bims-bac4me Biomed News
on Microbiome and trained immunity
Issue of 2023‒08‒20
39 papers selected by
Chun-Chi Chang
University Hospital Zurich

  1. Zhonghua Wei Zhong Bing Ji Jiu Yi Xue. 2023 Aug;35(8): 889-892
      Respiratory microbiome is extensively involved in human life activities and affects lung health and disease states through metabolism and immune regulation. Based on 16S rRNA gene sequencing and other methods, it is obvious that the diversity and the changes in the structure of respiratory microbiome and the dominant proliferation of pathogens are strongly related to the occurrence, development and clinical prognosis of ventilator-associated pneumonia (VAP). The mechanism by which respiratory microbiota promotes the clearance of pathogens may include the following aspects: (1) pre-stimulating innate immune system to increase the number of immune effector cells; (2) regulating pattern recognition receptor (PRR) to moderately promote the production of cytokines; (3) inducing the differentiation of neutrophils into specific subtypes and increasing the expression of antimicrobial genes; (4) producing free fatty acids and organic compounds that are capable of positively modulating the immune system. In conclusion, intervention of microbiome is beneficial to VAP patients. Therefore, this review illustrates the changes of respiratory flora in VAP and its effect on host immunity. At the same time, based on the review of the adjuvant treatment of VAP with probiotics, we put forward the prospect of respiratory commensal bacteria as a new clinical probiotic, in order to deepen the clinical understanding of the role of respiratory flora in VAP, and then provide new ideas for the evaluation of treatment and prognosis.
  2. Cell Host Microbe. 2023 Aug 10. pii: S1931-3128(23)00303-7. [Epub ahead of print]
      The intestinal microbiota regulates immunity across organ systems. Which symbionts control systemic immunity, the mechanisms they use, and how they avoid widespread inflammatory damage are unclear. We uncover host tolerance and resistance mechanisms that allow Firmicutes from the human microbiota to control systemic immunity without inducing immunopathology. Intestinal processing releases Firmicute glycoconjugates that disseminate, resulting in release of cytokine IL-34 that stimulates macrophages and enhances defenses against pneumonia, sepsis, and meningitis. Despite systemic penetration of Firmicutes, immune homeostasis is maintained through feedback control whereby IL-34-mediated mTORC1 activation in macrophages clears polymeric glycoconjugates from peripheral tissues. Smaller glycoconjugates evading this clearance mechanism are tolerated through sequestration by albumin, which acts as an inflammatory buffer constraining their immunological impact. Without these resistance and tolerance mechanisms, Firmicutes drive catastrophic organ damage and cachexia via IL-1β. This reveals how Firmicutes are safely assimilated into systemic immunity to protect against infection without threatening host viability.
    Keywords:  infectious disease; microbiota; systemic immunity; tolerance
  3. Microbiology (Reading). 2023 08;169(8):
      In Gram-positive bacteria such as Staphylococcus aureus and the coagulase-negative staphylococci (CoNS), the accessory gene regulator (agr) is a highly conserved but polymorphic quorum-sensing system involved in colonization, virulence and biofilm development. Signalling via agr depends on the interaction of an autoinducing peptide (AIP) with AgrC, a transmembrane sensor kinase that, once phosphorylated activates the response regulator AgrA. This in turn autoinduces AIP biosynthesis and drives target gene expression directly via AgrA or via the post-transcriptional regulator, RNAIII. In this review we describe the molecular mechanisms underlying the agr-mediated generation of, and response to, AIPs and the molecular basis of AIP-dependent activation and inhibition of AgrC. How the environment impacts on agr functionality is considered and the consequences of agr dysfunction for infection explored. We also discuss the concept of AIP-driven competitive interference between S. aureus and the CoNS and its anti-infective potential.
    Keywords:  Staphylococcus aureus; agr; autoinducing peptides; inter-bacterial competition; quorum sensing; staphylococci
  4. Antimicrob Steward Healthc Epidemiol. 2023 ;3(1): e130
      Surgical site infections (SSIs) are important healthcare-associated infections, leading to increased morbidity and mortality, healthcare costs, and prolonged hospital stays. Staphylococcus aureus is an important and common microbial cause of SSI. Nasal carriage of S. aureus has been shown to be an important determinant for the development of SSI, and interventions aimed at eradicating preoperative nasal carriage are associated with a reduced risk of infection. Yet, it is not entirely clear how the nasally residing S. aureus causes SSI at distant body sites. In this commentary, we describe our view on how S. aureus can be transported from the nares to the incision site during surgery. In addition, we shed light on the implications of our view for infection prevention research.
  5. Curr Opin Infect Dis. 2023 Aug 18.
      PURPOSE OF REVIEW: The human gut harbors a diverse community of microorganisms known as the gut microbiota. Extensive research in recent years has shed light on the profound influence of the gut microbiome on human health and disease. This review aims to explore the role of the gut microbiome in various clinical conditions and highlight the emerging therapeutic potential of targeting the gut microbiota for disease management.RECENT FINDINGS: Knowledge of the influence of gut microbiota on human physiology led to the development of various therapeutic possibilities such as fecal microbiota transplant (FMT), phage therapy, prebiotics, and probiotics. Recently, the U.S. FDA approved two FMT products for the treatment of recurrent Clostridioides difficile infection with ongoing research for the treatment of various disease conditions.
    SUMMARY: Advancement in the knowledge of the association between gut microbiota and various disease processes has paved the way for novel therapeutics.
  6. Signal Transduct Target Ther. 2023 08 14. 8(1): 300
      As a family of cationic host defense peptides, defensins are mainly synthesized by Paneth cells, neutrophils, and epithelial cells, contributing to host defense. Their biological functions in innate immunity, as well as their structure and activity relationships, along with their mechanisms of action and therapeutic potential, have been of great interest in recent years. To highlight the key research into the role of defensins in human and animal health, we first describe their research history, structural features, evolution, and antimicrobial mechanisms. Next, we cover the role of defensins in immune homeostasis, chemotaxis, mucosal barrier function, gut microbiota regulation, intestinal development and regulation of cell death. Further, we discuss their clinical relevance and therapeutic potential in various diseases, including infectious disease, inflammatory bowel disease, diabetes and obesity, chronic inflammatory lung disease, periodontitis and cancer. Finally, we summarize the current knowledge regarding the nutrient-dependent regulation of defensins, including fatty acids, amino acids, microelements, plant extracts, and probiotics, while considering the clinical application of such regulation. Together, the review summarizes the various biological functions, mechanism of actions and potential clinical significance of defensins, along with the challenges in developing defensins-based therapy, thus providing crucial insights into their biology and potential clinical utility.
