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Ivashkiv, L. B.

Publications and source records attributed to Ivashkiv, L. B..

13 recordsLinked to original sources

Sexual dimorphism in zymosan-induced arthritis is linked with a higher IFN response in myeloid cell subsets that faithfully recapitulate RA synovial cell clusters

A key feature of rheumatoid arthritis (RA) is sexual dimorphism, with a higher incidence of RA in females. Myeloid cells are key drivers of the inflammatory effector phase of RA, but little is known about their contribution to a sexually dimorphic arthritis phenotype. We wished to utilize an arthritis model that recapitulates RA pathogenic myeloid cell subsets defined by single cell transcriptome analysis to investigate sex differences in human disease-relevant cell types and related molecular pathways. We developed a computational strategy that rigorously maps scRNAseq-defined mouse arthritis myeloid cells and clusters onto previously defined RA subsets. Synovial myeloid cells in the zymosan-induced arthritis (ZIA) model closely recapitulated four pathogenic RA myeloid cell subsets, strongly supporting the disease-relevance of the ZIA model. ZIA also effectively modeled myeloid cells in immune checkpoint inhibitor arthritis (ICI-A). These RA, ICI-A and ZIA myeloid cells express genes in TNF-NF-kB, PGE2, and IFN-STAT pathways. In ZIA, an induction phase dominated by cell clusters expressing NF-kB and PGE2 pathways transitioned to peak arthritis characterized by cell subsets co-expressing NF-kB and IFN pathways, as occurs in RA and various inflammatory diseases. Female mice exhibited increased arthritis linked with early induction of interferon-stimulated genes and increased expansion of IFN signature-expressing cell subsets. Our study identifies a computational strategy and animal model that enables investigation of recently described pathogenic myeloid cell subsets, and links increased arthritis in female mice with specific myeloid cell subsets that exhibit a stronger IFN response.

immunology↗

Pathologic profibrotic activation of distinct myeloid cell subsets in a model of impaired healing after anterior cruciate ligament reconstruction

Anterior cruciate ligament reconstruction (ACLR) may fail due to poor bone-to-tendon integration, yet the cellular mechanisms underlying this process remain incompletely understood. Using a murine model of ACLR, we show that host-derived immune cells are the primary drivers of early healing, while tendon graft-derived stromal cells also contribute at the tendon-bone interface. We developed a model of impaired post-ACLR healing by a surgical approach, that led to increased infiltration of immune cells at the tendon-bone interface, particularly CX3CR1+ monocytes/macrophages (MonoMacs). Single-cell RNA sequencing revealed dynamic monocyte-to-macrophage transitions, with an enrichment of fibrotic, mechanosensitive CX3CR1+ MonoMacs in the impaired healing model. These findings suggest that excessive recruitment or functional shifts in host-derived MonoMacs may disrupt normal healing dynamics. Our study identifies CX3CR1+ MonoMacs as a key cell population related to inferior bone-to-tendon healing after ACLR and potential therapeutic targets to improve surgical outcomes.

immunology↗

Beyond Antagonism: IL-4 Exploits TNF signaling to Shape Its Gene Expression Signature in Monocytes and Macrophages.

Investigation of crosstalk between antagonistic pro- and anti-inflammatory cytokines has focused on mechanisms and functional consequences of cross-inhibition. We investigated cross-regulation between proinflammatory TNF and anti-inflammatory IL-4 in primary human monocytes and in a skin wound-healing model. Surprisingly, TNF functioned mainly as a costimulator of IL-4-induced gene expression, whereas IL-4 selectively inhibited the TNF-induced IFN response, leaving inflammatory gene expression mostly intact. TNF and IL-4 synergistically induced gene sets important for regulating inflammation and tissue repair, which were highly induced during the phase of wound healing when these cytokines are co-expressed. Crosstalk between TNF and IL-4 was mediated by epigenetic chromatin-mediated mechanisms associated with cooperation between NF-{kappa}B and STAT6 transcription factors, erasure of negative histone mark H3K27me3, and selective inhibition of IRF1. These results identify a long-sought mechanism for expansion of the IL-4 response, and highlight the complexity of crosstalk between antagonistic cytokines that includes cooperation for select gene responses important in immune response and tissue repair.

