bims-bac4me 2023-06-11 papers

bims-bac4me

Biomed News

on Microbiome and trained immunity

Issue of 2023–06–11
24 papers selected by
Chun-Chi Chang, University Hospital Zurich

Heterogeneous regulation of Staphylococcus aureus by different Staphylococcus epidermidis agr types in atopic dermatitis.
Functional diversity of staphylococcal surface proteins at the host-microbe interface.
Immunometabolic changes of β-glucan-trained immunity induction and inhibition on neonatal calf immune innate cells.
A high-throughput cytotoxicity screening platform reveals agr-independent mutations in bacteraemia-associated Staphylococcus aureus that promote intracellular persistence.
Plasmacytoid dendritic cells: A dendritic cell in disguise.
Monocyte regulation by gut microbial signals.
Trained immunity in the pathogenesis of vitiligo.
Intestinal colonization regulates systemic anti-commensal immune sensitivity and hyperreactivity.
Extracellular vesicles from human plasma dampen inflammation and promote tissue repair functions in macrophages.
STAT1 is required to establish but not maintain interferon-γ-induced transcriptional memory.
Mutual interaction of microbiota and host immunity during health and diseases.
TNF licenses macrophages to undergo rapid caspase-1, -11, and -8-mediated cell death that restricts Legionella pneumophila infection.
Probiotics and their beneficial health effects.
Speaking the host language: how Salmonella effector proteins manipulate the host.
Acute and chronic lung inflammation drives changes in epithelial glycans.
Persistence of obligate intracellular pathogens: alternative strategies to overcome host-specific stresses.
Evolutionary implications of host genetic control for engineering beneficial microbiomes.
Editorial: Recent approaches in exploring metabolic inflammation.
Editorial: Ecology, environment, and human microbiome interaction with infection.
Colonization and Dissemination of Klebsiella pneumoniae is Dependent on Dietary Carbohydrates.
Meta-omics profiling of the gut-lung axis illuminates metabolic networks and host-microbial interactions associated with elevated lung elastance in a murine model of obese allergic asthma.
It's all relative: analyzing microbiome compositions, its significance, pathogenesis and microbiota derived biofilms: Challenges and opportunities for disease intervention.
Comparison of culture media reveals that non-essential amino acids strongly affect the phenotype of human monocyte-derived macrophages.
Control of enhancer and promoter activation in the type I interferon response by the histone demethylase Kdm4d/JMJD2d.

J Invest Dermatol. 2023 Jun 02. pii: S0022-202X(23)02138-3. [Epub ahead of print]

Heterogeneous regulation of Staphylococcus aureus by different Staphylococcus epidermidis agr types in atopic dermatitis.

Yuan Zhou, Xiaoqiang Xu, Yang Liu, Ao Wang, Yang Luo, Xiaochun Liu, Xiaokai Wang, Wei Li, Xu Yao.

  The skin commensal Staphylococcus epidermidis exhibits a protective role in skin inflammation; however, the exact functions of S. epidermidis and their mechanisms in atopic dermatitis (AD) are not fully understood. Here, whole-genome sequencing was conducted on strains of S. epidermidis isolated from pediatric patients with AD and revealed significant strain-level heterogeneity in functional genes. Specific sequence analysis of S. epidermidis identified four types of accessory gene regulator (agr) according to locus variations in the agr operon, which was consistent with the metagenomic data of the contextual microbiota. The number of S. epidermidis agr type I was slightly decreased among AD isolates, while agr type IV was hardly detected in AD isolates. Functional experiments demonstrated that strains of S. epidermidis agr type I and IV, but not type II and III, inhibited the expression of S. aureus agr-mediated virulence factors in vitro, and suppressed S. aureus epidermal colonization and attenuated skin inflammation in a mouse model. The delineation of genome signatures of S. epidermidis at the strain level in AD and the quorum-sensing interference between S. epidermidis agr type IV and S. aureus provide a foundation for the modulation of the skin microbiota and the treatment of AD.

Keywords:  Atopic dermatitis; Staphylococcus aureus; Staphylococcus epidermidis; accessory gene regulator; quorum sensing; skin microbiome; whole-genome sequencing

DOI:  https://doi.org/10.1016/j.jid.2023.05.014
Front Microbiol. 2023 ;14 1196957

Functional diversity of staphylococcal surface proteins at the host-microbe interface.

Nicoletta Schwermann, Volker Winstel.

  Surface proteins of Gram-positive pathogens are key determinants of virulence that substantially shape host-microbe interactions. Specifically, these proteins mediate host invasion and pathogen transmission, drive the acquisition of heme-iron from hemoproteins, and subvert innate and adaptive immune cell responses to push bacterial survival and pathogenesis in a hostile environment. Herein, we briefly review and highlight the multi-facetted roles of cell wall-anchored proteins of multidrug-resistant Staphylococcus aureus, a common etiological agent of purulent skin and soft tissue infections as well as severe systemic diseases in humans. In particular, we focus on the functional diversity of staphylococcal surface proteins and discuss their impact on the variety of clinical manifestations of S. aureus infections. We also describe mechanistic and underlying principles of staphylococcal surface protein-mediated immune evasion and coupled strategies S. aureus utilizes to paralyze patrolling neutrophils, macrophages, and other immune cells. Ultimately, we provide a systematic overview of novel therapeutic concepts and anti-infective strategies that aim at neutralizing S. aureus surface proteins or sortases, the molecular catalysts of protein anchoring in Gram-positive bacteria.

