Biology subjects

Tsingos, E.

Publications and source records attributed to Tsingos, E..

9 recordsLinked to original sources

bioRxiv2026

Laminin and Fibronectin Cooperate to Guide Endothelial Self-Organization During Intersegmental Vessel Formation

Endothelial sprouts must integrate cell-intrinsic self-organization with external guidance cues to build stereotyped vascular patterns. During zebrafish intersegmental vessel (ISV) formation, the extra-cellular matrix in the intersomitic space is enriched in laminin and fibronectin, but how these cues guide sprouting remains unclear. We integrated live imaging, perturbation experiments, rescue assays, and mathematical modeling to test whether these matrix components canalize endothelial behavior. Partial loss of laminin or fibronectin slowed endothelial sprouting without abolishing overall ISV formation. In a hybrid mathematical model coupling endothelial self-organization to a deformable extracellular matrix, reduced matrix density predicted slower sprouting and increased vessel fusion. Consistent with this prediction, combined laminin and fibronectin knockdown produced severe ISV mispatterning, including ectopic fusion events and network-like vascular arrangements. Chimeric fibronectin mRNAs rescued vascular patterning and associated somite defects. Comparison of lama1/lama4/fn1a and lama1/lama4/fn1b morphants suggested that somite disorganization exacerbates ISV defects, but is not required for them. Together, our results support a guided self-organization model in which laminin and fibronectin cooperate with other tissue cues to confine endothelial self-organization to the intersomitic space and ensure robust angiogenic patterning.

developmental biology↗

bioRxiv2024

Quantitative modelling of fate specification in the C. elegans postembryonicM lineage reveals a missing spatiotemporal signal

The invariant lineages of C. elegans provide tractable cell fate models to study how developing organisms robustly integrate spatial signals at the single-cell level via gene regulatory networks. For instance, during postembryonic development, a mesoderm lineage arises through a sequence of oriented cell divisions from a single progenitor. This mesoblast initially gives rise to 18 cells with three distinct fates - 14 body wall muscles (BWMs), 2 coelomocytes (CCs; dorsal), and 2 sex myoblasts (SMs; ventral). The latter cells migrate and then proliferate to contribute 16 smooth muscles to the nematodes reproductive organs. Prior work identified key symmetry breaking cues: i) ventrally restricted activation of the LIN-12 Notch pathway promoting SM over CC fate and ii) asymmetric re-distribution of SYS-1 {beta}-catenin and POP-1 TCF among daughter cells along the anteroposterior (A-P) axis, i.e. the Wnt/{beta}-catenin asymmetry pathway. However, it remains unclear whether these pathways are sufficient to specify all cell fates accordingly or whether additional symmetry breaking cues are necessary. In this study, we use quantitative modelling to better understand fate specification in the postembryonic M lineage. Specifically, we focus on the anteroposterior symmetry break by creating increasingly complex models towards robustly reproducing fate specification in wild type larvae and mutants. This iterative process resulted in two alternative models that explain the experimental observations by either introducing an additional spatial (spatial symmetry break) or temporal cue (temporal symmetry break). Finally, we evaluate their plausibility and propose a series of experiments to provide support for alternative models. Overall, our study highlights how a quantitative examination of mechanistic ideas can identify knowledge gaps and guide experimental follow-up.

systems biology↗

bioRxiv2024

How cells align to structured collagen fibrils: A hybrid cellular Potts and molecular dynamics model with dynamic mechanosensitive focal adhesions.

