Biology subjects

Elias, S.

Publications and source records attributed to Elias, S..

9 recordsLinked to original sources

bioRxiv2025

CenSegNet: a generalist high-throughput deep learning framework for centrosome phenotyping at spatial and single-cell resolution in heterogeneous tissues

Centrosome abnormalities (CA) are a hallmark of epithelial cancers, yet their spatial complexity and phenotypic heterogeneity remain poorly resolved due to limitations in conventional image analysis. We present CenSegNet (Centrosome Segmentation Network), a modular deep learning framework for high-resolution, context-aware segmentation of centrosomes and epithelial architecture across diverse tissue types. Integrating a dual-branch architecture with uncertainty-guided refinement, CenSegNet achieves state-of-the-art performance and generalisability across both immunofluorescence and immunohistochemistry modalities, outperforming existing models in accuracy and morphological fidelity. Applied to tissue microarrays (TMAs) containing 911 breast cancer sample cores from 127 patients, CenSegNet enables the first large-scale, spatially resolved quantification of numerical and structural CA at single-cell resolution. These CA subtypes are mechanistically uncoupled, exhibiting distinct spatial distributions, age-dependent dynamics, and associations with histological tumour grade, hormone receptor status, genomic alterations, and nodal involvement. Structural CA levels are additionally associated with overall survival, supporting the clinical relevance of spatially resolved CA patterns. Discordant CA profiles at tumour margins are linked to local aggressiveness and stromal remodelling. To support broad adoption and reproducibility, CenSegNet is released as an open-source Python library. Together, our findings establish CenSegNet as a scalable, generalisable platform for spatially resolved centrosome phenotyping in intact tissues, enabling systematic dissection of the biology of this organelle and its dysregulation in cancer and other epithelial diseases.

cell biology↗

bioRxiv2023

Systemic Lupus Erythematosus Serum Stimulation of Human Intestinal Organoids Induces Changes in Goblet Cell Differentiation and Mitochondrial Fitness

Human intestinal epithelial cells are the interface between potentially harmful luminal content and basally residing immune cells. Their role is not only nutrient absorption but also the formation of a tight monolayer that constantly secrets mucus creating a multi-layered protective barrier. Alterations in this barrier can lead to increased gut permeability which is frequently seen in individuals with chronic extraintestinal autoimmune diseases, such as Systemic Lupus Erythematosus (SLE). Despite recent advances in identifying alterations in gut microbiota composition in SLE patients, not much attention has been given to the epithelial barrier itself. To date, it remains largely unexplored which role and function intestinal epithelial cells have in SLE pathology. Here, we present a unique near-physiologic in vitro model specifically designed to examine the effects of SLE on the epithelial cells. We utilize human colon organoids that are stimulated with serum obtained from SLE patients. Combining bulk and scRNA transcriptomic analysis with functional assays revealed that SLE serum stimulation induced a unique expression profile marked by a type I interferon gene signature. Additionally, organoids exhibited decreased mitochondrial fitness, alterations in mucus composition and imbalanced cellular composition. Similarly, transcriptomic analysis of SLE human colon biopsies revealed a downregulation of epithelial secretory markers. Our work uncovers a crucial connection between SLE and intestinal homeostasis that might be promoted in vivo through the blood, offering insights into the causal connection of barrier dysfunction and autoimmune diseases.

cell biology↗

bioRxiv2023

Crosstalk between the plasma membrane and cell-cell adhesion maintains epithelial identity for correct polarised cell divisions