immunology↗

Epigenetic Regulation of Inflammatory NF-κB Target Genes by IFN-γ via IRF1

The regulation of inflammatory gene expression involves complex interactions between transcription factors (TFs), signaling pathways and epigenetic chromatin-mediated mechanisms. This study investigated mechanisms by which by IFN-{gamma}-mediated priming augments TLR-induced expression of NF-{kappa}B target genes in primary human monocytes. IFN-{gamma} priming enhanced the expression of signature inflammatory genes such as IL6, TNF, IL1B, and CXCL10 when monocytes were exposed to various TLR agonists. RNA-seq analysis identified genes synergistically activated by IFN-{gamma} and LPS, which were enriched in inflammatory pathways. Similar synergistic activation was observed with the TLR1/2 agonist PAM3CYS, suggesting a shared regulatory mechanism. ATAC-seq analysis revealed that TLR ligands induce IRF1 TF activity independently of IFN-{gamma}. JAK1/2 inhibitor (iJAK) treatment reduced IRF1 expression and protein levels, especially in IFN-{gamma}-treated monocytes, but not in LPS-stimulated monocytes, suggesting LPS-induced IRF1 may compensate for loss of IFN-{gamma}-induced IRF1. We applied CRISPR-Cas9 to knock out IRF1 in primary human monocytes and found loss of IRF1 abrogates synergistic activation of key inflammatory genes, suggesting a pivotal role for IRF1. This genetic data was corroborated by IRF1 CUT&RUN data showing resistance of IRF1 binding to JAK inhibition under (IFN-{gamma} + LPS) costimulated conditions, and co-occupancy of IRF1 binding sites by NF-{kappa}B. This study enhances our understanding of inflammatory gene regulation, highlighting IRF1 as a key player and a potential therapeutic target for inflammatory diseases.

immunology↗

Opposing Regulation of TNF Responses and IL-1b+ Macrophages by PGE2-cAMP and IFN-g Signaling

IL-1{beta}-expressing macrophages have been described in rheumatoid arthritis (RA), immune checkpoint inhibitor-induced inflammatory arthritis (ICI-arthritis), and pancreatic cancer and proposed to be pathogenic. In RA and pancreatic cancer IL-1{beta}+ macrophages express genes cooperatively induced by PGE2 and TNF signaling, but mechanisms that induce these cells and the extent to which they contribute to arthritic phenotypes are not known. In this study we used an integrated transcriptomic and epigenomic analysis in primary human monocytes to study PGE2-TNF crosstalk, and how it is regulated by IFN-{gamma}, as occurs in RA synovial macrophages. We identified a TNF + PGE2 (TP) induced gene expression signature that is enriched in a previously identified IL1{beta}+ RA monocytic subset defined by scRNAseq and includes genes in pathogenic IL-1, Notch and neutrophil chemokine pathways. A similar TP gene expression signature was apparent in an IL-1{beta}+ macrophage subset newly identified by scRNAseq in ICI-arthritis. Reference mapping revealed that ICI-arthritis myeloid cells map primarily onto four previously defined RA synovial monocytic clusters, and the TP signature extends beyond IL-1{beta}+ cells to subsets of adjacent clusters, suggestive of a new functional monocyte subset. TP signature genes are distinct from canonical inflammatory NF-{kappa}B target genes such as TNF, IL6 and IL12B and are activated by cooperation of PGE2-induced AP-1, CEBP and NR4A family transcription factors with TNF-induced NF-{kappa}B activity. Unexpectedly, IFN-{gamma} suppressed induction of AP-1, CEBP and NR4A activity to ablate induction of IL-1, Notch and neutrophil chemokine genes, while promoting expression of distinct inflammatory genes such as TNF and T cell chemokines like CXCL10. The opposing cross-regulation of PGE2 and IFN signaling in vitro was reflected in vivo in mutually exclusive expression of TP and IFN signatures in different cell clusters in RA and ICI-arthritis monocytes. These results reveal the basis for synergistic induction of inflammatory genes by PGE2 and TNF, and a novel regulatory axis whereby IFN-{gamma} and PGE2 oppose each other to determine the balance between two distinct TNF-induced inflammatory gene expression programs relevant for RA and ICI-arthritis.

