Biology subjects

Gerovska, D.

Publications and source records attributed to Gerovska, D..

6 recordsLinked to original sources

bioRxiv2025

NEURO-IMMUNE CRYPT-ASSOCIATED CELLS DRIVE COLORECTAL CARCINOGENESIS VIA REST-MEDIATED PHENOTYPIC REPROGRAMMING: IMPLICATIONS FOR TUMORIGENESIS AND VIRAL SUSCEPTIBILITY

Colorectal cancer (CRC) pathogenesis remains linked to poorly defined cellular origins and microenvironmental drivers. We identify Neuro-Immune Crypt-Associated (NICA) cells as a privileged pathogen portal and a plausible epithelial cell of origin. During carcinogenesis, the repressor REST drives a neuroendocrine-to-epithelial transition by silencing NICA-associated neuroendocrine markers, a lineage loss reversible via epigenetic modulation or genetic ablation in CRC models. This landscape is further shaped by EBV-infected B-lineage cells (BLEICS), which transactivate HERV-H/F elements in CRC cells through paracrine signaling, establishing a niche-restricted viral scar. While tumor crypts sense this retroviral pressure, they exhibit an abortive antiviral signature marked by RNase L downregulation, creating a functional execution gap. We propose a pathogen-first model where chronic inflammatory pressure triggers mutation-silencing -the simultaneous genotoxic and epigenetic inactivation of tumor suppressors. Together, the convergence of NICA plasticity, BLEICS-mediated HERV induction, and compromised antiviral surveillance redefines CRC as a pathogen-driven disruption of the neuro-immune niche.

cancer biology↗

bioRxiv2024

Technical and biological variations in the purification of extrachromosomal circular DNA (eccDNA) and the finding of more eccDNA in the plasma of lung adenocarcinoma patients compared with healthy donors

Human plasma DNA originates from all tissues and organs, holding the potential as a versatile marker for diseases such as cancer, as fragments of cancer-specific alleles can be found circulating in the blood. While linear DNA has been studied intensely as a liquid biomarker, the role of circular circulating DNA in cancer is more unknown due, in part, to a lack of comprehensive testing methods. Our developed method profiles extrachromosomal circular DNA (eccDNA) in plasma, integrating Solid-Phase Reversible Immobilization (SPRI) bead purification, the removal of linear DNA and mitochondrial DNA, and DNA sequencing. As an initial assessment, we examined the method, biological variations, and technical variations using plasma samples from four patients with lung adenocarcinoma and four healthy and physically fit individuals. Despite the small sample group, we observed a significant eccDNA increase in cancer patients in two independent laboratories and that eccDNA covered up to 0.4 % of the genome/mL plasma. We found a subset of eccDNA from recurrent genes present in cancer samples but not in every control. In conclusion, our data reflect the large variation found in eccDNA sequence content and show that the variability observed among replicates in eccDNA stems from a biological source and can cause inconclusive findings for biomarkers. This suggests the need to explore other biological markers, such as epigenetic features on eccDNA.

molecular biology↗

bioRxiv2024

TET3 regulates cellular terminal differentiation at the metabolic level

TET-family members play an essential role in cell fate commitment and their dysfunctions result in arrested differentiation. TET3 is ubiquitously expressed in differentiated cells and essential in postnatal development due to yet unknown reasons. To define TET3 function in cell differentiation, we profiled the intestinal epithelium at the single-cell level from wild-type and Tet3 knockout mice. Here we show that, in the absence of TET3, enterocytes exhibit an aberrant differentiation trajectory and do not acquire a physiological cell identity due to an impairment in oxidative phosphorylation, specifically due to an ATP synthase assembly deficiency. Furthermore, our analysis demonstrates that the loss of TET3 compromises mitochondrial metabolic maturation and leads to a metabolic profile enriched in glycolysis-dependent anabolic pathways similar to those observed in undifferentiated cells. Collectively, our study has revealed the molecular mechanism by which TET3 regulates terminal differentiation at the metabolic level.

developmental biology↗

bioRxiv2020

Human skeletal muscle organoids model fetal myogenesis and sustain uncommitted PAX7 myogenic progenitors

In vitro culture systems that structurally model human myogenesis and promote PAX7+ myogenic progenitor maturation have not been established. Here we report that human skeletal muscle organoids can be differentiated from induced pluripotent stem cell lines to contain paraxial mesoderm and neuromesodermal progenitors and develop into organized structures reassembling neural plate border and dermomyotome. Culture conditions instigate neural lineage arrest and promote fetal hypaxial myogenesis towards limb axial anatomical identity, with generation of sustainable uncommitted PAX7 myogenic progenitors and fibroadipogenic (PDGFRa+) progenitor populations equivalent to those from the second trimester of human gestation. Single cell comparison to human fetal and adult myogenic progenitors reveals distinct molecular signatures for non-dividing myogenic progenitors in activated (CD44High/CD98+/MYOD1+) and dormant (PAX7High/FBN1High/SPRY1High) states. Our approach provides a robust 3D in vitro developmental system for investigating muscle tissue morphogenesis and homeostasis.

