Biology subjects

Srinivas, S.

Publications and source records attributed to Srinivas, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Quantitative multi-scale morphodynamic analysis reveals ratchet-like collective DVE migration and epiblast retrograde cell flow during anterior patterning in the mouse embryo

The collective unidirectional migration of distal visceral endoderm (DVE) cells in the early mouse embryo is required to pattern the anterior-posterior (A-P) axis in the epiblast. It is unknown to what extent A-P axial asymmetries exist prior to DVE migration, how migration becomes channeled towards one side of the embryo, and whether the epiblast cells they migrate over have coordinated movements. We developed a quantitative embryo-wide, tissue-tracking approach to analyse visceral endoderm and epiblast tissue morphodynamics in a longitudinal light-sheet imaged, multi-embryo data-set. Here we show that asymmetric morphology of the ectoplacental cone already present prior to DVE migration correlates with the alignment of the A-P axis but not its polarity. DVE cell movements are initiated with a relatively low cell coordination and small net migration, then get channelled in an abrupt transition to a highly coordinated, uni-directional anterior motion. This anteriorwards migration is characterised by a ratchet-like, intermittent motion. Vertex modelling demonstrates that tissue rheology can account for DVE start-stop motion, and suggests that T1-mediated stress relaxation in the surrounding tissue can facilitate intermittent DVE motion without requiring intrinsic fluctuations in DVE velocity. Finally, comparing cell movement of the DVE with the underlying epiblast reveals a previously unknown coordinated motion in the anterior epiblast, opposite to the direction of DVE migration. Together these data provide insights into the origin of embryonic axial asymmetry and a previously unappreciated coordination between VE and epiblast tissue-motion during anterior-posterior patterning. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/720339v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1cfe4fdorg.highwire.dtl.DTLVardef@1c2c3e6org.highwire.dtl.DTLVardef@1cb6a5corg.highwire.dtl.DTLVardef@1b3ed19_HPS_FORMAT_FIGEXP M_FIG C_FIG See supplemental movie: animated abstract

developmental biology↗

bioRxiv2026

Uncoupling of seagrass host selection and succession for microbial guilds in meadow chronosequence

Succession is an ecosystem building process in which a habitat and its community interact predictably by increasing diversity, habitat engineering, and ultimately reaching a climax community, where other ecological processes influence its dynamic. Key to succession is the establishment of primary producing habitat forming species, which drives niche differentiation leading to increasing diversity. Here, we use the primary colonizing and habitat forming seagrass, Halophila ovalis, to demonstrate that it drives bacterial succession in a meadow ecosystem, and its microbiome, both rhizoplane and phylloplane, are under host selection. Many of the characteristics attributed to plants for habitat modification are microbial processes such as nitrogen fixation and sulfide detoxification and succession is often extrapolated to such processes. To determine if succession (increasing diversity) or selection (reducing diversity) drives changes in diversity (16S rRNA gene) or habitat modifying processes (nifH, soxB, aprA, dsrA), molecular analysis was performed along chronosequences (as a proxy for succession) of seagrass patches. Bacterial communities were sampled within the meadow ecosystem and the microbiomes of H. ovalis (both rhizoplane and phylloplane). Genes involved in biogeochemical cycling are differentially impacted within the microbiome and meadow sediments, with only nifH under succession. All genes from all niches sampled for community analysis are under directional community trajectories, despite being subjected to distinct ecological processes, signifying that many ecological processes, including succession and host association, drive community assemblage.

ecology↗

bioRxiv2026

Machine Learning Ensemble Reveals Distinct Molecular Pathways of Retinal Damage in Spaceflown Mice

