Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst

Forces Shaping the Blastocyst

The blastocyst forms during the first days of mammalian development. The structure of the blastocyst is conserved among placental mammals and is paramount to the establishment of the first mammalian lineages. The blastocyst is composed of an extraembryonic epithelium, the trophectoderm (TE), that envelopes a fluid-filled lumen and the inner cell mass (ICM). To shape the blastocyst, embryos transit through three stages driven by forces that have been characterized in the mouse embryo over the past decade. The morphogenetically quiescent cleavage stages mask dynamic cytoskeletal remodeling. Then, during the formation of the morula, cells pull themselves together and the strongest ones internalize. Finally, the blastocyst forms after the pressurized lumen breaks the radial symmetry of the embryo before expanding in cycles of collapses and regrowth. In this review, we delineate the force patterns sculpting the blastocyst, based on our knowledge on the mouse and, to some extent, human embryos.

HAND1, partially mediated through ape-specific LTR binding, is essential for human extra-embryonic mesenchyme derivation from iPSCs

The specification of extra-embryonic mesenchyme (ExMC) is a prime example of developmental divergence between mouse and human. Derived from definitive mesoderm during mouse gastrulation, the human ExMC first appears at peri-implantation prior to gastrulation and therefore its human cellular origin, still unknown, must differ. In a human pluripotent stem cell model, we report that ExMC shares progenitor cells with trophoblast, suggesting a trophectoderm origin. This ability to form ExMC appears to extend to human trophoblast stem cell lines. We define HAND1 as an essential regulator of ExMC specification, with null cells remaining in the trophoblast lineage. Bound by HAND1, ape-specific, endogenous retrovirus-derived LTR2B contributes to unique features of ExMC. Additionally, ExMC supports the maintenance of pluripotent stem cells, possibly reflecting a role in maintaining epiblast pluripotency through peri-implantation development. Our data emphasize the nascent evolutionary innovation in human early development and provide a cellular system to study this.

Single-cell 5-hydroxymethylcytosine landscapes of mouse early embryos at single-base resolution

DNA methylation and hydroxymethylation are extensively reprogrammed during mammalian early embryogenesis, and studying their regulatory functions requires comprehensive DNA hydroxymethylation maps at base resolution. Here, we develop single-cell 5-hydroxymethylcytosine (5hmC) chemical-assisted C-to-T conversion-enabled sequencing (schmC-CATCH), a method leveraging selective 5hmC labeling for a quantitative, base-resolution, genome-wide landscape of the DNA hydroxymethylome in mouse gametes and preimplantation embryos spanning from the zygote to blastocyst stage. We revealed that, in addition to late zygotic stages, onset of ten-eleven translocation (TET)-mediated DNA hydroxymethylation initiates immediately after fertilization and is characterized by the distinct 5hmC patterns on the parental genomes shaped by TET3 demethylase. We identified persistent clusters of 5hmC hotspots throughout early embryonic stages, which are highly associated with young retroelements. 5hmC is also associated with different regulatory elements, indicating a potential regulatory function during early embryogenesis. Collectively, our work elucidates the dynamics of active DNA demethylation during mouse preimplantation development and provides a valuable resource for functional studies of epigenetic reprogramming in early embryos.

Cavity oscillation drives pattern formation in early mammalian embryos

During the second cell fate in mouse embryos, the inner cell mass (ICM) segregates into the spatially distinct epiblast (EPI) and primitive endoderm (PrE) layers. The mechanism driving this pattern formation, however, remains unresolved. Here, we report that, concomitant with the segregation process of EPI/PrE precursors starting from mid-blastocyst, the blastocyst cavity begins to oscillate cyclically with rapid contraction yet slow expansion, triggering a phase transition in the ICM to a fluid-like state. This asymmetric oscillation of the blastocyst cavity facilitates EPI/PrE segregation by enhancing cell-cell contact fluctuations within the ICM and initiating convergent cell flows, which induce movement of these two cell types in opposite directions, wherein PrE precursors move toward the ICM-lumen interface, whereas EPI precursors move toward the trophectoderm. Last, we found that both PDGFRα expression and YAP nuclear accumulation in PrE precursors increase in response to blastocyst cavity oscillation. This study reveals the foundational role of physical oscillation in driving embryonic pattern formation during early mammalian embryonic development.

Role of tristability in the robustness of the differentiation mechanism

During cell differentiation, identical pluripotent cells undergo a specification process marked by changes in the expression of key genes, regulated by transcription factors that can inhibit the transcription of a competing gene or activate their own transcription. This specification is orchestrated by gene regulatory networks (GRNs), encompassing transcription factors, biochemical reactions, and signalling cascades. Mathematical models for these GRNs have been proposed in various contexts, to replicate observed robustness in differentiation properties. This includes reproducible proportions of differentiated cells with respect to parametric or stochastic noise and the avoidance of transitions between differentiated states. Understanding the GRN components controlling these features is crucial. Our study thoroughly explored an extended version of the Toggle Switch model with auto-activation loops. This model represents cells evolving from common progenitors in one out of two fates (A or B, bistable regime) or, additionally, remaining in their progenitor state (C, tristable regime). Such a differentiation into populations with three distinct cell fates is observed during blastocyst formation in mammals, where inner cell mass cells can remain in that state or differentiate into epiblast cells or primitive endoderm. Systematic analysis revealed that the existence of a stable non-differentiated state significantly impacts the GRN's robustness against parametric variations and stochastic noise. This state reduces the sensitivity of cell populations to parameters controlling key gene expression asymmetry and prevents cells from making transitions after acquiring a new identity. Stochastic noise enhances robustness by decreasing sensitivity to initial expression levels and helping the system escape from the non-differentiated state to differentiated cell fates, making the differentiation more efficient.

Coupling of cell shape, matrix and tissue dynamics ensures embryonic patterning robustness

Tissue patterning coordinates morphogenesis, cell dynamics and fate specification. Understanding how precision in patterning is robustly achieved despite inherent developmental variability during mammalian embryogenesis remains a challenge. Here, based on cell dynamics quantification and simulation, we show how salt-and-pepper epiblast and primitive endoderm (PrE) cells pattern the inner cell mass of mouse blastocysts. Coupling cell fate and dynamics, PrE cells form apical polarity-dependent actin protrusions required for RAC1-dependent migration towards the surface of the fluid cavity, where PrE cells are trapped due to decreased tension. Concomitantly, PrE cells deposit an extracellular matrix gradient, presumably breaking the tissue-level symmetry and collectively guiding their own migration. Tissue size perturbations of mouse embryos and their comparison with monkey and human blastocysts further demonstrate that the fixed proportion of PrE/epiblast cells is optimal with respect to embryo size and tissue geometry and, despite variability, ensures patterning robustness during early mammalian development.

Divergent destinies: insights into the molecular mechanisms underlying EPI and PE fate determination

Mammalian pre-implantation development is entirely devoted to the specification of extra-embryonic lineages, which are fundamental for embryo morphogenesis and support. The second fate decision is taken just before implantation, as defined by the epiblast (EPI) and the primitive endoderm (PE) specification. Later, EPI forms the embryo proper and PE contributes to the formation of the yolk sac. The formation of EPI and PE as molecularly and morphologically distinct lineages is the final step of a multistage process, which begins when bipotent progenitor cells diverge into separate fates. Despite advances in uncovering the molecular mechanisms underlying the differential transcriptional patterns that dictate how apparently identical cells make fate decisions and how lineage integrity is maintained, a detailed overview of these mechanisms is still lacking. In this review, we dissect the EPI and PE formation process into four stages (initiation, specification, segregation, and maintenance) and we provide a comprehensive understanding of the molecular mechanisms involved in lineage establishment in the mouse. In addition, we discuss the conservation of key processes in humans, based on the most recent findings.

Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in early mouse embryos

During the first lineage segregation, mammalian embryos generate the inner cell mass (ICM) and trophectoderm (TE). ICM gives rise to the epiblast (EPI) that forms all cell types of the body, an ability referred to as pluripotency. The molecular mechanisms that induce pluripotency in embryos remain incompletely elucidated. Using knockout (KO) mouse models in conjunction with low-input ATAC-seq and RNA-seq, we found that Oct4 and Sox2 gradually come into play in the early ICM, coinciding with the initiation of Sox2 expression. Oct4 and Sox2 activate the pluripotency-related genes through the putative OCT-SOX enhancers in the early ICM. Furthermore, we observed a substantial reorganization of chromatin landscape and transcriptome from the morula to the early ICM stages, which was partially driven by Oct4 and Sox2, highlighting their pivotal role in promoting the developmental trajectory toward the ICM. Our study provides new insights into the establishment of the pluripotency network in mouse preimplantation embryos.

TBX3 is Essential for Zygotic Genome Activation and Embryonic Development in Pigs

The pluripotency-related T-box family transcription factor TBX3 maintains mESC self-renewal and plays a key role in the development of several tissues, including the heart, mammary glands, limbs, and lungs. However, the role of TBX3 during porcine preimplantation embryo development remains unclear. In our research, TBX3 was knocked down by injecting dsRNA to explore the function of TBX3. TBX3 expression gradually increases during early embryonic development. TBX3 knockdown resulted in decreased in the rate of four-cell and blastocyst. Depletion of TBX3 decreased the level of H3K9Ac/H3K27Ac and decreased ZGA gene expression at the four-cell stage. Furthermore, TBX3 knockdown led to a decrease in ZSACN4 protein level, DNMT1 and intracellular 5mc levels were increased, and then induced telomeres shorten and DNA damaged. Additionally, TBX3 knockdown significantly decreased histone acetylation and pluripotency genes NANOG/OCT4 expression in blastocysts. TBX3 knockdown induced apoptosis in blastocysts. Taken together, TBX3 regulate histone acetylation and play important roles in zygotic genome activation and early embryonic development in pigs.

PI3K/AKT signaling controls ICM maturation and proper epiblast and primitive endoderm specification in mice

The inner cell mass (ICM) of early mouse embryos is specified into epiblast (Epi) and primitive endoderm (PrE) lineages during blastocyst formation. The antagonistic transcription factors (TFs) NANOG and GATA-binding protein 6 (GATA6) in combination with fibroblast growth factor (FGF)/extracellular-signal-regulated kinase (ERK) signaling are central actors in ICM fate choice. However, what initiates the specification of ICM progenitors into Epi or PrE and whether other factors are involved in this process has not been fully understood yet. Here, we show that phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) is constitutively active during preimplantation development. Using pharmacological inhibition, we demonstrate that PI3K/AKT enables the formation of a functional ICM capable of giving rise to both the Epi and the PrE: it maintains the expression of the TF NANOG, which specifies the Epi, and confers responsiveness to FGF4, which is essential for PrE specification. Our work thus identifies PI3K/AKT signaling as an upstream regulator controlling the molecular events required for both Epi and PrE specification.

Blastocoel expansion and AMOT degradation cooperatively promote YAP nuclear localization during epiblast formation

The epiblast is a pluripotent cell population formed in the late blastocyst stage of preimplantation embryos. During the process of epiblast formation from the inner cell mass (ICM) of the early blastocyst, activation of the Hippo pathway transcription factor TEAD by the nuclear translocation of the coactivator protein YAP is required for the robust expression of pluripotency factors. However, the mechanisms that alter YAP localization during epiblast formation remain unknown. Here, we reveal two such mechanisms. Expansion of the blastocoel promotes nuclear YAP localization by increasing cytoplasmic F-actin and reducing YAP phosphorylation. Additionally, cell differentiation regulates YAP. Expression of the junctional Hippo component, AMOT, gradually decreases during epiblast formation through a tankyrase-mediated degradation. SOX2 expression in the ICM is necessary for the reduction of AMOT and YAP phosphorylation. These two mechanisms function in parallel. Thus, the blastocoel-F-actin and SOX2-AMOT axes cooperatively suppress YAP phosphorylation and promote YAP nuclear localization during epiblast formation. The cooperation of these two distinct mechanisms likely contributes to the robustness of epiblast cell differentiation.

Fate specification triggers a positive feedback loop of TEAD-YAP and NANOG to promote epiblast formation in preimplantation embryos

In preimplantation embryos, epiblast (EPI) fate specification from the inner cell mass is controlled by the segregation of NANOG and GATA6 expression. TEAD-YAP interaction is activated during EPI formation and is required for pluripotency factor expression. These events occur asynchronously with similar timing during EPI formation, and their relationship remains elusive. Here, we examined the relationship between NANOG-GATA6 and TEAD-YAP. The nuclear accumulation of YAP takes place only in EPI-specified cells, and a positive feedback loop operates between NANOG and TEAD-YAP. The effects of TEAD-YAP on SOX2 upregulation in EPI-specified cells are likely indirect. EPI fate specification also alters the response of Nanog, Sox2 and Cdx2 to TEAD-YAP. These results suggest that EPI-fate specification alters the transcriptional network from the morula-like to the EPI-specified state and activates TEAD-YAP to trigger a positive feedback loop with NANOG, which stabilizes the EPI fate. The coordinated occurrence of these processes in individual cells likely supports proper EPI formation under the condition of asynchronous EPI-fate specification.

TMELand: An End-to-End Pipeline for Quantification and Visualization of Waddington's Epigenetic Landscape Based on Gene Regulatory Network

Waddington's epigenetic landscape is a framework depicting the processes of cell differentiation and reprogramming under the control of a gene regulatory network (GRN). Traditional model-driven methods for landscape quantification focus on the Boolean network or differential equation-based models of GRN, which need sophisticated prior knowledge and hence hamper their practical applications. To resolve this problem, we combine data-driven methods for inferring GRNs from gene expression data with model-driven approach to the landscape mapping. Specifically, we build an end-to-end pipeline to link data-driven and model-driven methods and develop a software tool named TMELand for GRN inference, visualizing Waddington's epigenetic landscape, and calculating state transition paths between attractors to uncover the intrinsic mechanism of cellular transition dynamics. By integrating GRN inference from real transcriptomic data with landscape modeling, TMELand can facilitate studies of computational systems biology, such as predicting cellular states and visualizing the dynamical trends of cell fate determination and transition dynamics from single-cell transcriptomic data.

