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

2021 ◽  
Author(s):  
Stanley E. Strawbridge ◽  
Agata Kurowski ◽  
Elena Corujo-Simon ◽  
Alexander G. Fletcher ◽  
Jennifer Nichols
Keyword(s):  
Cell Fate ◽  
Spatial Information ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Three Dimensional ◽  
Mathematical Framework ◽  
Cell Fate Decision ◽  
Machine Learning Approach ◽  
Quantitative Immunofluorescence ◽  
Fate Decision

AbstractA crucial aspect of embryology is relating the position of individual cells to the broader geometry of the embryo. A classic example can be seen in the first cell-fate decision of the mouse embryo, where interior cells become inner cell mass and exterior cells become trophectoderm. Advances in image acquisition and processing technology used by quantitative immunofluorescence have resulted in the production of embryo images with increasingly rich spatial information that demand accessible analytical methods. Here, we describe a simple mathematical framework and an unsupervised machine learning approach for classifying interior and exterior points of a three-dimensional point-cloud. We benchmark our method to demonstrate that it yields higher classification rates for pre-implantation mouse embryos and greater accuracy when challenged with local surface concavities. This method should prove useful to experimentalists within and beyond embryology, with broader applications in the biological and life sciences.

scholarly journals Cell fate clusters in ICM organoids arise from cell fate heredity and division: a modelling approach

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Tim Liebisch ◽  
Armin Drusko ◽  
Biena Mathew ◽  
Ernst H. K. Stelzer ◽  
Sabine C. Fischer ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Cell Division ◽  
Cell Fate ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Cell Lineage ◽  
Cell Fate Decision ◽  
Cell Fate Decisions ◽  
Chemical Signalling ◽  
Fate Decision

AbstractDuring the mammalian preimplantation phase, cells undergo two subsequent cell fate decisions. During the first decision, the trophectoderm and the inner cell mass are formed. Subsequently, the inner cell mass segregates into the epiblast and the primitive endoderm. Inner cell mass organoids represent an experimental model system, mimicking the second cell fate decision. It has been shown that cells of the same fate tend to cluster stronger than expected for random cell fate decisions. Three major processes are hypothesised to contribute to the cell fate arrangements: (1) chemical signalling; (2) cell sorting; and (3) cell proliferation. In order to quantify the influence of cell proliferation on the observed cell lineage type clustering, we developed an agent-based model accounting for mechanical cell–cell interaction, i.e. adhesion and repulsion, cell division, stochastic cell fate decision and cell fate heredity. The model supports the hypothesis that initial cell fate acquisition is a stochastically driven process, taking place in the early development of inner cell mass organoids. Further, we show that the observed neighbourhood structures can emerge solely due to cell fate heredity during cell division.

scholarly journals Three-dimensional cell neighbourhood impacts differentiation in the inner mass cells of the mouse blastocyst

2017 ◽  
Author(s):  
Sabine C. Fischer ◽  
Elena Corujo-Simón ◽  
Joaquín Lilao-Garzón ◽  
Ernst H. K. Stelzer ◽  
Silvia Muñoz-Descalzo
Keyword(s):  
Cell Fate ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Three Dimensional ◽  
Mouse Blastocyst ◽  
Blastocyst Development ◽  
Cell Position ◽  
Fate Decision ◽  
Early Mouse ◽  
Dimensional Cell

AbstractDuring mammalian blastocyst development, inner cell mass (ICM) cells differentiate into epiblast (Epi) or primitive endoderm (PrE). These two fates are characterised by the transcription factors NANOG and GATA6, respectively. Here, we present quantitative three-dimensional single cell-based neighbourhood analyses to investigate the spatial distribution of NANOG and GATA6 expression in the ICM of the mouse blastocyst. The cell neighbourhood is characterised by the expression levels of the fate markers in the surrounding cells, together with the number of surrounding cells and cell position. We find that cell neighbourhoods are established in early blastocysts and different for cells expressing different levels of NANOG and GATA6. Highest NANOG expressing cells occupy specific positions within the ICM and are surrounded by 9 neighbours, while GATA6 expressing cells cluster according to their GATA6 levels. The analysis of mutants reveals that NANOG local neighbourhood is regulated by GATA6.Summary statementThree-dimensional cell neighbourhood, which includes fate marker levels, number of neighbouring cells and cell position, determines cell fate decision in early mouse embryos.

scholarly journals Cell Fate Clusters in ICM Organoids Arise from Cell Fate Heredity & Division – a Modelling Approach