Keywords:  Staphylococcus aureus; abscess; sortase A; surface proteins; vaccine

DOI:  https://doi.org/10.3389/fmicb.2023.1196957
Mol Immunol. 2023 Jun 02. pii: S0161-5890(23)00111-6. [Epub ahead of print]159 58-68

Immunometabolic changes of β-glucan-trained immunity induction and inhibition on neonatal calf immune innate cells.

Miriam Angulo, Carlos Angulo.

  The growing antibiotic resistance and low-efficient vaccines make searching for alternatives a need to fight infectious diseases in newborn calves. Thus, trained immunity could be used as a tool to optimize immune response against a wide range of pathogens. Although β-glucans have shown to induce trained immunity, it has not been demonstrated in bovines yet. Uncontrolled trained immunity activation can generate chronic inflammation in mice and humans, and inhibiting it might reduce excessive immune activation. The aim of this study is to demonstrate that in vitro β-glucan training induces metabolic changes in calf monocytes, characterized by an increase in lactate production and glucose consumption upon restimulation with lipopolysaccharide. These metabolic shifts can be abolished by co-incubation with MCC950, a trained immunity inhibitor. Moreover, the dose-response relationship of β-glucan on the viability of calf monocytes was demonstrated. In newborn calves, in vivo β-glucan oral administration also induced a trained phenotype in innate immune cells, leading to immunometabolic changes, upon ex vivo challenge with E.coli. β-glucan-induced trained immunity improved phagocytosis, nitric oxide production, myeloperoxidase activity, and TNF-α gene expression through up-regulation genes of the TLR2/NF-κB pathway. Furthermore, β-glucan oral doses enhanced consumption and production of glycolysis metabolites (glucose and lactate, respectively), as well as up-regulated expression of mTOR and HIF1-α mRNA. Therefore, the results suggest that β-glucan immune training may confer calf protection from a secondary bacterial challenge, and trained phenotype induced by β-glucan can be inhibited.

Keywords:  Calves; Innate immune memory; Metabolic reprogramming

DOI:  https://doi.org/10.1016/j.molimm.2023.05.008
Elife. 2023 Jun 08. pii: e84778. [Epub ahead of print]12

A high-throughput cytotoxicity screening platform reveals agr-independent mutations in bacteraemia-associated Staphylococcus aureus that promote intracellular persistence.

Abderrahman Hachani, Stefano G Giulieri, Romain Guérillot, Calum J Walsh, Marion Herisse, Ye Mon Soe, Sarah L Baines, David R Thomas, Shane Doris Cheung, Ashleigh S Hayes, Ellie Cho, Hayley J Newton, Sacha Pidot, Ruth C Massey, Benjamin P Howden, Timothy P Stinear.

  Staphylococcus aureus infections are associated with high mortality rates. Often considered an extracellular pathogen, S. aureus can persist and replicate within host cells, evading immune responses, and causing host cell death. Classical methods for assessing S. aureus cytotoxicity are limited by testing culture supernatants and endpoint measurements that do not capture the phenotypic diversity of intracellular bacteria. Using a well-established epithelial cell line model, we have developed a platform called InToxSa (intracellular toxicity of S. aureus) to quantify intracellular cytotoxic S. aureus phenotypes. Studying a panel of 387 S. aureus bacteraemia isolates, and combined with comparative, statistical, and functional genomics, our platform identified mutations in S. aureus clinical isolates that reduced bacterial cytotoxicity and promoted intracellular persistence. In addition to numerous convergent mutations in the Agr quorum sensing system, our approach detected mutations in other loci that also impacted cytotoxicity and intracellular persistence. We discovered that clinical mutations in ausA, encoding the aureusimine non-ribosomal peptide synthetase, reduced S. aureus cytotoxicity, and increased intracellular persistence. InToxSa is a versatile, high-throughput cell-based phenomics platform and we showcase its utility by identifying clinically relevant S. aureus pathoadaptive mutations that promote intracellular residency.

Keywords:  GWAS; Staphylococcus aureus; bacterial population genomics; cytotoxicity; evolutionary convergence analysis; genetics; genomics; infectious disease; intracellular; microbiology

DOI:  https://doi.org/10.7554/eLife.84778
Mol Immunol. 2023 Jun 01. pii: S0161-5890(23)00102-5. [Epub ahead of print]159 38-45

Plasmacytoid dendritic cells: A dendritic cell in disguise.

Rebeca Arroyo Hornero, Juliana Idoyaga.

