Innate immune perturbations, accumulating DAMPs and inflammasome dysregulation: a ticking time bomb in ageing

Ageing has pronounced effects on the immune system, including on innate immune cells. Whilst most studies suggest that total numbers of different innate immune cell populations do not change dramatically during ageing, many of their functions such as phagocytosis, antigen presentation and inflammatory molecule secretion decline. In contrast, many endogenous damage-associated molecular patterns (DAMPs) accumulate during ageing. These include reactive oxygen species (ROS) released from damaged mitochondria, extracellular nucleotides like ATP, high mobility group box (HMGB) 1 protein, oxidized low density lipoprotein, amyloid-beta (Aβ), islet amyloid polypeptide and particulates like monosodium urate (MSU) crystals and cholesterol crystals. Some of these DAMPs trigger the activation of inflammasomes, cytosolic danger sensing signalling platforms that drive both the maturation of specific pro-inflammatory mediators such as IL-1β, as well as the initiation of pro-inflammatory pyroptotic cell death. Herein, we review the evidence that dysregulated inflammasome activation, via altered innate immune cell functions and elevated levels of DAMPs, contributes to the establishment of chronic, low-grade inflammation (characterized by elevated levels of IL-6 and C-reactive protein) and the development of age-related pathological processes

Identification and annotation of conserved promoters and macrophage-expressed genes in the pig genome.

BACKGROUND: The FANTOM5 consortium used Cap Analysis of Gene Expression (CAGE) tag sequencing to produce a comprehensive atlas of promoters and enhancers within the human and mouse genomes. We reasoned that the mapping of these regulatory elements to the pig genome could provide useful annotation and evidence to support assignment of orthology. RESULTS: For human transcription start sites (TSS) associated with annotated human-mouse orthologs, 17% mapped to the pig genome but not to the mouse, 10% mapped only to the mouse, and 55% mapped to both pig and mouse. Around 17% did not map to either species. The mapping percentages were lower where there was not clear orthology relationship, but in every case, mapping to pig was greater than to mouse, and the degree of homology was also greater. Combined mapping of mouse and human CAGE-defined promoters identified at least one putative conserved TSS for >16,000 protein-coding genes. About 54% of the predicted locations of regulatory elements in the pig genome were supported by CAGE and/or RNA-Seq analysis from pig macrophages. CONCLUSIONS: Comparative mapping of promoters and enhancers from humans and mice can provide useful preliminary annotation of other animal genomes. The data also confirm extensive gain and loss of regulatory elements between species, and the likelihood that pigs provide a better model than mice for human gene regulation and function

Interleukin-1β Maturation Triggers Its Relocation to the Plasma Membrane for Gasdermin-D-Dependent and -Independent Secretion

IL-1β requires processing by caspase-1 to generate the active, pro-inflammatory cytokine. Acute IL-1β secretion from inflammasome-activated macrophages requires caspase-1-dependent GSDMD cleavage, which also induces pyroptosis. Mechanisms of IL-1β secretion by pyroptotic and non-pyroptotic cells, and the precise functions of caspase-1 and GSDMD therein, are unresolved. Here, we show that, while efficient early secretion of endogenous IL-1β from primary non-pyroptotic myeloid cells in vitro requires GSDMD, later IL-1β release in vitro and in vivo proceeds independently of GSDMD. IL-1β maturation is sufficient for slow, caspase-1/GSDMD-independent secretion of ectopic IL-1β from resting, non-pyroptotic macrophages, but the speed of IL-1β release is boosted by inflammasome activation, via caspase-1 and GSDMD. IL-1β cleavage induces IL-1β enrichment at PIP2-enriched plasma membrane ruffles, and this is a prerequisite for IL-1β secretion and is mediated by a polybasic motif within the cytokine. We thus reveal a mechanism in which maturation-induced IL-1β trafficking facilitates its unconventional secretion

