Biology subjects

Simone, D.

Publications and source records attributed to Simone, D..

5 recordsLinked to original sources

bioRxiv2023

Trained immunity in human monocyte enhances myeloid-T-cell pathogenic crosstalk in Ankylosing Spondylitis

Recent studies in infectious, cardiovascular and neurodegenerative diseases have established the presence of memory in innate immune cells. This "trained immunity (TI)" leads to an enhanced response to a second challenge. Monocytes in Ankylosing Spondylitis (AS), a common form of inflammatory arthritis, are known to be hyper-responsive to microbial stimulus lipopolysaccharide (LPS). We asked if TI is present in AS monocytes and, if so, how it contributes to disease pathology. Using Single-cell RNA sequencing (scRNA-seq), flow cytometry and enzyme-linked immunosorbent assays (ELISA), we identify a subset of monocytes from AS patients exhibiting features of trained immunity and being hyperresponsive to LPS stimulation. Surprisingly, both trained monocytes in AS and {beta}-glucan-trained monocytes from healthy donors are hyper-responsive to T-cell-induced activation. scRNA-seq of AS synovial mononuclear cells shows enrichment of a monocyte population with these/analogous features. Additionally, T cell-stimulated monocytes act back on T-cells to support Th17 responses (of established pathology in AS). Lastly, using genetic and chemical perturbations we show that ERN1, an AS risk gene enriched in this trained monocyte population, contributes to T-cell-induced monocyte activation. Our data provide strong evidence for the first time for the key role of TI in common human inflammatory arthritis.

molecular biology↗

bioRxiv2022

Deficiencies of Runx3 and tissue-resident CD4+ intestinal epithelial lymphocytes link intestinal dysbiosis and inflammation in mouse and human spondyloarthropathy

ObjectiveDisturbances in immune regulation, intestinal microbial dysbiosis and intestinal inflammation characterize ankylosing spondylitis (AS), which is associated with RUNX3 loss-of-function variants. ZAP70W163C mutant (SKG) mice have reduced ZAP70 signaling, spondyloarthritis and ileitis. At intestinal epithelial interfaces, lamina propria Foxp3+ regulatory T cells (Treg) and intraepithelial CD4+CD8+TCR{beta}+ lymphocytes (CD4-IEL) control inflammation. TGF-{beta} and retinoic acid (RA)-producing dendritic cells are required for induction of Treg and for CD4-IEL differentiation from CD4+ conventional or Treg precursors, with upregulation of Runx3 and suppression of ThPOK. We investigated Treg, CD4-IEL, ZAP70 and Runx3 in SKG mice and AS patients. MethodsWe compared ileal Treg and CD4-IEL numbers and differentiation in BALB/c and SKG mice, and with ZAP70 inhibition, and related differentially-expressed genes in terminal ileum to ChIP-seq-identified Runx3-regulated genes. We compared proportions of CD4-IEL in ileum and CD4+8+ T cells in blood of AS patients and healthy controls. ResultsZAP70W163C or ZAP70 inhibition prevented intestinal CD4-IEL but not Foxp3+ Treg differentiation in context of TGF-{beta} and RA in vitro and in vivo, resulting in Runx3 and ThPOK dysregulation. CD4-IEL frequency and expression of tissue resident memory T-cell and Runx3-regulated genes was reduced in SKG intestine. Multiple under-expressed genes were shared with risk SNPs identified in human spondyloarthropathies. CD4-IEL were decreased in AS intestine. Double-positive T cells were reduced and Treg increased in AS peripheral blood. ConclusionHigh-affinity TCR-ZAP70 signalling is required for Runx3-mediated intestinal CD4-IEL differentiation from Treg. Genetically-encoded relative immunodeficiency of T cells underpins poor intestinal barrier control in mouse and human spondyloarthropathy. What is already known about this subject?Ankylosing spondylitis (AS) is associated with RUNX3 loss-of-function variants. Capacity of the AS T cell receptor repertoire to expand in response to infectious antigens is reduced. Foxp3+ regulatory T cells (Treg) are increased in AS intestine. ZAP70W163C mutant (SKG) mice have reduced ZAP70 signaling, spondyloarthritis (SpA) and ileitis. Intestinal epithelial Foxp3+ Treg and CD4+CD8+ cytotoxic lymphocytes (CD4-IEL) control local inflammation. CD4-IEL differentiate from Treg, with upregulation of Runx3 and suppression of ThPOK transcription factors. What does this study add?High-affinity TCR-ZAP70 signalling is required for Runx3-mediated intestinal CD4-IEL differentiation from Treg Intestinal CD4-IEL and circulating CD4+CD8+ T cells are reduced in AS while circulating Treg are increased. Impaired CD8 expression may be correctible by TNF inhibition in AS CD4+ T cells. Deficiencies of Runx3 and tissue-resident CD4-IEL link intestinal dysbiosis and inflammation in mouse and human SpA. How might this influence clinical practice or future developments?Genetically-encoded relative T immunodeficiency underpins poor intestinal barrier control in SpA