  Since their discovery, the identity of plasmacytoid dendritic cells (pDCs) has been at the center of a continuous dispute in the field, and their classification as dendritic cells (DCs) has been recently re-challenged. pDCs are different enough from the rest of the DC family members to be considered a lineage of cells on their own. Unlike the exclusive myeloid ontogeny of cDCs, pDCs may have dual origin developing from myeloid and lymphoid progenitors. Moreover, pDCs have the unique ability to quickly secrete abundant levels of type I interferon (IFN-I) in response to viral infections. In addition, pDCs undergo a differentiation process after pathogen recognition that allows them to activate T cells, a feature that has been shown to be independent of presumed contaminating cells. Here, we aim to provide an overview of the historic and current understanding of pDCs and argue that their classification as either lymphoid or myeloid may be an oversimplification. Instead, we propose that the capacity of pDCs to link the innate and adaptive immune response by directly sensing pathogens and activating adaptive immune responses justify their inclusion within the DC network.

Keywords:  Antigen presentation; Plasmacytoid dendritic cells; Transitional dendritic cells; Type I interferon

DOI:  https://doi.org/10.1016/j.molimm.2023.05.007
Trends Microbiol. 2023 Jun 02. pii: S0966-842X(23)00159-2. [Epub ahead of print]

Monocyte regulation by gut microbial signals.

Panayota Kolypetri, Howard L Weiner.

  Monocytes are innate immune cells that sense environmental changes and participate in the immunoregulation of autoimmune, neurologic, cardiovascular, and metabolic diseases as well as cancer. Recent studies have suggested that the gut microbiome shapes the biology of monocytes via microbial signals at extraintestinal sites. Interestingly, in chronic diseases, communication between microbial signals and monocytes can either promote or inhibit disease activity, suggesting that some of these pathways can be harnessed for clinical therapies. In this review, we discuss the newer concepts of regulation of monocyte homeostasis and function by gut microbial signals during steady state and inflammation. We also highlight the therapeutic potential of microbial signal-based approaches for modulation in the context of various diseases.

Keywords:  gut microbiome; microbial signals; monocytes

DOI:  https://doi.org/10.1016/j.tim.2023.05.006
Pigment Cell Melanoma Res. 2023 Jun 09.

Trained immunity in the pathogenesis of vitiligo.

Nicoline F Post, Greta Ginski, Rens Peters, Nathalie O P Van Uden, Marcel W Bekkenk, Albert Wolkerstorfer, Mihai G Netea, Rosalie M Luiten.

  Vitiligo is caused by an autoimmune reaction against melanocytes leading to melanocyte loss. The cause of vitiligo is an interaction between genetic susceptibility and environmental factors. Both the adaptive immune system-through cytotoxic CD8+ T cells and melanocyte specific antibodies-and the innate immune system are involved in these immune processes in vitiligo. While recent data stressed the importance of innate immunity in vitiligo, the question remains why vitiligo patients' immune response becomes overly activated. Could a long-term increase in innate memory function, described as trained immunity after vaccination and in other inflammatory diseases, play a role as an enhancer and continuous trigger in the pathogenesis of vitiligo? After exposure to certain stimuli, innate immune system is able to show an enhanced immunological response to a secondary trigger, indicating a memory function of the innate immune system, a concept termed trained immunity. Trained immunity is regulated by epigenetic reprogramming, including histone chemical modifications and changes in chromatin accessibility that cause sustained changes in the transcription of specific genes. In responses to an infection, trained immunity is beneficial. However, there are indications of a pathogenic role of trained immunity in inflammatory and autoimmune diseases, with monocytes presenting features of a trained phenotype, resulting in increased cytokine production, altered cell metabolism through mTOR signaling, and epigenetic modifications. This hypothesis paper focusses on vitiligo studies that have shown these indications, suggesting the involvement of trained immunity in vitiligo. Future studies focusing on metabolic and epigenetic changes in innate immune cell populations in vitiligo could help in elucidating the potential role of trained immunity in vitiligo pathogenesis.

Keywords:  innate immunity; pathogenesis; trained immunity; vitiligo

DOI:  https://doi.org/10.1111/pcmr.13101
Front Immunol. 2023 ;14 1030395

Intestinal colonization regulates systemic anti-commensal immune sensitivity and hyperreactivity.

Regula Burkhard, Mia Koegler, Kirsty Brown, Kirsten Wilson, Lukas F Mager, Amanda Z Zucoloto, Carolyn Thomson, Roopa Hebbandi Nanjundappa, Isla Skalosky, Shokouh Ahmadi, Braedon McDonald, Markus B Geuking.

  Healthy host-microbial mutualism with our intestinal microbiota relies to a large degree on compartmentalization and careful regulation of adaptive mucosal and systemic anti-microbial immune responses. However, commensal intestinal bacteria are never exclusively or permanently restricted to the intestinal lumen and regularly reach the systemic circulation. This results in various degrees of commensal bacteremia that needs to be appropriately dealt with by the systemic immune system. While most intestinal commensal bacteria, except for pathobionts or opportunistic pathogen, have evolved to be non-pathogenic, this does not mean that they are non-immunogenic. Mucosal immune adaptation is carefully controlled and regulated to avoid an inflammatory response, but the systemic immune system usually responds differently and more vigorously to systemic bacteremia. Here we show that germ-free mice have increased systemic immune sensitivity and display anti-commensal hyperreactivity in response to the addition of a single defined T helper cell epitope to the outer membrane porin C (OmpC) of a commensal Escherichia coli strain demonstrated by increased E. coli-specific T cell-dependent IgG responses following systemic priming. This increased systemic immune sensitivity was not observed in mice colonized with a defined microbiota at birth indicating that intestinal commensal colonization also regulates systemic, and not only mucosal, anti-commensal responses. The observed increased immunogenicity of the E. coli strain with the modified OmpC protein was not due to a loss of function and associated metabolic changes as a control E. coli strain without OmpC did not display increased immunogenicity.

