Biology subjects

Trusina, A.

Publications and source records attributed to Trusina, A..

12 recordsLinked to original sources

bioRxiv2025

Mechanical cues organize planar cell polarity during vertebrate morphogenesis and embryonic wound repair

Planar cell polarity (PCP) is a phenomenon of coordinated cell orientation in many epithelia and is required for early morphogenetic events, such as vertebrate gastrulation or neural tube closure that place embryonic tissues in their proper locations. Known PCP complexes segregate to opposite edges of each cell due to regulatory feedback interactions, however, whether and how PCP is connected to the tension-sensing machinery has been elusive. Here we observed dynamic polarization of Afadin- and -Actinin-interacting protein (ADIP) in the epithelia adjacent to the involuting marginal zone and the folding neural plate of Xenopus embryos, suggesting that it is controlled by mechanical cues. Supporting this hypothesis, ADIP puncta relocated in response to the pulling forces of neighboring ectoderm cells undergoing apical constriction. Moreover, ADIP puncta rapidly polarized in embryos subjected to stretching and during embryonic wound healing. ADIP formed a mechanosensitive complex with the PCP protein Diversin that was distinct from known core PCP complexes and required for wound repair. We propose that mechanically controlled planar polarization of the ADIP-Diversin complex guides cell behaviors in normal morphogenesis and during wound healing. HighlightsO_LIADIP is a mechanosensing protein that is planar polarized together with Diversin in epithelia during morphogenesis and wound repair C_LIO_LIEpithelial wound healing redistributes ADIP-containing complexes towards the wound. C_LIO_LIADIP and Diversin are interdependent and form a complex regulating morphogenesis and wound healing C_LIO_LIPositive regulatory feedback between mechanical forces and PCP signaling drives morphogenesis C_LI

developmental biology↗

bioRxiv2024

Tipping-point transition from transient to persistent inflammation in pancreatic islets

Type 2 diabetes (T2D) is associated with a systemic increase in the pro-inflammatory cytokine IL-1{beta}. While transient exposure to low IL-1{beta} concentrations improves insulin secretion and {beta}-cell proliferation in pancreatic islets, prolonged exposure leads to impaired insulin secretion and collective {beta}-cell death. IL-1 is secreted locally by islet-resident macrophages and {beta}-cells; however it is unknown if and how the two opposing modes may emerge at single islet level. We investigated the duality of IL-1{beta} with a quantitative in-silico model of the IL-1 regulatory network in pancreatic islets. We find that the network can produce either transient or persistent IL-1 responses, when induced by pro-inflammatory and metabolic cues. This suggests that the duality of IL-1 may be regulated at the single islet level. We use two core feedbacks in the IL-1 regulation to explain both modes: First, a fast positive feedback in which IL-1 induces its own production through IL-1R/IKK/NF-{kappa}B pathway. Second, a slow negative feedback where NF{kappa}-{kappa}B upregulates inhibitors acting at different levels along the IL-1R/IKK/NF-{kappa}B pathway - IL-1 receptor antagonist and A20 among others. A transient response ensues when the two feedbacks are balanced. When positive feedback is dominating over the negative islets transit into the persistent inflammation mode. Consistent with several observations, where the size of islets was implicated in its inflammatory state, we find that large islets and islets with high density of IL-1{beta} amplifying cells are more prone to transit into persistent IL-1{beta} mode. Our results are likely not limited to IL-1{beta} but general for the combined effect of multiple pro-inflammatory cytokines and chemokines. Generalizing complex regulations in terms of two feedbacks of opposing nature and acting on different time scales provides a number of testable predictions, which call for dynamic monitoring of pro-inflammatory cytokines at the single islet level. AUTHOR SUMMARYDifferent expression or activity dynamics of the same proteins or signaling molecules can lead to opposing fates in cells and tissues. While it is known that brief and prolonged exposure to pro-inflammatory cytokine IL-1{beta} have opposing effects on the functionality and viability of pancreatic {beta}-cells, it is unclear if and how these differences in dynamics may arise at the single islet level. We use a mathematical model of the core feedback loops in the IL-1{beta} regulatory network to show that transient and persistent responses are the two characteristic dynamic modes of the IL-1{beta} response. The likelihood of each mode depends on systemic inflammation and elevated glycaemia and free fatty acids levels. We find that large islets are more prone to transit into the persistent mode, which may provide an explanation for why large islets are underrepresented in type 2 diabetes patients.