A gene expression atlas of the domestic pig

<p>Abstract</p> <p>Background</p> <p>This work describes the first genome-wide analysis of the transcriptional landscape of the pig. A new porcine Affymetrix expression array was designed in order to provide comprehensive coverage of the known pig transcriptome. The new array was used to generate a genome-wide expression atlas of pig tissues derived from 62 tissue/cell types. These data were subjected to network correlation analysis and clustering.</p> <p>Results</p> <p>The analysis presented here provides a detailed functional clustering of the pig transcriptome where transcripts are grouped according to their expression pattern, so one can infer the function of an uncharacterized gene from the company it keeps and the locations in which it is expressed. We describe the overall transcriptional signatures present in the tissue atlas, where possible assigning those signatures to specific cell populations or pathways. In particular, we discuss the expression signatures associated with the gastrointestinal tract, an organ that was sampled at 15 sites along its length and whose biology in the pig is similar to human. We identify sets of genes that define specialized cellular compartments and region-specific digestive functions. Finally, we performed a network analysis of the transcription factors expressed in the gastrointestinal tract and demonstrate how they sub-divide into functional groups that may control cellular gastrointestinal development.</p> <p>Conclusions</p> <p>As an important livestock animal with a physiology that is more similar than mouse to man, we provide a major new resource for understanding gene expression with respect to the known physiology of mammalian tissues and cells. The data and analyses are available on the websites <url>http://biogps.org and http://www.macrophages.com/pig-atlas</url>.</p

Structural and functional annotation of the porcine immunome

Background: The domestic pig is known as an excellent model for human immunology and the two species share many pathogens. Susceptibility to infectious disease is one of the major constraints on swine performance, yet the structure and function of genes comprising the pig immunome are not well-characterized. The completion of the pig genome provides the opportunity to annotate the pig immunome, and compare and contrast pig and human immune systems.[br/] Results: The Immune Response Annotation Group (IRAG) used computational curation and manual annotation of the swine genome assembly 10.2 (Sscrofa10.2) to refine the currently available automated annotation of 1,369 immunity-related genes through sequence-based comparison to genes in other species. Within these genes, we annotated 3,472 transcripts. Annotation provided evidence for gene expansions in several immune response families, and identified artiodactyl-specific expansions in the cathelicidin and type 1 Interferon families. We found gene duplications for 18 genes, including 13 immune response genes and five non-immune response genes discovered in the annotation process. Manual annotation provided evidence for many new alternative splice variants and 8 gene duplications. Over 1,100 transcripts without porcine sequence evidence were detected using cross-species annotation. We used a functional approach to discover and accurately annotate porcine immune response genes. A co-expression clustering analysis of transcriptomic data from selected experimental infections or immune stimulations of blood, macrophages or lymph nodes identified a large cluster of genes that exhibited a correlated positive response upon infection across multiple pathogens or immune stimuli. Interestingly, this gene cluster (cluster 4) is enriched for known general human immune response genes, yet contains many un-annotated porcine genes. A phylogenetic analysis of the encoded proteins of cluster 4 genes showed that 15% exhibited an accelerated evolution as compared to 4.1% across the entire genome.[br/] Conclusions: This extensive annotation dramatically extends the genome-based knowledge of the molecular genetics and structure of a major portion of the porcine immunome. Our complementary functional approach using co-expression during immune response has provided new putative immune response annotation for over 500 porcine genes. Our phylogenetic analysis of this core immunome cluster confirms rapid evolutionary change in this set of genes, and that, as in other species, such genes are important components of the pig’s adaptation to pathogen challenge over evolutionary time. These comprehensive and integrated analyses increase the value of the porcine genome sequence and provide important tools for global analyses and data-mining of the porcine immune response

Metal ions in macrophage antimicrobial pathways: emerging roles for zinc and copper

The immunomodulatory and antimicrobial properties of zinc and copper have long been appreciated. In addition, these metal ions are also essential for microbial growth and survival. This presents opportunities for the host to either harness their antimicrobial properties or limit their availability as defence strategies. Recent studies have shed some light on mechanisms by which copper and zinc regulation contribute to host defence, but there remain many unanswered questions at the cellular and molecular levels. Here we review the roles of these two metal ions in providing protection against infectious diseases in vivo, and in regulating innate immune responses. In particular, we focus on studies implicating zinc and copper in macrophage antimicrobial pathways, as well as the specific host genes encoding zinc transporters (SLC30A, SLC39A family members) and CTRs (copper transporters, ATP7 family members) that may contribute to pathogen control by these cells

