Single-cell Embryo Research Articles

Perspectives in Genome-Editing Techniques for Livestock.

Genome editing of farm animals has undeniable practical applications. It helps to improve production traits, enhances the economic value of livestock, and increases disease resistance. Gene-modified animals are also used for biomedical research and drug production and demonstrate the potential to be used as xenograft donors for humans. The recent discovery of site-specific nucleases that allow precision genome editing of a single-cell embryo (or embryonic stem cells) and the development of new embryological delivery manipulations have revolutionized the transgenesis field. These relatively new approaches have already proven to be efficient and reliable for genome engineering and have wide potential for use in agriculture. A number of advanced methodologies have been tested in laboratory models and might be considered for application in livestock animals. At the same time, these methods must meet the requirements of safety, efficiency and availability of their application for a wide range of farm animals. This review aims at covering a brief history of livestock animal genome engineering and outlines possible future directions to design optimal and cost-effective tools for transgenesis in farm species.

Integrative analysis of single-cell embryo data reveals transcriptome signatures for the human pre-implantation inner cell mass.

As the source of embryonic stem cells (ESCs), inner cell mass (ICM) can form all tissues of the embryo proper, however, its role in early human lineage specification remains controversial. Although a stepwise differentiation model has been proposed suggesting the existence of ICM as a distinct developmental stage, the underlying molecular mechanism remains unclear. In the present study, we perform an integrated analysis on the public human preimplantation embryonic single-cell transcriptomic data and apply a trajectory inference algorithm to measure the cell plasticity. In our results, ICM population can be clearly discriminated on the dimension-reduced graph and confirmed by compelling evidences, thus validating the two-step hypothesis of lineage commitment. According to the branch probabilities and differentiation potential, we determine the precise time points for two lineage segregations. Further analysis on gene expression dynamics and regulatory network indicates that transcription factors including GSC, PRDM1, and SPIC may underlie the decisions of ICM fate. In addition, new human ICM marker genes, such as EPHA4 and CCR8 are discovered and validated by immunofluorescence. Given the potential clinical applications of ESCs, our analysis provides a further understanding of human ICM cells and facilitates the exploration of more unique characteristics in early human development.

Detecting Embryo Developmental Potential by Single Blastomere RNA-Seq.

Recent advances in preimplantation embryo diagnostics enable a wide range of applications using single cell biopsy and molecular-based selection techniques without compromising embryo production. This study was conducted to develop a single cell embryo biopsy technique and gene expression analysis method with a very low input volume to ensure normal embryo development and to see if there are differences in gene expression profiles between day-5 biopsied bovine embryos that developed into blastocysts and embryos arrested at morula stage. Out of the 65 biopsied morulae, 32 developed to blastocysts (49.2%). Out of the 13,580 successfully annotated genes, 1204 showed a difference in mRNA expression level. Out of these, 155 genes were expressed in embryos developing to blastocysts. The pathway enrichment analysis revealed significant enrichment in "organelle biogenesis and maintenance", "mRNA splicing" and "mitochondrial translation" pathways. These findings suggest principal differences in gene expression patterns and functional networks of embryos able to reach the blastocyst stage compared to embryos arrested in development. Our preliminary data suggest that single blastomere biopsy and selected gene expression profiles at morula stage could offer additional possibilities for early preimplantation embryo selection before transfer.

A hexa-species transcriptome atlas of mammalian embryogenesis delineates metabolic regulation across three different implantation modes

Mammalian embryogenesis relies on glycolysis and oxidative phosphorylation to balance the generation of biomass with energy production. However, the dynamics of metabolic regulation in the postimplantation embryo in vivo have remained elusive due to the inaccessibility of the implanted conceptus for biochemical studies. To address this issue, we compiled single-cell embryo profiling data in six mammalian species and determined their metabolic dynamics through glycolysis and oxidative phosphorylation associated gene expression. Strikingly, we identify a conserved switch from bivalent respiration in the late blastocyst towards a glycolytic metabolism in early gastrulation stages across species, which is independent of embryo implantation. Extraembryonic lineages followed the dynamics of the embryonic lineage, except visceral endoderm. Finally, we demonstrate that in vitro primate embryo culture substantially impacts metabolic gene regulation by comparison to in vivo samples. Our work reveals a conserved metabolic programme despite different implantation modes and highlights the need to optimise postimplantation embryo culture protocols.