BackgroundSpaceflight-associated neuro-ocular syndrome (SANS) poses significant risks to astronaut visual health during long-duration missions, yet its underlying molecular mechanisms remain incompletely understood. Oxidative stress and apoptosis are candidate molecular drivers, but their transcriptomic signatures in spaceflight-exposed retinal tissue have not been systematically characterized. MethodsWe applied a machine learning ensemble of linear regression models to predict two ocular phenotypes: 4-hydroxynonenal (4-HNE) immunostaining as a marker of lipid peroxidation-mediated oxidative damage; and TUNEL positivity as a marker of apoptotic cell death. In this observational study, we use bulk retinal gene expression data obtained from a controlled experiment with ground control and spaceflown mice to predict these phenotypes. Gene Ontology pathway enrichment was performed on the most predictive gene sets for each phenotype. ResultsThe 4-HNE phenotype was predicted by genes that converge on membrane-associated pathways, photoreceptor protein modification, synaptic dysfunction, and extracellular matrix dysregulation, including B2m, Tf, Cnga1, mt-Nd1, Snap25, and Efemp1. The genes predicting the TUNEL phenotype revealed a distinct signature emphasizing stress-induced apoptosis, rod photoreceptor degeneration, and endoplasmic reticulum dysfunction, with Ddit4, Nrl, Rom1, Reep6, and Gabarapl1 emerging as central regulators. ConclusionsOxidative lipid peroxidation and apoptotic cell death represent complementary and molecularly distinct pathological mechanisms in spaceflight-exposed murine retinal tissue. The gene signatures provide a putative molecular framework for developing noninvasive biomarkers and therapeutic targets to monitor and protect astronaut visual health during long-duration and deep-space missions.

bioinformatics↗

bioRxiv2024

Calcium signalling is required for anterior patterning in the mouse embryo

Anterior-Posterior axis formation in the mouse embryo requires the active migration of the DVE cell population at E5.5. While intracellular Ca2+ signalling has been shown to control cell migration in multiple cell contexts, it is unknown whether it is required for DVE migration. The pattern of Ca2+ activity in the mouse embryo at early peri-implantation stages is also unknown. Using the GCaMP6f Ca2+ reporter line we performed a detailed assessment of Ca2+ dynamics between E0.5 - E5.5 using live imaging. We find that prior to implantation, Ca2+ transients are rare, but at E5.5 widespread, periodic, Ca2+ transients in extra-embryonic tissues can be observed, including in the VE and ExE. In contrast, cells of the E5.5 epiblast remain relatively quiescent but show sporadic large-scale multi-cellular waves. Inhibition of SERCA at E5.5 abolishes Ca2+ transients and leads to DVE arrest, indicative that these transients are required for axial patterning. Together these results reveal the pattern of Ca2+ handling in the early mouse embryo and a novel requirement in anterior-posterior axis formation.

developmental biology↗

bioRxiv2024

Geographical distribution, disease association and diversity of Klebsiella pneumoniae KL and O antigens in India: roadmap for vaccine development

