Interferon Regulatory Factor 5 (IRF5): An important player in macrophage polarization and TNF regulation

Macrophages are dynamic and heterogeneous cells that can be divided into specific, phenotypic subsets. Based on Th1/Th2 polarization concept they are referred to as proinflammatory classical M1 (IL-12high, IL-23high, IL-10low) macrophages and anti-inflammatory M2 (IL-12low, IL-23low, IL-10high) macrophages. In contrast to T lymphocyte subsets, the transcription factor(s) underlying macrophage polarization remain largely unknown. My research has highlighted the importance of Interferon regulatory factor 5 (IRF5) for establishing the pro-inflammatory M1 macrophage phenotype. I was able to show that high expression of IRF5 is characteristic of M1 macrophages, in which it transcriptionally regulates M1-specific cytokines, chemokines and co-stimulatory molecules. Consequently, the depletion of IRF5 in human M1 macrophages results in down-regulation of M1-specific cytokines and further evidence for a role of IRF5 in effective immunity stems from my work using an in vivo model of polarizing inflammation. IRF5 deficient mice showed a significant reduction in serum levels of M1-specific cytokines compared to wild-type littermate controls. Therefore, the suppression of macrophage function via inhibition of IRF5 provides a new approach to attenuate the inflammatory response. Tumor necrosis factor (TNF) plays an essential role in the host defence against infections but is a major factor in the pathogenesis of chronic inflammatory diseases. The expression of TNF is therefore tightly regulated. I was able to demonstrate that IRF5 is not only involved in the induction of human TNF gene expression but also crucial for the late phase secretion of TNF by human myeloid cells. IRF5 is using a complex molecular mechanism to control the TNF gene with two spatially separated regulatory regions (5‟ upstream and 3‟ downstream of the gene) and two independent modes of action (direct DNA binding and formation of IRF5/RelA complex) being involved. The manipulation of the IRF5/RelA interaction could be a putative target for cell-specific modulation of TNF gene expression

Chromatin mapping and single-cell immune profiling define the temporal dynamics of ibrutinib response in CLL

The Bruton tyrosine kinase (BTK) inhibitor ibrutinib provides effective treatment for patients with chronic lymphocytic leukemia (CLL), despite extensive heterogeneity in this disease. To define the underlining regulatory dynamics, we analyze high-resolution time courses of ibrutinib treatment in patients with CLL, combining immune-phenotyping, single-cell transcriptome profiling, and chromatin mapping. We identify a consistent regulatory program starting with a sharp decrease of NF-kappa B binding in CLL cells, which is followed by reduced activity of lineage-defining transcription factors, erosion of CLL cell identity, and acquisition of a quiescence-like gene signature. We observe patient-to-patient variation in the speed of execution of this program, which we exploit to predict patient-specific dynamics in the response to ibrutinib based on the pre-treatment patient samples. In aggregate, our study describes time-dependent cellular, molecular, and regulatory effects for therapeutic inhibition of B cell receptor signaling in CLL, and it establishes a broadly applicable method for epigenome/transcriptome-based treatment monitoring

Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation.

Non-lymphoid tissues (NLTs) harbor a pool of adaptive immune cells with largely unexplored phenotype and development. We used single-cell RNA-seq to characterize 35,000 CD4+ regulatory (Treg) and memory (Tmem) T cells in mouse skin and colon, their respective draining lymph nodes (LNs) and spleen. In these tissues, we identified Treg cell subpopulations with distinct degrees of NLT phenotype. Subpopulation pseudotime ordering and gene kinetics were consistent in recruitment to skin and colon, yet the initial NLT-priming in LNs and the final stages of NLT functional adaptation reflected tissue-specific differences. Predicted kinetics were recapitulated using an in vivo melanoma-induction model, validating key regulators and receptors. Finally, we profiled human blood and NLT Treg and Tmem cells, and identified cross-mammalian conserved tissue signatures. In summary, we describe the relationship between Treg cell heterogeneity and recruitment to NLTs through the combined use of computational prediction and in vivo validation

Tissue Microenvironments Define and Get Reinforced by Macrophage Phenotypes in Homeostasis or during Inflammation, Repair and Fibrosis

