Biology subjects

Konstantopoulos, D.

Publications and source records attributed to Konstantopoulos, D..

9 recordsLinked to original sources

bioRxiv2025

Disease-specific fibroblast-myeloid interactions in rheumatoid arthritis synovium

Rheumatoid arthritis (RA) is characterized by profound remodeling of the synovial microenvironment. Here we show that enhanced fibroblast-macrophage cross-talk distinguishes RA from psoriatic arthritis (PsA). MerTK-SPP1 macrophages represent the dominant inflammatory myeloid population in RA, interacting with expanded fibroblast subsets through SPP1-mediated signaling. Lining fibroblasts display induction of antigen-presentation and IL-6/JAK-STAT pathways, while a CHI3L1-producing fibroblast population arises specifically in RA and may act as a source of autoantigens. These stromal populations interact closely with FABP5 iDC3 cells and T cells within a disrupted synovial lining, creating a niche driving adaptive immune activation. In contrast, PsA exhibits increased fibroblast- endothelial interactions without major endothelial transcriptional changes. Our data identify SPP1 signaling and fibroblast-myeloid-dendritic interactions as core drivers of RA synovial inflammation that links innate immune activation to the initiation of autoimmunity. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/688477v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@c76e39org.highwire.dtl.DTLVardef@11563a9org.highwire.dtl.DTLVardef@141f3fborg.highwire.dtl.DTLVardef@f90742_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

WNT inhibition primes the transcriptional landscape of mesoderm to initiate a phased ventricular cardiomyocyte specification programme

Background and AimsCardiac reprogramming holds promise for treating ischemic heart diseases and advancing personalised medicine, but current approaches do not yet reliably generate human functional, homogeneous cardiomyocyte cultures. This limited success likely reflects our incomplete understanding of hierarchical transcriptional programmes guiding cardiomyocyte specification. Here, we modelled cardiomyocyte differentiation aiming to uncover gene regulatory networks (GRNs) guiding early human ventricular cardiomyocyte development. Our study focused on defining how inhibition of WNT signalling remodels the transcriptional landscape underlying human cardiomyocyte differentiation, since both in vivo cardiac development and in vitro cardiomyocyte differentiation protocols require WNT inhibition. MethodsWe modelled left ventricular cardiomyocyte differentiation from human pluripotent stem cells and experimentally manipulated WNT signalling to uncover transcriptional responses using single-cell RNA sequencing. Bioinformatics analysis defined cell identities, reconstructed differentiation trajectories, and inferred WNT inhibition-dependent gene expression and regulatory networks driving cardiomyocyte specification. ResultsWe found that WNT inhibition (WNTi) decisively redirects mesoderm cells towards a cardiomyocyte progenitor fate, expanding their numbers while limiting alternative trajectories. GRN inference revealed both WNTi-dependent and -independent programmes and a hierarchical cascade of transcription factors driving the mesoderm-to-cardiomyocyte progenitor transition. Notably, MEIS2 emerged as a central WNTi-independent regulator, while WNTi-responsive networks featured early (ISL1, PBX3, TBX5 and KLF1) and late (MEF2-related genes, GATA-related genes, PBX1, CREM, FOXP1 and NKX3-1) factors. Mesodermal GRNs were primed for cardiomyocyte specification in WNTi-treated cultures but, in the absence of WNTi, mesodermal GRNs remained ambiguous, activating ISL1 and PBX3 but failing to establish cardiomyocyte commitment and subsequent differentiation into contractile cells. ConclusionThis work provides the first comprehensive dissection of WNTi-dependent and -independent regulatory hierarchies guiding human ventricular cardiomyocyte specification and highlights new transcriptional players which could improve cardiac reprogramming efficiency and fidelity. Translational PerspectiveDeciphering the transcriptional programmes that drive early cardiomyocyte specification has clear translational potential for regenerative therapies and cardiac reprogramming. By modelling left ventricular cardiomyocyte differentiation from hPSCs, our study highlights how inhibition of WNT signalling promotes ventricular cardiomyocyte progenitor commitment while restricting alternative fates. The discovery of both WNTi-dependent and -independent transcriptional activators, including some not previously linked to cardiomyocyte development, provides new insights for improving the efficiency and fidelity of direct cardiac reprogramming. Importantly, these TF candidates may also guide the development of targeted therapies for ischemic heart disease and inform personalised approaches for repairing and regenerating damaged myocardium.

developmental biology↗

bioRxiv2025

A single-cell transcriptomic atlas of developing inhibitory neurons reveals expanding and contracting modes of diversification.