Klebsiella pneumoniae poses a significant healthcare challenge due to its multidrug resistance and diverse serotype landscape. This study aimed to explore the serotype diversity of 1072 K. pneumoniae and its association with geographical distribution, disease severity and antimicrobial/virulence patterns in India. Whole-genome sequencing was performed on the Illumina platform, and genomic analysis was carried out using the Kleborate tool. KL64 (n=264/1072, 26%), KL51 (249/1072, 24%), KL2 (n=88/1072, 8%), O1/O2v1 (n=471/1072, 44%), O1/O2v2 (n=353/1072, 33%), and OL101 (n=66/1072, 6%) were the most prevalent serotypes. The study identified 119 different sequence types (STs) with varying serotypes, with KL64 being the most predominant in ST231 (26%). O serotypes were strongly linked with STs, with O1/O2v1 predominantly associated with ST231 (44%). Simpsons diversity index and Fishers exact test revealed higher serotype diversity in the north and east regions, along with intriguing associations between specific serotypes and resistance profiles. No significant association between KL or O types and disease severity was observed. Furthermore, we found no specific association of virulence factors with KL types or O antigen types (P>0.05). Conventionally described hypervirulent clones (i.e., KL1 and KL2) in India lacked typical virulent markers (i.e., aerobactin), contrasting with other regional serotypes. The cumulative distribution of KL and O serotypes suggests that future vaccines may have to include either [~]20 KL types or 4 O types to cover >85% of the carbapenemase-producing Indian K. pneumoniae population. The findings underscore the need for a vaccine with broad coverage to address the diverse landscape of K. pneumoniae strains in different regions of India. Understanding regional serotype dynamics is pivotal for targeted surveillance, interventions, and tailored vaccine strategies to tackle the diverse landscape of K. pneumoniae infections across India. Data SummaryO_LIAll the sequenced data has been submitted to the European Nucleotide Archive (ENA) under the Bioproject numbers PRJEB29740 and PRJEB50614. Run Accessions and Biosample numbers are provided in Supplementary Table 1 with corresponding metadata for each sample used in the study. C_LIO_LIThe Microreact link for the genomic analysis is provided (https://microreact.org/project/oqKM84GBszEPW9Emt2FKnP-klebsiella-pneumoniae-indian-serotypes). C_LIO_LIThe pipelines used in the study are published in gitlab (https://gitlab.com/cgps/ghru/pipelines). C_LIO_LIThe tools details and the implementation of the pipelines are described in protocols.io (https://www.protocols.io/view/ghru-genomic-surveillance-of-antimicrobial-resista-bp2l6b11kgqe/v4). C_LIO_LIThe R scripts used with all the input files used for each script have been published in Fishare (https://doi.org/10.6084/m9.figshare.25414807.v1) C_LI Impact StatementKlebsiella pneumoniae produces polysaccharide capsules, which serve as both epidemiological markers and significant virulence factors. The increasing accessibility of whole genome sequencing has made it easier than ever to investigate this capsule diversity. This study is the first of its kind in India to comprehensively investigate the serotype diversity of K. pneumoniae strains and their association with disease severity, antimicrobial resistance/virulence patterns, and geographical distribution across various regions of the subcontinent. This multi-dimensional analysis not only provides valuable insights into the molecular epidemiology of K. pneumoniae in India but also offers crucial data for the development of targeted interventions, including vaccine formulations tailored to address the prevailing serotypes. These findings serve as a foundation for informed decision-making in the management and prevention of K. pneumoniae infections, ultimately contributing to improved public health outcomes in the region.

genomics↗

bioRxiv2023

Microbial Metamorphosis: Symbiotic bacteria and fungi proliferate during diapause and may enhance overwintering survival in a solitary bee

Host-microbe interactions underlie the development and fitness of many macroorganisms including bees. While many social bees benefit from vertically transmitted gut bacteria, solitary bees, which comprise the vast majority of species diversity within bees, lack a specialized gut microbiome. Here we examine the composition and abundance of bacteria and fungi throughout the complete life cycle of a ground-nesting solitary bee Anthophora bomboides standfordiana. In contrast to expectations, immature bee stages maintain a distinct core microbiome consisting of Actinobacteria and fungi in the genus Moniliella. Diapausing larval bees hosted the most abundant and distinctive bacteria and fungi, attaining 33 and 52 times their initial copy number, respectively. We tested two adaptive hypotheses regarding microbial functions for overwintering bees. First, using isolated bacteria and fungi, we found that Streptomyces from brood cells inhibited the growth of multiple pathogenic filamentous fungi, suggesting a role in pathogen protection during the long period of diapause. Second, sugar alcohol composition changed in tandem with major changes in microbial abundance suggesting links with bee metabolism or overwintering biology. Our results suggest that Anthophora bomboides hosts a conserved core microbiome that may provide key fitness advantages through larval development and overwintering, and raises the question of how this microbiome is transmitted between generations. The present work suggests that focus on adult gut microbiomes in solitary bees may overlook microbial symbionts within brood cells that could play diverse roles in bee fitness, and that exploration of microbes associated with immature bees may uncover novel microbial effects on insect hosts.

ecology↗

bioRxiv2023

Single-cell phenomics reveals behavioural and mechanical heterogeneities underpinning collective migration during mouse anterior patterning

