish, identifying blood cell losses in T, B, and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types, including two classes of natural killer immune cells, classically defined and erythroid-primed hematopoietic stem and progenitor cells, mucin-secreting kidney cells, and kidney stem/progenitor cells. In total, our work provides the first, comprehensive, single-cell, transcriptomic analysis of kidney and marrow cells in the adult zebrafish.

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

10.1101/461103 ◽

2018 ◽

Cited By ~ 3

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.

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Cardiac embryogenesis

ESC CardioMed ◽

10.1093/med/9780198784906.003.0004_update_001 ◽

2018 ◽

pp. 33-36

Author(s):

Robert G. Kelly

Keyword(s):

Progenitor Cells ◽

Progenitor Cell ◽

Congenital Heart ◽

Heart Defects ◽

Embryonic Heart ◽

Heart Tube ◽

Second Heart Field ◽

Heart Field ◽

Cell Niche ◽

The Right

The embryonic heart forms in anterior lateral splanchnic mesoderm and is derived from Mesp1-expressing progenitor cells. During embryonic folding, the earliest differentiating progenitor cells form the linear heart tube in the ventral midline. The heart tube extends in length and loops to the right as new myocardium is progressively added at the venous and arterial poles from multipotent second heart field cardiovascular progenitor cells in contiguous pharyngeal mesoderm. While the linear heart tube gives rise to the left ventricle, the right ventricle, outflow tract, and a large part of atrial myocardium are derived from the second heart field. Progressive myocardial differentiation is controlled by intercellular signals within the progenitor cell niche. The embryonic heart is the template for septation and growth of the four-chambered definitive heart and defects in progenitor cell deployment result in a spectrum of common forms of congenital heart defects.

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Single-Cell RNA Sequencing of Hematopoietic Stem and Progenitor Cells Treated with Gemcitabine and Carboplatin

Genes ◽

10.3390/genes11050549 ◽

2020 ◽

Vol 11 (5) ◽

pp. 549

Author(s):

Niclas Björn ◽

Ingrid Jakobsen ◽

Kourosh Lotfi ◽

Henrik Gréen

Keyword(s):

Cell Cycle ◽

Cell Proliferation ◽

Single Cell ◽

Progenitor Cells ◽

Myeloid Cell ◽

Enrichment Analysis ◽

Myelogenous Leukemia ◽

Transcriptional Level ◽

Hematopoietic Stem ◽

Stem And Progenitor Cells

Treatments that include gemcitabine and carboplatin induce dose-limiting myelosuppression. The understanding of how human bone marrow is affected on a transcriptional level leading to the development of myelosuppression is required for the implementation of personalized treatments in the future. In this study, we treated human hematopoietic stem and progenitor cells (HSPCs) harvested from a patient with chronic myelogenous leukemia (CML) with gemcitabine/carboplatin. Thereafter, scRNA-seq was performed to distinguish transcriptional effects induced by gemcitabine/carboplatin. Gene expression was calculated and evaluated among cells within and between samples compared to untreated cells. Cell cycle analysis showed that the treatments effectively decrease cell proliferation, indicated by the proportion of cells in the G2M-phase dropping from 35% in untreated cells to 14.3% in treated cells. Clustering and t-SNE showed that cells within samples and between treated and untreated samples were affected differently. Enrichment analysis of differentially expressed genes showed that the treatments influence KEGG pathways and Gene Ontologies related to myeloid cell proliferation/differentiation, immune response, cancer, and the cell cycle. The present study shows the feasibility of using scRNA-seq and chemotherapy-treated HSPCs to find genes, pathways, and biological processes affected among and between treated and untreated cells. This indicates the possible gains of using single-cell toxicity studies for personalized medicine.

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Single-cell RNA-seq reveals a distinct transcriptome signature of aneuploid hematopoietic cells

Blood ◽

10.1182/blood-2017-08-803353 ◽

2017 ◽

Vol 130 (25) ◽

pp. 2762-2773 ◽

Cited By ~ 26

Author(s):

Xin Zhao ◽

Shouguo Gao ◽

Zhijie Wu ◽

Sachiko Kajigaya ◽

Xingmin Feng ◽

...

Keyword(s):

Immune Response ◽

Single Cell ◽

Progenitor Cells ◽

Rna Seq ◽

Hematopoietic Stem ◽

Monosomy 7 ◽

Key Points ◽

Stem And Progenitor Cells ◽

Diploid Cells ◽

Transcriptome Signature

Key Points We distinguished aneuploid cells from diploid cells within the hematopoietic stem and progenitor cells using scRNA-seq. Monosomy 7 cells showed downregulated pathways involved in immune response and maintenance of DNA stability.

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