immunology↗

CXCL4 signaling and gene induction in human monocytes involve a TLR4 response divergent from LPS

The chemokine CXCL4 activates myeloid cells and contributes to the pathogenesis of inflammatory and fibrotic diseases. One mechanism of CXCL4 action is binding of nucleic acids to promote their internalization and activation of endosomal TLRs. However, the signaling pathways and receptors that mediate myeloid cell responses to CXCL4 alone are not well characterized. Here, we report that in primary human monocytes, CXCL4 activated NF-{kappa}B and a TBK1-JNK signaling axis that drive the expression of inflammatory, fibrotic and neutrophil chemokine genes, and also RIPK3-dependent necroptosis. Surprisingly, six distinct lines of evidence targeting TLR4 expression and function suggested a role for TLR4 in CXCL4 responses. However, we were not able to completely dissect the contributions of CXCL4 alone to the observed results versus a contribution from endotoxin contamination. Our findings suggest that the interactions between CXCL4 and TLR4 merit further study.

immunology↗

Costimulation of TLR8 responses by CXCL4 in Human Monocytes Mediated by TBK1-IRF5 Signaling and Epigenomic Remodeling

Regulation of endosomal TLR responses by the chemokine CXCL4 is implicated in inflammatory and fibrotic diseases. The current paradigm is that CXCL4 potentiates TLR responses by binding and facilitating endosomal delivery of nucleic acid TLR ligands. We report that in human monocytes/macrophages, CXCL4 initiates signaling cascades and downstream epigenomic reprogramming that change the profile of the TLR8 response by selectively and dramatically amplifying inflammatory gene transcription and IL-1{beta} production, while partially attenuating the IFN response. Mechanistically, costimulation by CXCL4 and TLR8 synergistically activated TBK1/IKK{varepsilon} and repurposed these kinases towards an inflammatory response via coupling with IRF5, and by activating the NLRP3 inflammasome without the need for an exogenous activator of a second signal for IL-1{beta} maturation. CXCL4 signaling strongly induced chromatin remodeling and de novo enhancers associated with inflammatory genes in a cooperative and synergistic manner with TLR8. These findings identify new mechanisms of regulation of TLR responses relevant for cytokine storm, and suggest targeting the TBK1/IKK{varepsilon}-IRF5 axis may be beneficial in inflammatory diseases.

immunology↗

Age-related Impairment of Implant Osseointegration is Associated with Immune Activation and Suppression of Angiogenic, Notch, and Wnt Pathways

The number of total joint replacements (TJRs) in the United States is increasing annually. Cementless implants are intended to improve upon traditional cemented implants by allowing bone growth directly on the surface to improve implant longevity. One major complication of TJR is implant loosening, which is related to deficient osseointegration in cementless TJRs. Although poor osseointegration in aged patients is typically attributed to decreased basal bone mass, little is known about the molecular pathways that compromise the growth of bone onto porous titanium implants. To identify the pathways important for osseointegration that are compromised by aging, we developed an approach for transcriptomic profiling of peri-implant tissue in young and aged mice using our murine model of osseointegration. Based on previous findings of changes of bone quality associated with aging, we hypothesized that aged mice have impaired activation of bone anabolic pathways at the bone-implant interface. We found that pathways most significantly downregulated in aged mice relative to young mice are related to angiogenic, Notch and Wnt signaling. Downregulation of these pathways is associated with markedly increased expression of inflammatory and immune genes at the bone-implant interface in aged mice. These results identify osseointegration pathways affected by aging and suggest that an increased inflammatory response in aged mice may compromise peri-implant bone healing. Targeting the Notch and Wnt pathways, promoting angiogenesis, or modulating the immune response at the peri-implant site may enhance osseointegration and improve the outcome of joint replacement in older patients.