The Origin of the Cyathea delgadii Sternb. Somatic Embryos Is Determined by the Developmental State of Donor Tissue and Mutual Balance of Selected Metabolites.

Somatic embryogenesis is the formation of a plant embryo from a cell other than the product of gametic fusion. The need to recognize the determinants of somatic cell fate has prompted investigations on how endogenous factors of donor tissues can determine the pattern of somatic embryo origin. The undertaking of this study was enabled by the newly developed experimental system of somatic embryogenesis of the tree fern Cyathea delgadii Sternb., in which the embryos are produced in hormone-free medium. The contents of 89 endogenous compounds (such as sugars, auxins, cytokinins, gibberellins, stress-related hormones, phenolic acids, polyamines, and amino acids) and cytomorphological features were compared between two types of explants giving rise to somatic embryos of unicellular or multicellular origin. We found that a large content of maltose, 1-kestose, abscisic acid, biologically active gibberellins, and phenolic acids was characteristic for single-cell somatic embryo formation pattern. In contrast, high levels of starch, callose, kinetin riboside, arginine, and ethylene promoted their multicellular origin. Networks for visualization of the relations between studied compounds were constructed based on the data obtained from analyses of a Pearson correlation coefficient heatmap. Our findings present for the first time detailed features of donor tissue that can play an important role in the somatic-to-embryogenic transition and the somatic embryo origin.

Multiscale analysis of single and double maternal-zygotic Myh9 and Myh10 mutants during mouse preimplantation development.

During the first days of mammalian development, the embryo forms the blastocyst, the structure responsible for implanting the mammalian embryo. Consisting of an epithelium enveloping the pluripotent inner cell mass and a fluid-filled lumen, the blastocyst results from a series of cleavage divisions, morphogenetic movements, and lineage specification. Recent studies have identified the essential role of actomyosin contractility in driving cytokinesis, morphogenesis, and fate specification, leading to the formation of the blastocyst. However, the preimplantation development of contractility mutants has not been characterized. Here, we generated single and double maternal-zygotic mutants of non-muscle myosin II heavy chains (NMHCs) to characterize them with multiscale imaging. We found that Myh9 (NMHC II-A) is the major NMHC during preimplantation development as its maternal-zygotic loss causes failed cytokinesis, increased duration of the cell cycle, weaker embryo compaction, and reduced differentiation, whereas Myh10 (NMHC II-B) maternal-zygotic loss is much less severe. Double maternal-zygotic mutants for Myh9 and Myh10 show a much stronger phenotype, failing most of the attempts of cytokinesis. We found that morphogenesis and fate specification are affected but nevertheless carry on in a timely fashion, regardless of the impact of the mutations on cell number. Strikingly, even when all cell divisions fail, the resulting single-celled embryo can initiate trophectoderm differentiation and lumen formation by accumulating fluid in increasingly large vacuoles. Therefore, contractility mutants reveal that fluid accumulation is a cell-autonomous process and that the preimplantation program carries on independently of successful cell division.

Microinjection quality control in zebrafish model for genetic manipulations

Microinjection technique is one of the essential methodologies that are used widely in zebrafish research. Microinjection is utilized to perform genetic manipulations within the developing zebrafish model. Further, this technique is used to study a wide range of genetic diseases and gene of interest role in early developmental processes. Thus, quality control for microinjection is an essential factor to ensure experimental reproducibility and consistency. In this technical note, in vitro transcribed synthetic mRNA encoding green fluorescence protein (eGFP), and red fluorescent protein (m-cherry) as well as fluorescein and rhodamine fluorescent dyes were injected into a single-cell zebrafish embryo for volume quality control. Given the importance of having quality control system and methodology to yield similar genetic manipulation within the zebrafish embryo:•We aimed to establish the unified delivery of injected material into zebrafish one cell stage embryo.•We aimed to establish consistency of the injected volume into mineral oil droplets that will serve as a quality control parameter to conforms a quality control practice to ensure the reproducibility of the microinjection technique.•The calibration of microinjection droplet size resulted in the visualization of fluorescent protein and dyes in the zebrafish embryo with precise volumes of delivered materials under the control of needle opening, injection pressure and time.