AI-powered simulation-based inference of a genuinely spatial-stochastic gene regulation model of early mouse embryogenesis

Understanding how multicellular organisms reliably orchestrate cell-fate decisions is a central challenge in developmental biology, particularly in early mammalian development, where tissue-level differentiation arises from seemingly cell-autonomous mechanisms. In this study, we present a multi-scale, spatial-stochastic simulation framework for mouse embryogenesis, focusing on inner cell mass (ICM) differentiation into epiblast (EPI) and primitive endoderm (PRE) at the blastocyst stage. Our framework models key regulatory and tissue-scale interactions in a biophysically realistic fashion, capturing the inherent stochasticity of intracellular gene expression and intercellular signaling, while efficiently simulating these processes by advancing event-driven simulation techniques. Leveraging the power of Simulation-Based Inference (SBI) through the AI-driven Sequential Neural Posterior Estimation (SNPE) algorithm, we conduct a large-scale Bayesian inferential analysis to identify parameter sets that faithfully reproduce experimentally observed features of ICM specification. Our results reveal mechanistic insights into how the combined action of autocrine and paracrine FGF4 signaling coordinates stochastic gene expression at the cellular scale to achieve robust and reproducible ICM patterning at the tissue scale. We further demonstrate that the ICM exhibits a specific time window of sensitivity to exogenous FGF4, enabling lineage proportions to be adjusted based on timing and dosage, thereby extending current experimental findings and providing quantitative predictions for both mutant and wild-type ICM systems. Notably, FGF4 signaling not only ensures correct EPI-PRE lineage proportions but also enhances ICM resilience to perturbations, reducing fate-proportioning errors by 10-20% compared to a purely cell-autonomous system. Additionally, we uncover a surprising role for variability in intracellular initial conditions, showing that high gene-expression heterogeneity can improve both the accuracy and precision of cell-fate proportioning, which remains robust when fewer than 25% of the ICM population experiences perturbed initial conditions. Our work offers a comprehensive, spatial-stochastic description of the biochemical processes driving ICM differentiation and identifies the necessary conditions for its robust unfolding. It also provides a framework for future exploration of similar spatial-stochastic systems in developmental biology.

Single Cell Isolation from Human Diabetic Fibrovascular Membranes for Single-Cell RNA Sequencing

Single-cell transcriptomic analyses have emerged as very powerful tools to query the gene expression changes at the single-cell level in physiological and pathological conditions. The quality of the analysis is heavily dependent on tissue digestion protocols, with the goal of preserving thousands of single live cells to submit to the subsequent processing steps and analysis. Multiple digestion protocols that use different enzymes to digest the tissues have been described. Harsh digestion can damage certain cell types, but this might be required to digest especially fibrotic tissue as in our experimental condition. In this paper, we summarize a collagenase type I digestion protocol for preparing the single-cell suspension from fibrovascular tissues surgically removed from patients with proliferative diabetic retinopathy (PDR) for single-cell RNA sequencing (scRNA-Seq) analyses. We also provide a detailed description of the data analysis that we implemented in a previously published study. Key features • Single-cell suspension from fibrovascular membranes isolated from PDR patients. • Single-cell RNA sequencing analyses performed using Seurat package in RStudio. • Trajectory analyses or pseudotime analyses to study the trajectory over (pseudo)time of specific cell types. • This protocol requires Illumina HiSEQ4000 instrument and knowledge of R and RStudio language for the analyses.

Exploring Mechanical Forces Shaping Self-Organization and Morphogenesis During Early Embryo Development

Embryonic development is a dynamic process orchestrated by a delicate interplay of biochemical and biophysical factors. While the role of genetics and biochemistry in embryogenesis has been extensively studied, recent research has highlighted the significance of mechanical regulation in shaping and guiding this intricate process. Here, we provide an overview of the current understanding of the mechanical regulation of embryo development. We explore how mechanical forces generated by cells and tissues play a crucial role in driving the development of different stages. We examine key morphogenetic processes such as compaction, blastocyst formation, implantation, and egg cylinder formation, and discuss the mechanical mechanisms and cues involved. By synthesizing the current body of literature, we highlight the emerging concepts and open questions in the field of mechanical regulation. We aim to provide an overview of the field, inspiring future investigations and fostering a deeper understanding of the mechanical aspects of embryo development.

Revisiting trophectoderm-inner cell mass lineage segregation in the mammalian preimplantation embryo

In the first days of life, cells of the mammalian embryo segregate into two distinct lineages, trophectoderm and inner cell mass. Unlike nonmammalian species, mammalian development does not proceed from predetermined factors in the oocyte. Rather, asymmetries arise de novo in the early embryo incorporating cues from cell position, contractility, polarity, and cell-cell contacts. Molecular heterogeneities, including transcripts and non-coding RNAs, have now been characterized as early as the 2-cell stage. However, it's debated whether these early heterogeneities bias cells toward one fate or the other or whether lineage identity arises stochastically at the 16-cell stage. This review summarizes what is known about early blastomere asymmetries and our understanding of lineage allocation in the context of historical models. Preimplantation development is reviewed coupled with what is known about changes in morphology, contractility, and transcription factor networks. The addition of single-cell atlases of human embryos has begun to reveal key differences between human and mouse, including the timing of events and core transcription factors. Furthermore, the recent generation of blastoid models will provide valuable tools to test and understand fate determinants. Lastly, new techniques are reviewed, which may better synthesize existing knowledge with emerging data sets and reconcile models with the regulative capacity unique to the mammalian embryo.

Dissecting SOX2 expression and function reveals an association with multiple signaling pathways during embryonic development and in cancer progression

SRY (Sex Determining Region) box 2 (SOX2) is an essential transcription factor that plays crucial roles in activating genes involved in pre- and post-embryonic development, adult tissue homeostasis, and lineage specifications. SOX2 maintains the self-renewal property of stem cells and is involved in the generation of induced pluripotency stem cells. SOX2 protein contains a particular high-mobility group domain that enables SOX2 to achieve the capacity to participate in a broad variety of functions. The information about the involvement of SOX2 with gene regulatory elements, signaling networks, and microRNA is gradually emerging, and the higher expression of SOX2 is functionally relevant to various cancer types. SOX2 facilitates the oncogenic phenotype via cellular proliferation and enhancement of invasive tumor properties. Evidence are accumulating in favor of three dimensional (higher order) folding of chromatin and epigenetic control of the SOX2 gene by chromatin modifications, which implies that the expression level of SOX2 can be modulated by epigenetic regulatory mechanisms, specifically, via DNA methylation and histone H3 modification. In view of this, and to focus further insights into the roles SOX2 plays in physiological functions, involvement of SOX2 during development, precisely, the advances of our knowledge in pre- and post-embryonic development, and interactions of SOX2 in this scenario with various signaling pathways in tumor development and cancer progression, its potential as a therapeutic target against many cancers are summarized and discussed in this article.

Microbiological toxicity tests using standardized ISO/OECD methods-current state and outlook

Microbial toxicity tests play an important role in various scientific and technical fields including the risk assessment of chemical compounds in the environment. There is a large battery of normalized tests available that have been standardized by ISO (International Organization for Standardization) and OECD (Organization for Economic Co-operation and Development) and which are worldwide accepted and applied. The focus of this review is to provide information on microbial toxicity tests, which are used to elucidate effects in other laboratory tests such as biodegradation tests, and for the prediction of effects in natural and technical aqueous compartments in the environment. The various standardized tests as well as not normalized methods are described and their advantages and disadvantages are discussed. In addition, the sensitivity and usefulness of such tests including a short comparison with other ecotoxicological tests is presented. Moreover, the far-reaching influence of microbial toxicity tests on biodegradation tests is also demonstrated. A new concept of the physiological potential of an inoculum (PPI) consisting of microbial toxicity tests whose results are expressed as a chemical resistance potential (CRP) and the biodegradation adaptation potential (BAP) of an inoculum is described that may be helpful to characterize inocula used for biodegradation tests. KEY POINTS: • Microbial toxicity tests standardized by ISO and OECD have large differences in sensitivity and applicability. • Standardized microbial toxicity tests in combination with biodegradability tests open a new way to characterize inocula for biodegradation tests. • Standardized microbial toxicity tests together with ecotoxicity tests can form a very effective toolbox for the characterization of toxic effects of chemicals.