  7. J Allergy Clin Immunol. 2023 Aug 11. pii: S0091-6749(23)00985-5. [Epub ahead of print]
      Viral infections are the most common cause of upper respiratory infections; they frequently infect adults once or twice and children 6 to 8 times annually. In most cases, these infections are self-limiting and resolve. However, many patients with chronic rhinosinusitis (CRS) relay that their initiating event began with an upper respiratory infection that progressed in both symptom severity and duration. Viruses bind to sinonasal epithelia through specific receptors, thereby entering cells and replicating within them. Viral infections stimulate interferon-mediated innate immune responses. Recent studies suggest that viral infections may also induce type 2 immune responses and stimulate the aberrant production of cytokines that can result in loss of barrier function, which is a hallmark in CRS. The main purpose of this review will be to highlight common viruses and their associated binding receptors and highlight pathophysiologic mechanisms associated with alterations in mucociliary clearance, epithelial barrier function, and dysfunctional immune responses that might lead to a further understanding of the pathogenesis of CRS.
    Keywords:  Chronic rhinosinusitis; airway epithelium; barrier function; genetics; innate immunity; upper respiratory tract infection; virus
  8. Int Immunopharmacol. 2023 Aug 16. pii: S1567-5769(23)01044-5. [Epub ahead of print]123 110719
      Uniquely positioned as sentinel cells constantly exposed to the environment, pulmonary macrophages are vital for the maintenance of the lung lining. These cells are responsible for the clearance of xenobiotics, pathogen detection and clearance, and homeostatic functions such as surfactant recycling. Among the spectrum of phenotypes that may be expressed by macrophages in the lung, the pulmonary lipid-laden phenotype is less commonly studied in comparison to its circulatory counterpart, the atherosclerotic lesion-associated foam cell, or the acutely activated inflammatory macrophage. Herein, we propose that lipid-laden macrophage formation in the lung is governed by lipid acquisition, storage, metabolism, and export processes. The cellular balance of these four processes is critical to the maintenance of homeostasis and the prevention of aberrant signaling that may contribute to lung pathologies. This review aims to examine mechanisms and signaling pathways that are involved in lipid-laden macrophage formation and the potential consequences of this phenotype in the lung.
    Keywords:  Foam cell; Immunometabolism; Inflammation; Lipid; Lung; Macrophage
  9. Curr Opin Microbiol. 2023 Aug 14. pii: S1369-5274(23)00101-7. [Epub ahead of print]75 102364
      Multiple factors contribute to establishment of skin microbial communities in early life, with perturbations in these ecosystems impacting health. This review provides an update on methods used to profile the skin microbiome and how this is helping enhance our understanding of infant skin microbial communities, including factors that influence composition and disease risk. We also provide insights into new interventional studies and treatments in this area. However, it is apparent that there are still research bottlenecks that include overreliance on high-income countries for skin microbiome 'surveys', many studies still focus solely on the bacterial microbiota, and also technical issues related to the lower microbial biomass of skin sites. These points link to pertinent open-research questions, such as how the whole infant skin microbiome interacts and how microbial-associated functions shape infant skin health and immunity.
  10. J Infect Dis. 2023 Aug 18. pii: jiad339. [Epub ahead of print]
      Mastitis caused by antibiotic-resistant strains of Staphylococcus aureus (S. aureus) is a significant concern in the livestock industry due to the economic losses it incurs. Regulating immunometabolism has emerged as a promising approach for preventing bacterial inflammation. To investigate the possibility of alleviating inflammation caused by S. aureus infection by regulating host glycolysis, we subjected the murine mammary epithelial cell line (EpH4-Ev) to S. aureus challenge. Our study revealed that S. aureus can colonize EpH4-Ev cells and promote inflammation through HIF1α-driven glycolysis. Notably, the activation of HIF1α was found to be dependent on the production of reactive oxygen species (ROS). By inhibiting PFKFB3, a key regulator in the host glycolytic pathway, we successfully modulated HIF1α-triggered metabolic reprogramming by reducing ROS production in S. aureus-induced mastitis. Our findings suggest that there is a high potential for the development of novel anti-inflammatory therapies that safely inhibit the glycolytic rate-limiting enzyme PFKFB3.
    Keywords:   Staphylococcus aureus ; HIF1α; PFKFB3; glycolysis; mastitis
  11. Int Immunopharmacol. 2023 Aug 13. pii: S1567-5769(23)01118-9. [Epub ahead of print]123 110793
      β-defensin-1 (BD-1) is a rich source of disulfide bonds and antibacterial peptides that exhibit direct bactericidal function. The expression of BD-1 is primarily induced by external stimulation and is known to correlate with TLR-mediated inflammation, suggesting its association with innate immune responses. Equine β-defensin-1 (eBD-1) belongs to the BD-1 family. Our previous study demonstrated that eBD-1 enhances cytokine expression and promotes macrophage phagocytosis of S. aureus, although the underlying mechanism remains unknown. In this study, we utilized a PI-3K inhibitor (PKI-402) to treat eBD-1 -treated S. aureus-infected macrophages in vitro. Our results revealed that PKI-402 decreased the expression of eBD-1-promoted TNF-α, IL-6, CXCL10, CD40, RANTES, and p65 mRNA. To further investigate the relationship between eBD-1 and phagocytosis, we examined the expression of paxillin and FcγRIII (CD16 receptor) using western blot and immunofluorescence techniques. Our findings demonstrated that eBD-1 enhanced CD16 and paxillin expression in S. aureus -infected macrophages. Considering the correlation between paxillin expression and focal adhesion kinase (FAK), we transfected FAK siRNA into macrophages and evaluated paxillin expression using western blot analysis. Additionally, we quantified the number of S. aureus phagocytosed by macrophages. The results indicated a reduction in both paxillin expression and the number of S. aureus phagocytosed by macrophages upon FAK siRNA treatment. Our study showed the eBD-1 promotes cytokine mRNA expression in S. aureus-infected macrophages regulated by PI-3K-NF-κB pathway, and it increases macrophage phagocytosis of S. aureus associated with the FAK-paxillin signaling pathway.