Current macrophage phenotype classifications are based on distinct in vitro culture conditions that do not adequately mirror complex tissue environments. In vivo monocyte progenitors populate all tissues for immune surveillance which supports the maintenance of homeostasis as well as regaining homeostasis after injury. Here we propose to classify macrophage phenotypes according to prototypical tissue environments, e.g. as they occur during homeostasis as well as during the different phases of (dermal) wound healing. In tissue necrosis and/or infection, damage- and/or pathogen-associated molecular patterns induce proinflammatory macrophages by Toll-like receptors or inflammasomes. Such classically activated macrophages contribute to further tissue inflammation and damage. Apoptotic cells and antiinflammatory cytokines dominate in postinflammatory tissues which induce macrophages to produce more antiinflammatory mediators. Similarly, tumor-associated macrophages also confer immunosuppression in tumor stroma. Insufficient parenchymal healing despite abundant growth factors pushes macrophages to gain a profibrotic phenotype and promote fibrocyte recruitment which both enforce tissue scarring. Ischemic scars are largely devoid of cytokines and growth factors so that fibrolytic macrophages that predominantly secrete proteases digest the excess extracellular matrix. Together, macrophages stabilize their surrounding tissue microenvironments by adapting different phenotypes as feed-forward mechanisms to maintain tissue homeostasis or regain it following injury. Furthermore, macrophage heterogeneity in healthy or injured tissues mirrors spatial and temporal differences in microenvironments during the various stages of tissue injury and repair. Copyright (C) 2012 S. Karger AG, Base

Macrophages: supportive cells for tissue repair and regeneration.

International audienceMacrophages, and more broadly inflammation, have been considered for a long time as bad markers of tissue homeostasis. However, if it is indisputable that macrophages are associated with many diseases in a deleterious way, new roles have emerged, showing beneficial properties of macrophages during tissue repair and regeneration. This discrepancy is likely due to the high plasticity of macrophages, which may exhibit a wide range of phenotypes and functions depending on their environment. Therefore, regardless of their role in immunity, macrophages play a myriad of roles in the maintenance and recovery of tissue homeostasis. They take a major part in the resolution of inflammation. They also exert various effects of parenchymal cells, including stem and progenitor cell, of which they regulate the fate. In the present review, few examples from various tissues are presented to illustrate that, beyond their specific properties in a given tissue, common features have been described that sustain a role of macrophages in the recovery and maintenance of tissue homeostasis

Cytokines and inflammatory mediators: 25. Certolizumab Pegol has a Different Profile from the other Anti-TNFS, Including Golimumab, in a Variety of in Vitro Assays

Background: Activities of the anti-TNFs, certolizumab pegol (CZP), etanercept (ETA), infliximab (IFX) and adalimumab (ADA), have been compared in a range of in vitro assays. CZP is the only licensed PEGylated Fab' anti-TNF; ETA is a fusion protein with an IgG1 Fc, and IFX and ADA are both antibodies with an IgG1 Fc. Golimumab (GLM) is a monoclonal IgG1 TNF inhibitor recently approved for a number of indications; it is thus of interest to assess the in vitro activity of GLM. In vitro assays previously used were neutralisation of TNF in the L929 bioassay, inhibition of LPS-driven cytokine production by monocytes, induction of apoptosis in activated lymphocytes and monocytes, and induction of neutrophil necrosis. Methods: Neutralisation of human TNF was assessed in the L929 bioassay using a range of concentrations of the anti-TNFs and a fixed concentration of TNF (100 pg/mL). Activity of the anti-TNFs at inhibiting LPS-driven IL-1β secretion by monocytes was assessed by incubating peripheral blood monocytes with various concentrations of the anti-TNF for 1 hour (hr) and then washing the cells. LPS was added for 4 hrs, the supernatants collected and the IL-1β level measured by ELISA. To assess induction of apoptosis, peripheral blood lymphocytes were activated for 2 days with 2 μg/mL CD3/CD28 and monocytes with 300 U/mL IL-4 and GMCSF for 3 days. The effect of the anti-TNFs on apoptosis was assessed by Annexin V staining using flow cytometry 24 hrs later. The effect of the anti-TNFs on neutrophil necrosis was determined by measuring myeloperoxidase release after 12 hrs. An isotype-matched control was used in all assays except the L929 bioassay. Results: IC90 neutralisation activity of the anti-TNFs in the L929 bioassay was 0.3 ng/mL for ETA, 4 ng/mL for GLM, 15 ng/mL for ADA, and 20 ng/mL for IFX, compared with 2.5 ng/mL for CZP. CZP was the most potent inhibitor of LPS-driven IL-1β secretion (IC50 ∼0.1 ng/mL), followed by GLM (20 ng/mL) and IFX (50 ng/mL). GLM, ADA, IFX and ETA induced apoptosis of monocytes and lymphocytes to a similar degree reaching a level of 23% and ∼40% at 100 μg/mL, respectively. CZP caused no increase in apoptosis above the levels seen with the isotype-matched control. In the neutrophil necrosis assay, ADA,IFX and GLM caused ∼70% necrosis at 100 μg/mL, and ETA 48%. CZP did not increase the level of necrosis above the level of the control. Conclusions: Bioactivity of the IgG1 molecules GLM, IFX and ADA in neutralising human TNF was inferior to that of CZP and ETA. CZP, the only PEGylated anti-TNF, had a different profile to the other anti-TNFs as it was the most potent at inhibiting LPS-driven IL-1β production by monocytes, did not induce apoptosis of activated monocytes and lymphocytes, and did not cause neutrophil necrosis. The clinical relevance of these in vitro effects is unknown. Nevertheless, these assays show interesting in vitro differences between the anti-TNFs. Disclosure statement: G.F. and A.N. are employees of UC