bioengineering↗

bioRxiv2019

FOntCell: Fusion of Ontologies of Cells

High-throughput cell-data technologies such as single-cell RNA-Seq create a demand for algorithms for automatic cell classification and characterization. There exist several classification ontologies of cells with complementary information. However, one needs to merge them in order to combine synergistically their information. The main difficulty in merging is to match the ontologies since they use different naming conventions. To overcome this obstacle we developed an algorithm that merges ontologies by integrating the name-matching search between class label names with the structure mapping between the ontology elements. To implement our algorithms, we developed FOntCell, a software module in Python for efficient automatic parallel-computed fusion of ontologies in the same or similar knowledge domains. It processes the ontology attributes to extract relations and class synonyms. FOntCell integrates the semantic, name with synonyms, mapping with a structure mapping based on graph convolution. Since the structure mapping assessment is time consuming process, we designed two methods to perform the graph convolution: vectorial structure matching and constraint-based structure matching. To perform the vectorial structure matching we designed a general method to calculate the similarities between vectors of different lengths for different metrics. Additionally, we adapted the slower Blondel method to work for structure matching. These functionalities of FOntCell allow the unification of dispersed knowledge in one domain into a unique ontology. FOntCell produces the results of the merged ontology in OBO format that can be iteratively reused by FOntCell to adapt continuously the ontologies with the new data, such of the Human Cell Atlas, endlessly produced by data-driven classification methods. To navigate easily across the fused ontologies, it generates HTML files with tabulated and graphic summaries, and an interactive circular Directed Acyclic Graphs of the merged results. We used FOntCell to fuse CELDA, LifeMap and LungMAP Human Anatomy cell ontologies to produce comprehensive cell ontology. Author SummaryThere is a strong belief in the research community that there exist more cell types than the described in the literature, therefore new technologies were developed to produce a high volume of data to discover new cells. One issue that arises once the cells are discovered is how to classify them. One way to perform such classification is to use already existing cell classifications from different ontology sources but it is difficult to merge them. An ontology has semantic information providing the meaning of each term and structural information providing the relationship between terms as a graph. We developed a new Python module, FOntCell that merges efficiently cell ontologies and integrates semantic and structure information with our own graph convolution technique. Since the structure mapping assessment is time-consuming process we designed two methods to optimize the graph convolution: vectorial and constraint-based structure matching. To perform the vectorial structure matching we designed a method that calculates the similarities between vectors describing the graphs of different sizes. The functionalities of FOntCell allow the unification of dispersed knowledge into a unique ontology, to adapt continuously from new data, and to navigate across the fused ontologies by a graphic use interface.

bioinformatics↗

bioRxiv2018

Newly developed single-cell computational approach elucidates the stabilization of Oct4 expression in the E3.25 mouse preimplantation embryo

The time of onset of the second cell fate decision in the mouse preimplantation embryo is still unknown. Ohnishi et al. (2014) looked for cell heterogeneity in the ICM at E3.25 that could indicate the time preceding the apparent segregation of PE and EPI at E3.5, but were not able to detect an early splitting transcriptomics event using state-of-the-art clustering techniques. We developed a new clustering algorithm, hierarchical optimal k-means (HOkM), and identified from single cell (sc) transcriptomics microarray data two groups of ICM cells during the 32 to 64 mouse embryo transition: from embryos with less than 34 cells, and more than 33 cells, corresponding to two developmental sub-stages. The genes defining these sub-stages indicate that the development of the embryo to 34 cells triggers a dramatic event as a result of which Bsg is high expressed, the canonical Wnt pathway is activated, Oct4 is stabilized to high expression and the chromatin remodeling program is initialized to establish a very early narve pluripotent state from the preceding totipotency. We characterized our HOkM partition comparing with independent scRNA-seq datasets. It was staggering to discover that from the 3.4360x1010 possible bi-partitions of the E3.25 data of Ohnishi et al. (2014), our HOkM discovered one partition that shares the biological features of the early and late 32 ICM cells of Posfai et al. (2017). We propose that the stabilization of Oct4 expression is a non-cell autonomous process that requires a minimal number of four inner cell contacts acquired during the transition from a homogeneous outer-cell environment to a heterogeneous inner/outer cell environment formed by the niche of a kernel of at least six inner cells covered by trophectoderm.

developmental biology↗