scholarly journals Single cell transcriptomics reveal temporal dynamics of critical regulators of germ cell fate during mouse sex determination

2019 ◽  
Author(s):  
Chloé Mayère ◽  
Yasmine Neirijnck ◽  
Pauline Sararols ◽  
Chris M Rands ◽  
Isabelle Stévant ◽  
...  
Keyword(s):  
Sex Determination ◽  
Germ Cell ◽  
Single Cell ◽  
Cell Fate ◽  
Gene Networks ◽  
Network Inference ◽  
Temporal Dynamics ◽  
Intron Retention ◽  
Gonad Development ◽  
Altered Expression

SummaryDespite the importance of germ cell (GC) differentiation for sexual reproduction, the gene networks underlying their fate remain unclear. Here, we comprehensively characterize the gene expression dynamics during sex determination based on single-cell RNA sequencing of 14,914 XX and XY mouse GCs between embryonic days (E) 9.0 and 16.5. We found that XX and XY GCs diverge transcriptionally as early as E11.5 with upregulation of genes downstream of the Bone morphogenic protein (BMP) and Nodal/Activin pathways in XY and XX GCs, respectively. We also identified a sex-specific upregulation of genes associated with negative regulation of mRNA processing and an increase in intron retention consistent with a reduction in mRNA splicing in XY testicular GCs by E13.5. Using computational gene regulation network inference analysis, we identified sex-specific, sequential waves of putative key regulator genes during GC differentiation and revealed that the meiotic genes are regulated by positive and negative master modules acting in an antagonistic fashion. Finally, we found that rare adrenal GCs enter meiosis similarly to ovarian GCs but display altered expression of master genes controlling the female and male genetic programs, indicating that the somatic environment is important for GC function. Our data is available on a web platform and provides a molecular roadmap of GC sex determination at single-cell resolution, which will serve as a valuable resource for future studies of gonad development, function and disease.

scholarly journals Single‐cell transcriptomics reveal temporal dynamics of critical regulators of germ cell fate during mouse sex determination

2021 ◽  
Vol 35 (4) ◽  
Author(s):  
Chloé Mayère ◽  
Yasmine Neirijnck ◽  
Pauline Sararols ◽  
Chris M. Rands ◽  
Isabelle Stévant ◽  
...  
Keyword(s):  
Sex Determination ◽  
Germ Cell ◽  
Single Cell ◽  
Cell Fate ◽  
Temporal Dynamics

scholarly journals Biological network inference from single-cell multi-omics data using heterogeneous graph transformer

2021 ◽  
Author(s):  
Anjun Ma ◽  
Xiaoying Wang ◽  
Cankun Wang ◽  
Jingxian Li ◽  
Tong Xiao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Single Cell ◽  
Gene Networks ◽  
Network Inference ◽  
Lung Tumor ◽  
Superior Performance ◽  
Omics Data ◽  
Learning Platform ◽  
Cell Clustering ◽  
Cell Cell

We present DeepMAPS, a deep learning platform for cell-type-specific biological gene network inference from single-cell multi-omics (scMulti-omics). DeepMAPS includes both cells and genes in a heterogeneous graph to infer cell-cell, cell-gene, and gene-gene relations simultaneously. The graph attention neural network considers a cell and a gene with both local and global information, making DeepMAPS more robust to data noises. We benchmarked DeepMAPS on 18 datasets for cell clustering and network inference, and the results showed that our method outperforms various existing tools. We further applied DeepMAPS on a case study of lung tumor leukocyte CITE-seq data and observed superior performance in cell clustering, and predicted biologically meaningful cell-cell communication pathways based on the inferred gene networks. To improve the feasibility and ensure the reproducibility of analyzing scMulti-omics data, we deployed a webserver with multi-functions and various visualizations. Overall, we valued DeepMAPS as a novel platform of the state-of-the-art deep learning model in the single-cell study and can promote the use of scMulti-omics data in the community.

scholarly journals The Chromatin State during Gonadal Sex Determination

2021 ◽  
pp. 1-9
Author(s):  
Shannon Dupont ◽  
Blanche Capel
Keyword(s):  
Sex Determination ◽  
Cell Fate ◽  
Granulosa Cell ◽  
Histone Modifications ◽  
Granulosa Cells ◽  
Gonad Development ◽  
Chromatin State ◽  
Supporting Cells ◽  
Direct Role ◽  
Specific Factors