immunology↗

Bone Marrow Stromal Cells in a Mouse Model of Implant Osseointegration

Metal implants are commonly used in orthopaedic surgery. The mechanical stability and longevity of implants depend on adequate bone deposition along the implant surface. The cellular and molecular mechanisms underlying peri-implant bone formation (i.e. osseointegration) are incompletely understood. Herein, our goal was to determine the specific bone marrow stromal cell populations that contribute to bone formation around metal implants. To do this, we utilized a mouse tibial implant model that is clinically representative of human joint replacement procedures. Using a lineage-tracing approach with the Acta2.creERT2 and Tmem100.creERT2 transgenic alleles, we found that Pdgfra- and Ly6a/Sca1-expressing stromal cells (PS cells) multiply and differentiate in the peri-implant environment to give rise to osteocytes in newly formed bone tissue. Single cell RNA-seq analysis indicated that PS cells are quiescent in uninjured bone tissue; however, they express markers of proliferation and osteogenic differentiation shortly after implantation surgery. Our findings indicate that PS cells are mobilized to repair bone tissue and facilitate implant osseointegration following surgery. Biologic therapies targeting PS cells might improve osseointegration in patients undergoing orthopaedic procedures.

cell biology↗

HBEGF+ macrophages identified in rheumatoid arthritis promote joint tissue invasiveness and are reshaped differentially by medications

Macrophages tailor their function to the signals found in tissue microenvironments, taking on a wide spectrum of phenotypes. In human tissues, a detailed understanding of macrophage phenotypes is limited. Using single-cell RNA-sequencing, we define distinct macrophage subsets in the joints of patients with the autoimmune disease rheumatoid arthritis (RA), which affects ~1% of the population. The subset we refer to as HBEGF+ inflammatory macrophages is enriched in RA tissues and shaped by resident fibroblasts and the cytokine TNF. These macrophages promote fibroblast invasiveness in an EGF receptor dependent manner, indicating that inflammatory intercellular crosstalk reshapes both cell types and contributes to fibroblast-mediated joint destruction. In an ex vivo tissue assay, the HBEGF+ inflammatory macrophage is targeted by several anti-inflammatory RA medications, however, COX inhibition redirects it towards a different inflammatory phenotype that is also expected to perpetuate pathology. These data highlight advances in understanding the pathophysiology and drug mechanisms in chronic inflammatory disorders can be achieved by focusing on macrophage phenotypes in the context of complex interactions in human tissues. One Sentence SummaryA newly identified human macrophage phenotype from patients with the autoimmune condition RA is found to promote joint tissue invasiveness and demonstrates variable sensitivities to anti-inflammatory medications used to treat the disease.

immunology↗

High dimensional analyses of cells dissociated from cryopreserved synovial tissue