Keywords:  commensal E. coli; immunogenicity; immunoglobulins; metabolism; microbiota

DOI:  https://doi.org/10.3389/fimmu.2023.1030395
J Extracell Vesicles. 2023 Jun;12(6): e12331

Extracellular vesicles from human plasma dampen inflammation and promote tissue repair functions in macrophages.

Alan M Adamczyk, María Luz Leicaj, Martina Paula Fabiano, Gonzalo Cabrerizo, Nadia Bannoud, Diego O Croci, Kenneth W Witwer, Federico Remes Lenicov, Matías Ostrowski, Paula Soledad Pérez.

  Although inflammation is a vital defence response to infection, if left uncontrolled, it can lead to pathology. Macrophages are critical players both in driving the inflammatory response and in the subsequent events required for restoring tissue homeostasis. Extracellular vesicles (EVs) are membrane-enclosed structures released by cells that mediate intercellular communication and are present in all biological fluids, including blood. Herein, we show that extracellular vesicles from plasma (pEVs) play a relevant role in the control of inflammation by counteracting PAMP-induced macrophage activation. Indeed, pEV-treatment of macrophages simultaneously with or prior to PAMP exposure reduced the secretion of pro-inflammatory IL-6 and TNF-α and increased IL-10 response. This anti-inflammatory activity was associated with the promotion of tissue-repair functions in macrophages, characterized by augmented efferocytosis and pro-angiogenic capacity, and increased expression of VEGFa, CD300e, RGS2 and CD93, genes involved in cell growth and tissue remodelling. We also show that simultaneous stimulation of macrophages with a PAMP and pEVs promoted COX2 expression and CREB phosphorylation as well as the accumulation of higher concentrations of PGE2 in cell culture supernatants. Remarkably, the anti-inflammatory activity of pEVs was abolished if cells were treated with a pharmacological inhibitor of COX2, indicating that pEV-mediated induction of COX2 is critical for the pEV-mediated inhibition of inflammation. Finally, we show that pEVs added to monocytes prior to their M-CSF-induced differentiation to macrophages increased efferocytosis and diminished pro-inflammatory cytokine responses to PAMP stimulation. In conclusion, our results suggest that pEVs are endogenous homeostatic modulators of macrophages, activating the PGE2/CREB pathway, decreasing the production of inflammatory cytokines and promoting tissue repair functions.

Keywords:  CREB; PGE2; exosomes; extracellular vesicles; human plasma; infection; inflammation; macrophages; resolution; tissue homeostasis; wound-healing

DOI:  https://doi.org/10.1002/jev2.12331
EMBO J. 2023 Jun 05. e112259

STAT1 is required to establish but not maintain interferon-γ-induced transcriptional memory.

Sahar Sh Tehrani, Pawel Mikulski, Izma Abdul-Zani, João F Mata, Wojciech Siwek, Lars Et Jansen.

  Exposure of human cells to interferon-γ (IFNγ) results in a mitotically heritable yet reversible state called long-term transcriptional memory. We previously identified the clustered GBP genes as strongly primed by IFNγ. Here, we discovered that in primed cells, both interferon-responsive transcription factors STAT1 and IRF1 target chromatin with accelerated kinetics upon re-exposure to IFNγ, specifically at promotors of primed genes. Priming does not alter the degree of IFNγ-induced STAT1 activation or nuclear import, indicating that memory does not alter upstream JAK-STAT signaling. We found STAT1 to be critical to establish transcriptional memory but in a manner that is independent of mere transcription activation. Interestingly, while Serine 727 phosphorylation of STAT1 was maintained during the primed state, STAT1 is not required for the heritability of GBP gene memory. Our results suggest that the memory of interferon exposure constitutes a STAT1-mediated, heritable state that is established during priming. This renders GBP genes poised for subsequent STAT1 and IRF1 binding and accelerated gene activation upon a secondary interferon exposure.

Keywords:  GBPs; IRF1; STAT1; epigenetic memory; epigenetics; trained immunity

DOI:  https://doi.org/10.15252/embj.2022112259
Biophys Rep. 2021 Aug 31. 7(4): 326-340

Mutual interaction of microbiota and host immunity during health and diseases.

Di Wu, Yinlian Zhang, Suwei Dong, Chao Zhong.

