Biology subjects

Stavropoulou, A.

Publications and source records attributed to Stavropoulou, A..

6 recordsLinked to original sources

bioRxiv2026

The genome organizer SMC1A mediates the gene expression response in inflammation by dissociating from nuclear-speckles and redistributing to the nuclear periphery

Nuclear architectural proteins are increasingly recognized as multifunctional regulators whose roles extend well beyond static genome organization. Here we report that SMC1A, a core subunit of the cohesin complex, undergoes a striking redistribution upon inflammatory stimulation in human monocytes, dissociating from nuclear speckles and accumulating at genomic regions enriched for stress-response genes with distinct exon-intron architectural properties. Through integrative analysis of RNA-seq, chromatin organization, and nuclear spatial data, we demonstrate that this redistribution has functional consequences at multiple levels of gene expression. SMC1A dissociation from speckles is accompanied by a reduction in intron retention events -consistent with a transition from a poised, pre-loaded transcriptional state toward active, efficient co-transcriptional processing- and by selective engagement with genes whose exon-intron architecture favors exon definition splicing, shorter nuclear mRNA residence times, and peripheral radial positioning. Genes affected by SMC1A silencing, by contrast, occupy more central nuclear positions and display fundamentally different structural properties, demonstrating that the two modes of SMC1A perturbation -stress-induced redistribution and depletion- are functionally and spatially non-equivalent. These findings suggest a genome compartmentalization in which DNA compositional preferences, gene architecture, radial positioning, and splicing mode converge to define gene sets capable of rapid, precise activation. SMC1A navigates this pre-existing landscape upon inflammatory cues, coordinating transcriptional and post-transcriptional responses simultaneously. We propose that stress-induced redistribution of architectural proteins within a largely invariant nuclear compartmental framework represents a general regulatory mechanism, one whose logic is encoded in the structural organization of the genome itself.

genomics↗

bioRxiv2025

High-resolution integrative analysis allows characterization and spatial annotation of normal and cancer-associated colon fibroblasts

Fibroblasts represent key regulators of colon homeostasis, and cancer-associated fibroblasts (CAFs) play pivotal roles in colorectal cancer (CRC). Despite their critical influence, a consensus view of adult human colon fibroblast and CRC CAF heterogeneity, spatial organization, and developmental trajectories is currently lacking. Here, we address this gap by performing a comprehensive characterization of colonic fibroblasts and CRC CAFs. Using large-scale integration of single-cell RNA-sequencing datasets from normal colon and CRC we mapped the fibroblast subpopulations. Spatial transcriptomics, immunohistochemistry, and in situ hybridization were used for validation and computational analyses to predict developmental trajectories and transcription factors underlying CAF activation. Subepithelial myofibroblasts (SEMFs), mucosa-associated fibroblasts (MAFs), and submucosa-associated fibroblasts (SAFs) were identified as the main colon fibroblast subtypes, and in mice, further divided into location-based subclusters. We also identified a novel colon fibroblast subset: muscle-embedded interstitial fibroblasts (MIFs). CRCs contained normal fibroblasts as well as four cancer-specific CAF populations: inflammatory CAFs (iCAFs), matrix CAFs (mCAFs), and two precursor CAF (preCAF) subtypes. Our data suggested that iCAFs originate from SEMFs through a preCAF1 intermediate phenotype, while mCAFs derive from SAFs/MIFs via preCAF2s. Transcription factors PRRX1, MAFB, and TWIST1 were uncovered as potential regulators of CAF identity and CTHRC1 was identified as a specific and sensitive pan-CAF marker in CRC. Our study presents a detailed framework for understanding colon fibroblast and CRC CAF heterogeneity. This work lays the groundwork for future research into the roles and potential therapeutic relevance of different CRC CAF subsets.

cancer biology↗

bioRxiv2025

Notch3 regulates pericyte phenotypic plasticity in colorectal cancer

Pericytes undergo phenotypic alterations that influence cancer progression, yet the molecular mechanisms governing these changes remain poorly understood. Here, we investigated the role of Notch3 signaling in pericyte phenotype and functions in colorectal cancer (CRC). Using lineage tracing approaches, we showed that tumor pericytes originate from normal tissue-resident pericytes, which proliferate inside tumors. In vivo genetic manipulation revealed that Notch3 pathway activation promotes pericyte proliferation, while suppressing contractile protein expression, and leads to increased endothelial cell proliferation. In contrast, Notch3 deletion leads to reduced endothelial proliferation and a significant decrease in. This effect is associated with a shift toward a contractile phenotype. Single-cell RNA sequencing analysis uncovered significant pericyte heterogeneity in both mouse colitis-associated cancer and human CRC. It specifically identified functionally distinct subpopulations characterized by differential Notch3 activity, which supported our in vivo and in vitro findings. Our results establish Notch3 as a key regulator of pericyte phenotypic plasticity in CRC and suggest that targeting this pathway could represent a promising strategy for improving therapeutic outcomes through vascular normalization.

