Biology subjects

Somma, D.

Publications and source records attributed to Somma, D..

8 recordsLinked to original sources

bioRxiv2026

Cell DiffErential Expression by Pooling (CellDEEP) highlights issues in differential gene expression in scRNA-seq

Accurate identification of differentially expressed genes (DEGs) in single-cell RNA sequencing (scRNA-seq) data remains challenging. Single-cell-specific statistical models often report large numbers of candidate genes but can exhibit inflated false positive rates, whereas pseudobulk approaches improve false discovery control at the cost of reduced sensitivity. To overcome the noise and bias that other tools have, and allow the user to have more control of the DEG process, we present CellDEEP, which uses a cell aggregation (metacell) approach. This tool provides a framework for flexible selection of pooling strategies and parameterisation for differential expression analysis (DE). Benchmarking on simulated and real datasets, including COVID-19 and rheumatoid arthritis, shows that CellDEEP often outperforms other methods, consistently reduces false positives compared to single-cell methods and recovers more true positives than pseudobulk methods. Our work shifts the focus from selecting a single "best" method to an approach that reduces cell-level noise while preserving biological signal, together with transparent validation framework, advancing more reliable differential-expression analysis in single-cell transcriptomics. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=189 HEIGHT=200 SRC="FIGDIR/small/710522v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@14692f9org.highwire.dtl.DTLVardef@5b37d6org.highwire.dtl.DTLVardef@aece11org.highwire.dtl.DTLVardef@5ade3d_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

The ontogeny of myeloid-stromal synovial tissue niches in rheumatoid arthritis.

Recent single-cell multi-omic and spatial analyses of synovial biopsies have transformed our understanding of myeloid cell-driven mechanisms underlying human joint pathology and tissue homeostasis in Rheumatoid arthritis (RA). However, the developmental trajectories of synovial tissue macrophage (STM) subsets in humans remain poorly understood, due in part to the lack of models that faithfully replicate synovial tissue niches. This hinders the exploration of the therapeutic potential of targeting specific synovial myeloid cell clusters. Using multi-omics analyses of synovial tissue from an allogeneic bone marrow transplant recipient, we show that joint-specific tissue-resident STM subsets, including both health- and disease-associated clusters, can derive from peripheral blood monocytes. Analysis of embryonic synovial joints revealed that macrophage localization and maturation in the joints are preceded by local stromal niche specialisation, indicating that synovial fibroblasts (FLS) provide tissue-specific instructive cues to STM precursors. To elucidate human STM developmental trajectories, we established a SNP-based fate-tracking human synovial organoid system by embedding distinct blood-derived myeloid precursors, together with FLS clusters from RA synovial biopsies and endothelial cells, into 3D structures. These organoids reproduced key synovial tissue features, including lining and sublining architecture and stromal-myeloid cell cluster composition. Importantly, they supported differentiation of all resident STM subsets: homeostatic lining TREM2pos macrophages, their pathogenic TREM2lowSPP1pos counterparts that characterize the RA hyperplastic lining, and both homeostatic and RA-associated perivascular LYVE1pos STM clusters, all traced to monocytic precursors. In summary, we show that development of STM subsets is driven by fibroblast-conditioned spatial niches. We have established a novel, tractable ex vivo platform to dissect the niche-specific cues driving homeostatic versus pathogenic phenotypic clusters. One Sentence SummaryHuman tissue-resident STMs develop from monocytes under the guidance of cues from FLS within discrete spatial locations.

immunology↗

bioRxiv2025

Macrophages amplify the spontaneous activity of damaged sensory neurons in a human co-culture model of neuropathic pain

Neuropathic pain is a highly prevalent condition for which treatments are hampered by low efficacy and dose-limiting side-effects. Injury to the somatosensory nervous system causes maladaptive plasticity that initiates and maintains chronic pain. Emerging evidence suggests that inflammatory cells of the innate immune system shape the response of the injured nervous system and thereby contribute to the pathogenesis of pain. Data from preclinical models and human patient biopsies have specifically implicated peripheral macrophage populations for a pro-algesic role, yet how these cell types influence damaged sensory neurons and whether they directly contribute to neuronal hyperexcitability is unclear. Here, we have developed an iPSC co-culture system to study the interactions of macrophages and sensory neurons in a fully humanised experimental model. We found that analogous to endogenous counterparts, iPSC-derived macrophages (iMacs) display a dynamic molecular and functional profile that is highly dependent on neuronal state. Co-culture with injured iPSC-derived sensory neurons (iSNs) induces morphological, gene expression, and secretory profile changes in iMacs that are consistent with the response of macrophages to nerve injury in vivo. iMacs in turn amplify spontaneous firing in damaged sensory neurons, implicating macrophages in this cardinal feature of neuropathic pain. These results illustrate the utility of an iPSC-based model to study signalling between these two cell types; they support a role for macrophages in directly amplifying damaged sensory neuron activity and highlight disrupting pathological signalling between these cell types as a promising strategy for future analgesic drug development.

neuroscience↗

bioRxiv2024

PROS1 released by human lung basal cells upon SARS-CoV-2 infection facilitates epithelial cell repair and limits inflammation.

