Biology subjects

Sfikakis, P. P.

Publications and source records attributed to Sfikakis, P. P..

5 recordsLinked to original sources

bioRxiv2026

Development of a multi-organ single-cell atlas of systemic sclerosis reveals shared and tissue-specific pathogenic pathways.

Objectives: Systemic sclerosis (SSc) is a multi-organ autoimmune disease for which no broadly effective disease-modifying treatment exists. We developed an integrated multi-organ single-cell atlas of SSc to identify shared and organ specific disease-associated transcriptional programmes and potential therapeutic targets. Methods: We integrated single-cell RNA-sequencing data from skin, lung, synovium, and peripheral blood mononuclear cells (six studies, 401,902 cells, 90 individuals) using Harmony. Pseudobulk differential expression and gene set enrichment analysis were performed at the tissue cell-compartment, cell-type, and subpopulation levels, including independent reclustering of lymphoid, myeloid and fibroblast populations. Results: Disease-associated transcriptional programmes showed marked tissue dependence, even within the same cell lineage, highlighting the importance of organ-specific mechanisms in SSc. Nevertheless, recurrent extracellular matrix (ECM) remodelling programmes were identified in lung, skin and synovium, and interferon signalling programmes in skin, synovium and peripheral blood mononuclear cells, across immune and fibroblast cell populations. Although no subpopulation was exclusive to SSc, a shared myofibroblast subpopulation expressing SFRP2, COL1A1, POSTN, ACTA2, and COMP was identified across lung, skin, and synovium. In addition, perivascular and mitotic fibroblast subpopulations exhibited both profibrotic and inflammatory signatures, including interferon- and IL-2-related signalling programmes. Conclusions: SSc is characterised by two complementary axes: a tissue-dependent cellular programme and a recurrent fibrotic and interferon-associated signature extending across multiple organs and cell populations. These findings are consistent with current organ-based therapeutic approaches while highlighting interferon signalling as a potential multi-organ therapeutic target. The resulting interactive single-cell atlas provides a resource for investigating shared and organ-specific disease mechanisms and guiding future therapeutic research.

immunology↗

bioRxiv2026

Pharmacologic METTL3 inhibition attenuates TGF-beta-driven profibrotic signature in systemic sclerosis

Systemic sclerosis (SSc) is a devastating fibrosing disorder affecting the skin and internal organs, associated with the highest mortality among all rheumatic diseases. The mechanisms underlying excessive fibrogenesis in SSc are incompletely defined and treatment options are limited. N6-methyladenosine (m6A), the most abundant internal mRNA modification, is a reversible and pharmacologically tractable determinant of RNA fate. Here we mapped the m6A epitranscriptome of peripheral blood mononuclear cells (PBMCs) from patients with SSc using two orthogonal single-nucleotide-resolution platforms, a MazF-based m6A microarray and nanopore direct RNA sequencing. SSc PBMCs showed coordinated upregulation of the m6A writer complex (METTL3, METTL14, WTAP), a two-fold increase in global m6A, and redistribution of m6A marks from 3' untranslated regions toward coding sequences. Both platforms converged on TGF-b signaling as the most enriched pathway among differentially methylated transcripts, with hypermethylation of TGFB1, JUNB and KLF10 transcripts. Pharmacologic inhibition of METTL3 with STM2457 significantly reversed TGF-b-induced transcriptomic changes in skin fibroblasts preventing their transformation into pathological myofibroblasts. Together, these findings uncover an epitranscriptomic signature driving profibrotic transcriptional alterations in SSc, including enhanced TGF-b signaling, which can be effectively reversed by clinically available enzymatic m6A inhibitors. Our data suggest that targeting m6A methylation may offer a novel therapeutic strategy to mitigate fibrosis in SSc.

molecular biology↗

bioRxiv2025

Stabilin levels are related to atherosclerotic plaque burden in type 2 diabetes mellitus individuals

Type 2 diabetes mellitus (T2DM) is a global burgeoning health problem that increases the risk of atherosclerotic cardiovascular disease (ASCVD). Infiltration and oxidative modification of low-density lipoprotein (LDL) cholesterol in the arterial wall and chronic inflammation comprise central pathogenetic mechanisms in ASCVD. Scavenger receptors, particularly Stabilin-1 (Stab1) and Stabilin-2 (Stab2), are pivotal in the clearance of oxidized LDL (oxLDL) cholesterol and pro-atherogenic ligands from circulation. However, their role in atherosclerosis development in the spectrum of T2DM remains poorly characterized. We assessed circulating levels of Stab1, Stab2, and their ligands (TGFbI, Periostin and Reelin) in a cohort of 33 T2DM and 21 non-diabetic individuals, stratified by their atherosclerotic plaque burden as assessed by high-resolution vascular ultrasound. Associations between stabilins, their ligands and conventional cardiovascular risk factors were evaluated. Stab1 levels were significantly elevated in individuals with higher atherosclerotic plaque burden (p<0.05), while Reelin levels were marginally elevated, both in the total study cohort and among T2DM patients. Stab1 levels positively correlated with body mass index and inversely correlated with total cholesterol, LDL, and high-density lipoprotein (HDL) cholesterol levels. Our findings indicate that Stab1 may serve as a marker of dysregulated lipid metabolism and increased atherosclerotic plaque burden in individuals with T2DM. Larger prospective studies are warranted to establish the prognostic and potentially therapeutic value of Stab1 and to clarify its mechanistic role in diabetic atherosclerosis.

physiology↗

bioRxiv2025

Exercise induces anti-inflammatory reprogramming in macrophages via Hsp60

Physical activity exerts systemic anti-inflammatory effects and reduces the risk for multiple non-communicable diseases, with 7.2% of all-cause deaths globally being attributed to physical inactivity. However, the cellular and molecular components of the exercise-induced anti-inflammatory effects remain only partly understood. Herein we show that moderate-intensity exercise promotes anti-inflammatory reprograming of macrophages orchestrated by the skeletal muscle cells secretome. Primary bone marrow-derived macrophages (BMDMs) exposed to the secretome of mechanically-loaded myotubes (exercise-conditioned medium, exCM) acquire an anti-inflammatory transcriptional profile and increased reliance on oxidative phosphorylation, as shown by Seahorse real-time cell metabolic analysis, compatible with an M2-like phenotypic switch. Using an unbiased proteomic analysis of the exCM we identify the chaperonin Hsp60 as a key mediator of the anti-inflammatory effects of exercise. Hsp60 expression increases in mechanically loaded myotubes in vitro, in the quadriceps muscle and serum of mice following an 8-week program of moderate-intensity aerobic exercise, as well as in human muscle after resistance training. Importantly, treatment of BMDMs with Hsp60 in vitro recapitulates the exCM-induced transcriptional reprograming, promoting an M2-like phenotype. Taken together, our data highlight Hsp60 as a novel component of the skeletal muscle cell-macrophage crosstalk, providing mechanistic insights into the anti-inflammatory effects of exercise.

physiology↗

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↗