Many mammalian cells, including endothelial cells and fibroblasts, tend to align and elongate with the orientation of extracellular matrix (ECM) fibers in a gel when cultured in vitro. During cell elongation, clusters of focal adhesions (FAs) form near the poles of the elongating cells. FAs are mechanosensitive clusters of adhesions that grow under mechanical tension due to the cells pulling on the ECM, and shrink when the tension is released. Using a mathematical modeling approach, we study the hypothesis that reciprocity between cells and the ECM drives cell shape changes. We show that FAs are preferentially stabilized along the orientation of ECM fibers, where the cells can generate more tension than perpendicular to the ECM fibers. We present a hybrid cellular Potts model that represents the ECM as an off-the-lattice network of cross-linked deformable fibers, whereas the cell is represented on the lattice. Multiple FAs are modeled individually by an independent rate of FA assembly and a mechanoresponsive FA disassembly. The resulting computational model predicts stiffness-dependent cell spreading and local ECM remodelling, and ECM-alignment dependent cell elongation. The effects combined suffice to explain how cell morphology is determined by local ECM structure and mechanics.

biophysics↗

bioRxiv2024

Altered thymic niche synergistically drives the massive proliferation of malignant thymocytes

The discovery of genetic alterations in patient samples over the last decades has reinforced a cell-autonomous view of proliferative expansion during T- cell acute lymphoblastic leukemia (T-ALL) development in the thymus. However, the potential contribution of non-cell-autonomous factors, particularly the impact of thymic epithelial cells (TECs) within the thymic niche during the initiation phase, remains unexplored. In this study, we combine a cell-based computational model of the thymus with complementary in vivo experiments in medaka (Oryzias latipes) to systematically analyze the impact of 12 cell-autonomous and non- autonomous factors, individually and in combination, on the proliferation of normal and malignant thymocytes carrying interleukin-7 receptor (IL7R) gain-of-function mutations or elevated IL7R levels, as observed in T-ALL patients. By simulating over 1500 scenarios, we show that while a dense TEC network favored the proliferation of normal thymocytes, it inhibited the proliferation of malignant lineages, which achieved their maximal proliferative capacity when TECs were sparsely distributed. Our in silico model further predicts that specific mutations could accelerate proliferative expansion within a few days. This prediction was experimentally validated, revealing the rapid onset of thymic lymphoma and systemic infiltration of malignant T-cells within just 8 days of embryonic development. These findings demonstrate that synergistic interaction between oncogenic alterations and modifications in the thymic niche can significantly accelerate disease progression. Our results also suggest that negative feedback from the proliferative state suppresses thymocyte differentiation. Overall, this multidisciplinary work reveals the critical role of TEC-thymocyte interactions in both the initiation and progression of T-ALL, highlighting the importance of the thymic microenvironment in early leukemogenesis.

cancer biology↗

bioRxiv2022

Modelling the mechanical cross-talk between cells and fibrous extracellular matrices using hybrid cellular Potts and molecular dynamics methods

The mechanical interaction between cells and the extracellular matrix (ECM) is fundamental to coordinate collective cell behavior in multicellular tissues. Relating individual cell-level mechanics to tissue-scale collective behavior is an outstanding challenge which cell-based models such as the cellular Potts model (CPM) are well-positioned to address. These models generally represent the ECM with mean-field approaches, which assume substrate homogeneity. This assumption breaks down with fibrous ECM, which has non-trivial structure and mechanics. Here, we extend the CPM with a bead-spring chain model of ECM fiber networks modelled using molecular dynamics. We model contractile cells pulling with discrete focal adhesion-like sites on the ECM fiber network, and demonstrate agreement with experimental spatiotemporal fiber densification and displacement. We show that contractile cell forces propagate over multiple cell radii scaling with power law exponent of {approx} -0.5 typical of viscoelastic ECM. Further, we use in silico atomic force microscopy to measure local cell-induced network stiffening consistent with experiments. Our model lays the foundation to investigate how local and long-ranged cell-ECM mechanobiology contributes to multicellular morphogenesis.

biophysics↗

bioRxiv2021

The Medaka Inbred Kiyosu-Karlsruhe (MIKK) Panel

Unraveling the relationship between genetic variation and phenotypic traits remains a fundamental challenge in biology. Mapping variants underlying complex traits while controlling for confounding environmental factors is often problematic. To address this, we have established a vertebrate genetic resource specifically to allow for robust genotype-to-phenotype investigations. The teleost medaka (Oryzias latipes) is an established genetic model system with a long history of genetic research and a high tolerance to inbreeding from the wild. Here we present the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel: the first near-isogenic panel of 80 inbred lines in a vertebrate model derived from a wild founder population. Inbred lines provide fixed genomes that are a prerequisite for the replication of studies, studies which vary both the genetics and environment in a controlled manner and functional testing. The MIKK panel will therefore enable phenotype-to-genotype association studies of complex genetic traits while allowing for careful control of interacting factors, with numerous applications in genetic research, human health, and drug development and fundamental biology. Here we present a detailed characterisation of the genetic variation across the MIKK panel, which provides a rich and unique genetic resource to the community by enabling large-scale experiments for mapping complex traits.