2019 ◽  
Author(s):  
Tim Liebisch ◽  
Armin Drusko ◽  
Biena Mathew ◽  
Ernst H. K. Stelzer ◽  
Sabine C. Fischer ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Cell Division ◽  
Cell Fate ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Cell Lineage ◽  
Cell Fate Decision ◽  
Agent Based ◽  
Cell Fate Decisions ◽  
Fate Decision

ABSTRACTDuring the mammalian preimplantation phase, cells undergo two subsequent cell fate decisions. During the first cell fate decision, cells become either part of an outer trophectoderm or part of the inner cell mass. Subsequently, the inner cell mass (ICM) segregates into an embryonic and an extraembryonic lineage, giving rise to the epiblast and the primitive endoderm, respectively. Inner cell mass organoids represent an experimental model system for preimplantation development, mimicking the second cell fate decision taking place in in vivo mouse embryos. In a previous study, the spatial pattern of the different cell lineage types was investigated. The study revealed that cells of the same fate tend to cluster stronger than expected for purely random cell fate decisions. Three major processes are hypothesised to contribute to the final cell fate arrangements at the mid and late blastocysts or 24 h old and 48 h old ICM organoids, respectively: 1) intra- and intercellular chemical signalling; 2) a cell sorting process; 3) cell proliferation. In order to quantify the influence of cell proliferation on the emergence of the observed cell lineage type clustering behaviour, we developed an agent-based model. Hereby, cells are mechanically interacting with direct neighbours, and exert adhesion and repulsion forces. The model was applied to compare several current assumptions of how inner cell mass neighbourhood structures are generated. We tested how different assumptions regarding cell fate switches affect the observed neighbourhood relationships. The model supports the hypothesis that initial cell fate acquisition is a stochastically driven process, taking place in the early development of inner cell mass organoids. The model further shows that the observed neighbourhood structures can emerge due to cell fate heredity during cell division and allows the inference of a time point for the cell fate decision.STATEMENT OF SIGNIFICANCECell fate decisions in early embryogenesis have been considered random events, causing a random cell fate distribution. Using an agent-based mathematical model, fitted to ICM organoid data, we show that the assumed random distribution of cell fates occurs only for a short time interval, as cell fate heredity and cell division quickly lead to spatial cell fate clustering. Our results show that neighbourhood clustering can emerge without specific neighbourhood interactions affecting the cell fate decision. The approach indicates four consecutive phases of early development: 1) co-expression of cell fate markers, 2) cell fate decision, 3) division and local cell fate clustering, and 4) phase separation, whereby only the phases 1-3 occur in ICM organoids during the first 24h of growth.

scholarly journals Origin of cellular asymmetries in the pre-implantation mouse embryo: a hypothesis

2014 ◽  
Vol 369 (1657) ◽  
pp. 20130536 ◽  
Author(s):  
Katsuyoshi Takaoka ◽  
Hiroshi Hamada
Keyword(s):  
Dna Methylation ◽  
Cell Fate ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Cell Fate Decision ◽  
Mouse Development ◽  
Cell Stage ◽  
Stage Embryo ◽  
A Cell ◽  
Fate Decision

The first cell fate decision during mouse development concerns whether a blastomere will contribute to the inner cell mass (ICM; which gives rise to the embryo proper) or to trophectoderm (TE; which gives rise to the placenta). The position of a cell within an 8- to 16-cell-stage embryo correlates with its future fate, with outer cells contributing to TE and inner cells to the ICM. It remains unknown, however, whether an earlier pre-pattern exists. Here, we propose a hypothesis that could account for generation of such a pre-pattern and which is based on epigenetic asymmetry (such as in histone or DNA methylation) between maternal and paternal genomes in the zygote.

scholarly journals The first cell-fate decision of mouse preimplantation embryo development: integrating cell position and polarity

Open Biology ◽  
2017 ◽  
Vol 7 (11) ◽  
pp. 170210 ◽  
Author(s):  
Aleksandar I. Mihajlović ◽  
Alexander W. Bruce
Keyword(s):  
Cell Fate ◽  
Embryo Development ◽  
Preimplantation Embryo ◽  
Cell Mass ◽  
Cell Fate Decision ◽  
Preimplantation Embryo Development ◽  
Cell Lineages ◽  
Mouse Preimplantation Embryo ◽  
Fate Decision ◽  
Mouse Preimplantation Embryo Development