Epigenetic control of cell fate - an interview with Maria-Elena Torres-Padilla.

Maria-Elena Torres-Padilla's research is focused on how cell fate arises from a single-cell embryo, the fertilized egg or zygote. After the initial divisions, cell potency becomes restricted, originating the first cell lineage fates. She studies how epigenetic information controls transitions in cell identity and cellular reprogramming during embryonic development. Currently, she is the founding Director of the Institute of Epigenetics and Stem Cells, Helmholtz Centre, and Professor of Stem Cell Biology at the Ludwigs Maximilians University in Munich. In this interview, Maria-Elena Torres-Padilla talks to us about her beginnings in the biology field in Mexico. She also tells us about how she became interested in the control of genome regulation within the nucleus during the transition from totipotency to pluripotency and how the control of gene regulation and chromatin organization during the early stages of cell fate decision in the one-cell embryo occurs. She considers that science has no borders; visiting Mexico gives her the possibility to discuss her work with colleagues and the new generation of students trained in Mexico.

Transient droplets are key to cellular biochemistry

Clifford P. Brangwynne smashed the single-celled embryo between a microscope slide and a thin glass cover slip. Then he peered into the microscope to get a look at the cell, taken from a worm commo...

Defining Human Pluripotency.

Human pluripotent stem cells harbor the capacity to differentiate into cells from the three embryonic germ layers, and this ability grants them a central role in modeling human disorders and in the field of regenerative medicine. Here, we review pluripotency in human cells with respect to four different aspects: (1) embryonic development, (2) transcriptomes of pluripotent cell stages, (3) genes and pathways that reprogram somatic cells into pluripotent stem cells, and finally (4) the recent identification of the human pluripotent stem cell essentialome. These four aspects of pluripotency collectively culminate in a broader understanding of what makes a cell pluripotent.

Agilent Technologies OnePGT solution: External verification on both blastomere and trophectoderm biopsies

Objectives OnePGT is a genome-wide next-generation sequencing haplarithmisis-based solution designed to reinforce ranking of IVF embryos. The single workflow solution, consisting of wet-lab reagents and dedicated data analysis software, allows concurrent PGT-M (preimplantation genetic testing of monogenic disorders), PGT-SR (preimplantation genetic testing of structural rearrangements) and PGT-A (preimplantation genetic testing of aneuploidies) hence enabling enhanced genetic profiling. In collaboration with MUMC and KU Leuven, a study was set up to assess the level of concordance between OnePGT and Gold Standard analysis of both single and few cell embryo biopsies for PGT-M, PGT-SR and PGT-A. Methods A total of 227 embryo samples (191 PGT-M; 36 PGT-SR) were included in the study, consisting of 179 blastomere and 48 trophectoderm biopsies, of which 118 embryos were obtained from KU Leuven, and 109 from MUMC. For the KU Leuven site of the study, left-over whole genome amplified (WGAed) DNA from the embryo biopsies was processed, while in the MUMC site, a second biopsy was taken and WGAed. Libraries for NGS were generated using proprietary OnePGT reagents for all WGAed embryo biopsies and for bulk DNA samples from parents and reference family member(s) in case of PGT-M. Libraries were sequenced on NextSeq500 (Illumina) and resulting data were analyzed with the dedicated proprietary OnePGT software suite. Results For PGT-M analysis, a OnePGT conclusion was made for 91 % of embryos determined to be of sufficient quality (n=161). Of these, four were shown to have mitotic aberrations resulting from chromosome instability phenomenon and three did not receive a conclusion from the Gold Standard. The remaining 154 embryos showed 100% concordance with the standard PGT techniques. For PGT-SR analysis (n=36), three embryos were shown to have mitotic aberrations resulted from chromosome instability phenomenon, the remaining 33 embryos 100% concordance with the standard PGT methods. For PGT-A analysis, 100% concordance (> 50 Mb) was shown between OnePGT and standard PGT methods for which a PGT-A result was available (n=118). Conclusion The proprietary OnePGT solution, consisting of all-in-one library preparation reagents and dedicated software suite for concurrent PGT-M, PGT-SR and PGT-A in a single assay, successfully identified the presence of 26 different monogenic disorders, translocations and chromosomal aneuploidies in over 200 embryo biopsies, with a concordance rate of 100%. This indicates that this innovative genome-wide solution is expected to boost the current PGT practice and to facilitate effective ranking of IVF embryos based on enhanced genetic profiling.