BackgroundDetailed molecular analyses of cells from rheumatoid arthritis (RA) synovium hold promise in identifying cellular phenotypes that drive tissue pathology and joint damage. The Accelerating Medicines Partnership (AMP) RA/SLE network aims to deconstruct autoimmune pathology by examining cells within target tissues through multiple high-dimensional assays. Robust standardized protocols need to be developed before cellular phenotypes at a single cell level can be effectively compared across patient samples.\n\nMethodsMultiple clinical sites collected cryopreserved synovial tissue fragments from arthroplasty and synovial biopsy in a 10%-DMSO solution. Mechanical and enzymatic dissociation parameters were optimized for viable cell extraction and surface protein preservation for cell sorting and mass cytometry, as well as for reproducibility in RNA sequencing (RNA-seq). Cryopreserved synovial samples were collectively analyzed at a central processing site by a custom-designed and validated 35-marker mass cytometry panel. In parallel, each sample was flow sorted into fibroblast, T cell, B cell, and macrophage suspensions for bulk population RNA-seq and plate-based single cell CEL-Seq2 RNA-seq.\n\nResultsUpon dissociation, cryopreserved synovial tissue fragments yielded a high frequency of viable cells, comparable to samples undergoing immediate processing. Optimization of synovial tissue dissociation across six clinical collection sites with [~]30 arthroplasty and [~]20 biopsy samples yielded a consensus digestion protocol using 100{micro}g/mL of Liberase TL enzyme. This protocol yielded immune and stromal cell lineages with preserved surface markers and minimized variability across replicate RNA-seq transcriptomes. Mass cytometry analysis of cells from cryopreserved synovium distinguished: 1) diverse fibroblast phenotypes, 2) distinct populations of memory B cells and antibody-secreting cells, and 3) multiple CD4+ and CD8+ T cell activation states. Bulk RNA sequencing of sorted cell populations demonstrated robust separation of synovial lymphocytes, fibroblasts, and macrophages. Single cell RNA-seq produced transcriptomes of over 1000 genes/cell, including transcripts encoding characteristic lineage markers identified.\n\nConclusionWe have established a robust protocol to acquire viable cells from cryopreserved synovial tissue with intact transcriptomes and cell surface phenotypes. A centralized pipeline to generate multiple high-dimensional analyses of synovial tissue samples collected across a collaborative network was developed. Integrated analysis of such datasets from large patient cohorts may help define molecular heterogeneity within RA pathology and identify new therapeutic targets and biomarkers.

immunology↗

Single Cell Transcriptomics And Flow Cytometry Reveal Disease-Associated Fibroblast Subsets In Rheumatoid Arthritis

Fibroblasts mediate normal tissue matrix remodeling, but they can cause fibrosis or tissue destruction following chronic inflammation. In rheumatoid arthritis (RA), synovial fibroblasts expand, degrade cartilage, and drive joint inflammation. Little is known about fibroblast heterogeneity or if aberrations in fibroblast subsets relate to disease pathology. Here, we used an integrative strategy, including bulk transcriptomics on targeted subpopulations and unbiased single-cell transcriptomics, to analyze fibroblasts from synovial tissues. We identify 7 phenotypic fibroblast subsets with distinct surface protein phenotypes, and these collapsed into 3 subsets based on transcriptomics data. One subset expressing PDPN, THY1, but lacking CD34 was 3-fold expanded in RA relative to osteoarthritis (P=0.007); most of these cells expressed CDH11. The subsets were found to differ in expression of cytokines and matrix metalloproteinases, localization in synovial microanatomy, and in response to TNF. Our approach provides a template to identify pathogenic stromal cellular subsets in complex diseases.

immunology↗

Single-Cell RNA-Seq Of Rheumatoid Arthritis Synovial Tissue Using Low Cost Microfluidic Instrumentation

Droplet-based single cell RNA-seq has emerged as a powerful technique for massively parallel cellular profiling. While these approaches offer the exciting promise to deconvolute cellular heterogeneity in diseased tissues, the lack of cost-effective, reliable, and user-friendly instrumentation has hindered widespread adoption of droplet microfluidic techniques. To address this, we have developed a microfluidic control instrument that can be easily assembled from 3D printed parts and commercially available components costing approximately $540. We adapted this instrument for massively parallel scRNA-seq and deployed it in a clinical environment to perform single cell transcriptome profiling of disaggregated synovial tissue from a rheumatoid arthritis patient. We sequenced 8,716 single cells from a synovectomy, revealing 16 transcriptomically distinct clusters. These encompass a comprehensive and unbiased characterization of the autoimmune infiltrate, including inflammatory T and NK subsets that contribute to disease biology. Additionally, we identified fibroblast subpopulations that are demarcated via THY1 (CD90) and CD55 expression. Further experiments confirm that these represent synovial fibroblasts residing within the synovial intimal lining and subintimal lining, respectively, each under the influence of differing microenvironments. We envision that this instrument will have broad utility in basic and clinical settings, enabling low-cost and routine application of microfluidic techniques, and in particular single-cell transcriptome profiling.

genomics↗