genomics↗

bioRxiv2021

Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

The teleost medaka (Oryzias latipes) is a well-established vertebrate model system, with a long history of genetic research, and multiple high-quality reference genomes available for several inbred strains (HdrR, HNI and HSOK). Medaka has a high tolerance to inbreeding from the wild, thus allowing one to establish inbred lines from wild founder individuals. We have exploited this feature to create an inbred panel resource: the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. This panel of 80 near-isogenic inbred lines contains a large amount of genetic variation inherited from the original wild population. We used Oxford Nanopore Technologies (ONT) long read data to further investigate the genomic and epigenomic landscapes of a subset of the MIKK panel. Nanopore sequencing allowed us to identify a much greater variety of high-quality structural variants compared with Illumina sequencing. We also present results and methods using a pan-genome graph representation of 12 individual medaka lines from the MIKK panel. This graph-based reference MIKK panel genome revealed novel differences between the MIKK panel lines compared to standard linear reference genomes. We found additional MIKK panel-specific genomic content that would be missing from linear reference alignment approaches. We were also able to identify and quantify the presence of repeat elements in each of the lines. Finally, we investigated line-specific CpG methylation and performed differential DNA methylation analysis across the 12 lines. We thus present a detailed analysis of the MIKK panel genomes using long and short read sequence technologies, creating a MIKK panel specific pan genome reference dataset allowing for the investigation of novel variation types that would be elusive using standard approaches.

genomics↗

bioRxiv2018

Retinal stem cells modulate proliferative parameters to coordinate post-embryonic morphogenesis in the eye of fish

A fundamental question in biology is how anatomically and functionally distinct tissues coordinate to direct growth and shape in complex organs. We address this question using as a model the eye of teleost fish, which grow while maintaining the precise shape needed for vision throughout the animals life.\n\nCombining clonal analysis in the eye of the teleost medaka (Oryzias latipes) with a computational agent based model, we find that the neural retina (NR) and retinal pigmented epithelium (RPE) differentially modulate cell divisions to coordinate their growth rates. Cell divisions in the NR are less stochastic, consistent with an upstream role as an inducer of growth in nearby tissues. Cells in the RPE display much higher stochasticity, consistent with a downstream role responding to inductive signals.\n\nOur simulation predicts that the segregation of stem- and progenitor cell domains in the retinal ciliary marginal zone niche is an emergent property, as the topology of the niche preconditions the system to undergo a spatially biased stochastic neutral drift. Clone properties in the NR support this prediction, and further suggest that NR cells control the direction of division axes to regulate organ shape and retinal cell topology.\n\nThis work highlights an as yet unappreciated mechanism for growth coordination in a complex organ, where one tissue integrates external and internal cues as a hub to synchronize growth rates in nearby tissues. In the eye of fish, proliferation parameters of neuroretinal stem cells are a minimal target node for evolution to exploit to adapt whole-organ morphogenesis in a complex vertebrate organ.

developmental biology↗

bioRxiv2018

Efficient single-copy HDR by 5’ modified long dsDNA donors

CRISPR/Cas9 efficiently induces targeted mutations via non-homologous-end-joining but for genome editing, precise, homology-directed repair (HDR) of endogenous DNA stretches is a prerequisite. To favor HDR, many approaches interfere with the repair machinery or manipulate Cas9 itself. Using Medaka we show that the modification of 5 ends of long dsDNA donors strongly enhances HDR, favors efficient single-copy integration by retaining a monomeric donor conformation thus facilitating successful gene replacement or tagging.

genetics↗