  Microbiota-host interaction has attracted more and more attentions in recent years. The association between microbiota and host health is largely attributed to its influence on host immune system. Microbial-derived antigens and metabolites play a critical role in shaping the host immune system, including regulating its development, activation, and function. However, during various diseases the microbiota-host communication is frequently found to be disordered. In particular, gut microbiota dysbiosis associated with or led to the occurrence and progression of infectious diseases, autoimmune diseases, metabolic diseases, and neurological diseases. Pathogenic microbes and their metabolites disturb the protective function of immune system, and lead to disordered immune responses that usually correlate with disease exacerbation. In the other hand, the immune system also regulates microbiota composition to keep host homeostasis. Here, we will discuss the current advances of our knowledge about the interactions between microbiota and host immune system during health and diseases.

Keywords:  Composition of microbiota; Host health and diseases; Immune system; Microbial-derived antigens and metabolites; Microbiota

DOI:  https://doi.org/10.52601/bpr.2021.200045
PLoS Pathog. 2023 Jun 06. 19(6): e1010767

TNF licenses macrophages to undergo rapid caspase-1, -11, and -8-mediated cell death that restricts Legionella pneumophila infection.

Tzvi Y Pollock, Víctor R Vázquez Marrero, Igor E Brodsky, Sunny Shin.

The inflammatory cytokine tumor necrosis factor (TNF) is necessary for host defense against many intracellular pathogens, including Legionella pneumophila. Legionella causes the severe pneumonia Legionnaires' disease and predominantly affects individuals with a suppressed immune system, including those receiving therapeutic TNF blockade to treat autoinflammatory disorders. TNF induces pro-inflammatory gene expression, cellular proliferation, and survival signals in certain contexts, but can also trigger programmed cell death in others. It remains unclear, however, which of the pleiotropic functions of TNF mediate control of intracellular bacterial pathogens like Legionella. In this study, we demonstrate that TNF signaling licenses macrophages to die rapidly in response to Legionella infection. We find that TNF-licensed cells undergo rapid gasdermin-dependent, pyroptotic death downstream of inflammasome activation. We also find that TNF signaling upregulates components of the inflammasome response, and that the caspase-11-mediated non-canonical inflammasome is the first inflammasome to be activated, with caspase-1 and caspase-8 mediating delayed pyroptotic death. We find that all three caspases are collectively required for optimal TNF-mediated restriction of bacterial replication in macrophages. Furthermore, caspase-8 is required for control of pulmonary Legionella infection. These findings reveal a TNF-dependent mechanism in macrophages for activating rapid cell death that is collectively mediated by caspases-1, -8, and -11 and subsequent restriction of Legionella infection.

DOI: https://doi.org/10.1371/journal.ppat.1010767
Mini Rev Med Chem. 2023 Jun 08.

Probiotics and their beneficial health effects.

Sumera Zaib, Aqsa Hayat, Imtiaz Khan.

  Probiotics are living microorganisms that are present in cultured milk and fermented food. Fermented foods are a rich source for the isolation of probiotics. They are known as good bacteria. They have various beneficial effects on human health including antihypertensive effects, anti-hypercholesterolemic effects, prevention of bowel disease, and improving the immune system. Microorganisms including bacteria, yeast, and mold are used as probiotics but the major microorganisms that are used as probiotics are bacteria from the genus Lactobacillus, Lactococcus, Streptococcus, and Bifidobacterium. Probiotics are beneficial in the prevention of harmful effects. Recently, the use of probiotics for the treatment of various oral and skin diseases has also gained significant attention. Clinical studies indicate that the usage of probiotics can alter gut microbiota composition and provoke immune modulation in a host. Due to their various health benefits, probiotics are attaining more interest as a substitute for antibiotics or anti-inflammatory drugs leading to the growth of the probiotic market.

Keywords:  Cardiovascular; Eczema; Immune modulation; Irritable bowel syndrome.; Probiotics

DOI:  https://doi.org/10.2174/1389557523666230608163823
Microbiology (Reading). 2023 06;169(6):

Speaking the host language: how Salmonella effector proteins manipulate the host.

Timesh D Pillay, Sahampath U Hettiarachchi, Jiyao Gan, Ines Diaz-Del-Olmo, Xiu-Jun Yu, Janina H Muench, Teresa L M Thurston, Jaclyn S Pearson.

  Salmonella injects over 40 virulence factors, termed effectors, into host cells to subvert diverse host cellular processes. Of these 40 Salmonella effectors, at least 25 have been described as mediating eukaryotic-like, biochemical post-translational modifications (PTMs) of host proteins, altering the outcome of infection. The downstream changes mediated by an effector's enzymatic activity range from highly specific to multifunctional, and altogether their combined action impacts the function of an impressive array of host cellular processes, including signal transduction, membrane trafficking, and both innate and adaptive immune responses. Salmonella and related Gram-negative pathogens have been a rich resource for the discovery of unique enzymatic activities, expanding our understanding of host signalling networks, bacterial pathogenesis as well as basic biochemistry. In this review, we provide an up-to-date assessment of host manipulation mediated by the Salmonella type III secretion system injectosome, exploring the cellular effects of diverse effector activities with a particular focus on PTMs and the implications for infection outcomes. We also highlight activities and functions of numerous effectors that remain poorly characterized.

