Biology subjects

Bonelli, M.

Publications and source records attributed to Bonelli, M..

7 recordsLinked to original sources

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↗

bioRxiv2025

SummArIzeR: Simplifying cross-database enrichment result clustering and annotation via large language models

MotivationEnrichment analysis across multiple databases often results in a high level of redundancy due to overlapping terms, complicating the interpretation of biological data. To address this, we developed SummArIzeR, an R package to cluster and annotate enrichment results across multiple databases, enabling fast, intuitive interpretation and comparison across multiple conditions. SummArIzeR clusters enrichment results based on shared genes, calculates a pooled p-value for each cluster and facilitates the cluster annotation using large-language models. It further allows an easyly interpretable vizualisisation of the results. ResultsCompared to existing tools, SummArIzeR provides unbiased and fast cluster annotation using large language models. We demonstrate that SummArIzeR achieves clustering comparable to manual curation while offering superior grouping based on shared underlying genes. Availability and ImplementationThe SummArIzeR package is available as an open-source R package, with a comprehensive user manual provided in its GitHub repository: https://github.com/bonellilab/SummArIzeR.

bioinformatics↗

bioRxiv2025

Primulagenin A is a potent inverse agonist of the nuclear receptor RAR-related orphan receptor gamma (RORγ)

Throughout history, herbal medicines and natural products have played a crucial role as therapeutics for humans, yet their molecular mechanisms of action often remain elusive. Here, we ask whether primulagenin A (PGA) from the traditionally used herbal substance Primula root, acts via the nuclear receptor ROR{gamma}, a key regulator of pro-inflammatory Th17 cells, which are linked to autoimmune diseases like psoriasis. Luciferase assays revealed a high potency (IC50 ~100 nM) and efficacy (Imax ~ 90%) of PGA as an inverse agonist of ROR{gamma}. To ensure sufficient supply, we established methods to isolate and synthesize PGA. Its binding to the human ROR{gamma} ligand binding domain was confirmed by nano differential scanning fluorimetry, and a structure-activity relationship was proposed by docking and site-directed mutagenesis. PGA downregulated ROR{gamma} target gene expression and inhibited murine and human Th17 differentiation in a concentration-dependent manner. It also reduced the proportion of IL-17A-producing Th17 cells. In this work, we identify PGA as a new, potent, and efficacious inverse agonist of ROR{gamma}, with potential for modulating immune responses in inflammatory and autoimmune diseases.

pharmacology and toxicology↗

bioRxiv2025

Preserved suppressive function despite loss of Foxp3: insights into the identity of regulatory T cells

Regulatory T (Treg) cells are essential for maintaining immune homeostasis, with Foxp3 acting as the master transcription factor governing their differentiation and function. The acquisition of effector signatures in Treg cells is closely tied to the surrounding tissue-specific immune environment and typically occurs alongside Foxp3 expression. In this study, we investigated the transcriptomic and functional consequences of Treg-mediated regulation in a Th2-driven disease setting. The application of both in vitro systems and in vivo disease models allowed us to mimic Th2-mediated environments. We could demonstrate Th2-driven loss of Foxp3 expression in Treg cells in vitro and in vivo. Transcriptomic analysis revealed a maintained Treg signature despite the loss of active Foxp3 expression. Functional characterization of Tregs both in vitro and in vivo uncovered a preserved suppressive capacity even in the absence of Foxp3. Our findings unveil that, despite loss of Foxp3, a preserved Treg signature remains intact enabling the regulation of Th2-mediated diseases. The persistence of this regulatory transcriptome highlights the importance for developing Treg-cell therapy strategies in cancer and autoimmune diseases independent of Foxp3 expression.

immunology↗

bioRxiv2025

Targeting histone acetylation enables epigenetic modulation of inflammatory pathways, a novel therapeutic strategy for rheumatoid arthritis