cancer biology↗

bioRxiv2024

Senescent cells cluster CTCF on nuclear speckles to sustain their splicing program

Senescence --the endpoint of replicative lifespan for normal cells-- is established via a complex sequence of molecular events. One such event is the dramatic reorganization of CTCF into senescence-induced clusters (SICCs). However, the molecular determinants, genomic consequences, and functional purpose of SICCs remained unknown. Here, we combine functional assays, super-resolution imaging, and 3D genomics with computational modelling to dissect SICC emergence. We establish that the competition between CTCF-bound and non-bound loci dictates clustering propensity. Upon senescence entry, cells repurpose SRRM2 --a key component of nuclear speckles-- and BANF1 --a molecular glue for chromosomes-- to cluster CTCF and rewire genome architecture. This CTCF-centric reorganization in reference to nuclear speckles functionally sustains the senescence splicing program, as SICC disruption fully reverts alternative splicing patterns. We therefore uncover a new paradigm, whereby cells translate changes in nuclear biochemistry into architectural changes directing splicing choices so as to commit to the fate of senescence. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/603680v1_ufig1.gif" ALT="Figure 1"> View larger version (85K): org.highwire.dtl.DTLVardef@cfb561org.highwire.dtl.DTLVardef@8cfdf3org.highwire.dtl.DTLVardef@7485d5org.highwire.dtl.DTLVardef@1fe9051_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIHMGB2-bound loci compete with CTCF-bound ones for nuclear speckle association C_LIO_LISenescent cells repurpose SRRM2 and BANF1 to cluster CTCF on speckles C_LIO_LIBANF1 is essential, but not sufficient for CTCF clustering C_LIO_LIThe SRRM2 RNA-binding domain directs CTCF clustering C_LIO_LISICCs rewire chromatin positioning to sustain the senescence splicing program C_LI

cell biology↗

bioRxiv2023

Rapid and synchronous chemical induction of replicative-like senescence via a small molecule inhibitor

Cellular senescence is now acknowledged as a key contributor to organismal ageing and late-life disease. Although popular, the study of senescence in vitro can be complicated by the prolonged and asynchronous timing of cells committing to it and its paracrine effects. To address these issues, we repurposed the small molecule inhibitor inflachromene (ICM) to induce senescence to human primary cells. Within six days of treatment with ICM, senescence hallmarks, including the nuclear eviction of HMGB1 and -B2, are uniformly induced across IMR90 cell populations. By generating and comparing various high throughput datasets from ICM-induced and replicative senescence, we uncovered significant similarity of the two states. Notably though, ICM suppresses the proinflammatory secretome associated with senescence, thus alleviating most paracrine effects. In summary, ICM induces a senescence-like phenotype rapidly and synchronously thereby allowing the study of its core regulatory program without any confounding heterogeneity.

genomics↗

bioRxiv2022

Distinct chromosomal niches in the genome of S. cerevisiae provide the background for genomic innovation and shape the fate of gene duplicates

Gene duplication is a major source of genomic innovation in all eukaryotes, with large proportions of genes being the result of either small-scale (SSD) or genome-wide duplication (WGD) events. In the model unicellular eukaryote Saccharomyces cerevisiae, of which nearly one third of the genome corresponds to gene duplicates, the two modes of duplication have been shown to follow different evolutionary fates, with SSD genes being more prone to acquire novel functionalities (neofunctionalization) and WGD more likely to retain different parts of the original ancestral function (subfunctionalization). Having previously described aspects of functional compartmentalization for the genes of S. cerevisiae, in this work we set out to investigate the existence of positional preferences of gene duplicates. We found that SSD and WGD genes are organized in distinct gene clusters that are, furthermore, segregated, occupying different regions, with SSD being more peripheral and WGD more centrally positioned close to centromeric chromatin. Duplicate gene clusters differ from the rest of the genome in terms of gene size and spacing, gene expression variability and regulatory complexity. What is more interesting, some of these properties are also shared by singleton genes residing in duplicate-rich regions in a position-dependent manner. Our analysis further reveals particular chromatin architectures in the promoters of duplicate genes, which are generally longer, with less pronounced nucleosome-free regions, strong structural constraints and a larger number of regulatory elements. Such structural features appear to be important for gene evolution as we find SSD gene-pair co-expression to be strongly associated with the similarity of nucleosome positioning patterns. We propose that specific regions of the yeast genome provide a favourable environment for the generation and maintenance of small-scale gene duplicates. The existence of such genomic "niches" is supported by the enrichment of these regions in singleton genes bearing similarities with gene "relics", remnants of recent duplications that have reverted to single gene status. Our findings provide a valuable framework for the study of genomic innovation and suggest taking into account positional preferences in the study of gene emergence and fixation in experimentally and naturally evolving populations.

genomics↗