Factors governing the coagulopathy and pneumonitis associated with severe viral infections remain unresolved. We previously found that the expression of protein S (PROS1) is increased in lung epithelium of patients with mild COVID-19 as compared to severe COVID-19. We hypothesised that PROS1 may exert a local effect that protects the upper airway against severe inflammation by modulating epithelial and myeloid cell responses. To test this, in vitro air-interface cultures, seeded from primary healthy human lung epithelial cells, were infected with different SARS-CoV-2 clades. This model, validated by single-cell RNAseq analysis, recapitulated the dynamic cell-profile and pathogenic changes of COVID-19. We showed that PROS1 was located in the basal cells of healthy pseudostratified epithelium. During SARS-Cov-2 infection, PROS1 was released by basal cells, which was partially mediated by interferon. Transcriptome analysis showed that SARS-CoV-2 infection induced proinflammatory phenotypes (CXCL10/11high, PTGS2posF3high, S100A8/A9high) of basal and transitional cells. PROS1 strongly downregulated these cells and transformed the proinflammatory CXCL10/11high basal cells into the regenerative S100A2posKRThigh basal cell phenotype. In addition, SARS-CoV-2 infection elevated M-CSF secretion from epithelium, which induced MERTK, a receptor for PROS1, on monocytes added into 3D lung epithelial culture. We demonstrated that SARS-CoV-2 drives monocyte phenotypes expressing coagulation (F13A1) and complement (C1O) genes. PROS1 significantly downregulated these phenotypes and induced higher expression of MHC class II. Overall, this study demonstrated that the epithelium-derived PROS1 during SARS-CoV-2 infection inhibits the proinflammatory epithelial phenotypes, favours basal cell regeneration, and inhibits myeloid inflammation while enhancing antigen presentation. These findings highlight the importance of basal epithelial cells and PROS1 protection from viral infection induced severe lung pathology. O_FIG O_LINKSMALLFIG WIDTH=193 HEIGHT=200 SRC="FIGDIR/small/612489v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@324deaorg.highwire.dtl.DTLVardef@994f30org.highwire.dtl.DTLVardef@11de2e0org.highwire.dtl.DTLVardef@11a0fe2_HPS_FORMAT_FIGEXP M_FIG 1) SARS-CoV2 infection of the epithelium results in release of IFN. 2) IFN secretion has an autocrine effect on epithelial cells 3) Infection and IFN cause release of PROS1 from the basal cells, as well as M-CSF from the epithelium 4) PROS1 acts on basal cells which express MERTK, a PROS1 receptor 5) PROS1 downregulated the proinflammatory phenotypes expanded by viral infection, while upregulating KRThigh basal cells with repair phenotypes 6) The secreted M-CSF drives MERTK expression on monocytes in cocultures with epithelium. 7) PROS1 induces downregulation of monocyte clusters characteristic of viral infection that express pro-coagulation and complement genes, while upregulating clusters with higher MHC class II. 8) In summary, PROS1 mediates phenotypic switch of SARS-Cov2 induced pathogenic myeloid clusters with complement and coagulation phenotypes into phenotype with efficient antigen presentation, reduces proinflammatory activation of epithelium and induces epithelial barrier repair, resulting in mild COVID-19. C_FIG

cell biology↗

bioRxiv2024

paraCell: A novel software tool for the interactive analysis and visualization of standard and dual host-parasite single cell RNA-Seq data

Advances in sequencing technology have led to a dramatic increase in the number of single-cell transcriptomic datasets available. In the field of parasitology these datasets typically describe the gene expression patterns of a given parasite species under specific experimental conditions, in specific hosts or tissues, or at different life-cycle stages. However, while this wealth of available data represents a significant resource for further research, the analysis of these datasets often requires significant computational skills, preventing a considerable proportion of the parasitology community from meaningfully incorporating existing single-cell data into their work. Here, we present paraCell, a novel software tool that automates the advanced analysis of published single-cell data without requiring any programming ability. On our free web-server, we demonstrated how to visualise data, re-analyse published Plasmodium and Trypanosoma datasets, and present novel Toxoplasma-mouse and Theileira-cow atlases to study the impact of IFN-{gamma} and host genetic susceptibility.

bioinformatics↗

bioRxiv2024

Distinct tissue-niche localization and function of synovial tissue myeloid DC subsets in health, and in active and remission Rheumatoid Arthritis