At embryonic day (E) 10.5, prior to gonadal sex determination, XX and XY gonads are bipotential and able to differentiate into either a testis or an ovary. At this point, they are transcriptionally and morphologically indistinguishable. Sex determination begins around E11.5 in the mouse when the supporting cell lineage commits to either Sertoli or granulosa cell fate. Testis-specific factors such as SRY and SOX9 drive differentiation of bipotential-supporting cells into the Sertoli cell pathway, whereas ovary-specific factors like WNT4 and FOXL2 guide differentiation into granulosa cells. It is known that these 2 pathways are mutually antagonistic, and repression of the alternative fate is critical for maintenance of the testis or ovary programs. While we understand much about the transcription factor networks guiding the process of sex determination, it is only more recently that we have begun to understand how this process is epigenetically controlled. Studies in the past decade have demonstrated the importance of the chromatin state for gene expression and cell fate commitment, with histone modifications and DNA accessibility having a direct role in gene regulation. It is now clear that the chromatin state during sex determination is dynamic and likely critical for the establishment and/or maintenance of the transcriptional programs. Prior to sex determination, supporting cells have similar chromatin structure and histone modification profiles, reflecting the bipotential nature of these cells. After differentiation to Sertoli or granulosa cells, the chromatin state acquires sex-specific profiles. The proteins that regulate the deposition of histone modifications or the opening of compact chromatin likely play an important role in Sertoli and granulosa cell fate commitment and gonad development. Here, we describe studies profiling the chromatin state during gonadal sex determination and one example in which depletion of <i>Cbx2</i>, a member of the Polycomb Repressive Complex 1 (PRC1), causes male-to-female sex reversal due to a failure to repress the ovarian pathway.

Data Integration of Hybrid Microarray and Single Cell Expression Data to Enhance Gene Network Inference

2019 ◽  
Vol 14 (3) ◽  
pp. 255-268 ◽  
Author(s):  
Wei Zhang ◽  
Wenchao Li ◽  
Jianming Zhang ◽  
Ning Wang
Keyword(s):  
Single Cell ◽  
In Silico ◽  
Gene Networks ◽  
Network Inference ◽  
Performance Metrics ◽  
Information Source ◽  
Inference Algorithm ◽  
Expression Data ◽  
Complementary Information ◽  
Cell Expression

Background: Gene Regulatory Network (GRN) inference algorithms aim to explore casual interactions between genes and transcriptional factors. High-throughput transcriptomics data including DNA microarray and single cell expression data contain complementary information in network inference. Objective: To enhance GRN inference, data integration across various types of expression data becomes an economic and efficient solution. Method: In this paper, a novel E-alpha integration rule-based ensemble inference algorithm is proposed to merge complementary information from microarray and single cell expression data. This paper implements a Gradient Boosting Tree (GBT) inference algorithm to compute importance scores for candidate gene-gene pairs. The proposed E-alpha rule quantitatively evaluates the credibility levels of each information source and determines the final ranked list. Results: Two groups of in silico gene networks are applied to illustrate the effectiveness of the proposed E-alpha integration. Experimental outcomes with size50 and size100 in silico gene networks suggest that the proposed E-alpha rule significantly improves performance metrics compared with single information source. Conclusion: In GRN inference, the integration of hybrid expression data using E-alpha rule provides a feasible and efficient way to enhance performance metrics than solely increasing sample sizes.

scholarly journals Single Cell Sequencing Reveals Early PGC-like Intermediates During Mouse Primed to Naïve Transition

2021 ◽  
Author(s):  
Jing Liu ◽  
Shengyong Yu ◽  
Chunhua Zhou ◽  
Jiangping He ◽  
Xingnan Huang ◽  
...  
Keyword(s):  
Germ Cell ◽  
Single Cell ◽  
Cell Fate ◽  
Single Cell Analysis ◽  
Primordial Germ Cell ◽  
Model System ◽  
Cell Analysis ◽  
Rna Seq ◽  
Single Cell Sequencing

Abstract Single cell analysis provides clarity unattainable with bulk approaches. Here we apply single cell RNA-seq to a newly established BMP4 induced mouse primed to naive transition (Bi-PNT) system and show that the reset is not a direct reversal of cell fate but through developmental intermediates. We first show that mEpiSCs bifurcate into c-Kit+ naïve and c-Kit- placenta-like cells, among which, the naive branch undergoes further transition through a primordial germ cell-like cells (PGCLCs) intermediate capable of spermatogenesis in vivo. Indeed, deficiency of Prdm1/Blimp1, the key regulator for PGC specification, blocks the induction of PGCLCs and naïve cells. Instead, Gata2 knockout arrests placenta-like fate, but facilitates the generation of PGCLCs. Our results not only reveal a newly cell fate dynamics between primed and naive states at single-cell resolution, but also provide a model system to explore mechanisms involved in regaining germline competence from primed pluripotency.

scholarly journals Single-cell transcriptomics of the mouse gonadal soma reveals the establishment of sexual dimorphism in distinct cell lineages