Polarised epithelial cell divisions represent a fundamental mechanism for tissue maintenance and morphogenesis; their dysregulation often leads to developmental disorders and cancer. Morphological and mechanical changes in the plasma membrane influence the organisation and crosstalk of microtubules and actin at the cell cortex, thereby regulating the mitotic spindle machinery and chromosome segregation. Yet, the precise mechanisms linking plasma membrane remodelling to cell polarity and cortical cytoskeleton dynamics to ensure accurate execution of mitosis in mammalian epithelial cells remain poorly understood. Here we experimentally manipulated the density of mammary epithelial cells in culture, which led to several mitotic defects. We found that perturbation of cell-cell adhesion integrity impairs the dynamics of the plasma membrane during mitosis, affecting the shape and size of mitotic cells and resulting in defects in mitosis progression and generating daughter cells with aberrant cytoarchitecture. In these conditions, F-actin-astral microtubule crosstalk is impaired leading to mitotic spindle misassembly and misorientation, which in turn contributes to chromosome mis-segregation. Mechanistically, we identify the S100 Ca2+-binding protein A11 (S100A11) as a key membrane-associated regulator that forms a complex with E-cadherin and LGN to coordinate plasma membrane remodelling with E-cadherin-mediated cell adhesion and LGN-dependent mitotic spindle machinery. We conclude that plasma membrane-mediated maintenance of mammalian epithelial cell identity is crucial for correct execution of polarised cell divisions, genome maintenance and safeguarding tissue integrity.

cell biology↗

bioRxiv2021

CXCR4+ Treg cells control serum IgM levels and natural IgM autoantibody production by B1 cells in the bone marrow

Regulatory T (Treg) cells represent a specialized lineage of suppressive CD4+ T cells, whose functionality is critically dependent on their ability to migrate to, and dwell in the proximity of cells they control. Here we show that continuous expression of the chemokine receptor CXCR4 in Treg cells is required for their ability to accumulate in the bone marrow (BM). Induced CXCR4 ablation in Treg cells led to their rapid depletion and consequent increase in mature B cells, foremost B-1 subset, observed exclusively in the BM without detectable changes in plasma cells or hematopoietic stem cells or any signs of systemic or local immune activation elsewhere. Dysregulation of BM B-1 B cells was associated with a highly specific increase in IgM autoantibodies and the total serum IgM levels. Thus, Treg cells control autoreactive B-1 B cells in a CXCR4-dependent manner. These findings have significant implications for understanding of regulation of B cell autoreactivity and malignancies.

immunology↗

bioRxiv2021

Annexin A1 is a polarity cue that directs planar mitotic spindle orientation during mammalian epithelial morphogenesis

Oriented cell divisions are critical for the formation and maintenance of structured epithelia. Proper mitotic spindle orientation relies on polarised anchoring of force generators to the cell cortex by the evolutionarily conserved Gi-LGN-NuMA complex. However, the polarity cues that control cortical patterning of this ternary complex remain largely unknown in mammalian epithelia. Here we identify the membrane-associated protein Annexin A1 (ANXA1) as a novel interactor of LGN in mammary epithelial cells. ANXA1 acts independently of Gi to instruct the accumulation of LGN and NuMA at the lateral cortex to ensure cortical anchoring of Dynein-Dynactin and astral microtubules and thereby planar alignment of the mitotic spindle. Loss of ANXA1 randomises mitotic spindle orientation, which in turn disrupts epithelial architecture and luminogenesis in three-dimensional cultures of primary mammary epithelial cells. Our findings establish ANXA1 as an upstream cortical cue that regulates LGN to direct planar cell divisions during mammalian epithelial morphogenesis.

cell biology↗

bioRxiv2021

Induction of specific antibodies, IgG-secreting plasmablasts and memory B cells following BCG vaccination

Many tuberculosis (TB) vaccine candidates are designed as a boost to BCG; an understanding of the BCG-induced immune response is therefore critical, and the opportunity to relate this to circumstances where BCG does protect may direct the design of more efficacious vaccines. While the T cell response to BCG vaccination has been well-characterised, little is known about the B cell and antibody response. We demonstrate BCG vaccine-mediated induction of specific antibodies in different human populations and macaque species which represent important preclinical models for TB vaccine development. We observe a strong correlation between antibody titres in serum versus plasma with modestly higher titres in serum. We also report for the first time the rapid and transient induction of antibody-secreting plasmablasts following BCG vaccination, together with a robust and durable memory B cell response in humans. Finally, we demonstrate a potential contribution of the antibody response to BCG vaccine-mediated control of mycobacterial growth in vitro. Taken together, our findings indicate that the humoral immune response in the context of BCG vaccination merits further attention to determine whether TB vaccine candidates could benefit from the induction of humoral as well as cellular immunity.