Single-cell transcriptional profiling: a window into embryonic cell-type specification.

During mammalian embryonic development, a single fertilized egg cell will proliferate and differentiate into all the cell lineages and cell types that eventually form the adult organism. Cell lineage diversification involves repeated cell fate choices that ultimately occur at the level of the individual cell rather than at the cell-population level. Improvements in single-cell technologies are transforming our understanding of mammalian development, not only by overcoming the limitations presented by the extremely low cell numbers of early embryos but also by enabling the study of cell fate specification in greater detail. In this Review, we first discuss recent advances in single-cell transcriptomics and imaging and provide a brief outline of current bioinformatics methods available to analyse the resulting data. We then discuss how these techniques have contributed to our understanding of pre-implantation and early post-implantation development and of in vitro pluripotency. Finally, we overview the current challenges facing single-cell research and highlight the latest advances and potential future avenues.

Gene-Editing Technology Accelerates Cardiovascular Research: Clinical Applications Being Explored.

The emergence of an inexpensive and efficient tool for gene editing is accelerating the pace of cardiovascular research and beginning to show potential as a treatment tool. The new gene-editing technology leverages a bacterial defense mechanism against viral infections. Bacteria store sections of viral DNA in repeated sequences called CRISPR within their own genomes and use those sequences to identify and destroy viruses. Now, scientists are inserting genes they would like to target into CRISPR and pairing it with CAS9, an enzyme that cuts DNA. This process allows scientists to efficiently remove or replace a targeted gene. “It’s been a transformative technology,” said Kiran Musunuru, MD, PhD, MPH, an associate professor of cardiovascular medicine and genetics at the University of Pennsylvania’s Perelman School of Medicine. Gene editing has been a common tool in research for decades—particularly for producing model organisms with a particular genetic mutation. However, older techniques were more time-consuming, expensive, and more error-prone. CRISPR-CAS is allowing scientists to more easily and quickly produce model animals or human cell lines with specific genetic variants allowing experiments to proceed at an unprecedented pace or scale. Some preliminary studies have suggested that it also may be a useful tool for treating some forms of heart disease. The most immediate impact of CRISPR-CAS9 has been speeding the production …

Single Cell Genetics and Epigenetics in Early Embryo: From Oocyte to Blastocyst.

Single cell technology has enormously changed the landscape of biomedical science, including single cell omics, gene editing, single cell imaging, single cell (embryo) manipulate, or non-invasive micro-test. Single cell technology also leads the research area of early embryo from basic research to reproductive medical application. We got the knowledge of programming/reprogramming and the epigenetics dynamics in the cell lineage differentiation. In the reproductive medicine, the genomic sequencing of embryo or polar body and the preimplantation genetic diagnosis rely on the single cell techniques. Those discoveries will improve the assisted reproductive technologies, human health, and livestock husbandry. In the future, the comprehensive atlas of cell state and lineage information can be generated for cellular systems by single-cell multi-omics approaches.