During the first cell-fate decision of mouse preimplantation embryo development, a population of outer-residing polar cells is segregated from a second population of inner apolar cells to form two distinct cell lineages: the trophectoderm and the inner cell mass (ICM), respectively. Historically, two models have been proposed to explain how the initial differences between these two cell populations originate and ultimately define them as the two stated early blastocyst stage cell lineages. The ‘positional’ model proposes that cells acquire distinct fates based on differences in their relative position within the developing embryo, while the ‘polarity’ model proposes that the differences driving the lineage segregation arise as a consequence of the differential inheritance of factors, which exhibit polarized subcellular localizations, upon asymmetric cell divisions. Although these two models have traditionally been considered separately, a growing body of evidence, collected over recent years, suggests the existence of a large degree of compatibility. Accordingly, the main aim of this review is to summarize the major historical and more contemporarily identified events that define the first cell-fate decision and to place them in the context of both the originally proposed positional and polarity models, thus highlighting their functional complementarity in describing distinct aspects of the developmental programme underpinning the first cell-fate decision in mouse embryogenesis.

scholarly journals Dynamic changes in Sox2 spatio-temporal expression promote the second cell fate decision through Fgf4/Fgfr2 signaling in preimplantation mouse embryos

2018 ◽  
Vol 475 (6) ◽  
pp. 1075-1089 ◽  
Author(s):  
Tapan Kumar Mistri ◽  
Wibowo Arindrarto ◽  
Wei Ping Ng ◽  
Choayang Wang ◽  
Leng Hiong Lim ◽  
...  
Keyword(s):  
Cell Fate ◽  
Target Genes ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Correlation Spectroscopy ◽  
Binding Interaction ◽  
Regulatory Motifs ◽  
Sox2 Expression ◽  
Spatio Temporal ◽  
Fate Decision

Oct4 and Sox2 regulate the expression of target genes such as Nanog, Fgf4, and Utf1, by binding to their respective regulatory motifs. Their functional cooperation is reflected in their ability to heterodimerize on adjacent cis regulatory motifs, the composite Sox/Oct motif. Given that Oct4 and Sox2 regulate many developmental genes, a quantitative analysis of their synergistic action on different Sox/Oct motifs would yield valuable insights into the mechanisms of early embryonic development. In the present study, we measured binding affinities of Oct4 and Sox2 to different Sox/Oct motifs using fluorescence correlation spectroscopy. We found that the synergistic binding interaction is driven mainly by the level of Sox2 in the case of the Fgf4 Sox/Oct motif. Taking into account Sox2 expression levels fluctuate more than Oct4, our finding provides an explanation on how Sox2 controls the segregation of the epiblast and primitive endoderm populations within the inner cell mass of the developing rodent blastocyst.

scholarly journals Spatially Precise DNA Bending Is an Essential Activity of the Sox2 Transcription Factor

2001 ◽  
Vol 276 (50) ◽  
pp. 47296-47302 ◽  
Author(s):  
Paola Scaffidi ◽  
Marco E. Bianchi
Keyword(s):  
Cell Fate ◽  
Inner Cell Mass ◽  
Dna Bending ◽  
Cell Mass ◽  
Three Dimensional ◽  
High Mobility ◽  
High Mobility Group ◽  
Cell Fate Decisions ◽  
Activation Of Transcription ◽  
Sox Proteins

Sox proteins, a subclass of high mobility group box proteins, govern cell fate decisions by acting both as classical transcription factors and architectural components of chromatin. We aimed to demonstrate that the DNA bending activity of Sox proteins is essential to regulate gene expression. We focused on mouse Sox2, which participates in the transactivation of theFgf4(fibroblastgrowthfactor4) gene in the inner cell mass of the blastocyst. We generated six substitutions in the high mobility group box of Sox2. One mutant showed a reduced DNA bending activity on theFgf4enhancer (46° instead of 80°), which resulted in more powerful transactivation compared with the wild type protein. We then selected two single-base mutations in theFgf4enhancer that make the DNA less bendable by the Sox2 protein. Again, a different DNA bend (0° and 42° instead of 80°) resulted in a different activation of transcription, but in this case reduced bending corresponded to decreased transcription. We found that the opposite effect on transcription of similar DNA bending angles is due to a 20° difference in the relative orientation of the DNA bends, proving that a correct three-dimensional geometry of enhanceosome complexes is necessary to promote transcription.

scholarly journals p38 (Mapk14/11) occupies a regulatory node governing entry into primitive endoderm differentiation during preimplantation mouse embryo development

Open Biology ◽  
2016 ◽  
Vol 6 (9) ◽  
pp. 160190 ◽  
Author(s):  
Vasanth Thamodaran ◽  
Alexander W. Bruce
Keyword(s):  
Cell Fate ◽  
Embryo Development ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Active Role ◽  
Primitive Endoderm ◽  
Fgf Receptor ◽  
Preimplantation Embryo Development ◽  
Critical Window ◽  
Fate Decision

