Revealing cellular and molecular transitions in neonatal germ cell differentiation using single cell RNA sequencing

Abstract Motivation The immune system has diverse types of cells that are differentiated or activated via various signaling pathways and transcriptional regulation upon challenging conditions. Immunophenotyping by flow and mass cytometry are the major approaches for identifying key signaling molecules and transcription factors directing the transition between the functional states of immune cells. However, few proteins can be evaluated by flow cytometry in a single experiment, preventing researchers from obtaining a comprehensive picture of the molecular programs involved in immune cell differentiation. Recent advances in single-cell RNA sequencing (scRNA-seq) have enabled unbiased genome-wide quantification of gene expression in individual cells on a large scale, providing a new and versatile analytical pipeline for studying immune cell differentiation. Results We present VirtualCytometry, a web-based computational pipeline for evaluating immune cell differentiation by exploiting cell-to-cell variation in gene expression with scRNA-seq data. Differentiating cells often show a continuous spectrum of cellular states rather than distinct populations. VirtualCytometry enables the identification of cellular subsets for different functional states of differentiation based on the expression of marker genes. Case studies have highlighted the usefulness of this subset analysis strategy for discovering signaling molecules and transcription factors for human T-cell exhaustion, a state of T-cell dysfunction, in tumor and mouse dendritic cells activated by pathogens. With more than 226 scRNA-seq datasets precompiled from public repositories covering diverse mouse and human immune cell types in normal and disease tissues, VirtualCytometry is a useful resource for the molecular dissection of immune cell differentiation. Availability and implementation www.grnpedia.org/cytometry

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Transcriptional dynamics of pluripotent stem cell-derived endothelial cell differentiation revealed by single-cell RNA sequencing

European Heart Journal ◽

10.1093/eurheartj/ehz351 ◽

2019 ◽

Cited By ~ 2

Author(s):

Ian R McCracken ◽

Richard S Taylor ◽

Fatma O Kok ◽

Fernando de la Cuesta ◽

Ross Dobie ◽

...

Keyword(s):

Stem Cell ◽

Endothelial Cell ◽

Cell Differentiation ◽

Single Cell ◽

Rna Sequencing ◽

Pluripotent Stem Cell ◽

Transcriptional Dynamics ◽

Endothelial Cell Differentiation ◽

Single Cell Rna Sequencing

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Single-cell RNA sequencing reveals species-specific time spans of cell cycle transitions in early oogenesis

Human Molecular Genetics ◽

10.1093/hmg/ddab048 ◽

2021 ◽

Author(s):

Zheng-Hui Zhao ◽

Tie-Gang Meng ◽

Hong-Yong Zhang ◽

Yi Hou ◽

Heide Schatten ◽

...

Keyword(s):

Cell Cycle ◽

Germ Cell ◽

Single Cell ◽

Rna Sequencing ◽

Germ Cells ◽

Cell Cycle Regulators ◽

Sequencing Data ◽

Interspecies Differences ◽

Single Cell Rna Sequencing ◽

Female Germ Cell

Abstract Oogenesis is a highly regulated process and its basic cellular events are evolutionarily conserved. However, the time spans of oogenesis differ substantially among species. To explore these interspecies differences in oogenesis, we performed single-cell RNA-sequencing on mouse and monkey female germ cells and downloaded the single-cell RNA-sequencing data of human female germ cells. The cell cycle analyses indicate that the period and extent of cell cycle transitions are significantly different between the species. Moreover, hierarchical clustering of critical cell cycle genes and the interacting network of cell cycle regulators also exhibit distinguished patterns across species. We propose that differences in the regulation of cell cycle transitions may underlie female germ cell developmental allochrony between species. A better understanding of the cell cycle transition machinery will provide new insights into the interspecies differences in female germ cell developmental time spans.

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Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing

Genome Biology ◽

10.1186/s13059-018-1426-0 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 34

Author(s):

Xiaoping Han ◽

Haide Chen ◽

Daosheng Huang ◽

Huidong Chen ◽

Lijiang Fei ◽

...

Keyword(s):

Stem Cell ◽

Cell Differentiation ◽

Single Cell ◽

Rna Sequencing ◽

High Throughput ◽

Pluripotent Stem Cell ◽

Stem Cell Differentiation ◽

Human Pluripotent Stem Cell ◽

Single Cell Rna Sequencing ◽

Differentiation Pathways

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Single cell RNA sequencing reveals regulation of fetal ovary development in the monkey (Macaca fascicularis)

10.1101/2020.05.22.110064 ◽

2020 ◽

Author(s):

Zheng-Hui Zhao ◽

Chun-Yang Li ◽

Tie-Gang Meng ◽

Yan Wang ◽

Wen-Bo Liu ◽

...

Keyword(s):

Germ Cell ◽

Single Cell ◽

Rna Sequencing ◽

Germ Cells ◽

Leydig Cells ◽

Macaca Fascicularis ◽

Ovary Development ◽

Single Cell Rna Sequencing ◽

Female Germ Cell ◽

Fetal Ovary

ABSTRACTGerm cells are vital for reproduction and heredity. However, the mechanisms underlying female germ cell development in primates, especially in late embryonic stages, remain elusive. Here, we performed single-cell RNA sequencing of 12471 cells from whole fetal ovaries, and explored the communications between germ cells and niche cells. We depicted the two waves of oogenesis at single cell resolution and demonstrated that progenitor theca cells exhibit similar characteristics to Leydig cells in fetal monkey ovaries. Notably, we found that ZGLP1 displays differentially expressed patterns between mouse and monkey, which is not overlapped with NANOG in monkey germ cells, suggesting its role in meiosis entry but not in activating oogenic program in primates. Furthermore, the majority of germ cell clusters that highly expressed PRDM9 and SPO11 might undergo apoptosis after cyst breakdown, leading to germ cell attrition. Overall, our work provides new insights into the molecular and cellular basis of primate fetal ovary development at single-cell resolution.

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Single-cell RNA sequencing reveals regulation of fetal ovary development in the monkey (Macaca fascicularis)

Cell Discovery ◽

10.1038/s41421-020-00219-0 ◽

2020 ◽

Vol 6 (1) ◽

Author(s):

Zheng-Hui Zhao ◽

Chun-Yang Li ◽

Tie-Gang Meng ◽

Yan Wang ◽

Wen-Bo Liu ◽

...

Keyword(s):

Germ Cell ◽

Single Cell ◽

Rna Sequencing ◽

Germ Cells ◽

Leydig Cells ◽

Macaca Fascicularis ◽

Ovary Development ◽

Single Cell Rna Sequencing ◽

Female Germ Cell ◽

Fetal Ovary

AbstractGerm cells are vital for reproduction and heredity. However, the mechanisms underlying female germ cell development in primates, especially in late embryonic stages, remain elusive. Here, we performed single-cell RNA sequencing of 12,471 cells from whole fetal ovaries, and explored the communications between germ cells and niche cells. We depicted the two waves of oogenesis at single-cell resolution and demonstrated that progenitor theca cells exhibit similar characteristics to Leydig cells in fetal monkey ovaries. Notably, we found that ZGLP1 displays differentially expressed patterns between mouse and monkey, which is not overlapped with NANOG in monkey germ cells, suggesting its role in meiosis entry but not in activating oogenic program in primates. Furthermore, the majority of germ cell clusters that sharply express PRDM9 and SPO11 might undergo apoptosis after cyst breakdown, leading to germ cell attrition. Overall, our work provides new insights into the molecular and cellular basis of primate fetal ovary development at single-cell resolution.

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