immunology↗

bioRxiv2021

Single cell analysis of spondyloarthritis regulatory T cells identifies distinct synovial gene expression patterns and clonal fates

Regulatory T cells (Tregs) play an important role in controlling inflammation and limiting autoimmunity, but their phenotypes at inflammatory sites in human disease are poorly understood. We here analyze the single-cell transcriptome of >16,000 Tregs obtained from peripheral blood and synovial fluid of two patients with HLA-B27+ ankylosing spondylitis and three patients with psoriatic arthritis, closely related forms of inflammatory spondyloarthritis. We identify multiple Treg clusters with distinct transcriptomic profiles, including, among others, a regulatory CD8+ subset expressing cytotoxic markers/genes, and a Th17-like RORC+ Treg subset characterized by IL-10 and LAG-3 expression. Synovial Tregs show upregulation of interferon signature and TNF receptor superfamily genes, and marked clonal expansion, consistent with tissue adaptation and antigen contact respectively. Individual synovial Treg clones map to different clusters indicating cell fate divergence. Finally, we demonstrate that LAG-3 directly inhibits IL-12/23 and TNF secretion by patient-derived monocytes, a mechanism with translational potential in SpA. Our detailed characterization of Tregs at an important inflammatory site illustrates the marked specialization of Treg subpopulations.

immunology↗

bioRxiv2020

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

Extremely oligotrophic deep groundwaters host organisms attuned to the low-end of the bioenergetics spectrum. While all domains of life along with viruses are active in this habitat, the evolutionary and ecological constraints on colonization and niche shifts and their consequences for the microbiome convergence are unknown. Here we provide a comparative genome-resolved analysis of the prokaryotic community in disconnected fracture fluids of the Fennoscandian Shield. The data show that the oligotrophic deep groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common deep groundwater core microbiome. Based on this high resolution "multi-omics" enabled understanding of the underlying mechanisms via functional expression analysis, we conclude that deep groundwater ecosystems foster highly diverse, yet cooperative microbial communities adapted to this setting. The fitness of primary energy producers is increased by ecological traits such as aggregate or biofilm formation. This also facilitates reciprocal promiscuous partnerships with diverse and prevalent epi-bionts, alleviating the "tragedy of common goods". Hence, instead of a lifestyle where microbes predominantly invest in functions related to maintenance and survival, an episodic and cooperative lifestyle ensures the subsistence of the deep groundwater microbiome. We suggest the name "halt and catch fire" for this way of life.

microbiology↗

bioRxiv2019

Single-cell sequencing reveals a clonal expansion of pro-inflammatory synovial CD8 T cells expressing tissue homing receptors in psoriatic arthritis

Psoriatic arthritis (PsA) is a debilitating immune-mediated inflammatory arthritis of unknown pathogenesis commonly affecting patients with skin psoriasis. We used three complementary single cell approaches to study leukocytes from PsA joints. Mass cytometry (CyTOF) demonstrated marked (>3 fold) expansion of memory CD8 T cells in the joints compared to matched blood. Further exploration of the memory CD8 compartment using both droplet and plate based single cell RNA sequencing of paired alpha and beta chain T cell receptor sequences identified pronounced CD8 T cell clonal expansions within the joints, strongly suggesting antigen driven expansion. These clonotypes exhibited distinct gene expression profiles including cycling, activation, tissue homing and tissue residency markers. Pseudotime analysis of these clonal CD8 populations identified trajectories in which tissue residency can represent an intermediate developmental state giving rise to activated, cycling and exhausted CD8 populations. Comparing T-cell clonality across patients further revealed specificity convergence of clones against a putative common antigen. We identify chemokine receptor CXCR3 as upregulated in expanded synovial clones, and elevation of two CXCR3 ligands, CXCL9 and CXCL10, in PsA synovial fluid.

immunology↗