Distal Visceral Endoderm (DVE) cells show a stereotypic unidirectional migration essential for correct orientation of the anterior-posterior axis. They migrate within a simple epithelium, the Visceral Endoderm (VE). It is unknown how DVE cells negotiate their way amongst the surrounding VE cells, what determines the bounds of DVE migration within the VE, and the relative contributions of different cell behaviours to this migration. To address these questions, we used lightsheet microscopy to generate a multi-embryo, singlecell resolution, longitudinal dataset of cell behaviour and morphology. We developed a machine learning based pipeline to segment cells and a data-informed systematic computational framework to extract and compare select morphological, behavioural and molecular parameters of all VE cells in a unified coordinate space. Unbiased clustering of this single-cell phenomic dataset reveals considerable patterned phenotypic heterogeneity within the VE and a previously unknown sub-grouping within the DVE. While migrating, DVE cells retain regular morphology, do not exchange neighbours and are crowded, all hallmarks of the jammed state. In contrast, VE cells immediately ahead of them deform and undergo neighbour exchange. We show that DVE cells are characterised by higher levels of apical F-actin and elevated tension relative to the VE cells immediately ahead of them through which they migrate, but stop migrating upon reaching a region of the VE with matching elevated tension. Lefty1 mutants, known to show abnormal over-migration of DVE cells, show disruption to this patterned tension in the VE. Our findings provide novel insights into the control of cell behaviour during the remodelling of curved epithelia, indicating that the collective migration of sub-sets of cells can be circumscribed by modulating the mechanical properties of surrounding cells and that migrating cells in this context remain as a jammed solid flock, with surrounding cells facilitating their movement by becoming unjammed. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/534937v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@10a7153org.highwire.dtl.DTLVardef@963a1forg.highwire.dtl.DTLVardef@c1fcd0org.highwire.dtl.DTLVardef@1bcdded_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2022

Molecular characterization of Left-Right symmetry breaking in the mouse embryo

The asymmetric morphology of the mammalian heart is essential to its function as the organ of pulmonary and systemic double circulation. Left-right asymmetry is established by a leftward flow in the node that results in the asymmetric expression of Nodal. This triggers a cascade of asymmetric expression of downstream genes, such as Pitx2c, in the lateral plate mesoderm that gives rise to the first morphologically recognizable primordial heart structure, the cardiac crescent. Relatively little is known about gene expression asymmetries in the cardiac crescent that might underpin asymmetric cardiac morphogenesis. To systematically identify asymmetrically expressed genes, we performed a single-cell transcriptional analysis of manually dissected left and right halves of the cardiac crescent at stages spanning symmetry breaking. This revealed both left and right-sided genes that have not previously been implicated in left-right symmetry breaking. Some of these were expressed in multiple cell types but showed asymmetric expression in only a sub-set of cell types. We validated these findings using multiplexed in situ Hybridization Chain Reaction (HCR) and high-resolution volume imaging to characterize the expression patterns of select genes. Using Dnahiv/iv mutant embryos that show randomized situs, we established that all the genes tested tracked the asymmetric expression of Pitx2c, indicating their asymmetric expression also arose from the early asymmetries at the node. This study provides a high-fidelity molecular characterization of left-right symmetry breaking during cardiac crescent formation, providing a basis for future mechanistic studies on asymmetric cardiac morphogenesis.

developmental biology↗

bioRxiv2022

Chromatin remodeller Chd7 is developmentally regulated in the neural crest by tissue-specific transcription factors