Current rheumatoid arthritis (RA) treatments do not restore immune tolerance. Investigating dendritic cell (DC) populations in human synovial tissue (ST) may reveal pathways to re-instate tolerance in RA. With single-cell and spatial-transcriptomics of synovial tissue biopsies, validated by micro co-culture systems, we identified condition and niche-specific myeloid DC clusters with distinct differentiation trajectories and functions. Healthy synovium contains a unique tolerogenic AXLpos DC2 cluster in the superficial sublining layer. In active RA, a macrophage-rich lining-layer niche becomes populated with inflammatory DC3 clusters that specifically activate memory CCL5pos TEM and CCL5posCXCL13pos TPH, promoting synovitis. In the sublining lymphoid niche, CCR7pos DC2 mReg specifically interact with naive-T-cells, potentially driving the local expansion of new effector T-cells. Sustained remission sees the resolution of these niches but lacks the recovery of tolerogenic AXLpos DC2, indicating latent potential for disease flare. A human RA disease-flare model showed that the activation of blood predecessor of ST-DC3 clusters precedes the onset of inflammation in joints. Therapeutic strategies targeting pathogenic ST-DC3 clusters, or reinstating tolerogenic AXLpos DC2, may restore immune homeostasis in RA. In briefDeconstruction of human RA synovium, using single-cell spatial transcriptomics and micro-culture systems, reveals distinct neighbourhoods within the synovial architecture across health, and RA patients with active disease or sustained remission. Discrete niches are identified that contain distinct myeloid DC clusters that differ in frequency, differentiation trajectories, and effector functions. HighlightsO_LIHuman RA synovium exhibits condition and niche specific myeloid DC clusters that vary in their tissue differentiation trajectories and functions. C_LIO_LIST-CD14pos DC3 (iDC3) support inflammatory CCL5pos TEM and CCL5pos TPH cell activation in the hyperplastic lining layer. C_LIO_LIST-CCR7pos DC2 (mReg), driven by MIR155, interact with naive-T-cells in sublining lymphoid niches. C_LIO_LIA specific inflammatory signature of blood predecessors of ST-DC3s predict flare in RA. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/600758v1_ufig1.gif" ALT="Figure 1"> View larger version (74K): org.highwire.dtl.DTLVardef@27ab01org.highwire.dtl.DTLVardef@4be238org.highwire.dtl.DTLVardef@1f10734org.highwire.dtl.DTLVardef@1102056_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2020

COVID-19 and Rheumatoid Arthritis share myeloid pathogenic and resolving pathways

BackgroundWe recently delineated the functional biology of pathogenic and inflammation resolving synovial tissue macrophage clusters in rheumatoid arthritis (RA). Whilst RA is not a viral respiratory syndrome, it represents a pro-inflammatory cytokine-driven chronic articular condition often accompanied by cardiovascular and lung pathologies. We hypothesised that functionally equivalent macrophage clusters in the lung might govern inflammation and resolution of COVID-19 pneumonitis. MethodsTo provide insight into the targetable functions of COVID-19 bronchoalveolar lavage (BALF) macrophage clusters, a comparative analysis of BALF macrophage single cell transcriptomics (scRNA-seq) with synovial tissue (ST) macrophage scRNA-seq and functional biology was performed. The function of shared BALF and ST MerTK inflammation-resolving pathway was confirmed with inhibitor in primary macrophage-synovial fibroblast co-cultures. Results. Distinct BALF FCNpos and FCNposSPP1pos macrophage clusters emerging in severe COVID-19 patients were closely related to ST CD48highS100A12pos and CD48posSPP1pos clusters driving synovitis in active RA. They shared transcriptomic profile and pathogenic mechanisms. Healthy lung resident alveolar FABP4pos macrophages shared a regulatory transcriptomic profile, including TAM (Tyro, Axl, MerTK) receptors pathway with synovial tissue TREM2pos macrophages that govern RA remission. This pathway was substantially altered in BALF macrophages of severe COVID-19. In vitro dexamethasone inhibited tissue inflammation via macrophages MerTK function. ConclusionPathogenesis and resolution of COVID-19 pneumonitis and RA synovitis might be driven by similar macrophage clusters and pathways. The MerTK-dependent anti-inflammatory mechanisms of dexamethasone, and the homeostatic function of TAM pathways that maintain RA in remission advocate the therapeutic MerTK agonism to ameliorate the cytokine storm and pneumonitis of severe COVID-19.

immunology↗

bioRxiv2018

The IκB-Protein BCL-3 Controls MAPK Activity by Promoting TPL-2 Degradation in the Nucleus.

The ability of the innate immune system to distinguish between low level microbial presence and invasive pathogens is fundamental for immune homeostasis and immunity. However, the molecular mechanisms underlying threat discrimination by innate immune cells are not clearly defined. Here we describe the integration of the NF-B and MAPK pathways in the nucleus by the IB protein BCL-3 and the MAP3K TPL-2. Our data reveals that TPL-2 is a nucleocytoplasmic shuttling protein and demonstrates that the nucleus is the primary site for TPL-2 ubiquitination and proteasomal degradation. BCL-3 promotes TPL-2 degradation through interaction in the nucleus. As a consequence, Bcl3-/- macrophages have increased TPL-2 stability and MAPK activity following TLR stimulation. The enhanced stability of TPL-2 in Bcl3-/- macrophages lowers the MAPK activation threshold and the level of TLR ligand required to initiate an inflammatory response. This study establishes the nucleus as a key regulatory site for TLR-induced MAPK activity and identifies BCL-3 as a regulator of the cellular decision to initiate inflammation

immunology↗