The cerebral cortex relies on vastly different types of inhibitory neurons to compute. How this diversity emerges during development remains an open question. The rarity of individual inhibitory neuron types often leads to their underrepresentation in single-cell RNA sequencing (scRNAseq) datasets, limiting insights into their developmental trajectories. To address this problem, we developed a computational pipeline to enrich and integrate rare cell types across multiple datasets. Applying this approach to somatostatin-expressing (SST+) inhibitory neurons--the most diverse inhibitory cell class in the cortex--we constructed the transcriptomic maps, Dev-SST-v1 and Dev-SST-v2, a comprehensive resource containing mouse scRNAseq data of over 51,000 SST+ neurons. We identify three principal groups--Martinotti cells (MCs), non-Martinotti cells (nMCs), and long-range projecting neurons (LRPs)--each following distinct diversification trajectories. MCs commit early, with distinct embryonic and neonatal clusters that map directly to adult counterparts. In contrast, nMCs diversify gradually, with each developmental cluster giving rise to multiple adult cell types. LRPs follow a unique contracting mode. Initially, two clusters are present until postnatal day 5 (P5), but by P7, one type is eliminated through programmed cell death, leaving a single surviving population. This transient LRP type is also found in the fetal human cortex, revealing an evolutionarily conserved feature of cortical development. Together, these findings highlight three distinct modes of SST+ neuronal diversification--invariant, expanding, and contracting--offering a new framework to understand how the large repertoire of inhibitory neurons emerges during development.

neuroscience↗

bioRxiv2023

Urolithin A induces cardioprotection and enhanced mitochondrial quality during natural aging and heart failure

Cardiovascular diseases remain the primary cause of global mortality, necessitating effective strategies to alleviate their burden. Mitochondrial dysfunction is a driving force behind aging and chronic conditions, including heart disease. Here, we investigate the potential of Urolithin A (UA), a gut microbiome-derived postbiotic that enhances mitophagy, to ameliorate both age-related decline in cardiac function and cardiac failure. We highlight the significance of targeting mitochondria, by comparing gene expression changes in aging human hearts and cardiomyopathies. UA oral administration successfully counteracts mitochondrial and cardiac dysfunctions in preclinical models of aging and heart failure. UA improves both systolic and diastolic heart functions, distinguishing it from other mitochondrial interventions. In cardiomyocytes, UA recovers mitochondrial ultrastructural defects and decline in mitochondrial biomarkers occurring with aging and disease. These findings extend UAs benefits to heart health, making UA a promising nutritional intervention to evaluate in the clinic to promote healthy cardiovascular function as we age.

cell biology↗

bioRxiv2022

SCALA: A web application for multimodal analysis of single cell next generation sequencing data

Analysis and interpretation of high-throughput transcriptional and chromatin accessibility data at single cell resolution are still open challenges in the biomedical field. In this article, we present SCALA, a bioinformatics tool for analysis and visualization of single cell RNA sequencing (scRNA-seq) and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) datasets. SCALA combines standard types of analysis by integrating multiple software packages varying from quality control to identification of distinct cell population and cell states. Additional analysis options enable functional enrichment, cellular trajectory inference, ligand-receptor analysis and regulatory network reconstruction. SCALA is fully parameterizable at every step of the analysis, presenting data in tabular format and produces publication-ready 2D and 3D visualizations including heatmaps, barcharts, scatter, violin and volcano plots. We demonstrate the functionality of SCALA through two use-cases related to TNF-driven arthritic mice, handling data from both scRNA-seq and scATAC-seq experiments. SCALA is mainly developed in R, Shiny and JavaScript and is available as a web application at http://scala.pavlopouloslab.info or https://scala.fleming.gr.

bioinformatics↗

bioRxiv2022

Upregulation of CD55 complement regulator in distinct PBMC subpopulations of COVID-19 patients is associated with suppression of interferon responses.

Complement activation has been verified in COVID-19 patients by both increased serum levels of complement factors C3a and C5b-9 and increased complement deposition at the tissue levels. Complement regulatory proteins (CRPs) CD55, CD46, CD59 and CR1 act to control complement overactivation and eliminate complement deposition and cell lysis. The aim of the study was to investigate the expression of CRPs in COVID-19 in order to identify potential dysregulated expression patterns of CRPs and address whether these may contribute to disease pathogenesis. Single cell RNA-sequencing (scRNA-seq) analysis performed on isolated PBMCs revealed an increase of CD55 expression in severe and critical COVID-19 patients compared to healthy controls. This increase was also detected upon integrated subclustering analysis of the monocyte, T cell and B cell populations. Flow cytometric analysis verified the distinct pattern of upregulated CD55 expression in monocyte and T cell sub populations of severe COVID-19 patients. This upregulation was associated with decreased expression of interferon stimulated genes (ISGs) in patients with severe COVID-19 suggesting a potential suppressor effect of CD55 on interferon responses. The present study identifies a COVID-19 specific CD55 expression pattern in PBMC subpopulations that coincides with reduced interferon responses thus indicating that the complement regulator CD55 may contribute to COVID-19 pathogenesis.

immunology↗

bioRxiv2022

miR-221/222 drive synovial fibroblast expansion and pathogenesis of TNF-mediated arthritis