2018 ◽  
Author(s):  
Isabelle Stévant ◽  
Françoise Kühne ◽  
Andy Greenfield ◽  
Marie-Christine Chaboissier ◽  
Emmanouil T. Dermitzakis ◽  
...  
Keyword(s):  
Time Series ◽  
Sex Determination ◽  
Single Cell ◽  
Cell Fate ◽  
Somatic Cells ◽  
Supporting Cells ◽  
Single Population ◽  
Cell Lineages ◽  
Multipotent Progenitors ◽  
Distinct Cell

SummarySex determination is a unique process that allows the study of multipotent progenitors and their acquisition of sex-specific fates during differentiation of the gonad into a testis or an ovary. Using time-series single-cell RNA sequencing (scRNA-seq) on ovarian Nr5a1-GFP+ somatic cells during sex determination, we identified a single population of early progenitors giving rise to both pre-granulosa cells and potential steroidogenic precursor cells. By comparing time-series scRNA-seq of XX and XY somatic cells, we demonstrate that the supporting cells emerge from the early progenitors with a non-sex-specific transcriptomic program, before pre-granulosa and Sertoli cells acquire their sex-specific identity. In XX and XY steroidogenic precursors similar transcriptomic profiles underlie the acquisition of cell fate, but with a delay in XX cells. Our data provide a novel framework, at single-cell resolution, for further interrogation of the molecular and cellular basis of mammalian sex determination.

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 Crosstalk Between Retinoic Acid and Sex-Related Genes Controls Germ Cell Fate and Gametogenesis in Medaka

2021 ◽  
Vol 8 ◽  
Author(s):  
Mateus C. Adolfi ◽  
Amaury Herpin ◽  
Anabel Martinez-Bengochea ◽  
Susanne Kneitz ◽  
Martina Regensburger ◽  
...  
Keyword(s):  
Retinoic Acid ◽  
Cell Differentiation ◽  
Sex Determination ◽  
Germ Cell ◽  
Cell Fate ◽  
Germ Cells ◽  
Sex Differentiation ◽  
Model Species ◽  
Fish Model ◽  
Germ Cell Differentiation

Sex determination (SD) is a highly diverse and complex mechanism. In vertebrates, one of the first morphological differences between the sexes is the timing of initiation of the first meiosis, where its initiation occurs first in female and later in male. Thus, SD is intimately related to the responsiveness of the germ cells to undergo meiosis in a sex-specific manner. In some vertebrates, it has been reported that the timing for meiosis entry would be under control of retinoic acid (RA), through activation of Stra8. In this study, we used a fish model species for sex determination and lacking the stra8 gene, the Japanese medaka (Oryzias latipes), to investigate the connection between RA and the sex determination pathway. Exogenous RA treatments act as a stress factor inhibiting germ cell differentiation probably by activation of dmrt1a and amh. Disruption of the RA degrading enzyme gene cyp26a1 induced precocious meiosis and oogenesis in embryos/hatchlings of female and even some males. Transcriptome analyzes of cyp26a1–/–adult gonads revealed upregulation of genes related to germ cell differentiation and meiosis, in both ovaries and testes. Our findings show that germ cells respond to RA in a stra8 independent model species. The responsiveness to RA is conferred by sex-related genes, restricting its action to the sex differentiation period in both sexes.

scholarly journals GATA2-Dependent Developmental and Regenerative Networks

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1182-1182
Author(s):  
Alexandra Soukup ◽  
Kirby D Johnson ◽  
Daniel J Conn ◽  
Evgenia Shishkova ◽  
Koichi Ricardo Katsumura ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Progenitor Cell ◽  
Fetal Liver ◽  
Single Cells ◽  
Wild Type ◽  
Monocytic Differentiation ◽  
Hematopoietic Stem ◽  
Altered Expression ◽  
Myeloid Progenitor