The asymmetric cell division machinery in the spiral-cleaving egg and embryo of the marine annelid Platynereis dumerilii

BackgroundOver one third of all animal phyla utilize a mode of early embryogenesis called ‘spiral cleavage’ to divide the fertilized egg into embryonic cells with different cell fates. This mode is characterized by a series of invariant, stereotypic, asymmetric cell divisions (ACDs) that generates cells of different size and defined position within the early embryo. Astonishingly, very little is known about the underlying molecular machinery to orchestrate these ACDs in spiral-cleaving embryos. Here we identify, for the first time, cohorts of factors that may contribute to early embryonic ACDs in a spiralian embryo.ResultsTo do so we analyzed stage-specific transcriptome data in eggs and early embryos of the spiralian annelid Platynereis dumerilii for the expression of over 50 candidate genes that are involved in (1) establishing cortical domains such as the partitioning defective (par) genes, (2) directing spindle orientation, (3) conveying polarity cues including crumbs and scribble, and (4) maintaining cell-cell adhesion between embryonic cells. In general, each of these cohorts of genes are co-expressed exhibiting high levels of transcripts in the oocyte and fertilized single-celled embryo, with progressively lower levels at later stages. Interestingly, a small number of key factors within each ACD module show different expression profiles with increased early zygotic expression suggesting distinct regulatory functions. In addition, our analysis discovered several highly co-expressed genes that have been associated with specialized neural cell-cell recognition functions in the nervous system. The high maternal contribution of these ‘neural’ adhesion complexes indicates novel general adhesion functions during early embryogenesis.ConclusionsSpiralian embryos are champions of ACD generating embryonic cells of different size with astonishing accuracy. Our results suggest that the molecular machinery for ACD is already stored as maternal transcripts in the oocyte. Thus, the spiralian egg can be viewed as a totipotent yet highly specialized cell that evolved to execute fast and precise ACDs during spiral cleaving stages. Our survey identifies cohorts of factors in P. dumerilii that are candidates for these molecular mechanisms and their regulation, and sets the stage for a functional dissection of ACD in a spiral-cleaving embryo.

Single-Cell Reprogramming in Mouse Embryo Development through a Critical Transition State

Our previous work on the temporal development of the genome-expression profile in single-cell early mouse embryo indicated that reprogramming occurs via a critical transition state, where the critical-regulation pattern of the zygote state disappears. In this report, we unveil the detailed mechanism of how the dynamic interaction of thermodynamic states (critical states) enables the genome system to pass through the critical transition state to achieve genome reprogramming right after the late 2-cell state. Self-organized criticality (SOC) control of overall expression provides a snapshot of self-organization and explains the coexistence of critical states at a certain experimental time point. The time-development of self-organization is dynamically modulated by changes in expression flux between critical states through the cell nucleus milieu, where sequential global perturbations involving activation-inhibition of multiple critical states occur from the middle 2-cell to the 4-cell state. Two cyclic fluxes act as feedback flow and generate critical-state coherent oscillatory dynamics. Dynamic perturbation of these cyclic flows due to vivid activation of the ensemble of low-variance expression (sub-critical state) genes allows the genome system to overcome a transition state during reprogramming. Our findings imply that a universal mechanism of long-term global RNA oscillation underlies autonomous SOC control, and the critical gene ensemble at a critical point (CP) drives genome reprogramming. Identification of the corresponding molecular players will be essential for understanding single-cell reprogramming.

Cytoplasmic flows as signatures for the mechanics of mitotic positioning.

The proper positioning of mitotic spindle in the single-cell Caenorhabditis elegans embryo is achieved initially by the migration and rotation of the pronuclear complex (PNC) and its two associated astral microtubules (MTs). Pronuclear migration produces global cytoplasmic flows that couple the mechanics of all MTs, the PNC, and the cell periphery with each other through their hydrodynamic interactions (HIs). We present the first computational study that explicitly accounts for detailed HIs between the cytoskeletal components and demonstrate the key consequences of HIs for the mechanics of pronuclear migration. First, we show that, because of HIs between the MTs, the cytoplasm-filled astral MTs behave like a porous medium, with its permeability decreasing with increasing the number of MTs. We then directly study the dynamics of PNC migration under various force-transduction models, including the pushing or pulling of MTs at the cortex and the pulling of MTs by cytoplasmically bound force generators. Although achieving proper position and orientation on reasonable time scales does not uniquely choose a model, we find that each model produces a different signature in its induced cytoplasmic flow. We suggest that cytoplasmic flows can be used to differentiate between mechanisms.