Keywords:  Salmonella pathogenesis; biochemical mechanism; intracellular pathogen; post-translational modification; type III effector protein

DOI:  https://doi.org/10.1099/mic.0.001342
Front Immunol. 2023 ;14 1167908

Acute and chronic lung inflammation drives changes in epithelial glycans.

Carlos A Alvarez, Emily Qian, Leandre M Glendenning, Kalob M Reynero, Emily N Kukan, Brian A Cobb.

   Introduction: Asthma is the most common chronic inflammatory disease and it is characterized by leukocyte infiltration and tissue remodeling, with the latter generally referring to collagen deposition and epithelial hyperplasia. Changes in hyaluronin production have also been demonstrated, while mutations in fucosyltransferases reportedly limit asthmatic inflammation.
Methods: Given the importance of glycans in cellular communication and to better characterize tissue glycosylation changes associated with asthma, we performed a comparative glycan analysis of normal and inflamed lungs from a selection of murine asthma models.
Results: We found that among other changes, the most consistent was an increase in fucose-α1,3-N-acetylglucosamine (Fuc-α1,3-GlcNAc) and fucose-α1,2-galactose (Fuc-α1,2-Gal) motifs. Increases in terminal galactose and N-glycan branching were also seen in some cases, whereas no overall change in O-GalNAc glycans was observed. Increased Muc5AC was found in acute but not chronic models, and only the more human-like triple antigen model yielded increased sulfated galactose motifs. We also found that human A549 airway epithelial cells stimulated in culture showed similar increases in Fuc-α1,2-Gal, terminal galactose (Gal), and sulfated Gal, and this matched transcriptional upregulation of the α1,2-fucosyltransferase Fut2 and the α1,3-fucosyltransferases Fut4 and Fut7.
Conclusions: These data suggest that airway epithelial cells directly respond to allergens by increasing glycan fucosylation, a known modification important for the recruitment of eosinophils and neutrophils.

Keywords:  asthma; epithelium; glycobiology; inflammation; lung; mouse

DOI:  https://doi.org/10.3389/fimmu.2023.1167908
Front Cell Infect Microbiol. 2023 ;13 1185571

Persistence of obligate intracellular pathogens: alternative strategies to overcome host-specific stresses.

Camille M Riffaud, Elizabeth A Rucks, Scot P Ouellette.

  In adapting to the intracellular niche, obligate intracellular bacteria usually undergo a reduction of genome size by eliminating genes not needed for intracellular survival. These losses can include, for example, genes involved in nutrient anabolic pathways or in stress response. Living inside a host cell offers a stable environment where intracellular bacteria can limit their exposure to extracellular effectors of the immune system and modulate or outright inhibit intracellular defense mechanisms. However, highlighting an area of vulnerability, these pathogens are dependent on the host cell for nutrients and are very sensitive to conditions that limit nutrient availability. Persistence is a common response shared by evolutionarily divergent bacteria to survive adverse conditions like nutrient deprivation. Development of persistence usually compromises successful antibiotic therapy of bacterial infections and is associated with chronic infections and long-term sequelae for the patients. During persistence, obligate intracellular pathogens are viable but not growing inside their host cell. They can survive for a long period of time such that, when the inducing stress is removed, reactivation of their growth cycles resumes. Given their reduced coding capacity, intracellular bacteria have adapted different response mechanisms. This review gives an overview of the strategies used by the obligate intracellular bacteria, where known, which, unlike model organisms such as E. coli, often lack toxin-antitoxin systems and the stringent response that have been linked to a persister phenotype and amino acid starvation states, respectively.

Keywords:  Chlamydia; Coxiella; interferon-gamma; iron starvation; obligate intracellular bacteria; persistence; stringent response; tryptophan starvation

DOI:  https://doi.org/10.3389/fcimb.2023.1185571
Curr Opin Syst Biol. 2023 Jun;34 None

Evolutionary implications of host genetic control for engineering beneficial microbiomes.

Lucas P Henry, Joy Bergelson.

Engineering new functions in the microbiome requires understanding how host genetic control and microbe-microbe interactions shape the microbiome. One key genetic mechanism underlying host control is the immune system. The immune system can promote stability in the composition of the microbiome by reshaping the ecological dynamics of its members, but the degree of stability will depend on the interplay between ecological context, immune system development, and higher-order microbe-microbe interactions. The eco-evolutionary interplay affecting composition and stability should inform the strategies used to engineer new functions in the microbiome. We conclude with recent methodological developments that provide an important path forward for both engineering new functionality in the microbiome and broadly understanding how ecological interactions shape evolutionary processes in complex biological systems.

DOI: https://doi.org/10.1016/j.coisb.2023.100455
Curr Opin Clin Nutr Metab Care. 2023 Jul 01. 26(4): 307-308

Editorial: Recent approaches in exploring metabolic inflammation.

Anastasia Z Kalea, Dorothy Klimis-Zacas.

DOI: https://doi.org/10.1097/MCO.0000000000000941
Front Public Health. 2023 ;11 1217927

Editorial: Ecology, environment, and human microbiome interaction with infection.

Yukiko Koizumi, Fumito Maruyama.



