Biology subjects

Micheroli, R.

Publications and source records attributed to Micheroli, R..

9 recordsLinked to original sources

bioRxiv2026

Serum Calprotectin as predictor of Rheumatoid Arthritis disease severity and Mortality

Objective: To evaluate the clinical utility of serum calprotectin (sCAL) as a biomarker of disease activity, disease severity, cardiovascular risk, and mortality in inflammatory rheumatic diseases (IRDs). Methods: Serum calprotectin was measured in 2677 patients with IRDs, including 1472 rheumatoid arthritis (RA), 771 axial spondyloarthritis (axSpA), and 434 psoriatic arthritis (PsA) patients enrolled in the Swiss Clinical Quality Management in Rheumatic Diseases registry, as well as 248 healthy blood donors. Associations with disease activity, radiographic progression, cardiovascular biomarkers, incident major adverse cardiovascular events (MACE), and mortality were evaluated using receiver operating characteristic, Cox regression, and Kaplan-Meier models. Results: sCAL concentrations were significantly higher in RA than in axSpA, PsA, or healthy blood donors. Although diagnostic discrimination between IRDs was modest (Area under the curve (AUC): 0.56), elevated sCAL identified a subset of patients with RA characterized by higher disease activity, higher autoantibody levels, and accelerated radiographic progression, performing better than CRP for the assessment of inflammatory activity, particularly for the discrimination of active synovitis (SJC28[≥]4, AUC 0.67 vs 0.62, p=0.012), even in patients with normal CRP concentrations. Elevated sCAL was independently associated with increased all-cause mortality (HR:2.99; 95% confidence interval (95%CI):1.87-4.78), cardiovascular mortality (HR:7.49;95%CI:1.50-37.55), respiratory mortality (HR: 5.89; 95%CI:1.97-17.62), and incident MACE (HR: 2.10; 95%CI: 1.04-4.24). Furthermore, sCAL correlated with high-sensitivity cardiac troponin T and NT-proBNP concentrations, independently of lipid profile. Conclusions: Serum calprotectin is a clinically relevant biomarker in RA that reflects both disease activity and severity, independently identifying patients at increased cardiovascular risk and mortality, supporting its potential role in disease monitoring and risk stratification.

immunology↗

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

Synovitis in systemic sclerosis is an interferon-driven stromal condition distinct from rheumatoid arthritis

Joint involvement is a major driver of disability in systemic sclerosis (SSc), yet its pathophysiology remains poorly understood. In the absence of specific evidence, SSc synovitis is treated by analogy with rheumatoid arthritis (RA). Here, we present the first comprehensive molecular characterization of SSc synovitis, integrating histology, single-cell RNA sequencing, and spatial multi-omics of synovial biopsies from SSc patients, RA patients, and non-inflammatory controls with in vitro validation. We show that SSc synovitis is characterized by distinct pathomechanisms from RA. Histologically, most SSc biopsies displayed a pauci-immune pathotype with sparse immune infiltrates and predominant stromal cells. At molecular level, synovial fibroblasts in SSc were characterized by a disease-specific type I interferon (IFN) response program, in contrast to the TNF-dominant profile of RA, accompanied by dysregulation of the complement cascade. This IFN program extended across multiple synovial cell types, including monocyte-derived macrophages and endothelial cells, and was spatially organized into focal myeloid niches and a diffuse stromal program. Systemically, elevated serum IFN-2a levels were associated with the presence of clinical synovitis in an independent cohort of SSc patients. We furthermore show that similar IFN-driven programs are shared between skin and synovium in SSc. Genes downregulated by IFNAR1 blockade in SSc skin were enriched in SSc synovium, supporting IFN receptor blockade as a multi-organ target therapeutic strategy. These findings reframe SSc synovitis as a less destructive, IFN-driven stromal condition distinct from RA and provide a mechanistic basis for dedicated clinical trials for joint inflammation in SSc. One Sentence SummarySSc synovitis is a pauci-immune, IFN-driven stromal condition distinct from RA, supporting IFNAR1 blockade as a therapeutic strategy. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/733140v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@d85bb5org.highwire.dtl.DTLVardef@6cffe6org.highwire.dtl.DTLVardef@148eb4org.highwire.dtl.DTLVardef@1a4cd83_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2026