Neurocristopathies such as CHARGE syndrome result from aberrant neural crest development. A large proportion of CHARGE cases are attributed to mutations in the gene encoding CHD7, chromodomain helicase DNA binding protein 7, which remodels chromatin. While the role for CHD7 in neural crest development is well documented, it remains elusive how this seemingly ubiquitous factor is specifically upregulated in neural crest cells. Here, we use epigenomic profiling of chick neural crest to identify a cohort of enhancers regulating Chd7 expression in neural crest cells and other tissues. We functionally validate upstream transcription factor binding at candidate enhancers, revealing novel epistatic relationships between neural crest master regulators and Chd7. To our knowledge, this is the first report of tissue-specific regulation of a chromatin remodeller. Furthermore, we find conserved enhancer features in human embryonic epigenomic data and validate the activity of the human equivalent CHD7 enhancers in the chick embryo. Collectively our findings embed Chd7 in the neural crest gene regulatory network and offer potentially clinically relevant elements for interpreting CHARGE syndrome cases without causative allocation.

developmental biology↗

bioRxiv2022

CIARA: a cluster-independent algorithm for the identification of markers of rare cell types from single-cell RNA seq data

A powerful feature of single-cell RNA-sequencing data analysis is the possibility to identify novel rare cell types. However, rare cell types are often missed by standard clustering approaches. We have developed CIARA (Cluster Independent Algorithm for the identification of markers of RAre cell types), a computational tool available in R and Python that outperforms existing methods for rare cell type detection. With CIARA, we found a small group of precursor cells among mouse embryonic stem cells and previously uncharacterized rare populations of cells in a human gastrula.

bioinformatics↗

bioRxiv2021

Characterisation of the transcriptional dynamics underpinning the function, fate, and migration of the mouse Anterior Visceral Endoderm

During early post-implantation development of the mouse embryo, the Anterior Visceral Endoderm (AVE) differs from surrounding visceral endoderm (VE) in its migratory behaviour and ability to restrict primitive streak formation to the opposite side of the egg cylinder. In order to characterise the molecular basis for the unique properties of the AVE, we combined single-cell RNA-sequencing of the VE prior to and during AVE migration, with high-resolution imaging, short-term lineage labelling, phosphoproteomics and pharmacological intervention. This revealed the transient nature of the AVE, the emergence of heterogeneities in AVE transcriptional states relative to position of cells, and its prominence in establishing gene expression asymmetries within the spatial constraints of the embryo. We identified a previously unknown requirement of Ephrin- and Semaphorin-signalling for AVE migration. These findings point to a tight coupling of transcriptional state and position in the AVE and reveal molecular heterogeneities underpinning its migratory behaviour and function.

developmental biology↗

bioRxiv2020

Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis

Transcriptional and epigenetic profiling of single-cells has advanced our knowledge of the molecular bases of gastrulation and early organogenesis. However, current approaches rely on dissociating cells from tissues, thereby losing the crucial spatial context that is necessary for understanding cell and tissue interactions during development. Here, we apply an image-based single-cell transcriptomics method, seqFISH, to simultaneously and precisely detect mRNA molecules for 387 selected target genes in 8-12 somite stage mouse embryo tissue sections. By integrating spatial context and highly multiplexed transcriptional measurements with two single-cell transcriptome atlases we accurately characterize cell types across the embryo and demonstrate how spatially-resolved expression of genes not profiled by seqFISH can be imputed. We use this high-resolution spatial map to characterize fundamental steps in the patterning of the midbrain-hindbrain boundary and the developing gut tube. Our spatial atlas uncovers axes of resolution that are not apparent from single-cell RNA sequencing data - for example, in the gut tube we observe early dorsal-ventral separation of esophageal and tracheal progenitor populations. In sum, by computationally integrating high-resolution spatially-resolved gene expression maps with single-cell genomics data, we provide a powerful new approach for studying how and when cell fate decisions are made during early mammalian development.

developmental biology↗

bioRxiv2020

ASPP2/PP1 complexes maintain the integrity of pseudostratified epithelia undergoing remodelling during morphogenesis