Naive pluripotent stem cell-based models capture FGF-dependent human hypoblast lineage specification

The hypoblast is an essential extraembryonic tissue set aside within the inner cell mass in the blastocyst. Research with human embryos is challenging. Thus, stem cell models that reproduce hypoblast differentiation provide valuable alternatives. We show here that human naive pluripotent stem cell (PSC) to hypoblast differentiation proceeds via reversion to a transitional ICM-like state from which the hypoblast emerges in concordance with the trajectory in human blastocysts. We identified a window when fibroblast growth factor (FGF) signaling is critical for hypoblast specification. Revisiting FGF signaling in human embryos revealed that inhibition in the early blastocyst suppresses hypoblast formation. In vitro, the induction of hypoblast is synergistically enhanced by limiting trophectoderm and epiblast fates. This finding revises previous reports and establishes a conservation in lineage specification between mice and humans. Overall, this study demonstrates the utility of human naive PSC-based models in elucidating the mechanistic features of early human embryogenesis.

The Advancement and Application of the Single-Cell Transcriptome in Biological and Medical Research

Single-cell RNA sequencing technology (scRNA-seq) has been steadily developing since its inception in 2009. Unlike bulk RNA-seq, scRNA-seq identifies the heterogeneity of tissue cells and reveals gene expression changes in individual cells at the microscopic level. Here, we review the development of scRNA-seq, which has gone through iterations of reverse transcription, in vitro transcription, smart-seq, drop-seq, 10 × Genomics, and spatial single-cell transcriptome technologies. The technology of 10 × Genomics has been widely applied in medicine and biology, producing rich research results. Furthermore, this review presents a summary of the analytical process for single-cell transcriptome data and its integration with other omics analyses, including genomes, epigenomes, proteomes, and metabolomics. The single-cell transcriptome has a wide range of applications in biology and medicine. This review analyzes the applications of scRNA-seq in cancer, stem cell research, developmental biology, microbiology, and other fields. In essence, scRNA-seq provides a means of elucidating gene expression patterns in single cells, thereby offering a valuable tool for scientific research. Nevertheless, the current single-cell transcriptome technology is still imperfect, and this review identifies its shortcomings and anticipates future developments. The objective of this review is to facilitate a deeper comprehension of scRNA-seq technology and its applications in biological and medical research, as well as to identify avenues for its future development in alignment with practical needs.

Lineage regulators TFAP2C and NR5A2 function as bipotency activators in totipotent embryos

During the first lineage segregation, a mammalian totipotent embryo differentiates into the inner cell mass (ICM) and trophectoderm (TE). However, how transcription factors (TFs) regulate this earliest cell-fate decision in vivo remains elusive, with their regulomes primarily inferred from cultured cells. Here, we investigated the TF regulomes during the first lineage specification in early mouse embryos, spanning the pre-initiation, initiation, commitment, and maintenance phases. Unexpectedly, we found that TFAP2C, a trophoblast regulator, bound and activated both early TE and inner cell mass (ICM) genes at the totipotent (two- to eight-cell) stages ('bipotency activation'). Tfap2c deficiency caused downregulation of early ICM genes, including Nanog, Nr5a2, and Tdgf1, and early TE genes, including Tfeb and Itgb5, in eight-cell embryos. Transcription defects in both ICM and TE lineages were also found in blastocysts, accompanied by increased apoptosis and reduced cell numbers in ICMs. Upon trophoblast commitment, TFAP2C left early ICM genes but acquired binding to late TE genes in blastocysts, where it co-bound with CDX2, and later to extra-embryonic ectoderm (ExE) genes, where it cooperatively co-occupied with the former ICM regulator SOX2. Finally, 'bipotency activation' in totipotent embryos also applied to a pluripotency regulator NR5A2, which similarly bound and activated both ICM and TE lineage genes at the eight-cell stage. These data reveal a unique transcription circuity of totipotency underpinned by highly adaptable lineage regulators.

Unveiling gene regulatory networks during cellular state transitions without linkage across time points

Time-stamped cross-sectional data, which lack linkage across time points, are commonly generated in single-cell transcriptional profiling. Many previous methods for inferring gene regulatory networks (GRNs) driving cell-state transitions relied on constructing single-cell temporal ordering. Introducing COSLIR (COvariance restricted Sparse LInear Regression), we presented a direct approach to reconstructing GRNs that govern cell-state transitions, utilizing only the first and second moments of samples between two consecutive time points. Simulations validated COSLIR's perfect accuracy in the oracle case and demonstrated its robust performance in real-world scenarios. When applied to single-cell RT-PCR and RNAseq datasets in developmental biology, COSLIR competed favorably with existing methods. Notably, its running time remained nearly independent of the number of cells. Therefore, COSLIR emerges as a promising addition to GRN reconstruction methods under cell-state transitions, bypassing the single-cell temporal ordering to enhance accuracy and efficiency in single-cell transcriptional profiling.

LogicGep: Boolean networks inference using symbolic regression from time-series transcriptomic profiling data

Reconstructing the topology of gene regulatory network from gene expression data has been extensively studied. With the abundance functional transcriptomic data available, it is now feasible to systematically decipher regulatory interaction dynamics in a logic form such as a Boolean network (BN) framework, which qualitatively indicates how multiple regulators aggregated to affect a common target gene. However, inferring both the network topology and gene interaction dynamics simultaneously is still a challenging problem since gene expression data are typically noisy and data discretization is prone to information loss. We propose a new method for BN inference from time-series transcriptional profiles, called LogicGep. LogicGep formulates the identification of Boolean functions as a symbolic regression problem that learns the Boolean function expression and solve it efficiently through multi-objective optimization using an improved gene expression programming algorithm. To avoid overly emphasizing dynamic characteristics at the expense of topology structure ones, as traditional methods often do, a set of promising Boolean formulas for each target gene is evolved firstly, and a feed-forward neural network trained with continuous expression data is subsequently employed to pick out the final solution. We validated the efficacy of LogicGep using multiple datasets including both synthetic and real-world experimental data. The results elucidate that LogicGep adeptly infers accurate BN models, outperforming other representative BN inference algorithms in both network topology reconstruction and the identification of Boolean functions. Moreover, the execution of LogicGep is hundreds of times faster than other methods, especially in the case of large network inference.

The SWI/SNF ATP-dependent chromatin remodeling complex in cell lineage priming and early development

ATP dependent chromatin remodelers have pivotal roles in transcription, DNA replication and repair, and maintaining genome integrity. SWI/SNF remodelers were first discovered in yeast genetic screens for factors involved in mating type switching or for using alternative energy sources therefore termed SWI/SNF complex (short for SWItch/Sucrose NonFermentable). The SWI/SNF complexes utilize energy from ATP hydrolysis to disrupt histone-DNA interactions and shift, eject, or reposition nucleosomes making the underlying DNA more accessible to specific transcription factors and other regulatory proteins. In development, SWI/SNF orchestrates the precise activation and repression of genes at different stages, safe guards the formation of specific cell lineages and tissues. Dysregulation of SWI/SNF have been implicated in diseases such as cancer, where they can drive uncontrolled cell proliferation and tumor metastasis. Additionally, SWI/SNF defects are associated with neurodevelopmental disorders, leading to disruption of neural development and function. This review offers insights into recent developments regarding the roles of the SWI/SNF complex in pluripotency and cell lineage primining and the approaches that have helped delineate its importance. Understanding these molecular mechanisms is crucial for unraveling the intricate processes governing embryonic stem cell biology and developmental transitions and may potentially apply to human diseases linked to mutations in the SWI/SNF complex.