Autoimmune diseases like rheumatoid arthritis (RA) are characterized by a systemic inflammation caused by autoreactive immune cells. Epigenomic modulation of these cells offers a strategy to reprogram pathogenic pathways without altering the genome, potentially restoring immune balance. Epigenetic inhibitors are already utilized in oncology but often exhibit adverse effects due to lack of selectivity and cytotoxic concentrations. Applying these drugs to treat autoimmune diseases necessitates more selective inhibitors and the use of tolerable concentrations. In this study, we screened a library of 25 compounds with varying degrees of target selectivity and different concentrations. Spectral cytometry enabled the analysis of cell-subset distribution and activation, followed by bulk RNA-sequencing for transcriptomic profiling. We could demonstrate cell-subset specific and concentration-dependent immune modulation in PBMCs. Transcriptomic analysis showed that inhibitors of histone acetylation-modulating enzymes significantly altered gene expression, particularly in immune regulation pathways relevant to autoimmune diseases. Comparative analysis between in-vitro treated healthy controls and RA patients demonstrated both shared and selective drug effects, with some inhibitors like Ricolinostat overlapping with established RA drug pathways. Our findings highlight the potential of epigenetic inhibitors, especially those targeting histone acetylation, to modulate immune responses in a target-selective manner. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/632975v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@30f4faorg.highwire.dtl.DTLVardef@23578borg.highwire.dtl.DTLVardef@4890ceorg.highwire.dtl.DTLVardef@1acbb5_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Time-resolved immune dynamics in rheumatoid arthritis under Methotrexate therapy

Rheumatoid arthritis (RA) is characterized by immune dysregulation, including alterations in peripheral blood mononuclear cell (PBMC) populations and aberrant cytokine signaling. Methotrexate (MTX) is the preferred first-line treatment for RA, yet its precise mechanisms of action remain incompletely understood. This study employed a multi-omics strategy--combining single-cell RNA sequencing (scRNA-seq) and immunophenotyping--to identify key effector peripheral immune cells and their cellular responses in RA patients over 12 weeks of MTX treatment. In our study, MTX was associated with significant immune modulation, including the restoration of naive T and B cells and reductions in T cell memory subsets with these effects detectable as early as three weeks post-treatment. Plasmablast levels also emerged as a potential biomarker for early therapeutic response, reflecting MTXs impact on immune homeostasis. Transcriptional analysis revealed modulation of key pathways, including TNF- signaling, B cell receptor signaling, and T cell receptor-mediated apoptosis. Network analysis identified critical regulatory hubs, such as EGR1, JAK2, and SOCS1, in monocytes and CD4 memory T cells, highlighting these cell types as key mediators of MTXs effects. In conclusion, these findings advance our understanding of MTXs effects on immune cell dynamics at different stages of treatment, showing for the first time the early cellular changes leading to immune modulation in RA. Altogether, our results provide the foundation for further mechanistic investigations into MTX.

genomics↗

bioRxiv2022

The guanine nucleotide exchange factor Rin-like acts as a gatekeeper for T follicular helper cell differentiation via regulating CD28 signaling

T follicular helper (Tfh) cells are essential for the development of germinal center B cells and high-affinity antibody producing B-cells in human and mice. Here, we identify the guanine nucleotide exchange factor (GEF) Rin-like (Rinl) as a negative regulator of Tfh generation. Loss of Rinl leads to an increase of Tfh in aging, upon in vivo immunization and acute LCMV Armstrong infection in mice, and in human CD4+ T cell in vitro cultures. Further, adoptive transfer experiments using WT and Rinl-KO naive CD4+ T cells unraveled T cell-intrinsic functions of Rinl. Mechanistically, Rinl regulates CD28 internalization and signaling, thereby shaping CD4+ T cell activation and differentiation. Thus, our results identify the GEF Rinl as a negative regulator of global Tfh differentiation in an immunological context and species-independent manner, and furthermore connect Rinl with CD28 internalization and signaling pathways in CD4+ T cells, demonstrating for the first-time the importance of endocytic processes for Tfh differentiation. HighlightsO_LIRinl-KO CD4+ T cells show increased Tfh differentiation in a context independent manner C_LIO_LIThe regulation of Tfh differentiation is T cell-intrinsic C_LIO_LIRinl controls CD28 endocytosis and shapes Tfh-specific CD28 signal transduction C_LIO_LIHuman Tfh differentiation is regulated by Rinl C_LI

immunology↗