During development, pseudostratified epithelia undergo large scale morphogenetic events associated with increased mechanical stress. The molecular mechanisms that maintain tissue integrity in this context are poorly understood. Using a variety of genetic and imaging approaches, we uncover that the ASPP2/PP1 complex ensures proper epiblast and proamniotic cavity architecture via a mechanism that specifically prevents the most apical daughter cells from delaminating apically following cell division events. The ASPP2/PP1 complex achieves this by maintaining the integrity and organisation of the F-actin cytoskeleton at the apical surface of dividing cells. ASPP2/PP1 is also essential during gastrulation in the primitive streak, in somites and in the head fold region, suggesting that this complex is required across a wide range of pseudostratified epithelia during morphogenetic events that are accompanied by intense tissue remodelling and high cell proliferation. Finally, our study also suggests that the interaction between ASPP2 and PP1 is essential to the tumour suppressor function of ASPP2 which may be particularly relevant in the context of tissues that are subject to increased mechanical stress.

developmental biology↗

bioRxiv2020

A spatially resolved single cell atlas of human gastrulation

Gastrulation is the fundamental process during the embryogenesis of all multicellular animals through which the basic body plan is first laid down. It is pivotal in generating cellular diversity coordinated with spatial patterning. Gastrulation in humans occurs in the third week following fertilization. Our understanding of this process in humans is extremely limited, and based almost entirely on experimental models. Here, we characterize in a spatially resolved manner the single cell transcriptional profile of an entire gastrulating human embryo approximately 16 to 19 days after fertilization. We used these data to provide the first unequivocal demonstration that human embryonic stem cells represent the early post implantation epiblast. We identified both primordial germ cells and red blood cells, which had never been characterized so early during human development. Comparison with mouse gastrula transcriptomes revealed many commonalities between the human and mouse but also several key differences, particularly in FGF signaling, that we validated experimentally. This unique dataset offers a unique glimpse into a central but generally inaccessible stage of our development, provides new context for interpreting experiments in other model systems and represents a valuable resource for guiding directed differentiation of human cells in vitro.

developmental biology↗

bioRxiv2020

An evolutionarily conserved metallophosphodiesterase is a determinant of lifespan in Drosophila

Evolutionarily conserved genes usually have a critical role to play during organismal aging and longevity. Here, we show that a previously uncharacterized Class III metallophosphoesterase in Drosophila, an ortholog of the MPPED1 and MPPED2 proteins in mammals, is necessary for optimal lifespan. dMPPED is the product of the gene CG16717 and hydrolyzed a variety of phosphodiester substrates in a metal-dependent manner. dMPPED was expressed widely during development and in the adult fly. Deletion of the gene in flies dramatically reduced lifespan, without affecting development or fecundity. Longevity was restored on ubiquitous expression of the protein, and neuronal expression of both wild type and the catalytically inactive form of dMPPED was also able to restore normal lifespan. Overexpression of the protein, both ubiquitously and neuronally in wild type flies extended lifespan by ~ 20%. RNA-seq analysis of dMPPEDKO flies revealed mis-regulation of innate immune pathways, a number of transcription factors and genes earlier reported to affect aging and lifespan. Importantly, neuronal expression of mammalian MPPED2 was able to rescue lifespan in dMPPEDKO flies, but not extend lifespan in wild type flies. This reports the first description of the biological role of an evolutionarily conserved metallophosphoesterase that may serve as a scaffolding protein in diverse signaling pathways to modulate longevity in the fly.

developmental biology↗

bioRxiv2020

An asymmetry in the frequency and position of mitosis in the epiblast precedes gastrulation and suggests a role for mitotic rounding in cell delamination during primitive streak epithelial-mesenchymal transition.