Inference of differentiation trajectories by transfer learning across biological processes

Stem cells differentiate into distinct fates by transitioning through a series of transcriptional states. Current computational approaches allow reconstruction of differentiation trajectories from single-cell transcriptomics data, but it remains unknown to what degree differentiation can be predicted across biological processes. Here, we use transfer learning to infer differentiation processes and quantify predictability in early embryonic development and adult hematopoiesis. Overall, we find that non-linear methods outperform linear approaches, and we achieved the best predictions with a custom variational autoencoder that explicitly models changes in transcriptional variance. We observed a high accuracy of predictions in embryonic development, but we found somewhat lower agreement with the real data in adult hematopoiesis. We demonstrate that this discrepancy can be explained by a higher degree of concordant transcriptional processes along embryonic differentiation compared with adult homeostasis. In summary, we establish a framework for quantifying and exploiting predictability of cellular differentiation trajectories.

Stem cell heterogeneity, plasticity, and regulation

As a population of homogeneous cells with both self-renewal and differentiation potential, stem cell pools are highly compartmentalized and contain distinct subsets that exhibit stable but limited heterogeneity during homeostasis. However, their striking plasticity is showcased under natural or artificial stress, such as injury, transplantation, cancer, and aging, leading to changes in their phenotype, constitution, metabolism, and function. The complex and diverse network of cell-extrinsic niches and signaling pathways, together with cell-intrinsic genetic and epigenetic regulators, tightly regulate both the heterogeneity during homeostasis and the plasticity under perturbation. Manipulating these factors offers better control of stem cell behavior and a potential revolution in the current state of regenerative medicine. However, disruptions of normal regulation by genetic mutation or excessive plasticity acquisition may contribute to the formation of tumors. By harnessing innovative techniques that enhance our understanding of stem cell heterogeneity and employing novel approaches to maximize the utilization of stem cell plasticity, stem cell therapy holds immense promise for revolutionizing the future of medicine.

The salt-and-pepper pattern in mouse blastocysts is compatible with signaling beyond the nearest neighbors

Embryos develop in a concerted sequence of spatiotemporal arrangements of cells. In the preimplantation mouse embryo, the distribution of the cells in the inner cell mass evolves from a salt-and-pepper pattern to spatial segregation of two distinct cell types. The exact properties of the salt-and-pepper pattern have not been analyzed so far. We investigate the spatiotemporal distribution of NANOG- and GATA6-expressing cells in the ICM of the mouse blastocysts with quantitative three-dimensional single-cell-based neighborhood analyses. A combination of spatial statistics and agent-based modeling reveals that the cell fate distribution follows a local clustering pattern. Using ordinary differential equations modeling, we show that this pattern can be established by a distance-based signaling mechanism enabling cells to integrate information from the whole inner cell mass into their cell fate decision. Our work highlights the importance of longer-range signaling to ensure coordinated decisions in groups of cells to successfully build embryos.

Rie1 and Sgn1 form an RNA-binding complex that enforces the meiotic entry cell fate decision

Budding yeast cells have the capacity to adopt few but distinct physiological states depending on environmental conditions. Vegetative cells proliferate rapidly by budding while spores can survive prolonged periods of nutrient deprivation and/or desiccation. Whether or not a yeast cell will enter meiosis and sporulate represents a critical decision that could be lethal if made in error. Most cell fate decisions, including those of yeast, are understood as being triggered by the activation of master transcription factors. However, mechanisms that enforce cell fates posttranscriptionally have been more difficult to attain. Here, we perform a forward genetic screen to determine RNA-binding proteins that affect meiotic entry at the posttranscriptional level. Our screen revealed several candidates with meiotic entry phenotypes, the most significant being RIE1, which encodes an RRM-containing protein. We demonstrate that Rie1 binds RNA, is associated with the translational machinery, and acts posttranscriptionally to enhance protein levels of the master transcription factor Ime1 in sporulation conditions. We also identified a physical binding partner of Rie1, Sgn1, which is another RRM-containing protein that plays a role in timely Ime1 expression. We demonstrate that these proteins act independently of cell size regulation pathways to promote meiotic entry. We propose a model explaining how constitutively expressed RNA-binding proteins, such as Rie1 and Sgn1, can act in cell fate decisions both as switch-like enforcers and as repressors of spurious cell fate activation.

Local cellular interactions during the self-organization of stem cells

Stem cell models for early mammalian development offer new experimental opportunities to access spatio-temporal details of the cell-cell interactions that govern cell differentiation and tissue patterning. This review summarizes recent studies that have used stem cell models to investigate the spatial range of developmental cell-cell communication systems. A key message from these works is that important biochemical signals for cell differentiation in these systems, such as Nodal and fibroblast growth factors (FGFs), often act over short distances of only a few cell diameters. The formation of long-range patterns at the tissue scale associated with these signals then results from signal relays and cell rearrangements. The modular view of differentiation and patterning emerging from research on stem cell models can offer a fresh perspective on the corresponding processes in the embryo.

Omics Views of Mechanisms for Cell Fate Determination in Early Mammalian Development

During mammalian preimplantation development, a totipotent zygote undergoes several cell cleavages and two rounds of cell fate determination, ultimately forming a mature blastocyst. Along with compaction, the establishment of apicobasal cell polarity breaks the symmetry of an embryo and guides subsequent cell fate choice. Although the lineage segregation of the inner cell mass (ICM) and trophectoderm (TE) is the first symbol of cell differentiation, several molecules have been shown to bias the early cell fate through their inter-cellular variations at much earlier stages, including the 2- and 4-cell stages. The underlying mechanisms of early cell fate determination have long been an important research topic. In this review, we summarize the molecular events that occur during early embryogenesis, as well as the current understanding of their regulatory roles in cell fate decisions. Moreover, as powerful tools for early embryogenesis research, single-cell omics techniques have been applied to both mouse and human preimplantation embryos and have contributed to the discovery of cell fate regulators. Here, we summarize their applications in the research of preimplantation embryos, and provide new insights and perspectives on cell fate regulation.

insideOutside: an accessible algorithm for classifying interior and exterior points, with applications in embryology

A crucial aspect of embryology is relating the position of individual cells to the broader geometry of the embryo. A classic example of this is the first cell-fate decision of the mouse embryo, where interior cells become inner cell mass and exterior cells become trophectoderm. Fluorescent labelling, imaging, and quantification of tissue-specific proteins have advanced our understanding of this dynamic process. However, instances arise where these markers are either not available, or not reliable, and we are left only with the cells' spatial locations. Therefore, a simple, robust method for classifying interior and exterior cells of an embryo using spatial information is required. Here, we describe a simple mathematical framework and an unsupervised machine learning approach, termed insideOutside, for classifying interior and exterior points of a three-dimensional point-cloud, a common output from imaged cells within the early mouse embryo. We benchmark our method against other published methods to demonstrate that it yields greater accuracy in classification of nuclei from the pre-implantation mouse embryos and greater accuracy when challenged with local surface concavities. We have made MATLAB and Python implementations of the method freely available. This method should prove useful for embryology, with broader applications to similar data arising in the life sciences.