Positioning of polarity formation by extracellular signaling during asymmetric cell division

Anterior–posterior (AP) polarity formation of cell membrane proteins plays a crucial role in determining cell asymmetry, which ultimately generates cell diversity. In Caenorhabditis elegans, a single fertilized egg cell (P0), its daughter cell (P1), and the germline precursors (P2 and P3 cells) form two exclusive domains of different PAR proteins on the membrane along the anterior–posterior axis. However, the phenomenon of polarity reversal has been observed in which the axis of asymmetric cell division of the P2 and P3 cells is formed in an opposite manner to that of the P0 and P1 cells. The extracellular signal MES-1/SRC-1 has been shown to induce polarity reversal, but the detailed mechanism remains elusive. Here, using a mathematical model, I explore the mechanism by which MES-1/SRC-1 signaling can induce polarity reversal and ultimately affect the process of polarity formation. I show that a positive correlation between SRC-1 and the on-rate of PAR-2 is the essential mechanism underlying polarity reversal, providing a mathematical basis for the orientation of cell polarity patterns.

Sample Preparation and Mounting of Drosophila Embryos for Multiview Light Sheet Microscopy.

Light sheet fluorescent microscopy (LSFM), and in particular its most widespread flavor Selective Plane Illumination Microscopy (SPIM), promises to provide unprecedented insights into developmental dynamics of entire living systems. By combining minimal photo-damage with high imaging speed and sample mounting tailored toward the needs of the specimen, it enables in toto imaging of embryogenesis with high spatial and temporal resolution. Drosophila embryos are particularly well suited for SPIM imaging because the volume of the embryo does not change from the single cell embryo to the hatching larva. SPIM microscopes can therefore image Drosophila embryos embedded in rigid media, such as agarose, from multiple angles every few minutes from the blastoderm stage until hatching. Here, we describe sample mounting strategies to achieve such a recording. We also provide detailed protocols to realize multiview, long-term, time-lapse recording of Drosophila embryos expressing fluorescent markers on the commercially available Zeiss Lightsheet Z.1 microscope and the OpenSPIM.

Males on demand: the environmental-neuro-endocrine control of male sex determination in daphnids.

Branchiopod crustaceans (e.g., Daphnia sp.) and some other taxa utilize both asexual and sexual reproduction to maximize population sustainability. The decision to switch from asexual to sexual reproduction is triggered by environmental cues that foretell a potentially detrimental change in environmental conditions. This review describes the cascade of events beginning with environmental cues and ending with changes in gene expression that dictate male sex determination in daphnids, the initial event in the switch to sexual reproduction. Several environmental cues have been identified which, either in isolation or in combination, stimulate male sex determination. These cues are typically associated with change of season, exhaustion of resources or loss of habitat. Maternal daphnids receive and respond to these cues, we propose, through the secretion of neuropeptides, which suppress (hyperglycemic hormone-like neuropeptides, allatostatin) or stimulate (allatotropin) the male sex differentiation program. In response, maternal daphnids produce the male sex-determining hormone, methyl farnesoate. Methyl farnesoate binds to a protein MET that dimerizes with the protein SRC forming an active transcription factor. This complex then regulates the expression of genes, primarily doublesex (dsx), involved in programming the single-celled embryo to develop into a male. In the absence of methyl farnesoate programming, the embryo develops into a female. Epigenetic modifications of the genome as a possible mode of methyl farnesoate action and the utility of this model to decipher the role of epigenetics in sex differentiation in other species are discussed.