The epiblast, a pseudostratified epithelium, is the precursor for the three main germ layers required for body shape and organogenesis: ectoderm, mesoderm, and endoderm. At gastrulation, a subpopulation of epiblast cells constitutes a transient posteriorly located structure called the primitive streak, where cells that undergo epithelial-mesenchymal transition make up the mesoderm and endoderm lineages. In order to observe the behavior of individual cells, epiblast cells were labeled ubiquitously or in a mosaic fashion using fluorescent membrane reporters. The cell shapes of individual cells and the packing and behaviour of neighbouring cells during primitive streak formation were recorded through live time-lapse imaging. Posterior epiblast displayed a higher frequency of rosettes, a signature of cell rearrangements, prior to primitive streak initiation. A third of rosettes were associated with a central cell undergoing mitosis. Interestingly, cells at the primitive streak, in particular delaminating cells, underwent mitosis twice more frequently than other epiblast cells, suggesting a role for cell division in epithelial-mesenchymal transition. Pseudostratified epithelia are characterized by interkinetic nuclear migration, where mitosis occurs at the apical side of the epithelium. However, we found that exclusively on the posterior side of the epiblast, mitosis was not restricted to the apical side. Non-apical mitosis was apparent as early as E5.75, just after the establishment of the anterior-posterior axis, and prior to initiation of epithelial-mesenchymal transition. Non-apical mitosis was associated with primitive streak morphogenesis, as it occurred specifically in the streak even when ectopically located. Most non-apical mitosis resulted in one or two daughter cells leaving the epiblast layer to become mesoderm. Furthermore, in contrast to what has been described in other pseudostratified epithelia such as neuroepithelium, the majority of cells dividing apically detached completely from the basal pole in the epiblast. Cell rearrangement associated with mitotic cell rounding in the posterior epiblast during gastrulation, in particular when it occurs on the basal side, might thus facilitate cell ingression through the PS and transition to a mesenchymal phenotype. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/959080v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@18530b2org.highwire.dtl.DTLVardef@1400a63org.highwire.dtl.DTLVardef@169f688org.highwire.dtl.DTLVardef@1b87931_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2020

Differences in mitochondrial activity trigger cell competition during early mouse development.

Cell competition is emerging as a quality control mechanism that eliminates unfit cells in a wide range of settings from development to the adult. However, the nature of the cells normally eliminated by cell competition and what triggers their elimination remains poorly understood. In mouse, prior to gastrulation 35% of epiblast cells are eliminated. Here we have performed single cell transcriptional profiling of these cells and find that they show the hallmarks of cell competition and have mitochondrial defects. We demonstrate that mitochondrial defects are common to a range of different loser cell types and that manipulating mitochondrial function is sufficient to trigger competition. Importantly, we show that in the embryo cell competition eliminates cells with mitochondrial DNA mutations and that even non-pathological changes in mitochondrial DNA sequence can induce cell competition. Our results therefore suggest that cell competition is a purifying selection that optimises mitochondrial performance prior to gastrulation.

developmental biology↗

bioRxiv2019

Position-sensing established duringcompaction dictates cell fate in themammalian embryo

Precise patterning within the 3-dimensional context of tissues, organs and embryos implies that cells can sense their relative position. We still understand relatively little about how cells sense their relative position within small groups of cells. During preimplantation development, outside and inside cells rely on apicobasal polarity and the Hippo pathway to choose their fate. Despite recent findings suggesting that mechanosensing may be central to this process, the relationship between blastomere geometry (i.e. shape and position) and the Hippo pathway effector YAP remains unknown. To address this, we used a highly quantitative approach to collect and analyse information on the geometry and YAP localisation of individual blastomeres of mouse and human embryos. We find that the fraction of YAP in the nucleus responds to the proportion of exposed cell surface area rather than blastomere shape. To directly test the influence of blastomere position on YAP localisation we developed an approach using hydrogel based cylindrical cavities to alter blastomere arrangement in cultured embryos. Unbiased clustering analyses of blastomeres from such embryos reveal that the ability to respond to position emerges as early as the 8-cell stage during compaction and that altering the relative position of a blastomere within an embryo can alter its fate. Finally, we demonstrate that this response is lost upon inhibiting PKC signalling, linking it to the cell polarity. Our results pinpoint when during early embryogenesis cell specification decisions are initiated and show how blastomeres can sense their position in a polarity dependent manner to alter YAP localisation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/856161v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@845b46org.highwire.dtl.DTLVardef@18473ceorg.highwire.dtl.DTLVardef@cf0124org.highwire.dtl.DTLVardef@53fc8b_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