Young LINE-1 transposon 5' UTRs marked by elongation factor ELL3 function as enhancers to regulate naïve pluripotency in embryonic stem cells

LINE-1s are the major clade of retrotransposons with autonomous retrotransposition activity. Despite the potential genotoxicity, LINE-1s are highly activated in early embryos. Here we show that a subset of young LINE-1s, L1Md_Ts, are marked by the RNA polymerase II elongation factor ELL3, and function as enhancers in mouse embryonic stem cells. ELL3 depletion dislodges the DNA hydroxymethylase TET1 and the co-repressor SIN3A from L1Md_Ts, but increases the enrichment of the Bromodomain protein BRD4, leading to loss of 5hmC, gain of H3K27ac, and upregulation of the L1Md_T nearby genes. Specifically, ELL3 occupies and represses the L1Md_T-based enhancer located within Akt3, which encodes a key regulator of AKT pathway. ELL3 is required for proper ERK activation and efficient shutdown of naïve pluripotency through inhibiting Akt3 during naïve-primed transition. Our study reveals that the enhancer function of a subset of young LINE-1s controlled by ELL3 in transcription regulation and mouse early embryo development.

Spatial positioning of preimplantation mouse embryo cells is regulated by mTORC1 and m7G-cap-dependent translation at the 8- to 16-cell transition

Preimplantation mouse embryo development involves temporal-spatial specification and segregation of three blastocyst cell lineages: trophectoderm, primitive endoderm and epiblast. Spatial separation of the outer-trophectoderm lineage from the two other inner-cell-mass (ICM) lineages starts with the 8- to 16-cell transition and concludes at the 32-cell stages. Accordingly, the ICM is derived from primary and secondary contributed cells; with debated relative EPI versus PrE potencies. We report generation of primary but not secondary ICM populations is highly dependent on temporal activation of mammalian target of Rapamycin (mTOR) during 8-cell stage M-phase entry, mediated via regulation of the 7-methylguanosine-cap (m7G-cap)-binding initiation complex (EIF4F) and linked to translation of mRNAs containing 5' UTR terminal oligopyrimidine (TOP-) sequence motifs, as knockdown of identified TOP-like motif transcripts impairs generation of primary ICM founders. However, mTOR inhibition-induced ICM cell number deficits in early blastocysts can be compensated by the late blastocyst stage, after inhibitor withdrawal; compensation likely initiated at the 32-cell stage when supernumerary outer cells exhibit molecular characteristics of inner cells. These data identify a novel mechanism specifically governing initial spatial segregation of mouse embryo blastomeres, that is distinct from those directing subsequent inner cell formation, contributing to germane segregation of late blastocyst lineages.

Single-cell transcriptional uncertainty landscape of cell differentiation

Background: Single-cell studies have demonstrated the presence of significant cell-to-cell heterogeneity in gene expression. Whether such heterogeneity is only a bystander or has a functional role in the cell differentiation process is still hotly debated. Methods: In this study, we quantified and followed single-cell transcriptional uncertainty - a measure of gene transcriptional stochasticity in single cells - in 10 cell differentiation systems of varying cell lineage progressions, from single to multi-branching trajectories, using the stochastic two-state gene transcription model. Results: By visualizing the transcriptional uncertainty as a landscape over a two-dimensional representation of the single-cell gene expression data, we observed universal features in the cell differentiation trajectories that include: (i) a peak in single-cell uncertainty during transition states, and in systems with bifurcating differentiation trajectories, each branching point represents a state of high transcriptional uncertainty; (ii) a positive correlation of transcriptional uncertainty with transcriptional burst size and frequency; (iii) an increase in RNA velocity preceding the increase in the cell transcriptional uncertainty. Conclusions: Our findings suggest a possible universal mechanism during the cell differentiation process, in which stem cells engage stochastic exploratory dynamics of gene expression at the start of the cell differentiation by increasing gene transcriptional bursts, and disengage such dynamics once cells have decided on a particular terminal cell identity. Notably, the peak of single-cell transcriptional uncertainty signifies the decision-making point in the cell differentiation process.

Influence of FGF4 and BMP4 on FGFR2 dynamics during the segregation of epiblast and primitive endoderm cells in the pre-implantation mouse embryo

Specification of the epiblast (EPI) and primitive endoderm (PE) in the mouse embryo involves fibroblast growth factor (FGF) signaling through the RAS/MAP kinase pathway. FGFR1 and FGFR2 are thought to mediate this signaling in the inner cell mass (ICM) of the mouse blastocyst and BMP signaling can also influence PE specification. In this study, we further explored the dynamics of FGFR2 expression through an enhanced green fluorescent protein (eGFP) reporter mouse line (FGFR2-eGFP). We observed that FGFR2-eGFP is present in the late 8-cell stage; however, it is absent or reduced in the ICM of early blastocysts. We then statistically correlated eGFP expression with PE and EPI markers GATA6 and NANOG, respectively. We detected that eGFP is weakly correlated with GATA6 in early blastocysts, but this correlation quickly increases as the blastocyst develops. The correlation between eGFP and NANOG decreases throughout blastocyst development. Treatment with FGF from the morula stage onwards did not affect FGFR2-eGFP presence in the ICM of early blastocysts; however, late blastocysts presented FGFR2-eGFP in all cells of the ICM. BMP treatment positively influenced FGFR2-eGFP expression and reduced the number of NANOG-positive cells in late blastocysts. In conclusion, FGFR2 is not strongly associated with PE precursors in the early blastocyst, but it is highly correlated with PE cells as blastocyst development progresses, consistent with the proposed role for FGFR2 in maintenance rather than initiating the PE lineage.

Neurotrophin-4 promotes the specification of trophectoderm lineage after parthenogenetic activation and enhances porcine early embryonic development

Neurotrophin-4 (NT-4), a neurotrophic factor, appears to affect early embryonic development because it is secreted not only by neurons but also by oviductal and uterine epithelial cells. However, no studies have characterized the effects of NT-4 on early embryonic development in pigs. In this study, we applied the experimental model of parthenogenetic-activation (PA)-derived embryos. Herein, we investigated the effect of NT-4 supplementation during the in vitro culture (IVC) of embryos, analyzed the transcription levels of specific genes, and outlined the first cell lineage specification for porcine PA-derived blastocysts. We confirmed that NT-4 and its receptor proteins were localized in both the inner cell mass (ICM) and trophectoderm (TE) in porcine blastocysts. Across different concentrations (0, 1, 10, and 100 ng/mL) of NT-4 supplementation, the optimal concentration of NT-4 to improve the developmental competence of porcine parthenotes was 10 ng/mL. NT-4 supplementation during porcine IVC significantly (p < 0.05) increased the proportion of TE cells by inducing the transcription of TE lineage markers (CDX2, PPAG3, and GATA3 transcripts). NT-4 also reduced blastocyst apoptosis by regulating the transcription of apoptosis-related genes (BAX and BCL2L1 transcripts) and improved blastocyst quality via the interaction of neurotrophin-, Hippo-yes-associated protein (Hippo-YAP) and mitogen-activated protein kinase/extracellular regulated kinase (MAPK/ERK) pathway. Additionally, NT-4 supplementation during IVC significantly (p < 0.05) increased YAP1 transcript levels and significantly (p < 0.01) decreased LATS2 transcript levels, respectively, in the porcine PA-derived blastocysts. We also confirmed through fluorescence intensity that the YAP1 protein was significantly (p < 0.001) increased in the NT-4-treated blastocysts compared with that in the control. NT-4 also promoted differentiation into the TE lineage rather than into the ICM lineage during porcine early embryonic development. In conclusion, 10 ng/mL NT-4 supplementation enhanced blastocyst quality by regulating the apoptosis- and TE lineage specification-related genes and interacting with neurotrophin-, Hippo-YAP-, and MAPK/ERK signaling pathway during porcine in vitro embryo development.