Coding and regulatory human GATA2 mutations that deregulate protein expression and/or function cause immunodeficiency that often progresses to MDS/AML (McReynolds et al., 2018). In the mouse, decreased GATA2 expression impairs hematopoietic stem/progenitor cell (HSPC) genesis and function (de Pater et al., 2013; Gao et al., 2013; Tsai et al., 1994). While prior studies demonstrated Gata2 +9.5 and -77 enhancers are essential for HSC emergence (+9.5) and/or progenitor cell fate (+9.5 and -77) (Johnson et al., 2012; Johnson et al., 2015; Mehta et al., 2017) and hematopoietic regeneration (+9.5) (Soukup et al., 2019), the mechanisms mediating these processes are not completely established. The -77 enhancer is required for fetal liver progenitors to undergo erythroid, megakaryocytic, granulocytic and monocytic differentiation. By contrast, progenitors with a -77 homozygous deletion (-77-/-) exhibit a predominant monocytic cell fate and generate macrophages ex vivo (Johnson et al., 2015). Using multiomic and single-cell strategies, we asked how this enhancer orchestrates a balance between fate-promoting and -suppressing circuitry in cell populations and single cells. Quantitative proteomics was conducted to discover the -77-regulated protein ensemble conferring multiple fates in a myeloid progenitor population [Common Myeloid Progenitor (CMP) and Granulocyte-Monocyte Progenitor (GMP)] from E14.5 fetal liver of -77+/+ and -77-/- mouse embryos. -77-/- progenitors exhibited decreased levels of GATA2 (4.7-fold) and proteins generated from GATA2 target genes (GATA1: 51-fold; HDC: 52-fold). The 202 proteins upregulated in -77-/- progenitors highlighted immune and inflammatory mechanisms, while the 232 downregulated proteins were linked to erythroid, megakaryocyte and granulocyte biology, indicative of loss of these fate potentials. Innate immune machinery was upregulated in -77-/- vs. -77+/+ progenitors, including interferon (IFN) signaling pathway components such as the IFN-inducible transcription factor and critical monocytic differentiation determinant Interferon Regulatory Factor 8 (IRF8; 2.7 fold higher) (Kurotaki et al., 2013) and diverse pathogen sensors. Expressing GATA2 at physiological levels in -77-/- progenitors normalized the aberrant transcriptome. Since -77 deletion downregulated Gata2 and upregulated Irf8, we tested whether this opposing expression pattern occurs in distinct and/or identical cells in the population using single cell transcriptomics. -77 deletion decreased Gata2 expression, which was anti-correlative with Irf8, and detailed single cell analyses indicated that -77 loss downregulates GATA2, corrupting the transcriptome/proteome, Irf8 expression increases, and IRF8 enables or drives the predominant monocytic differentiation. To determine how GATA2-dependent mechanisms governing progenitor fate relate to those guiding HSPC expansion and differentiation during regeneration, we utilized our +9.5 human disease Ets motif mutation that abrogates myeloablation-dependent GATA2 induction and hematopoietic regeneration in bone marrow (Soukup et al., 2019). While population RNA-seq with Lin-Sca1+c-Kit+ (LSK) cells revealed little to no perturbations in the steady-state, 5-FU treatment of mutants led to altered expression of only 14% of the transcripts regulated in regenerating wild type cells (423/2974). Gene Ontology analysis of differentially expressed genes indicated that genes dysregulated by the Ets motif mutation included those linked to cell cycle regulation and cellular proliferation. As LSKs consist of LT-HSCs, ST-HSCs, and MPPs, we used single-cell transcriptomics to elucidate defective regenerative circuits in individual cells. Analysis of 17000-20000 wild type and mutant LSK cells revealed GATA2-dependent mechanisms distinct from those mediating progenitor cell fate control in the fetal liver. These studies have revealed context-dependent GATA2 mechanisms governing developmental and regenerative hematopoiesis, which will enable the development of strategies to detect, diagnose, and treat GATA2-linked blood diseases. Disclosures No relevant conflicts of interest to declare.

scholarly journals Transcriptome Landscape Reveals Underlying Mechanisms of Ovarian Cell Fate Differentiation and Primordial Follicle Assembly

2019 ◽  
Author(s):  
Jun-Jie Wang ◽  
Wei Ge ◽  
Qiu-Yue Zhai ◽  
Jing-Cai Liu ◽  
Xiao-Wen Sun ◽  
...  
Keyword(s):  
Germ Cell ◽  
Single Cell ◽  
Cell Fate ◽  
Germ Cells ◽  
Granulosa Cells ◽  
Primordial Follicle ◽  
Gene Clusters ◽  
Bioinformatics Analyses ◽  
Primordial Follicles ◽  
New Genes

AbstractPrimordial follicle assembly in mammals occurs at perinatal ages and largely determines the ovarian reserve available to support the reproductive lifespan. The primordial follicle structure is generated by a complex network of interactions between oocytes and ovarian somatic cells that remain poorly understood. In the present research, using single-cell RNA sequencing performed over a time-series on mouse ovaries coupled with several bioinformatics analyses, the complete dynamic genetic programs of germ and granulosa cells from E16.5 to PD3 are reported for the first time. The time frame of analysis comprises the breakdown of germ cell cysts and the assembly of primordial follicles. Confirming the previously reported expression of genes by germ cells and granulosa cells, our analyses identified ten distinct gene clusters associated to germ cells and eight to granulosa cells. Consequently, several new genes expressed at significant levels at each investigated stage were assigned. Building single-cell pseudo temporal trajectories five states and two branch points of fate transition for the germ cells, and three states and one branch point for the granulosa cells were revealed. Moreover, GO and ClueGO term enrichment enabled identifying biological processes, molecular functions and cellular components more represented in germ cells and granulosa cells or common to both cell types at each specific stage. Finally, by SCENIC algorithm, we were able to establish a network of regulons that can be postulated as likely candidates for sustaining germ cell specific transcription programs throughout the investigated period.

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