biophysics↗

bioRxiv2023

Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics

To meet the physiological demands of the body, organs need to establish a functional tissue architecture and adequate size as the embryo develops to adulthood. In the liver, uni- and bipotent progenitor differentiation into hepatocytes and biliary epithelial cells (BECs), and their relative proportions comprise the functional architecture. Yet, the contribution of individual liver progenitors at the organ level to both fates, and their specific proportion is unresolved. Combining mathematical modelling with organ-wide, multispectral FRaeppli-NLS lineage tracing in zebrafish, we demonstrate that a precise BEC to hepatocyte ratio is established (i) fast, (ii) solely by heterogeneous lineage decisions from uni- and bipotent progenitors, and (iii) independent of subsequent cell type-specific proliferation. Extending lineage tracing to adulthood determined that embryonic cells undergo spatially heterogeneous three-dimensional growth associated with distinct environments. Strikingly, giant clusters comprising almost half a ventral lobe suggest lobe-specific dominant-like growth behaviours. We show substantial hepatocyte polyploidy in juveniles representing another hallmark of postembryonic liver growth. Our findings uncover heterogeneous progenitor contributions to tissue architecture-defining cell type proportions and postembryonic organ growth as key mechanisms forming the adult liver.

developmental biology↗

bioRxiv2022

A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation

Cooperative DNA binding of transcription factors (TFs) integrates external stimuli and context across tissues and time. Naive mouse embryonic stem cells are derived from early development and can sustain the pluripotent identity indefinitely. Here we ask whether TFs associated with pluripotency evolved to directly support this state, or if the state emerges from their combinatorial action. NANOG and ESRRB are key pluripotency factors that co-bind DNA. We find that when both factors are expressed, ESRRB supports pluripotency. However, when NANOG is not present, ESRRB supports a bistable culture of cells with an embryo-like primitive endoderm identity ancillary to pluripotency. The stoichiometry between NANOG and ESRRB quantitatively influences differentiation, and in silico modeling of bipartite TF activity suggests ESRRB safeguards plasticity in differentiation. Thus, the concerted activity of cooperative TFs can transform their effect to sustain intermediate cell identities and allow ex vivo expansion of highly stable stem cell models.

cell biology↗

bioRxiv2022

Transcriptional Heterogeneity and Cell Cycle Regulation as Central Determinants of Primitive Endoderm Priming.

During embryonic development cells acquire identity at the same time as they are proliferating, implying that an intrinsic facet of cell fate choice requires coupling lineage decisions to rates of cell division. How is the cell cycle regulated to promote or suppress heterogeneity and differentiation? We explore this question combining time lapse imaging with single cell RNA-seq in the contexts of self-renewal, priming and differentiation of embryonic stem cells (ESCs) towards the Primitive Endoderm lineage (PrE). Since ESCs are derived from the Inner Cell Mass of the mammalian blastocyst, ESCs in standard culture conditions are transcriptionally heterogeneous containing subfractions that are primed for either of the two ICM lineages, Epiblast and PrE. These subfractions represent dynamic states that can readily interconvert in culture, and the PrE subfraction is functionally primed for endoderm differentiation. Here we find that differential regulation of cell cycle can tip the balance between these primed populations, such that naive ESC culture conditions promote Epiblast-like expansion and PrE differentiation stimulates the selective proliferation of PrE-primed cells. In endoderm differentiation, we find that this change is accompanied by a counter-intuitive increase in G1 length that also appears replicated in vivo. While FGF/ERK signalling is a known key regulator of ESCs and PrE differentiation, we find it is not just responsible for ESCs heterogeneity, but also cell cycle synchronisation, required for the inheritance of similar cell cycles between sisters and cousins. Taken together, our results point to a tight relationship between transcriptional heterogeneity and cell cycle regulation in the context of lineage priming, with primed cell populations providing a pool of flexible cell types that can be expanded in a lineage-specific fashion while allowing plasticity during early determination.

developmental biology↗

bioRxiv2021

Spatiotemporal NF-κB dynamics encodes the position, amplitude and duration of local immune inputs