Macrophage biology in development, homeostasis and disease

Macrophages the most plastic cells of the hematopoietic system are found in all tissues and exhibit great functional diversity. They have roles in development, homeostasis, tissue repair, and immunity. While anatomically distinct, resident tissue macrophages exhibit different transcriptional profiles, and functional capabilities, they are all required for the maintenance of homeostasis. However, these reparative and homeostatic functions can be subverted by chronic insults, resulting in a causal association of macrophages with disease states. In this review, we discuss how macrophages regulate normal physiology and development and provide several examples of their pathophysiologic roles in disease. We define the “hallmarks” of macrophages performing particular functions, taking into account novel insights into the diversity of their lineages, identity, and regulation. This diversity is essential to understand because macrophages have emerged as important therapeutic targets in many important human diseases

Interferon Regulatory Factor 5 (IRF5) : an important player in macrophage polarization and TNF regulation

Macrophages are dynamic and heterogeneous cells that can be divided into specific, phenotypic subsets. Based on Th1/Th2 polarization concept they are referred to as proinflammatory classical M1 (IL-12high, IL-23high, IL-10low) macrophages and anti-inflammatory M2 (IL-12low, IL-23low, IL-10high) macrophages. In contrast to T lymphocyte subsets, the transcription factor(s) underlying macrophage polarization remain largely unknown. My research has highlighted the importance of Interferon regulatory factor 5 (IRF5) for establishing the pro-inflammatory M1 macrophage phenotype. I was able to show that high expression of IRF5 is characteristic of M1 macrophages, in which it transcriptionally regulates M1-specific cytokines, chemokines and co-stimulatory molecules. Consequently, the depletion of IRF5 in human M1 macrophages results in down-regulation of M1-specific cytokines and further evidence for a role of IRF5 in effective immunity stems from my work using an in vivo model of polarizing inflammation. IRF5 deficient mice showed a significant reduction in serum levels of M1-specific cytokines compared to wild-type littermate controls. Therefore, the suppression of macrophage function via inhibition of IRF5 provides a new approach to attenuate the inflammatory response. Tumor necrosis factor (TNF) plays an essential role in the host defence against infections but is a major factor in the pathogenesis of chronic inflammatory diseases. The expression of TNF is therefore tightly regulated. I was able to demonstrate that IRF5 is not only involved in the induction of human TNF gene expression but also crucial for the late phase secretion of TNF by human myeloid cells. IRF5 is using a complex molecular mechanism to control the TNF gene with two spatially separated regulatory regions (5‟ upstream and 3‟ downstream of the gene) and two independent modes of action (direct DNA binding and formation of IRF5/RelA complex) being involved. The manipulation of the IRF5/RelA interaction could be a putative target for cell-specific modulation of TNF gene expression.EThOS - Electronic Theses Online ServiceArthritis Research UK, Medical Research Council, the European Community Seventh Framework Programme and the Kennedy Institute trusteesGBUnited Kingdo

Correction: Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling

Correction to: The ISME Journal https://doi.org/10.1038/ismej.2016.40 Since publication of the original paper the authors realised the following funding body was missing from the article’s Acknowledgements: "FP and this work was also supported by the European Research Council (ERC, Advanced Grant Ares(2013)3687660)". The authors apologise for any inconvenience caused

Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling

The gut microbiome is significantly altered in inflammatory bowel diseases, but the basis of these changes is not well understood. We have combined metagenomic and metatranscriptomic profiling of the gut microbiome to assess modifications to both bacterial community structure and transcriptional activity in a mouse model of colitis. By using transcriptomic analysis of colonic tissue and luminal RNA derived from the host, we have also characterised how host transcription relates to the microbial transcriptional response in inflammation. In colitis, increased abundance and transcription of diverse microbial gene families involved in responses to nutrient deprivation, antimicrobial peptide production and oxidative stress support an adaptation of multiple commensal genera to withstand a diverse set of environmental stressors in the inflammatory environment. These data are supported by a transcriptional signature of activated macrophages and granulocytes in the gut lumen during colitis, a signature that includes the transcription of the key antimicrobial genes S100a8 and S100a9 (calprotectin). Genes involved in microbial resistance to oxidative stress, including Dps/ferritin, Fe-dependent peroxidase and glutathione S-transferase were identified as changing to a greater extent at the level of transcription than would be predicted by DNA abundance changes, implicating a role for increased oxygen tension and/or host-derived reactive oxygen species in driving transcriptional changes in commensal microbes