    Keywords:  Equine β-defensin 1; Macrophage; Paxillin-FAK-PI3K pathway; S. aureus infection
  12. Nature. 2023 Aug 16.
      Disruption of the lung endothelial-epithelial cell barrier following respiratory virus infection causes cell and fluid accumulation in the air spaces and compromises vital gas exchange function1. Endothelial dysfunction can exacerbate tissue damage2,3, yet it is unclear whether the lung endothelium promotes host resistance against viral pathogens. Here we show that the environmental sensor aryl hydrocarbon receptor (AHR) is highly active in lung endothelial cells and protects against influenza-induced lung vascular leakage. Loss of AHR in endothelia exacerbates lung damage and promotes the infiltration of red blood cells and leukocytes into alveolar air spaces. Moreover, barrier protection is compromised and host susceptibility to secondary bacterial infections is increased when endothelial AHR is missing. AHR engages tissue-protective transcriptional networks in endothelia, including the vasoactive apelin-APJ peptide system4, to prevent a dysplastic and apoptotic response in airway epithelial cells. Finally, we show that protective AHR signalling in lung endothelial cells is dampened by the infection itself. Maintenance of protective AHR function requires a diet enriched in naturally occurring AHR ligands, which activate disease tolerance pathways in lung endothelia to prevent tissue damage. Our findings demonstrate the importance of endothelial function in lung barrier immunity. We identify a gut-lung axis that affects lung damage following encounters with viral pathogens, linking dietary composition and intake to host fitness and inter-individual variations in disease outcome.
  13. Front Immunol. 2023 ;14 1224591
      Dendritic cells and macrophages are integral parts of the innate immune system and gatekeepers against infection. The protozoan pathogen, Toxoplasma gondii, is known to hijack host immune cells and modulate their immune response, making it a compelling model to study host-pathogen interactions. Here we utilize single cell Dual RNA-seq to parse out heterogeneous transcription of mouse bone marrow-derived dendritic cells (BMDCs) infected with two distinct genotypes of T. gondii parasites, over multiple time points post infection. We show that the BMDCs elicit differential responses towards T. gondii infection and that the two parasite lineages distinctly manipulate subpopulations of infected BMDCs. Co-expression networks define host and parasite genes, with implications for modulation of host immunity. Integrative analysis validates previously established immune pathways and additionally, suggests novel candidate genes involved in host-pathogen interactions. Altogether, this study provides a comprehensive resource for characterizing host-pathogen interplay at high-resolution.
    Keywords:  BMDCs; Dual single-cell RNA-seq; Toxoplasma gondii; bone marrow-derived dendritic cells; host-pathogen interactions; immune modulation; scDual-Seq
  14. bioRxiv. 2023 Aug 02. pii: 2023.07.31.551394. [Epub ahead of print]
      Rationale: Macrophages play a central role in the onset and progression of vascular disease in pulmonary hypertension (PH) and cell-based immunotherapies aimed at treating vascular remodeling are lacking.Objective: To evaluate the effect of pulmonary administration of macrophages modified to have an anti-inflammatory/pro-resolving phenotype in attenuating early pulmonary inflammation and progression of experimentally induced PH.
    Methods: Mouse bone marrow derived macrophages (BMDMs) were polarized in vitro to a regulatory (M2 reg ) phenotype. M2 reg profile and anti-inflammatory capacity were assessed in vitro upon lipopolysaccharide (LPS)/interferon-γ (IFNγ) restimulation, before their administration to 8- to 12-week-old mice. M2 reg protective effect was tested at early (2 to 4 days) and late (4 weeks) time points during hypoxia (8.5% O 2 ) exposure. Levels of inflammatory markers were quantified in alveolar macrophages and whole lung, while PH development was ascertained by right ventricular systolic pressure (RSVP) and right ventricular hypertrophy (RVH) measurements. Bronchoalveolar lavage (BAL) from M2 reg -transplanted hypoxic mice was collected, and its inflammatory potential tested on naïve BMDMs.
    Results: M2 reg macrophages demonstrated a stable anti-inflammatory phenotype upon a subsequent pro-inflammatory stimulus by maintaining the expression of specific anti-inflammatory markers (Tgfß, Il10 and Cd206) and downregulating the induction of proinflammatory cytokines and surface molecules (Cd86, Il6 and Tnfα). A single dose of M2 regs attenuated the hypoxic monocytic recruitment and perivascular inflammation. Early hypoxic lung and alveolar macrophage inflammation leading to PH development was significantly reduced and, importantly, M2 regs attenuated RVH, RVSP and vascular remodeling at 4 weeks post treatment.
    Conclusions: Adoptive transfer of M2 regs halts the recruitment of monocytes and modifies the hypoxic lung microenvironment, potentially changing the immunoreactivity of recruited macrophages and restoring normal immune functionality of the lung. These findings provide new mechanistic insights on the diverse role of macrophage phenotype on lung vascular homeostasis that can be explored as novel therapeutic targets.
  15. Ageing Res Rev. 2023 Aug 10. pii: S1568-1637(23)00191-5. [Epub ahead of print]90 102032
      Parkinson's disease (PD) is a slowly progressive neurodegenerative disease characterized by α-synuclein aggregation and dopaminergic neuronal death. Recent evidence suggests that neuroinflammation is an early event in the pathogenesis of PD. Microglia are resident immune cells in the central nervous system that can be activated into either pro-inflammatory M1 or anti-inflammatory M2 phenotypes as found in peripheral macrophages. To exert their immune functions, microglia respond to various stimuli, resulting in the flexible regulation of their metabolic pathways. Inflammasomes activation in microglia induces metabolic shift from oxidative phosphorylation to glycolysis, and leads to the polarization of microglia to pro-inflammatory M1 phenotype, finally causing neuroinflammation and neurodegeneration. In addition, iron accumulation induces microglia take an inflammatory and glycolytic phenotype. M2 phenotype microglia is more sensitive to ferroptosis, inhibition of which can attenuate neuroinflammation. Therefore, this review highlights the interplay between microglial polarization and metabolic reprogramming of microglia. Moreover, it will interpret how inflammasomes and iron regulate microglial metabolism and phenotypic shifts, which provides a promising therapeutic target to modulate neuroinflammation and neurodegeneration in PD and other neurodegenerative diseases.