Infected cells communicate through secreted signaling molecules like cytokines, which inform nearby cells about the type, severity and location of pathogens. How differences in cytokine secretion affect inflammatory signaling over space and time, and how responding cells decode information from propagating cytokine signals are not understood. By computationally and experimentally studying NF-{kappa}B dynamics in co-cultures of signal sending cells (macrophages) and receiving cells (fibroblasts), we found that cytokine signals are transmitted by wave-like propagation of NF-{kappa}B activity and create well-defined cellular activation zones in a responding cell population. Remarkably, NF-{kappa}B dynamics in responding cells can simultaneously encode information about cytokine dose, duration, and distance to the cytokine source. Spatially-resolved transcriptional analysis revealed that responding cells transmit local cytokine information to distance specific pro-inflammatory gene expression patterns, creating "gene expression zones" in the population. Despite single-cell variability, the size and duration of the signaling zone is tightly controlled by the macrophage cytokine secretion profile. Our results highlight how macrophages tune their cytokine secretion dynamics to control signal transmission distance, and how NF-{kappa}B interprets these signals to coordinate inflammatory response in space and time.

systems biology↗

bioRxiv2020

ICM cells can be partitioned robustly throughtransient synchronization using secreted FGF4

The differentiation of ICM cells into epiblast (EPI) and primitive endoderm (PE) is central in embryonic development. It is known that FGF4 signaling is important in this process, but it remains unclear how cells can be correctly partitioned. Here we model the NANOG-GATA6-FGF4 network, and test all 64 logical regulatory combinations for their ability to partition a group of cells. We found that nearly all the logic combinations allowed for correct partitioning, including a minimal network where self-activation of NANOG and GATA6 was inactivated. However such self-activation increased the robustness of the system. Furthermore, the model also captured the reported changes in cell proportions in response to FGF perturbations. This constrains the possible regulatory logic and predicts the presence of an "OR" gate in cell-cell communication. We repeatedly found that FGF4 coordinated the decision in two phases: A convergence and a bifurcation phase. First FGF4 negative feedback drives the cells to a balanced "battle" state where most cells have intermediate levels of both regulators, thus being double positive. Subsequent bifurcation happens at constant FGF4 level. Together our results suggest that the frequently observed state of multipotency during differentiation may be an emergent phenomenon resulting from inter-cellular negative feedbacks.

developmental biology↗

bioRxiv2019

Model to link cell shape and polarity with organogenesis

How do tubes -- gut or neural tube -- form from flat sheets of polarized cells? The prevalent view is that it is a two-step process: first cells wedge to bend the sheet, then cells intercalate and extend the initial invagination into a tube. We computationally challenged this model by asking if one mechanism (either cell wedging or intercalation) may suffice for the entire sheet-to-tube transition. Using a physical model with epithelial cells represented by polarized point particles, we show that either cell intercalation or wedging alone can be sufficient and each can both bend the sheet and extend the tube. When working in parallel, the two mechanisms increase the robustness of the tube formation. The successful simulations of Drosophila salivary gland, Sea urchin gastrulation and mammalian neurulation support the generality of our results.

developmental biology↗

bioRxiv2019

Chaperone-Mediated Reflux of Secretory Proteins to the Cytosol During Endoplasmic Reticulum Stress

Diverse perturbations to endoplasmic reticulum (ER) functions compromise the proper folding and structural maturation of secretory proteins. To study secretory pathway physiology during such \"ER stress\", we employed an ER-targeted, redox-responsive, green fluorescent protein--eroGFP--that reports on ambient changes in oxidizing potential. Here we find that diverse ER stress agents cause properly folded, ER-resident eroGFP (and other ER luminal proteins) to \"reflux\" back to the reducing environment of the cytosol as intact, folded proteins. By utilizing eroGFP in a comprehensive genetic screen in S. cerevisiae, we show that ER protein reflux during ER stress requires specific chaperones and co-chaperones residing in both the ER and the cytosol. Chaperone-mediated ER protein reflux does not require E3 ligase activity, and proceeds even more vigorously when these ER-associated degradation (ERAD) factors are crippled, suggesting that reflux may work in parallel with ERAD. In summary, chaperone-mediated ER-protein reflux may be a conserved protein quality control process that evolved to maintain secretory pathway homeostasis during ER protein-folding stress.\n\nSIGNIFICANCEApproximately one third of eukaryotic proteins are synthesized on ribosomes attached to the endoplasmic reticulum (ER) membrane. Many of these polypeptides co- or post-translationally translocate into the ER, wherein they fold and mature. An ER quality-control system proofreads these proteins by facilitating their folding and modification, while eliminating misfolded proteins through ER-associated degradation (ERAD). Yet, the fate of many secretory proteins during ER stress is not completely understood. Here, we uncovered an ER-stress induced \"protein reflux\" system that delivers intact, folded ER luminal proteins back to the cytosol without degrading them. We found that ER protein reflux works in parallel to ERAD and requires distinct ER-resident and cytosolic chaperones and co-chaperones.