Keywords:  One Health; biotic-abiotic interaction with infection pathobiont; dysbiosis; eco epidemiology; human microbiome

DOI:  https://doi.org/10.3389/fpubh.2023.1217927
bioRxiv. 2023 May 25. pii: 2023.05.25.542283. [Epub ahead of print]

Colonization and Dissemination of Klebsiella pneumoniae is Dependent on Dietary Carbohydrates.

Aaron L Hecht, Lisa C Harling, Elliot S Friedman, Ceylan Tanes, Junhee Lee, Jenni Firrman, Vincent Tu, LinShu Liu, Kyle Bittinger, Mark Goulian, Gary D Wu.

Dysbiosis of the gut microbiota is increasingly appreciated as both a consequence and precipitant of human disease. The outgrowth of the bacterial family Enterobacteriaceae is a common feature of dysbiosis, including the human pathogen Klebsiella pneumoniae . Dietary interventions have proven efficacious in the resolution of dysbiosis, though the specific dietary components involved remain poorly defined. Based on a previous human diet study, we hypothesized that dietary nutrients serve as a key resource for the growth of bacteria found in dysbiosis. Through human sample testing, and ex-vivo , and in vivo modeling, we find that nitrogen is not a limiting resource for the growth of Enterobacteriaceae in the gut, contrary to previous studies. Instead, we identify dietary simple carbohydrates as critical in colonization of K. pneumoniae . We additionally find that dietary fiber is necessary for colonization resistance against K. pneumoniae , mediated by recovery of the commensal microbiota, and protecting the host against dissemination from the gut microbiota during colitis. Targeted dietary therapies based on these findings may offer a therapeutic strategy in susceptible patients with dysbiosis.

DOI: https://doi.org/10.1101/2023.05.25.542283
Front Microbiomes. 2023 ;pii: 1153691. [Epub ahead of print]2

Meta-omics profiling of the gut-lung axis illuminates metabolic networks and host-microbial interactions associated with elevated lung elastance in a murine model of obese allergic asthma.

Victoria A Heinrich, Crystal Uvalle, Michelle L Manni, Kelvin Li, Steven J Mullett, Sri Ramya Donepudi, Jason Clader, Adam Fitch, Madeline Ellgass, Veronika Cechova, Shulin Qin, Fernando Holguin, Bruce A Freeman, Barbara A Methé, Alison Morris, Stacy L Gelhaus.

  Obesity and associated changes to the gut microbiome worsen airway inflammation and hyperresponsiveness in asthma. Obesogenic host-microbial metabolomes have altered production of metabolites that may influence lung function and inflammatory responses in asthma. To understand the interplay of the gut microbiome, metabolism, and host inflammation in obesity-associated asthma, we used a multi-omics approach to profile the gut-lung axis in the setting of allergic airway disease and diet-induced obesity. We evaluated an immunomodulator, nitro-oleic acid (NO2-OA), as a host- and microbial-targeted treatment intervention for obesity-associated allergic asthma. Allergic airway disease was induced using house dust mite and cholera toxin adjuvant in C57BL6/J mice with diet-induced obesity to model obesity-associated asthma. Lung function was measured by flexiVent following a week of NO2-OA treatment and allergen challenge. 16S rRNA gene (from DNA, taxa presence) and 16S rRNA (from RNA, taxa activity) sequencing, metabolomics, and host gene expression were paired with a Treatment-Measured-Response model as a data integration framework for identifying latent/hidden relationships with linear regression among variables identified from high-dimensional meta-omics datasets. Targeting both the host and gut microbiota, NO2-OA attenuated airway inflammation, improved lung elastance, and modified the gut microbiome. Meta-omics data integration and modeling determined that gut-associated inflammation, metabolites, and functionally active gut microbiota were linked to lung function outcomes. Using Treatment-Measured-Response modeling and meta-omics profiling of the gut-lung axis, we uncovered a previously hidden network of interactions between gut levels of amino acid metabolites involved in elastin and collagen synthesis, gut microbiota, NO2-OA, and lung elastance. Further targeted metabolomics analyses revealed that obese mice with allergic airway disease had higher levels of proline and hydroxyproline in the lungs. NO2-OA treatment reduced proline biosynthesis by downregulation of pyrroline-5-carboxylate reductase 1 (PYCR1) expression. These findings are relevant to human disease: adults with mild-moderate asthma and BMI ≥ 25 had higher plasma hydroxyproline levels. Our results suggest that changes to structural proteins in the lung airways and parenchyma may contribute to heightened lung elastance and serve as a potential therapeutic target for obese allergic asthma.

Keywords:  asthma; elastance; gut-lung axis; metabolomics; microbiome; multi-omics analyses; obesity; proline

DOI:  https://doi.org/10.3389/frmbi.2023.1153691
Arch Microbiol. 2023 Jun 06. 205(7): 257

It's all relative: analyzing microbiome compositions, its significance, pathogenesis and microbiota derived biofilms: Challenges and opportunities for disease intervention.

Sahar Zaidi, Khursheed Ali, Asad U Khan.