    Keywords:  Glycolysis; Inflammasome; Iron; Microglia; Neuroinflammation; Parkinson’s disease
  16. Nature. 2023 Aug 16.
      Certain bacterial strains from the microbiome induce a potent, antigen-specific T cell response1-5. However, the specificity of microbiome-induced T cells has not been explored at the strain level across the gut community. Here, we colonize germ-free mice with complex defined communities (roughly 100 bacterial strains) and profile T cell responses to each strain. The pattern of responses suggests that many T cells in the gut repertoire recognize several bacterial strains from the community. We constructed T cell hybridomas from 92 T cell receptor (TCR) clonotypes; by screening every strain in the community against each hybridoma, we find that nearly all the bacteria-specific TCRs show a one-to-many TCR-to-strain relationship, including 13 abundant TCR clonotypes that each recognize 18 Firmicutes. By screening three pooled bacterial genomic libraries, we discover that these 13 clonotypes share a single target: a conserved substrate-binding protein from an ATP-binding cassette transport system. Peripheral regulatory T cells and T helper 17 cells specific for an epitope from this protein are abundant in community-colonized and specific pathogen-free mice. Our work reveals that T cell recognition of commensals is focused on widely conserved, highly expressed cell-surface antigens, opening the door to new therapeutic strategies in which colonist-specific immune responses are rationally altered or redirected.
  17. Microbiol Immunol. 2023 Aug 13.
      The skin and mucous membranes are the primary sites of Staphylococcus aureus colonization, particularly those of health care personnel and patients in long-term care centers. We found that S. aureus colonized with a higher abundance ratio on skins which had recovered from pressure injury (PI) than on normal skins in our earlier research on the skin microbiota of bedridden patients. Multilocus sequence typing (MLST) is a useful tool for typing S. aureus isolated from clinical specimens. However, the MLST approach cannot be used in microbiota DNA owing to the contamination from other bacteria species. In this study, we developed a multiplex-nested PCR method to determine S. aureus MLST in samples collected from human skins. The seven pairs of forward and reverse primers were designed in the upstream and downstream regions, which were conserved specifically in S. aureus. The first amplifications of the seven pairs were conducted in a multiplex assay. The samples were diluted and applied to conventional PCR for MLST. We confirmed that the method amplified the seven allele sequences of S. aureus specifically in the presence of untargeted DNAs from human and other skin commensal bacteria. Using this assay, we succeeded in typing sequence types (STs) of S. aureus in the DNA samples derived from the skins healed from PI. Peaks obtained by Sanger sequencing showed that each sample contained one ST, which were mainly categorized into clonal complex 1 (CC1) or CC5. We propose that this culture-free approach may be used in detecting S. aureus in clinical specimens without isolation.
    Keywords:  Staphylococcus aureus; clinical samples; culture-free approach; multilocus sequence typing; multiplex PCR; pressure injury
  18. Nat Commun. 2023 Aug 14. 14(1): 4895
      The opportunistic fungal pathogen Cryptococcus neoformans causes lethal infections in immunocompromised patients. Macrophages are central to the host response to cryptococci; however, it is unclear how C. neoformans is recognised and phagocytosed by macrophages. Here we investigate the role of TLR4 in the non-opsonic phagocytosis of C. neoformans. We find that loss of TLR4 function unexpectedly increases phagocytosis of non-opsonised cryptococci by murine and human macrophages. The increased phagocytosis observed in Tlr4-/- cells was dampened by pre-treatment of macrophages with oxidised-LDL, a known ligand of scavenger receptors. The scavenger receptor, macrophage scavenger receptor 1 (MSR1) (also known as SR-A1 or CD204) was upregulated in Tlr4-/- macrophages. Genetic ablation of MSR1 resulted in a 75% decrease in phagocytosis of non-opsonised cryptococci, strongly suggesting that it is a key non-opsonic receptor for this pathogen. We go on to show that MSR1-mediated uptake likely involves the formation of a multimolecular signalling complex involving FcγR leading to SYK, PI3K, p38 and ERK1/2 activation to drive actin remodelling and phagocytosis. Altogether, our data indicate a hitherto unidentified role for TLR4/MSR1 crosstalk in the non-opsonic phagocytosis of C. neoformans.
  19. Zhonghua Wei Zhong Bing Ji Jiu Yi Xue. 2023 Aug;35(8): 884-888
      The systemic inflammatory response caused by various pathogenic factors is a key stage in the development of acute respiratory distress syndrome (ARDS). At present, suppression of the inflammatory response and symptomatic support are main methods for the treatment of ARDS. Alveolar epithelial autophagy has an important role in the regulation of the inflammatory response in ARDS. Autophagy is a normal immune mechanism in the body, and it is a metabolic process by which phagocytes degrade intracellular components with the help of lysosomes to maintain intracellular homeostasis. Current studies have shown that pathogenic factors both inside and outside the lung can cause alveolar epithelial cells to form an unfavorable internal environment of hypoxia, starvation, infection, and even apoptosis by triggering inflammatory responses, leading to autophagy dysfunction. Excessive autophagy activation can continue to aggravate inflammatory responses. Autophagy related proteins such as Beclin1, microtubule-associated protein 1 light chain 3 (LC3), mammalian target of rapamycin (mTOR), and p62 are common autophagic markers in current research, which play a crucial role in regulating the autophagic process and the development of lung injury. Therefore, the expression of cellular autophagy genes can be used as early markers and important mechanisms of lung injury in septic ARDS. The Hippo signaling pathway is derived from the protein kinase Hippo in Drosophila, and the Hippo and autophagy are two conserved pathways that are essential for the protection of homeostasis in vivo. The mutual regulation of Hippo signaling pathway and autophagy is currently a hot topic in the academic community. This paper reviews the relevant literature to explore whether the Hippo signaling pathway can regulate cellular autophagy to alleviate the inflammatory response in septic ARDS, so as to provide further research directions for the treatment of ARDS.