SNPic: SNP Topic Modeling for Interpretable Clustering of Complex phenotypes

Genome-wide association studies (GWAS) have cataloged thousands of disease-associated variants, yet a central challenge remains: decoding the shared, pleiotropic architecture that links complex phenotypes. Existing approaches, including dimensionality reduction methods and regression genetic models, either lack interpretability or rely on external linkage disequilibrium (LD) reference panels, limiting their ability to recover coherent biological mechanisms. Here we introduce the SNP topic model (SNPic), a generative probabilistic framework that reframes GWAS summary statistics as a structured corpus and models genetic architecture using principles from Natural Language Processing (NLP). By treating phenotypes as documents and genes or the whole corpus of traits as words, SNPic applies topic models, e.g. Latent Dirichlet Allocation (LDA), to infer latent "genetic topics", representing interpretable, overlapping biological modules that jointly explain complex traits. This formulation enables simultaneous reconstruction of trait relationships and identification of their underlying molecular drivers. SNPic integrates two complementary schemes: Sumstat-as-word for capturing global phenotypic structure and Gene-as-word for resolving mechanistic detail, within a unified modeling framework. To ensure robustness, we introduce a stability-optimized inference pipeline based on bootstrap resampling, allowing data-driven selection of topic number and filtering of stochastic signals. Across extensive simulations, SNPic consistently outperforms conventional dimensionality reduction methods in recovering latent structure under both linear and non-linear, highly overlapping genetic architectures. Applied to integrated FinnGen and UK Biobank datasets, SNPic identifies reproducible genetic topics corresponding to distinct biological programs, including HLA-mediated immune processes and transporter-driven metabolic regulation, with strong tissue-specific support. The framework further generalizes across species, organizing complex traits in maize, Arabidopsis thaliana, and cattle into biologically coherent modules. Together, these results establish SNPic as a scalable and interpretable framework that shifts GWAS analysis from association cataloging toward the construction of an interpretable knowledge graph representing the latent semantic architecture of the genome. By unifying statistical genetics with NLP, SNPic reframes GWAS analysis as a probabilistic language modeling task, enabling the systematic decoding of complex trait architectures and delivering a systemic graph of cross-phenotype relationships.

genetics↗

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

Distinct myeloid precursors and their interaction with mesenchymal cells orchestrate the spreading of psoriatic disease from the skin to the joints

Psoriatic disease initially affects the skin, but later extends to the joints. Herein, we describe a two-step process that orchestrates spreading of inflammation from the skin to the joints. Induction of psoriatic skin disease in photoconvertible mice, followed by sequencing and computational characterization of skin-derived cells in the joints, identified a unique population of CD2+ MHC-II+ CCR2+ myeloid precursors that built up a skin-derived myeloid cell compartment in the joints. Single-cell cross-species reference mapping and mitochondrial variant tracing showed an orthologue human cell population. Interactome analyses in the joints showed that in a second step, resident regulatory CD200+ fibroblasts critically regulate the priming of the CD2+ MHC-II+ CCR2+ myeloid precursors, which subsequently regulate the IL-17 expression in T cells. Hence, spreading of inflammation requires a distinct migratory myeloid precursor population and a permissive local tissue environment, similar to tumour metastasis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/665302v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@38c440org.highwire.dtl.DTLVardef@dc574dorg.highwire.dtl.DTLVardef@1e79f72org.highwire.dtl.DTLVardef@19508cf_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Human Fibroblast-Myeloid cell tissue atlas across lung, synovium, skin and heart