MicroRNAs (miRNAs) constitute fine tuners of gene expression and are implicated in a variety of diseases spanning from inflammation to cancer. miRNA expression is deregulated in rheumatoid arthritis (RA), however, their specific role in key arthritogenic cells such as the synovial fibroblast (SF) remains elusive. We have shown in the past that the expression of the miR-221/222 cluster is upregulated in RA SFs. Here, we demonstrate that miR-221/222 activation is downstream of major inflammatory cytokines, such as TNF and IL-1{beta}, which promote miR-221/222 expression independently. miR-221/222 expression in SFs from the huTNFtg mouse model of arthritis correlates with disease progression. Targeted transgenic overexpression of miR-221/222 in SFs of the huTNFtg mouse model led to further expansion of synovial fibroblasts and disease exacerbation. miR-221/222 overexpression altered the transcriptional profile of SFs igniting pathways involved in cell cycle progression and ECM regulation. Validated targets of miR-221/222 included p27 and p57 cell cycle inhibitors, as well as Smarca1 (a chromatin remodeling component). In contrast, complete genetic ablation of miR-221/222 in arthritic mice led to decreased proliferation of fibroblasts, reduced synovial expansion and attenuated disease. scATAC-seq data analysis revealed increased miR-221/222 gene activity in the pathogenic and activated clusters of the intermediate and lining compartment. Taken together, our results establish an SF-specific pathogenic role of the miR-221/222 cluster in arthritis and suggest that its therapeutic targeting in specific subpopulations should inform the design of novel fibroblast-targeted therapies for human disease.

cell biology↗

bioRxiv2021

Single-cell chromatin and transcriptome dynamics of Synovial Fibroblasts transitioning from homeostasis to pathology in modelled TNF-driven arthritis

Synovial fibroblasts (SFs) are specialized cells of the synovium that provide nutrients and lubricants for the maintenance of proper function of diarthrodial joints. Chronic TNF signals are known to trigger activation of SFs and orchestration of arthritic pathology via proinflammatory effector functions, secretion of cartilage degrading proteases and promotion of osteolysis. We performed single-cell (sc) profiling of SFs transcriptome by RNA-sequencing (scRNA-seq) and of chromatin accessibility by scATAC-seq in normal mouse SFs and SFs derived from early and advanced TNF-driven arthritic disease. We describe here distinct subsets of SFs in the homeostatic synovium, serving diverse functions such as chondro- and osteogenesis, tissue repair and immune regulation. Strikingly, development of spontaneous arthritis by transgenic TNF overexpression primes the emergence of distinct pathology-associated SF subtypes. We reveal 7 constitutive and 2 disease-specific SF subtypes. The latter emerge in the early stage, expand in late disease and are localized in areas at the interface between the invasive pannus and the articular bone. The associated transcription profiles are characterized by enhanced inflammatory responses, promigratory behaviour, neovascularization and collagen metabolic processes. Temporal reconstruction of transcriptomic events indicated which specific sublining cells may function as progenitors at the root of trajectories leading to intermediate subpopulations and culminating to a destructive lining inflammatory identity. Integrated analysis of chromatin accessibility and transcription changes revealed key transcription factors such as Bach and Runx1 to drive arthritogenesis. Parallel analysis of human arthritic SF data showed highly conserved core regulatory and transcriptional programs between the two species. Therefore, our study dissects the dynamic SF landscape in TNF-mediated arthritis and sets the stage for future investigations that might address the functions of specific SF subpopulations to understand joint pathophysiology and combat chronic inflammatory and destructive arthritic diseases.

cell biology↗

bioRxiv2019

Continuous transcription initiation guarantees robust repair of transcribed genes and regulatory regions in response to DNA damage

Inhibition of RNA synthesis caused by DNA damage-impaired RNA polymerase II (Pol II) elongation is found to conceal a local increase in de novo transcription, slowly progressing from Transcription Start Sites (TSSs) to gene ends. Although associated with accelerated repair of Pol II-encountered lesions and limited mutagenesis, it is still unclear how this mechanism is maintained during recovery from genotoxic stress. Here we uncover a surprising widespread gain in chromatin accessibility and preservation of the active histone mark H3K27ac after UV-irradiation. We show that the concomitant increase in Pol II release from promoter-proximal pause (PPP) sites of most active genes, PROMoter uPstream Transcripts (PROMPTs) and enhancer RNAs (eRNAs) favors unrestrained initiation, as demonstrated by the synthesis of short nascent RNAs, including TSS-associated RNAs (start-RNAs). In accordance, drug-inhibition of the transition into elongation replenished the post-UV reduced levels of pre-initiating pol II at TSSs. Continuous engagement of new Pol II thus ensures maximal transcription-driven DNA repair of active genes and non-coding regulatory loci. Together, our results reveal an unanticipated layer regulating the UV-triggered transcriptional-response and provide physiologically relevant traction to the emerging concept that transcription initiation rate is determined by pol II pause-release dynamics.

molecular biology↗