  Concept of microorganisms has largely been perceived from their pathogenic view point. Nevertheless, it is being gradually revisited in terms of its significance to human health and now appears to be the most dominant force that shapes the immune system of the human body and also determines an individual's predisposition to diseases. Human inhabits bacterial diversity (which is predominant among all microbial communities in human body) occupying 0.3% of body mass, known as microbiota. On birth, a part of microbiota that child obtains is essentially a mother's legacy. So, the review was initiated with this critical topic of microbiotal inheritance. Since, each body site has distinct physiological specifications; therefore, they contain discrete microbiome composition that has been separately discussed along with dysbiosis-induced pathologies originating in different body organs. Factors affecting microbiome composition and may cause dysbiosis like antibiotics, delivery, feeding method etc. as well as the strategies that immune system adopts to prevent dysbiosis have been highlighted. We also tried to bring into attention the topic of dysbiosis induced biofilms, that enables cohort to survive stresses, evolve, disseminate and infection resurgence that is still in dormancy. Eventually, we put spotlight on microbiome significance in medical therapeutics. We didn't merely confine article to gut microbiota, that is being studied more extensively. Numerous community forms at diverse body sites are inter-related, and being exposed to awfully variable perturbations appear to be challenging to evaluate perturbation risks holistically. All aspects have been elaborately discussed to achieve a global depiction of human microbiota in order to meet urgent necessity for protocol standardisation. Demonstrates that environmental challenges (antibiotic use, alterations in diet, stress, smoking etc.) might cause dysbiosis i.e. transition of healthy microbiome composition to the one in which pathogenic microorganisms become more abundant, and eventually results in an infected state.

Keywords:  Biofilm; Commensal; Microbiome; Microbiota; Microorganisms

DOI:  https://doi.org/10.1007/s00203-023-03589-7
Immunology. 2023 Jun 08.

Comparison of culture media reveals that non-essential amino acids strongly affect the phenotype of human monocyte-derived macrophages.

Kristian W Antonsen, Henriette N Friis, Boe S Sorensen, Anders Etzerodt, Søren K Moestrup, Holger J Møller.

  Macrophages are important innate immune cells with the ability to adapt their phenotype to environmental cues. Research on human macrophages often uses monocyte-derived macrophages cultured in vitro, but it is unclear if culture medium affects macrophage phenotype. The objective of this study was to determine the impact of culture medium composition on monocyte-derived macrophage phenotype. Monocyte-derived macrophages were generated in different formulations of culture media (RPMI 1640, DMEM, MEM, McCoy's 5a and IMDM). Viability, yield and cell size were monitored, and RT-qPCR, flow cytometry or ELISA was used to compare levels of phenotype markers (CD163, CD206, CD80, TNFα, IL-10, SIRPα, LILRB1 and Siglec-10). Yield, cell size, gene expression, membrane protein levels and release of soluble proteins were all affected by changes in culture medium composition. The most pronounced effects were observed after culture in DMEM, which lacks the non-essential amino acids asparagine, aspartic acid, glutamic acid and proline. Supplementation of DMEM with non-essential amino acids either fully or partly reversed most effects of DMEM on macrophage phenotype. The results suggest culture medium composition and amino acid availability affect the phenotype of human monocyte-derived macrophages cultured in vitro.

Keywords:  flow cytometry; human; macrophage

DOI:  https://doi.org/10.1111/imm.13670
Front Immunol. 2023 ;14 1146699

Control of enhancer and promoter activation in the type I interferon response by the histone demethylase Kdm4d/JMJD2d.

Rohit Chandwani, Terry C Fang, Scott Dewell, Alexander Tarakhovsky.

   Introduction: Transcriptional activation depends on the interplay of chromatin modifiers to establish a permissive epigenetic landscape. While histone 3 lysine 9 (H3K9) methylation has long been associated with gene repression, there is limited evidence to support a role for H3K9 demethylases in gene activation.
Methods: We leveraged knockdown and overexpression of JMJD2d / Kdm4d in mouse embryonic fibroblasts, coupled with extensive epigenomic analysesm to decipher the role of histone 3 lysine 9 demethylases in the innate immune response.
Results: Here we describe the H3K9 demethylase Kdm4d/JMJD2d as a positive regulator of type I interferon responses. In mouse embryonic fibroblasts (MEFs), depletion of JMJD2d attenuates the transcriptional response, conferring increased viral susceptibility, while overexpression of the demethylase results in more robust IFN activation. We find that the underlying mechanism of JMJD2d in type I interferon responses consists of an effect both on the transcription of enhancer RNAs (eRNAs) and on dynamic H3K9me2 at associated promoters. In support of these findings, we establish that JMJD2d is associated with enhancer regions throughout the genome prior to stimulation but is redistributed to inducible promoters in conjunction with transcriptional activation.
Discussion: Taken together, our data reveal JMJD2d as a chromatin modifier that connects enhancer transcription with promoter demethylation to modulate transcriptional responses.

Keywords:  IFN-β; JMJD2D; KDM4D; eRNA; enhancer chromatin; histone demethylation; innate immunity; type I interferon response

DOI:  https://doi.org/10.3389/fimmu.2023.1146699