Analyses of pig genomes provide insight into porcine demography and evolution

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model

Rôle de la voie Toll-Like Receptor 2 et de la phagocytose dans la production de cytokines par les cellules mononuclées phagocytaires en réponse à Staphylococcus aureus

Staphylococcus aureus est une bactérie à Gram positif responsable d'un nombre croissant de pathologies humaines. Notre étude a comme objectif d'étudier la production de cytokines par les cellules mononucléées phagocytaires (monocytes, macrophages péritonéaux et alvéolaires) en réponse à S. aureus. Nous avons confirmé que la présence de TLR2 n'était pas indispensable pour la reconnaissance de S. aureus par les macrophages péritonéaux. En revanche, l'activation du TLR2 et la phagocytose de la bactérie étaient requises simultanément pour les monocytes et les macrophages alvéolaires, afin d'obtenir une production optimale de cytokines. De plus, à l'aide d'inhibiteurs spécifiques, nous avons observé que p38 et la Pi3K avaient un rôle central dans ces deux voies d'activauon. Au contraire, Racl et ERK étaient important spécifiquement pour l'activation de la voie intracellulaire chez les macrophages péritonéaux ou alvéolaires. Nous avons cherché à identifier le récepteur intracellulaire permettant la détection de S. aureus après phagocytose. La transfection d'un dominant-négatif de NOD2 dans la lignée macrophagique RAW 264.7 inhibait fortement l'activation de NF-KB en réponse à S. aureus. Mais en utilisant des cellules primaires ne possédant pas NOD2, nous avons observé que l'absence de ce récepteur n'avait pas d'incidence sur la production de cytokines. Enfin, l'injection en intra-nasal d'une souche de S.aureus, n'a pas montré de différence entre les souris NOD2 déficientes et leurs congénères sauvages. Toutefois, les souris NOD2 déficientes semblaient se remettre plus rapidement de l'infection, que ce soit au niveau de la perte du poids que des lésions pulmonaires. En conclusion, nos travaux mettent en évidence une voie d'activauon des macrophages autre que le TLR2 et dépendante de la phagocytose. NOD2 ne semble pas jouer un rôle critique, lors de la réponse à S. aureus, que ce soit in vitro ou in vivo. Enfin, nous avons pu observer qu'au sein même de la population mononucléée phagocytaire, il existe de grandes différences quant au rôle de la phagocytose dans la réponse à S. aureus. Ceci souligne l'hétérogénéité de la réponse de ces phagocytes professionnels selon le compartiment dont ils proviennent.Staphylococcus aureus is a Gram positive bacteria leading to an increasing number of human pathologies. The goal of our work was to study the S. aureus-induced cytokine production by phagocytic mononuclear cells (i.e monocytes, peritoneal and alveolar macrophages). We confirmed that TLR2 was dispensable for peritoneal macrophage response to S. aureus. In contrast, TLR2 activation and phagocytosis were both required to obtain a full cytokine production in monocytes and alveolar macrophages. Furthermore, with specific inhibitors, we observed that p38 and Pi3K had a key role in both activation pathways. On the contrary, Racl and ERK were important for macrophages intracellular pathway. We then investigated which receptor was detecting S. aureus after phagocytosis. Transfection of a dominant-negative form of NOD2 in RAW 264.7 macrophagic cell line inhibited strongly NF-KB activation in response to S. aureus. However, using NOD2-deficient primary cells, we observed that the absence of NOD2 did not alter cytokine production. Finally, NOD2-/- animals responses were comparable to wild-type after intra-nasal injection of S. aureus. Nevertheless, NOD2-/- mice recovered faster than wild-type (weigh gain and pulmonary lesions). In conclusion, our work shows the existence of a TLR2-independant activation pathway that relies on phagocytosis. NOD2 does not play a critical role in S. aureus response, both in vivo and in vitro. Finally, we show that, in phagocytic mononuclear cells, there is a great discrepancy in the role of phagocytosis in the response to S. aureus. This work underlines the heterogeneity in the phagocytic cells response depending on the compartment they are derived from.PARIS5-BU Méd.Cochin (751142101) / SudocSudocFranceF