Inference on autoregulation in gene expression with variance-to-mean ratio

Some genes can promote or repress their own expressions, which is called autoregulation. Although gene regulation is a central topic in biology, autoregulation is much less studied. In general, it is extremely difficult to determine the existence of autoregulation with direct biochemical approaches. Nevertheless, some papers have observed that certain types of autoregulations are linked to noise levels in gene expression. We generalize these results by two propositions on discrete-state continuous-time Markov chains. These two propositions form a simple but robust method to infer the existence of autoregulation from gene expression data. This method only needs to compare the mean and variance of the gene expression level. Compared to other methods for inferring autoregulation, our method only requires non-interventional one-time data, and does not need to estimate parameters. Besides, our method has few restrictions on the model. We apply this method to four groups of experimental data and find some genes that might have autoregulation. Some inferred autoregulations have been verified by experiments or other theoretical works.

The Wnt/TCF7L1 transcriptional repressor axis drives primitive endoderm formation by antagonizing naive and formative pluripotency

Early during preimplantation development and in heterogeneous mouse embryonic stem cells (mESC) culture, pluripotent cells are specified towards either the primed epiblast or the primitive endoderm (PE) lineage. Canonical Wnt signaling is crucial for safeguarding naive pluripotency and embryo implantation, yet the role and relevance of canonical Wnt inhibition during early mammalian development remains unknown. Here, we demonstrate that transcriptional repression exerted by Wnt/TCF7L1 promotes PE differentiation of mESCs and in preimplantation inner cell mass. Time-series RNA sequencing and promoter occupancy data reveal that TCF7L1 binds and represses genes encoding essential naive pluripotency factors and indispensable regulators of the formative pluripotency program, including Otx2 and Lef1. Consequently, TCF7L1 promotes pluripotency exit and suppresses epiblast lineage formation, thereby driving cells into PE specification. Conversely, TCF7L1 is required for PE specification as deletion of Tcf7l1 abrogates PE differentiation without restraining epiblast priming. Taken together, our study underscores the importance of transcriptional Wnt inhibition in regulating lineage specification in ESCs and preimplantation embryo development as well as identifies TCF7L1 as key regulator of this process.

Comparative assessment of embryotoxicity of 2,4,6-triiodophenol to mouse blastoid and pre-implantation embryo models

Embryonic developmental effects of disinfection by-products, which are generated during drinking water treatment and widely detected in environment, have gained more and more attention nowadays, calling for construction of in vitro research models which can mimic early embryonic development to evaluate the embryotoxicity. The embryonic stem cell test offers a promising assay to predict embryotoxicity of environmental pollutions. However, it is not appropriate for the toxicological study of preimplantation embryos. Here, we used mouse extended stem cells (mEPS) to reconstruct embryo-like structures (blastoid), furtherly attempting to evaluate the reliability of this model for the prediction of possible developmental toxicity of 2,4,6-triiodophenol (TIP, 5-50 μM), a novel halogenated disinfection byproduct widely detected in water and even drinking water, to mammalian preimplantation embryo. To verify this, we treated mouse embryo derived from in vitro fertilization (IVF-embryo) as reference. The results showed that mEPS-blastoid was like natural blastocyst in morphology, cell composition, and could recapitulate key developmental events happened during mouse preimplantation stage. When blastoid and IVF-embryo models were separately exposed to TIP, their final blastocyst formation rates were not impaired, according to morphological features, meanwhile that TIP exposure caused slight cell apoptosis. Besides, TIP induced an ICM cell bias in cell fate decision, resulting in cell proportion change, which implied abnormal developmental potential. Though we could not evaluate TIP's embryotoxicity before 8-cell stage using blastoid model, its viability as a novel and high-throughput assessment platform for increasing environmental pollutants was still recognized.

BLTSA: pseudotime prediction for single cells by branched local tangent space alignment

MOTIVATION

The development of single-cell RNA sequencing (scRNA-seq) technology makes it possible to study the cellular dynamic processes such as cell cycle and cell differentiation. Due to the difficulties in generating genuine time-series scRNA-seq data, it is of great importance to computationally infer the pseudotime of the cells along differentiation trajectory based on their gene expression patterns. The existing pseudotime prediction methods often suffer from the high level noise of single-cell data, thus it is still necessary to study the single-cell trajectory inference methods.

RESULTS

In this study, we propose a branched local tangent space alignment (BLTSA) method to infer single-cell pseudotime for multi-furcation trajectories. By assuming that single cells are sampled from a low-dimensional self-intersecting manifold, BLTSA first identifies the tip and branching cells in the trajectory based on cells' local Euclidean neighborhoods. Local coordinates within the tangent spaces are then determined by each cell's local neighborhood after clustering all the cells to different branches iteratively. The global coordinates for all the single cells are finally obtained by aligning the local coordinates based on the tangent spaces. We evaluate the performance of BLTSA on four simulation datasets and five real datasets. The experimental results show that BLTSA has obvious advantages over other comparison methods.

AVAILABILITY AND IMPLEMENTATION

R codes are available at https://github.com/LiminLi-xjtu/BLTSA.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Reconstruction of Single-Cell Trajectories Using Stochastic Tree Search

The recent advancement in single-cell RNA sequencing technologies enables the understanding of dynamic cellular processes at the single-cell level. Using trajectory inference methods, pseudotimes can be estimated based on reconstructed single-cell trajectories which can be further used to gain biological knowledge. Existing methods for modeling cell trajectories, such as minimal spanning tree or k-nearest neighbor graph, often lead to locally optimal solutions. In this paper, we propose a penalized likelihood-based framework and introduce a stochastic tree search (STS) algorithm aiming at the global solution in a large and non-convex tree space. Both simulated and real data experiments show that our approach is more accurate and robust than other existing methods in terms of cell ordering and pseudotime estimation.

Early Cell Specification in Mammalian Fertilized and Somatic Cell Nuclear Transfer Embryos

Early cell specification in mammalian preimplantation embryos is an intricate cellular process that leads to coordinated spatial and temporal expression of specific genes. Proper segregation into the first two cell lineages, the inner cell mass (ICM) and the trophectoderm (TE), is imperative for developing the embryo proper and the placenta, respectively. Somatic cell nuclear transfer (SCNT) allows the formation of a blastocyst containing both ICM and TE from a differentiated cell nucleus, which means that this differentiated genome must be reprogrammed to a totipotent state. Although blastocysts can be generated efficiently through SCNT, the full-term development of SCNT embryos is impaired mostly due to placental defects. In this review, we examine the early cell fate decisions in fertilized embryos and compare them to observations in SCNT-derived embryos, in order to understand if these processes are affected by SCNT and could be responsible for the low success of reproductive cloning.