Single-cell RNA sequencing (scRNAseq) of human tissues has expanded our understanding of the complexity of cellular subsets and their changes in disease. The availability of scRNAseq data in different tissues and disease states provides an opportunity to compare cellular subsets and identify common and unique cellular activation. In this study, we aimed to characterize shared and tissue-specific myeloid and stromal phenotypes and uncover key cellular subtypes involved in pathogenic tissue activation. We analyzed scRNAseq data from 14 public datasets, comprising heart, lung, skin, and synovium in both healthy and diseased states. Our analysis identified distinct and overlapping myeloid and stromal cell populations in these tissues. Despite significant inter-individual variability, we were able to identify both shared and disease-specific changes in these cell populations. These findings provide insights into the conserved and tissue-specific roles of myeloid and stromal cells in health and disease and contribute to a better understanding of tissue pathology and potential therapeutic targets.

cell biology↗

bioRxiv2022

A comprehensive single-cell atlas of freshly dissociated human synovium in inflammatory arthritis with an optimized dissociation protocol for prospective fresh synovial biopsy collection

Single-cell RNA-sequencing is advancing our understanding of synovial pathobiology in inflammatory arthritis. Here, we optimized the protocol for the dissociation of fresh synovial biopsies and created a reference single-cell map of fresh human synovium in inflammatory arthritis. We utilized the published method for dissociating cryopreserved synovium and optimized it for dissociating small fresh synovial biopsies. The optimized protocol enabled the isolation of a good yield of consistently highly viable cells, minimizing the dropout rate of prospectively collected biopsies. Our reference synovium map comprised over 100000 unsorted single-cell profiles from 25 synovial tissues of patients with inflammatory arthritis. Synovial cells formed 11 lymphoid, 15 myeloid and 16 stromal cell clusters, including IFITM2+ synovial neutrophils. Using this reference map, we successfully annotated published synovial scRNA-seq datasets. Our dataset uncovered endothelial cell diversity and identified SOD2highSAA1+SAA2+ and SERPINE1+COL5A3+ fibroblast clusters, expressing genes linked to cartilage breakdown (SDC4) and extracellular matrix remodelling (LOXL2, TGFBI, TGFB1), respectively. We broadened the characterization of tissue resident FOLR2+COLEC12high and LYVE1+SLC40A1+ macrophages, inferring their extracellular matrix sensing and iron recycling activities. Our research brings an efficient synovium dissociation protocol and a reference annotation resource of fresh human synovium, while expanding the knowledge about synovial cell diversity in inflammatory arthritis.

genomics↗

bioRxiv2021

MAFB surrogates the glucocorticoid receptor ability to induce tolerogenesis in dendritic cells

Glucocorticoids (GCs) exert potent anti-inflammatory effects in immune cells through the glucocorticoid receptor (GR). Dendritic cells (DCs), central actors for coordinating immune responses, acquire tolerogenic properties in response to GCs. Tolerogenic DCs (tolDCs) have emerged as a potential treatment for various inflammatory diseases. To date, the underlying cell type-specific regulatory mechanisms orchestrating GC-mediated acquisition of immunosuppressive properties remain poorly understood. In this study, we investigated the transcriptomic and epigenomic remodeling associated with differentiation to DCs in the presence of GCs. Our analysis demonstrates a major role of MAFB in this process, in synergy with GR. GR and MAFB both interact with methylcytosine dioxygenase TET2 and bind to genomic loci that undergo specific demethylation in tolDCs. We also show that the role of MAFB is more extensive, binding to thousands of genomic loci in tolDCs. Finally, MAFB knockdown erases the tolerogenic properties of tolDCs and reverts the specific DNA demethylation and gene upregulation. The preeminent role of MAFB is also demonstrated in vivo for myeloid cells from synovium in rheumatoid arthritis following GC treatment. Our results imply that, once directly activated by GR, MAFB takes over the main roles to orchestrate the epigenomic and transcriptomic remodeling that define the tolerogenic phenotype.

immunology↗