  20. Cell Mol Immunol. 2023 Aug 15.
      The immune system is coordinated by an intricate network of stimulatory and inhibitory circuits that regulate host responses against endogenous and exogenous insults. Disruption of these safeguard and homeostatic mechanisms can lead to unpredictable inflammatory and autoimmune responses, whereas deficiency of immune stimulatory pathways may orchestrate immunosuppressive programs that contribute to perpetuate chronic infections, but also influence cancer development and progression. Glycans have emerged as essential components of homeostatic circuits, acting as fine-tuners of immunological responses and potential molecular targets for manipulation of immune tolerance and activation in a wide range of pathologic settings. Cell surface glycans, present in cells, tissues and the extracellular matrix, have been proposed to serve as "self-associated molecular patterns" that store structurally relevant biological data. The responsibility of deciphering this information relies on different families of glycan-binding proteins (including galectins, siglecs and C-type lectins) which, upon recognition of specific carbohydrate structures, can recalibrate the magnitude, nature and fate of immune responses. This process is tightly regulated by the diversity of glycan structures and the establishment of multivalent interactions on cell surface receptors and the extracellular matrix. Here we review the spatiotemporal regulation of selected glycan-modifying processes including mannosylation, complex N-glycan branching, core 2 O-glycan elongation, LacNAc extension, as well as terminal sialylation and fucosylation. Moreover, we illustrate examples that highlight the contribution of these processes to the control of immune responses and their integration with canonical tolerogenic pathways. Finally, we discuss the power of glycans and glycan-binding proteins as a source of immunomodulatory signals that could be leveraged for the treatment of autoimmune inflammation and chronic infection.
    Keywords:  Glycan-binding proteins; Glycans; Glycosylation; Immune response; Infection; Inflammation
  21. Clin Sci (Lond). 2023 Aug 16. 137(15): 1209
    Keywords:  airway remodelling; asthma; biologics; chronic rhinosinusitis; precision medicine; type 2 inflammation
  22. bioRxiv. 2023 Aug 02. pii: 2023.07.31.551245. [Epub ahead of print]
      Altering the route of Bacille Calmette-Guérin (BCG) immunization from low-dose intradermal vaccination to high-dose intravenous (IV) vaccination resulted in a high level of protection against Mycobacterium tuberculosis ( Mtb ) infection, providing an opportunity to uncover immune correlates and mechanisms of protection. In addition to strong T cell immunity, IV BCG vaccination was associated with a robust expansion of humoral immune responses that tracked with bacterial control. However, given the near complete protection afforded by high-dose IV BCG immunization, a precise correlate of immune protection was difficult to define. Here we leveraged plasma and bronchoalveolar lavage fluid (BAL) from a cohort of rhesus macaques that received decreasing doses of IV BCG and aimed to define the correlates of immunity across macaques that experienced immune protection or breakthrough infection following Mtb challenge. We show an IV BCG dose-dependent induction of mycobacterial-specific humoral immune responses, both in the plasma and in the airways. Moreover, antibody responses at peak immunogenicity significantly predicted bacterial control following challenge. Multivariate analyses revealed antibody-mediated complement and NK cell activating humoral networks as key functional signatures associated with protective immunity. Collectively, this work extends our understanding of humoral biomarkers and potential mechanisms of IV BCG mediated protection against Mtb .
  23. Am J Physiol Lung Cell Mol Physiol. 2023 Aug 15.
      Studies of pulmonary inflammation require unique considerations due to the complex structure and composition of the lungs. The lungs have multiple compartments and diverse immune cell populations, with inherently high autofluorescence, and are involved in the host response to pulmonary pathogens. We describe a protocol that accounts for these factors through a novel combination of methodologies - in vivo compartmental analysis and spectral flow cytometry with a broad panel of antibodies. In vivo compartmental analysis enables the precise localization of immune cells within the marginated vasculature, lung interstitium, non-lavageable airways, and lavageable airways of the lungs, as well as the pulmonary lymph nodes. Spectral flow cytometry with a broad panel of antibodies supports an unbiased exploratory approach to investigating diverse immune cell populations during pulmonary inflammation. Most importantly, spectral flow utilizes cellular autofluorescence to aid in the resolution and identification of immune cell populations. This methodology enables the acquisition of high-quality data compatible with informed gating and dimensionality reduction algorithms. Additionally, our protocol emphasizes considerations for compartmentalization of the inflammatory response, spectral flow panel design, and autofluorescence spectra analysis. These methodologies are critical for increasing the rigor of pulmonary research. We apply this protocol for the precise characterization and localization of leukocytes in the pulmonary host response to influenza A virus in C57BL/6J mice. In particular, we demonstrate that this protocol improves the quantification and localization of alveolar macrophages within the airways. The methodology is modifiable and expandable to allow for further characterization of leukocyte populations of special interest.
    Keywords:  compartmental analysis; full-spectrum flow cytometry; heterogeneous autofluorescence; influenza; pulmonary immune response
  24. RSC Med Chem. 2023 Aug 16. 14(8): 1410-1428
      The emergence of antimicrobial resistance, coupled with the occurrence of persistent systemic infections, has already complicated clinical therapy efforts. Moreover, infections are also accompanied by strong inflammatory responses, generated by the host's innate and adaptive immune systems. The closely intertwined relationship between bacterial infection and inflammation has multiple implications on the ability of antibacterial therapeutics to tackle infection and inflammation. Particularly, uncontrolled inflammatory responses to infection can lead to sepsis, a life-threatening physiological condition. In this review, we discuss dual-functional antibacterial therapeutics that have potential to be developed for treating inflammation associated with bacterial infections. Immense research is underway that aims to develop new therapeutic agents that, when administered, regulate the excess inflammatory response, i.e. they have immunomodulatory properties along with the desired antibacterial activity. The classes of antibiotics that have immunomodulatory function in addition to antibacterial activity have been reviewed. Host defense peptides and their synthetic mimics are amongst the most sought-after solutions to develop such dual-functional therapeutics. This review also highlights the important classes of peptidomimetics that exhibit both antibacterial and immunomodulatory properties.