The Beneficial Effects of Static Magnetic Field and Iron Oxide Nanoparticles on the Vitrification of Mature Mice Oocytes

This study was conducted to evaluate the effects of static magnetic field (SMF) and nanoparticles (NPs) on the vitrification of cumulus-oocyte-complex (COC). To this end, the non-vitrified (nVit) and vitrified groups (Vit) that contain NPs, with or without SMF were labeled nVit_NPs, nVit_NPs_SMF, Vit_NPs, and Vit_NPs_SMF, respectively. The non-toxic dosages of NPs were first determined to be 0.008% w/v. The survival, apoptosis, and necrosis, mitochondrial activity, fertilization rate, subsequent-derived embryo development, and gene expressions were examined. The viability rates obtained by trypan blue and Anx-PI staining were meaningfully smaller in the Vit groups, compared to the nVit groups. The JC1 red/green signal ratios were reduced considerably in the Vit group, compared to the nVit. Transmission electron microscopy (TEM) was performed to assess the entry of the NPs into the oocytes. TEM images showed that NPs were present in nVit_NPs, and Vit_NPs. Thereafter, the effects of NPs and SMF on in vitro fertilization (IVF) were examined. The difference in blastocyst rates between nVit and Vit_NPs_SMF groups was significant. Finally, Nanog, Cdx2, Oct4, and Sox2 genes were evaluated. There were substantial differences in Cdx2 gene expressions between the Vit_NPs and nVit groups. The expression of Nanog in Vit was significantly higher than those of the Vit_NPs, Vit_NPs_SMF, and nVit groups. The data presented here provide deeper insight into the application of iron oxide nanoparticles in COC vitrification. It appears that using SMF and supplemented CPA by NPs inhibits cryoinjury and promote the embryo development capacity of vitrified-warmed COCs.

Recent advances in high-throughput single-cell transcriptomics and spatial transcriptomics

Single-cell RNA sequencing (scRNA-seq) has been developed for characterizing the transcriptome of cells that are rare but of biological significance. With cell barcoding and microchip technologies, a suite of high-throughput scRNA-seq protocols enable transcriptome profiling in thousands of individual cells at single-cell resolution for classifying cell types, discovering novel cell populations, investigating cellular heterogeneity and elucidating lineage trajectories. Microchip technologies including microfluidics- and microwell-based platforms play a major role in high-throughput scRNA-seq. As the emerging technology, spatial transcriptomics integrates cellular transcriptomics with their spatial coordinates within tissues for spatially deciphering cellular composition, heterogeneity and cell-cell communications. Spatial transcriptomics has been increasingly recognized as one of the most powerful tools for discovering new biology and advancing precision medicine. Microfluidics as an enabling technology plays an increasingly important role in spatial transcriptomics. We review the technological spectrum and advances in high-throughput scRNA-seq and spatial transcriptomics, discuss their advantages and limitations, and pitch into new biology learned from these new tools.

Journey of the mouse primitive endoderm: from specification to maturation

The blastocyst is a conserved stage and distinct milestone in the development of the mammalian embryo. Blastocyst stage embryos comprise three cell lineages which arise through two sequential binary cell fate specification steps. In the first, extra-embryonic trophectoderm (TE) cells segregate from inner cell mass (ICM) cells. Subsequently, ICM cells acquire a pluripotent epiblast (Epi) or extra-embryonic primitive endoderm (PrE, also referred to as hypoblast) identity. In the mouse, nascent Epi and PrE cells emerge in a salt-and-pepper distribution in the early blastocyst and are subsequently sorted into adjacent tissue layers by the late blastocyst stage. Epi cells cluster at the interior of the ICM, while PrE cells are positioned on its surface interfacing the blastocyst cavity, where they display apicobasal polarity. As the embryo implants into the maternal uterus, cells at the periphery of the PrE epithelium, at the intersection with the TE, break away and migrate along the TE as they mature into parietal endoderm (ParE). PrE cells remaining in association with the Epi mature into visceral endoderm. In this review, we discuss our current understanding of the PrE from its specification to its maturation. This article is part of the theme issue 'Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom'.

Regulation of paternal 5mC oxidation and H3K9me2 asymmetry by ERK1/2 in mouse zygotes

Background

Extracellular-signal-regulated kinase (ERK) direct cell fate determination during the early development. The intricate interaction between the deposition of H3K9me2, de novo 5mC, and its oxides affects the remodeling of zygotic epigenetic modification. However, the role of fertilization-dependent ERK in the first cell cycle during zygotic reprogramming remains elusive.

Methods

In the present study, we used the small molecule inhibitor to construct the rapid ERK1/2 inactivation system in early zygotes in mice. The pronuclear H3K9me2 deposition assay and the pre-implantation embryonic development ability were assessed to investigate the effect of fertilization-dependent ERK1/2 on zygotic reprogramming and developmental potential. Immunofluorescence and RT-PCR were performed to measure the 5mC or its oxides and H3K9me2 deposition, and the expression of related genes.

Results

We reported that zygotic ERK1/2 inhibition impaired the development competence of pre-implantation embryos. Following the ERK1/2 inhibition, H3K9me2, as well as 5mC and its oxides, were all accumulated abnormally, and the excess accumulation of paternal H3K9me2 and 5mC resulted in reduced asymmetry between parental pronuclei. Furthermore, ERK1/2 inhibition triggered paternal pronuclear localization of the H3K9 methyltransferase G9a and Tet methylcytosine dioxygenase 3 (Tet3). Moreover, the excess localization of G9a antagonized the tight binding of Tet3 to paternal chromatin when ERK1/2 was inhibited.

Conclusions

In conclusion, we propose that zygotic H3K9me2 and 5mC are regulated by fertilization-dependent ERK1/2, which contributes to the development competence of pre-implantation embryos in mice.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13578-022-00758-x.

The physiological and pathological mechanisms of early embryonic development

Early embryonic development is a complex process. The zygote undergoes several rounds of division to form a blastocyst, and during this process, the zygote undergoes the maternal-to-zygotic transition to gain control of embryonic development and makes two cell fate decisions to differentiate into an embryonic and two extra-embryonic lineages. With the use of new molecular biotechnologies and animal models, we can now further study the molecular mechanisms of early embryonic development and the pathological causes of early embryonic arrest. Here, we first summarize the known molecular regulatory mechanisms of early embryonic development in mice. Then we discuss the pathological factors leading to the early embryonic arrest. We hope that this review will give researchers a relatively complete view of the physiology and pathology of early embryonic development.

Paracrine interactions through FGFR1 and FGFR2 receptors regulate the development of preimplantation mouse chimaeric embryo

The preimplantation mammalian embryo has the potential to self-organize, allowing the formation of a correctly patterned embryo despite experimental perturbation. To better understand the mechanisms controlling the developmental plasticity of the early mouse embryo, we used chimaeras composed of an embryonic day (E)3.5 or E4.5 inner cell mass (ICM) and cleaving 8-cell embryo. We revealed that the restricted potential of the ICM can be compensated for by uncommitted 8-cell embryo-derived blastomeres, thus leading to the formation of a normal chimaeric blastocyst that can undergo full development. However, whether such chimaeras maintain developmental competence depends on the presence or specific orientation of the polarized primitive endoderm layer in the ICM component. We also demonstrated that downregulated FGFR1 and FGFR2 expression in 8-cell embryos disturbs intercellular interactions between both components and results in an inverse proportion of primitive endoderm and epiblast within the resulting ICM and abnormal embryo development. This finding suggests that FGF signalling is a key part of the regulatory mechanism that assigns cells to a given lineage and ensures the proper composition of the blastocyst, which is a prerequisite for its successful implantation in the uterus and for further development.