immunology↗

bioRxiv2021

VEGFA's distal enhancer regulates its alternative splicing in CML

Enhancer demethylation in leukemia and lymphoma was shown to lead to overexpression of genes which promote cancer characteristics. The vascular endothelial growth factor A (VEGFA) enhancer, located 157 Kb downstream of its promoter, is demethylated in chronic myeloid leukemia (CML). VEGFA has several alternative splicing isoforms with different roles in vascularization and cancer progression. Since transcription and splicing are coupled in space and time, we hypothesized that the VEGFA enhancer can also regulate the genes alternative splicing to contribute to the pathology of CML. Our results show that mutating the VEGFA +157 enhancer promotes exclusion of exons 6b and 7 and activating the enhancer by tethering a chromatin activator has the opposite effect. In line with these results, CML patients display high enhancer activity and inclusion of VEGFA exons 6b and 7. To search for a key protein connecting transcription with alternative splicing, we analyzed 161 chromatin immunoprecipitation (ChIP)-seq experiments for DNA binding proteins and found that PML and CCNT2 bind VEGFAs promoter and enhancer. CCNT2 is a positive regulator of RNA polymerase II (RNAPII) transcription elongation and indeed its silencing promotes exclusion of exons 6b and 7. Slowing down RNAPII elongation promotes exclusion of exons 6b and 7. Thus our results suggest that VEGFAs +157 enhancer regulates its alternative splicing by increasing RNAPII elongation rate via CCNT2. Our work demonstrates the importance of the interplay between transcription and alternative splicing.

cancer biology↗

bioRxiv2019

Gene regulatory network of human GM-CSF secreting T helper cells

GM-CSF produced by autoreactive CD4 positive T helper cells is involved in the pathogenesis of autoimmune diseases, such as Multiple Sclerosis. However, the molecular regulators that establish and maintain the features of GM-CSF positive CD4 T cells are unknown. In order to identify these regulators, we isolated human GM-CSF producing CD4 T cells from human peripheral blood by using a cytokine capture assay. We compared these cells to the corresponding GM-CSF negative fraction, and furthermore, we studied naive CD4 T cells, memory CD4 T cells and bulk CD4 T cells from the same individuals as additional control cell populations. As a result, we provide a rich resource of integrated chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq) data from these primary human CD4 T cell subsets, and we show that the identified signatures are associated with human autoimmune disease, especially Multiple Sclerosis. By combining information about mRNA expression, DNA accessibility and predicted transcription factor binding, we reconstructed directed gene regulatory networks connecting transcription factors to their targets, which comprise putative key regulators of human GM-CSF positive CD4 T cells as well as memory CD4 T cells. Our results suggest potential therapeutic targets to be investigated in the future in human autoimmune disease.

bioinformatics↗

bioRxiv2017

An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems

We introduce a new conceptual framework and a model-based interventional calculus to steer, manipulate, and reconstruct the dynamics and generating mechanisms of non-linear dynamical systems from partial and disordered observations based on the contributions of each of the systems, by exploiting first principles from the theory of computability and algorithmic information. This calculus entails finding and applying controlled interventions to an evolving object to estimate how its algorithmic information content is affected in terms of positive or negative shifts towards and away from randomness in connection to causation. The approach is an alternative to statistical approaches for inferring causal relationships and formulating theoretical expectations from perturbation analysis. We find that the algorithmic information landscape of a system runs parallel to its dynamic attractor landscape, affording an avenue for moving systems on one plane so they can be controlled on the other plane. Based on these methods, we advance tools for reprogramming a system that do not require full knowledge or access to the systems actual kinetic equations or to probability distributions. This new approach yields a suite of universal parameter-free algorithms of wide applicability, ranging from the discovery of causality, dimension reduction, feature selection, model generation, a maximal algorithmic-randomness principle and a systems (re)programmability index. We apply these methods to static (e.coli Transcription Factor network) and to evolving genetic regulatory networks (differentiating naive from Th17 cells, and the CellNet database). We highlight their ability to pinpoint key elements (genes) related to cell function and cell development, conforming to biological knowledge from experimentally validated data and the literature, and demonstrate how the method can reshape a systems dynamics in a controlled manner through algorithmic causal mechanisms.

systems biology↗