  25. Cell Commun Signal. 2023 Aug 17. 21(1): 208
      BACKGROUND: Lung infections caused by Streptococcus pneumonia are a global leading cause of death. The reactive oxygen species H2O2 is one of the virulence factors of Streptococcus pneumoniae. The Golgi apparatus is essential for the inflammatory response of a eukaryotic cell. Golgi fragmentation was previously shown to be induced by bacterial pathogens and in response to H2O2 treatment. This led us to investigate whether the Golgi apparatus is actively involved and targeted in host-pathogen interactions during pneumococcal infections.METHODS: Following in vitro infection of BEAS-2B bronchial epithelial cells with Streptococcus pneumoniae for 16 h, the structure of the Golgi apparatus was assessed by fluorescence staining of the Golgi-associated protein, Golgin-97. To investigate the effect of H2O2 production on Golgi structure, BEAS-2B cells were treated with H2O2 or the H2O2 degrading enzyme Catalase, prior to Golgi staining. Artificial disruption of the Golgi apparatus was induced by treatment of cells with the GBF1 inhibitor, Golgicide A. A proinflammatory cellular response was induced by treatment of cells with the bacterial cell wall component and TLR4 ligand lipoteichoic acid.
    RESULTS: In vitro infection of bronchial epithelial cells with wild type Streptococcus pneumoniae led to a disruption of normal Golgi structure. Golgi fragmentation was not observed after deletion of the pneumococcal H2O2-producing gene, spxB, or neutralization of H2O2 by catalase treatment, but could be induced by H2O2 treatment. Streptococcus pneumoniae infection significantly reduced host cell protein glycosylation and artificial disruption of Golgi structure significantly reduced bacterial adherence, but increased bacterial counts in the supernatant. To understand if this effect depended on cell-contact or soluble factors, pneumococci were treated with cell-supernatant of cells treated with Golgicide A and/or lipoteichoic acid. This approach revealed that lipoteichoic acid conditioned medium inhibits bacterial replication in presence of host cells. In contrast, artificial Golgi fragmentation by Golgicide A treatment prior to lipoteichoic acid treatment rescued bacterial replication. This effect was associated with an increase of IL-6 and IL-8 in the supernatant of lipoteichoic acid treated cells. The increased cytokine release was abolished if cells were treated with Golgicide A prior to lipoteichoic acid treatment.
    CONCLUSION: Streptococcus pneumoniae disrupts the Golgi apparatus in an H2O2-dependent manner, thereby inhibiting paracrine anti-infective mechanisms. Video Abstract.
  26. Front Microbiol. 2023 ;14 1219942
      Asthma is one of the common chronic respiratory diseases in children, which poses a serious threat to children's quality of life. Respiratory infection is a risk factor for asthma. Compared with healthy children, children with early respiratory infections have a higher risk of asthma and an increased chance of developing severe asthma. Many clinical studies have confirmed the correlation between respiratory infections and the pathogenesis of asthma, but the underlying mechanism is still unclear. The gut microbiome is an important part of maintaining the body's immune homeostasis. The imbalance of the gut microbiome can affect the lung immune function, and then affect lung health and cause respiratory diseases. A large number of evidence supports that there is a bidirectional regulation between intestinal flora and respiratory tract infection, and both are significantly related to the development of asthma. The changes of intestinal microbial components and their metabolites in respiratory tract infection may affect the occurrence and development of asthma through the immune pathway. By summarizing the latest advancements in research, this review aims to elucidate the intricate connection between respiratory tract infections and the progression of asthma by highlighting its bridging role of the gut microbiome. Furthermore, it offers novel perspectives and ideas for future investigations into the mechanisms that underlie the relationship between respiratory tract infections and asthma.
    Keywords:  asthma; gut microbiome; interferon; respiratory virus infection; short-chain fatty acid; vitamin D
  27. Stem Cell Reports. 2023 Aug 08. pii: S2213-6711(23)00268-0. [Epub ahead of print]
      AT2 cells harbor alveolar stem cell activity in the lung and can self-renew and differentiate into AT1 cells during homeostasis and after injury. To identify epigenetic pathways that control the AT2-AT1 regenerative response in the lung, we performed an organoid screen using a library of pharmacological epigenetic inhibitors. This screen identified DOT1L as a regulator of AT2 cell growth and differentiation. In vivo inactivation of Dot1l leads to precocious activation of both AT1 and AT2 gene expression during lung development and accelerated AT1 cell differentiation after acute lung injury. Single-cell transcriptome analysis reveals the presence of a new AT2 cell state upon loss of Dot1l, characterized by increased expression of oxidative phosphorylation genes and changes in expression of critical transcription and epigenetic factors. Taken together, these data demonstrate that Dot1l controls the rate of alveolar epithelial cell fate acquisition during development and regeneration after acute injury.
    Keywords:  DOT1L; alveolar stem cell; lung regeneration; metabolism
  28. Front Cell Dev Biol. 2023 ;11 1206049
      Background: Leishmaniasis results in a wide spectrum of clinical manifestations, ranging from skin lesions at the site of infection to disseminated lesions in internal organs, such as the spleen and liver. While the ability of Leishmania-infected host cells to migrate may be important to lesion distribution and parasite dissemination, the underlying mechanisms and the accompanying role of host cells remain poorly understood. Previously published work has shown that Leishmania infection inhibits macrophage migration in a 2-dimensional (2D) environment by altering actin dynamics and impairing the expression of proteins involved in plasma membrane-extracellular matrix interactions. Although it was shown that L. infantum induces the 2D migration of dendritic cells, in vivo cell migration primarily occurs in 3-dimensional (3D) environments. The present study aimed to investigate the migration of macrophages and dendritic cells infected by Leishmania using a 3-dimensional environment, as well as shed light on the mechanisms involved in this process. Methods: Following the infection of murine bone marrow-derived macrophages (BMDM), human macrophages and human dendritic cells by L. amazonensis, L. braziliensis, or L. infantum, cellular migration, the formation of adhesion complexes and actin polymerization were evaluated. Results: Our results indicate that Leishmania infection inhibited 3D migration in both BMDM and human macrophages. Reduced expression of proteins involved in adhesion complex formation and alterations in actin dynamics were also observed in Leishmania-infected macrophages. By contrast, increased human dendritic cell migration in a 3D environment was found to be associated with enhanced adhesion complex formation and increased actin dynamics. Conclusion: Taken together, our results show that Leishmania infection inhibits macrophage 3D migration, while enhancing dendritic 3D migration by altering actin dynamics and the expression of proteins involved in plasma membrane extracellular matrix interactions, suggesting a potential association between dendritic cells and disease visceralization.