cell biology↗

bioRxiv2019

The fitness cost and benefit of phase separated protein deposits

Phase separation of soluble proteins into insoluble deposits is associated with numerous diseases. However, protein deposits can also function as membrane-less compartments for many cellular processes. What are the fitness costs and benefits of forming such deposits in different conditions? Using a model protein that phase separates into deposits, we distinguish and quantify the fitness contribution due to the loss or gain of protein function and deposit formation in yeast. The environmental condition and the cellular demand for the protein function emerge as key determinants of fitness. Protein deposit formation can lead to cell-to-cell differences in free protein abundance between individuals. This results in variable manifestation of protein function and a continuous range of phenotypes in a cell population, favoring survival of some individuals in certain environments. Thus, protein deposit formation by phase separation might be a mechanism to sense protein concentration in cells and to generate phenotypic variability. The selectable phenotypic variability, previously described for prions, could be a general property of proteins that can form phase separated assemblies and may influence cell fitness.\n\nStand-first textUsing a model protein that phase separates into deposits, we distinguish and quantify the fitness contribution due to the loss or gain of protein function and deposit formation in yeast.\n\nO_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY\n\nBullet pointsO_LIThe presented approach identifies and quantifies different fitness effects associated with protein deposit formation due to phase separation\nC_LIO_LIThe environmental condition and the cellular demand for the protein function emerge as key determinants of fitness upon protein deposit formation\nC_LIO_LIVariability in protein deposit formation can lead to cell-to-cell differences in free protein abundance between individuals\nC_LIO_LIProtein phase separation can generate a continuous range of phenotypes in a cell population\nC_LI

systems biology↗

bioRxiv2018

Theory bridging cell polarities with development of robust complex morphologies

Despite continual renewal and damages, a multicellular organism is able to maintain its complex morphology. How is this stability compatible with the complexity and diversity of living forms? Looking for answers at protein level may be limiting as diverging protein sequences can result in similar morphologies. Inspired by the progressive role of apical-basal and planar cell polarity in development, we propose that stability, complexity, and diversity are emergent properties in populations of proliferating polarized cells. We support our hypothesis by a theoretical approach, developed to effectively capture both types of polar cell adhesions. When applied to specific cases of development gastrulation and the origins of folds and tubes our theoretical tool suggests experimentally testable predictions pointing to the strength of polar adhesion, restricted directions of cell polarities, and the rate of cell proliferation to be major determinants of morphological diversity and stability.

biophysics↗

bioRxiv2016

Impact of Zygosity in Bimodal Phenotype Distributions

Allele number, or zygosity, is a clear determinant of gene expression in diploid cells. But the relationship between the number of copies of a gene and its expression can be hard to anticipate, especially when the gene in question is embedded in a regulatory circuit that contains feedbacks. Here we study this question making use of the natural genetic variability of human populations, which allows us to compare the expression profiles of a receptor protein in natural killer cells between donors infected with human cytomegalovirus (HCMV) with one or two copies of the allele. Crucially, the distribution of gene expression in many of the donors is bimodal, indicative of the presence of a positive feedback somewhere in the regulatory environment of the gene. Three separate gene-circuit models differing in the location of the positive feedback with respect to the gene can all reproduce well the homozygous data. However, when the resulting fitted models are applied to the hemizygous donors, only one model (the one with the positive feedback located at the level of gene transcription) reproduces the experimentally observed gene-expression profile. In that way, our work shows that zygosity can help us relate structure and function of gene regulatory networks.\n\nAuthor SummaryNearly all mammalian cells, including human cells, have two copies of each chromosome, and thus possess two potentially different copies of each gene (which might be in some cases non-functional or even absent). Naiively one might expect that two identical copies of the gene would lead to the protein being expressed at twice the rate, but many factors can alter this simple calculation. One of these factors is the existence of feedback mechanisms affecting in one way or another the regulatory circuit in which our gene of interest is embedded. Here we study the relationship between the number of gene copies and the expression of a receptor protein that plays a crucial role in the recognition of pathogens by natural killer cells, which are important elements of the innate immune system. Experimental data of virus-infected donors reveals a bimodal expression profile of this receptor, typical of a positive feedback, and a clear difference between donors with one or two copies of the gene. Mathematical modeling allows us to find the likely location of the feedback loop within the genes regulatory circuit, by requiring the correct model to reproduce the expression profiles of both types of donors.

systems biology↗