During mouse preimplantation embryo development, the classically described second cell-fate decision involves the specification and segregation, in blastocyst inner cell mass (ICM), of primitive endoderm (PrE) from pluripotent epiblast (EPI). The active role of fibroblast growth factor (Fgf) signalling during PrE differentiation, particularly in the context of Erk1/2 pathway activation, is well described. However, we report that p38 family mitogen-activated protein kinases (namely p38α/Mapk14 and p38β/Mapk11; referred to as p38-Mapk14/11) also participate in PrE formation. Specifically, functional p38-Mapk14/11 are required, during early-blastocyst maturation, to assist uncommitted ICM cells, expressing both EPI and earlier PrE markers, to fully commit to PrE differentiation. Moreover, functional activation of p38-Mapk14/11 is, as reported for Erk1/2, under the control of Fgf-receptor signalling, plus active Tak1 kinase (involved in non-canonical bone morphogenetic protein (Bmp)-receptor-mediated PrE differentiation). However, we demonstrate that the critical window of p38-Mapk14/11 activation precedes the E3.75 timepoint (defined by the initiation of the classical ‘salt and pepper’ expression pattern of mutually exclusive EPI and PrE markers), whereas appropriate lineage maturation is still achievable when Erk1/2 activity (via Mek1/2 inhibition) is limited to a period after E3.75. We propose that active p38-Mapk14/11 act as enablers, and Erk1/2 as drivers, of PrE differentiation during ICM lineage specification and segregation.

scholarly journals Modular HUWE1 architecture serves as hub for degradation of cell-fate decision factors

2020 ◽  
Author(s):  
Moritz Hunkeler ◽  
Cyrus Y. Jin ◽  
Michelle W. Ma ◽  
Daan Overwijn ◽  
Julie K. Monda ◽  
...  
Keyword(s):  
Cell Fate ◽  
Three Dimensional ◽  
Cellular Stress Response ◽  
Cell Fate Decision ◽  
Decision Factors ◽  
Link Functions ◽  
Wide Range ◽  
Essential Enzyme ◽  
Fate Decision ◽  
Molecular Picture

SummaryHECT ubiquitin ligases play essential roles in metazoan development and physiology. The HECT ligase HUWE1 is central to the cellular stress response by mediating degradation of key death or survival factors including Mcl1, p53, DDIT4, and Myc. As a step toward understanding regulation of HUWE1 engagement with its diverse substrates, we present here the cryo-EM structure of HUWE1, offering a first complete molecular picture of a HECT ubiquitin ligase. The ~4400 amino acid residue polypeptide forms an alpha solenoid-shaped assembly with a central pore decorated with protein interaction modules. This modularity enables HUWE1 to target a wide range of substrates for destruction. The locations of human mutations associated with severe neurodevelopmental disorders link functions of this essential enzyme with its three-dimensional organization.

scholarly journals Dynamic changes in Sox2 spatio-temporal expression direct the second cell fate decision throughFgf4/Fgfr2signaling in preimplantation mouse embryos

2016 ◽  
Author(s):  
Tapan Kumar Mistri ◽  
Wibowo Arindrarto ◽  
Wei Ping Ng ◽  
Choayang Wang ◽  
Leng Hiong Lim ◽  
...  
Keyword(s):  
Cell Fate ◽  
Target Genes ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Regulatory Elements ◽  
Correlation Spectroscopy ◽  
Binding Interaction ◽  
Preimplantation Mouse ◽  
Spatio Temporal ◽  
Fate Decision

ABSTRACTOct4 and Sox2 regulate the expression of target genes such asNanog, Fgf4andUtf1, by binding to their respective regulatory motifs. Their functional cooperation is reflected in their ability to heterodimerise on adjacentcisregulatory elements, the composite Sox/Oct motif. Given that Oct4 and Sox2 regulate many developmental genes, a quantitative analysis of their synergistic action on different Sox/Oct motifs would yield valuable insights into the mechanisms of early embryonic development. In this study, we measured binding affinities of Oct4 and Sox2 to different Sox/Oct motifs using fluorescence correlation spectroscopy (FCS). We found that the synergistic binding interaction is driven mainly by the level of Sox2 in the case of theFgf4Sox/Oct motif. Taking into accountSox2expression levels fluctuate more thanOct4, our finding provides an explanation on how Sox2 controls the segregation of the epiblast (EPI) and primitive endoderm (PE) populations within the inner cell mass (ICM) of the developing rodent blastocyst.

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