    Keywords:  3D migration; Leishmania; dendritic cells; dissemination; macrophages
  29. J Clin Invest. 2023 Aug 15. pii: e163402. [Epub ahead of print]
      Secondary lung infection by inhaled Staphylococcus aureus (SA) is a common and lethal event in individuals infected with influenza A virus (IAV). How IAV disrupts host defense to promote SA infection in lung alveoli, where fatal lung injury occurs, is not known. We addressed this issue using the first real-time determinations of alveolar responses to IAV in live, intact, perfused lungs. Our findings show IAV infection blocked defensive alveolar wall liquid (AWL) secretion and induced airspace liquid absorption, thereby reversing normal alveolar liquid dynamics and inhibiting alveolar clearance of inhaled SA. Loss of AWL secretion resulted from inhibition of the cystic fibrosis transmembrane conductance regulator (CFTR) ion channel in the alveolar epithelium, and airspace liquid absorption was caused by stimulation of the alveolar epithelial Na+ channel (ENaC). Loss of AWL secretion promoted alveolar stabilization of inhaled SA, but rescue of AWL secretion protected against alveolar SA stabilization and fatal SA-induced lung injury in IAV-infected mice. These findings reveal a central role for AWL secretion in alveolar defense against inhaled SA and identify AWL inhibition as a critical mechanism of IAV lung pathogenesis. AWL rescue may represent a new therapeutic approach for IAV-SA coinfection.
    Keywords:  Epithelial transport of ions and water; Influenza; Innate immunity; Pulmonology
  30. Am J Physiol Lung Cell Mol Physiol. 2023 Aug 15.
      BACKGROUND: Few new therapeutics exist to target airway inflammation in mild-to-moderate asthma. Alveolar macrophages regulate airway inflammation by producing pro-resolving eicosanoids. We hypothesized that stimulation of the purinergic receptor P2X7 in macrophages from individuals with asthma produces eicosanoids associated with airway inflammation and resolution, and that these responses are predicted, in part, by P2X-7 pore function.METHODS: Study subjects were recruited in an IRB approved study. Alveolar macrophages were recovered from bronchoalveolar lavage fluid following bronchoscopy. Purinergic receptor classification was performed using flow cytometry and fluorescent cell assay. Macrophages were stimulated in vitro and eicosanoids measured via ELISA or EIA in the presence and absence of P2X7-specific agonist (Bz-ATP) and antagonist (AZD9056).
    RESULTS: Functional P2X7 pore status was confirmed in a live cell assay utilizing P2X7-specific agonists and antagonists. Alveolar macrophages produced increased quantities of the oxylipins Lipoxin A4 (LXA4), Resolvin D1 (RvD1) and 15(S)-Hydroxyeicosatetraenoic acid (15(S)-HETE) following stimulation with Bz-ATP compared to vehicle controls, responses that were attenuated in the presence of the P2X7-selective antagonist, AZD9056. LXA4 and RvD1 production were greatest at 1 hour, while 15(S)-HETE was maximally produced 24 hours. Prostaglandin E-2 and Resolvin E1 were minimally produced by P2X7 activation, indicating differential signaling pathways involved in eicosanoid production in alveolar macrophages derived from individuals with asthma.
    CONCLUSIONS: The early production of the pro-resolving eicosanoids, LXA4 and Resolvin D1, is regulated by P2X7, whereas generation of the pro-inflammatory eicosanoid, 15(S)-HETE, is only partially regulated through P2X7 signaling and reaches maximal production after the peak in pro-resolving eicosanoids.
    Keywords:  Asthma; Eicosanoid; Lipoxin; Purinergic; Soluble Lipid Mediator
  31. Sci Adv. 2023 Aug 18. 9(33): eadg6262
      Lipid synthesis is necessary for formation of epithelial barriers and homeostasis with external microbes. An analysis of the response of human keratinocytes to several different commensal bacteria on the skin revealed that Cutibacterium acnes induced a large increase in essential lipids including triglycerides, ceramides, cholesterol, and free fatty acids. A similar response occurred in mouse epidermis and in human skin affected with acne. Further analysis showed that this increase in lipids was mediated by short-chain fatty acids produced by Cutibacterium acnes and was dependent on increased expression of several lipid synthesis genes including glycerol-3-phosphate-acyltransferase-3. Inhibition or RNA silencing of peroxisome proliferator-activated receptor-α (PPARα), but not PPARβ and PPARγ, blocked this response. The increase in keratinocyte lipid content improved innate barrier functions including antimicrobial activity, paracellular diffusion, and transepidermal water loss. These results reveal that metabolites from a common commensal bacterium have a previously unappreciated influence on the composition of epidermal lipids.
  32. Anaerobe. 2023 Aug 10. pii: S1075-9964(23)00081-1. [Epub ahead of print] 102772
      The gut is host to a diverse array of microbiota that constitute a complex ecological system crucial to human physiology. Disruptors to the normal host microbiota, such as antimicrobials, can cause a loss of species diversity in the gut, reducing its ability to resist colonization by invading pathogens, and potentially leading to colonization with antimicrobial resistant organisms (AROs). ARO negatively impact gut health by disrupting the usual heterogeneity of gut microbiota and have the potential to cause systemic disease. In recent years, fecal microbiota transplantation (FMT) has been increasingly explored in the management of specific disease states such as Clostridioides difficile infection (CDI). Promising data from management of CDI has led to considerable interest in understanding the role of therapeutics to restore the gut microbiota to a healthy state. This review aims to discuss key studies that highlight the current landscape, and explore existing clinical evidence, for the use of FMT and microbiome-based therapeutics in combating intestinal colonization with ARO. We also explore potential future directions of such therapeutics and discuss unaddressed needs in this field that merit further investigation.
    Keywords:  Antimicrobial-resistant organisms; FMT; Fecal microbiota transplantation; Gut health; Microbiome-based therapeutics
  33. Exp Mol Med. 2023 Aug 15.
      We present an in-depth single-cell atlas of in vitro multiculture systems on human primary airway epithelium derived from normal and diseased lungs of 27 individual donors. Our large-scale single-cell profiling identified new cell states and differentiation trajectories of rare airway epithelial cell types in human distal lungs. By integrating single-cell datasets of human lung tissues, we discovered immune-primed subsets enriched in lungs and organoids derived from patients with chronic respiratory disease. To demonstrate the full potential of our platform, we further illustrate transcriptomic responses to various respiratory virus infections in vitro airway models. Our work constitutes a single-cell roadmap for the cellular and molecular characteristics of human primary lung cells in vitro and their relevance to human tissues in vivo.
  34. PLoS Biol. 2023 Aug 17. 21(8): e3002231
      Mycobacterium tuberculosis (Mtb) defends host-mediated killing by repressing the autophagolysosome machinery. For the first time, we report NCoR1 co-repressor as a crucial host factor, controlling Mtb growth in myeloid cells by regulating both autophagosome maturation and lysosome biogenesis. We found that the dynamic expression of NCoR1 is compromised in human peripheral blood mononuclear cells (PBMCs) during active Mtb infection, which is rescued upon prolonged anti-mycobacterial therapy. In addition, a loss of function in myeloid-specific NCoR1 considerably exacerbates the growth of M. tuberculosis in vitro in THP1 differentiated macrophages, ex vivo in bone marrow-derived macrophages (BMDMs), and in vivo in NCoR1MyeKO mice. We showed that NCoR1 depletion controls the AMPK-mTOR-TFEB signalling axis by fine-tuning cellular adenosine triphosphate (ATP) homeostasis, which in turn changes the expression of proteins involved in autophagy and lysosomal biogenesis. Moreover, we also showed that the treatment of NCoR1 depleted cells by Rapamycin, Antimycin-A, or Metformin rescued the TFEB activity and LC3 levels, resulting in enhanced Mtb clearance. Similarly, expressing NCoR1 exogenously rescued the AMPK-mTOR-TFEB signalling axis and Mtb killing. Overall, our data revealed a central role of NCoR1 in Mtb pathogenesis in myeloid cells.
  35. Int J Pharm. 2023 Aug 12. pii: S0378-5173(23)00733-0. [Epub ahead of print] 123313
      Rapid development of tissue engineering in recent years has increased the importance of three-dimensional (3D) bioprinting technology as novel strategy for fabrication functional 3D tissue and organoid models for pharmaceutical research. 3D bioprinting technology gives hope for eliminating many problems associated with traditional cell culture methods during drug screening. However, there is a still long way to wider clinical application of this technology due to the numerous difficulties associated with development of bioinks, advanced printers and in-depth understanding of human tissue architecture. In this review, the work associated with relatively well-known extrusion-based bioprinting (EBB), jetting-based bioprinting (JBB), and vat photopolymerization bioprinting (VPB) is presented and discussed with the latest advances and limitations in this field. Next we discuss state-of-the-art research of 3D bioprinted in vitro models including liver, kidney, lung, heart, intestines, eye, skin as well as neural and bone tissue that have potential applications in the development of new drugs.
    Keywords:  3D printing; drug screening; organoid models; pharmaceutical application; tissue models
  36. Blood. 2023 Aug 18. pii: blood.2023020597. [Epub ahead of print]
      In this spotlight we review technical issues that compromise single cell analysis of tissue macrophages including limited and unrepresentative yields, fragmentation and generation of remnants and activation during tissue disaggregation. These issues may lead to misleading definition of subpopulations of macrophages and expression of macrophage-specific transcripts by unrelated cells. Recognition of the technical limitations of single cell approaches is required in order to map the full spectrum of tissue resident macrophage heterogeneity and to assess its biological significance.
  37. PLoS Biol. 2023 Aug 18. 21(8): e3002198
      Pathogenic bacteria proliferating inside mammalian host cells need to rapidly adapt to the intracellular environment. How they achieve this and scavenge essential nutrients from the host has been an open question due to the difficulties in distinguishing between bacterial and host metabolites in situ. Here, we capitalized on the inability of mammalian cells to metabolize mannitol to develop a stable isotopic labeling approach to track Salmonella enterica metabolites during intracellular proliferation in host macrophage and epithelial cells. By measuring label incorporation into Salmonella metabolites with liquid chromatography-mass spectrometry (LC-MS), and combining it with metabolic modeling, we identify relevant carbon sources used by Salmonella, uncover routes of their metabolization, and quantify relative reaction rates in central carbon metabolism. Our results underline the importance of the Entner-Doudoroff pathway (EDP) and the phosphoenolpyruvate carboxylase for intracellularly proliferating Salmonella. More broadly, our metabolic labeling strategy opens novel avenues for understanding the metabolism of pathogens inside host cells.
  38. J Cell Sci. 2023 Aug 15. pii: jcs260787. [Epub ahead of print]136(16):
      Cellular quiescence is a dormant, non-dividing cell state characterized by significant shifts in physiology and metabolism. Quiescence plays essential roles in a wide variety of biological processes, ranging from microbial sporulation to human reproduction and wound repair. Moreover, when the regulation of quiescence is disrupted, it can drive cancer growth and compromise tissue regeneration after injury. In this Review, we examine the dynamic changes in metabolism that drive and support dormant and transiently quiescent cells, including spores, oocytes and adult stem cells. We begin by defining quiescent cells and discussing their roles in key biological processes. We then examine metabolic factors that influence cellular quiescence in both healthy and disease contexts, and how these could be leveraged in the treatment of cancer.
    Keywords:  Metabolism; Oocytes; Quiescence; Stem cells