bims-bac4me Biomed News
on Microbiome and trained immunity
Issue of 2023–12–24
fifty-nine papers selected by
Chun-Chi Chang, Universitäts Spital Zürich
  1. Commensal skin bacteria exacerbate inflammation and delay skin healing.
  2. TLR4 sensing of IsdB of Staphylococcus aureus induces a proinflammatory cytokine response via the NLRP3-caspase-1 inflammasome cascade.
  3. Staphylococcus aureus suppresses the pentose phosphate pathway in human neutrophils via the adenosine receptor A2aR to enhance intracellular survival.
  4. Enduring echoes: Post-infectious long-term changes in innate immunity.
  5. CpsA mediates infection of recruited lung myeloid cells by Mycobacterium tuberculosis.
  6. Wound Microbiota and Its Impact on Wound Healing.
  7. Spatial resolution of host-microbiome interactions.
  8. Commensal production of a broad-spectrum and short-lived antimicrobial peptide polyene eliminates nasal Staphylococcus aureus.
  9. Current Understanding of Bacillus Calmette-Guérin-Mediated Trained Immunity and Its Perspectives for Controlling Intracellular Infections.
  10. Epithelial SIRT6 governs IL-17A pathogenicity and drives allergic airway inflammation and remodeling.
  11. HPV vaccines induce trained immunity and modulate pro-inflammatory cytokine expression in response to secondary Toll-like receptor stimulations.
  12. Lactate helps in tissue repair by promoting efferocytosis-induced macrophage proliferation.
  13. Pseudomonas aeruginosa kills Staphylococcus aureus in a polyphosphate-dependent manner.
  14. Innovative Approaches for Maintaining and Enhancing Skin Health and Managing Skin Diseases through Microbiome-Targeted Strategies.
  15. Human gut microbiota and endocrinology: paradigm shift from genome to its regulation.
  16. A distinct human cell type expressing MHCII and RORγt with dual characteristics of dendritic cells and type 3 innate lymphoid cells.
  17. IL-27 Alleviates Airway Inflammation and Airway Hyperresponsiveness in Asthmatic Mice by Targeting the CD39/ATP Axis of Dendritic Cells.
  18. Innate extracellular Hsp70 inflammatory properties are mediated by the interaction of Siglec-E and LOX-1 receptors.
  19. A Metabolic Axis of Immune Intractability.
  20. Don't lose sleep over chronic rhinosinusitis with nasal polyps.
  21. A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice.
  22. NET formation is a default epigenetic program controlled by PAD4 in apoptotic neutrophils.
  23. Protocol for the induction of innate immune memory in human smooth muscle cells and endothelial cells in vitro.
  24. Transcriptional Regulation of Suppressors of Cytokine Signaling During Infection with Mycobacterium tuberculosis in human THP-1-derived macrophages and in mice.
  25. Translational profiling identifies sex-specific metabolic and epigenetic reprogramming of cortical microglia/macrophages in APPPS1-21 mice with an antibiotic-perturbed-microbiome.
  26. How Neutrophils Shape the Immune Response: Reassessing Their Multifaceted Role in Health and Disease.
  27. Time-resolved single-cell transcriptomics defines immune trajectories in glioblastoma.
  28. From Mother to Infant, from Placenta to Gut: Understanding Varied Microbiome Profiles in Neonates.
  29. An Organotypic Human Lymph Node Model Reveals the Importance of Fibroblastic Reticular Cells for Dendritic Cell Function.
  30. Salmonella spvC gene suppresses macrophage/neutrophil antibacterial defense mediated by gasdermin D.
  31. A Bacterial and Ganglioside-based Nanoparticle Initiates Reprogramming of Macrophages and Promotes Antitumor Phenotypes.
  32. Early human lung immune cell development and its role in epithelial cell fate.
  33. CD115+ monocytes protect microbially experienced mice against E. coli-induced sepsis.
  34. A guide to cell death pathways.
  35. The multi-faceted role of NADPH in regulating inflammation in activated myeloid cells.
  36. Monocyte immunometabolic reprogramming in human pregnancy: contribution of trophoblast cells.
  37. Group A Streptococcus adaptation to diverse niches: lessons from transcriptomic studies.
  38. Single-cell immune profiling reveals markers of emergency myelopoiesis that distinguish severe from mild respiratory syncytial virus disease in infants.
  39. The RNA m6A demethylase ALKBH5 drives emergency granulopoiesis and neutrophil mobilization by upregulating G-CSFR expression.
  40. Gut-Antimicrobial Peptides: Synergistic Co-Evolution with Antibiotics to Combat Multi-Antibiotic Resistance.
  41. CTRP6 promotes the macrophage inflammatory response, and its deficiency attenuates LPS-induced inflammation.
  42. Distinct gene expression signatures comparing latent tuberculosis infection with different routes of Bacillus Calmette-Guérin vaccination.
  43. Extracellular Proteins Isolated from L. acidophilus as an Osteomicrobiological Therapeutic Agent to Reduce Pathogenic Biofilm Formation, Regulate Chronic Inflammation, and Augment Bone Formation In Vitro.
  44. Spatial resolution of host-microbiome interactions.
  45. CD69 is indispensable for the development of functional local immune memory in murine contact hypersensitivity.
  46. Apoptosis recognition receptors regulate skin tissue repair in mice.
  47. Experimental Modeling of Host-Bacterial Interactions in Head and Neck Squamous Cell Carcinoma.
  48. The tetrapeptide sequence of IL-18 and IL-1β regulates their recruitment and activation by inflammatory caspases.
  49. Nutrient inputs and social metabolic control of T cell fate.
  50. How Can Imbalance in Oral Microbiota and Immune Response Lead to Dental Implant Problems?
  51. Neutrophils - Biology and Diversity.
  52. Statistical prediction of microbial metabolic traits from genomes.
  53. Understanding the gut microbiota by considering human evolution: a story of fire, cereals, cooking, molecular ingenuity, and functional cooperation.
  54. Lactobacillus rhamnosus (LR) ameliorates pulmonary and extrapulmonary acute respiratory distress syndrome (ARDS) via targeting neutrophils.
  55. Neutrophils only die twice.
  56. The Pneumococcal Protein SufC Binds to Host Plasminogen and Promotes Its Conversion into Plasmin.
  57. Effects of clinically achievable pulmonary antibiotic concentrations on the recovery of bacteria: in vitro comparison of the BioFire FILMARRAY Pneumonia Panel versus conventional culture methods in bronchoalveolar lavage fluid.
  58. Culturing and Differentiation of Patient-Derived Ectocervical Epithelial Stem Cells Using Air-Liquid Interphase and Matrigel Scaffold.
  59. The Mycobacterium tuberculosis methyltransferase Rv2067c manipulates host epigenetic programming to promote its own survival.
  1. bioRxiv. 2023 Dec 04. pii: 2023.12.04.569980. [Epub ahead of print]
    Commensal skin bacteria exacerbate inflammation and delay skin healing.
    Veda D Khadka, Laura Markey, Magalie Boucher, Tami D Lieberman.
      The skin microbiome can both trigger beneficial immune stimulation and pose a potential infection threat. Previous studies have shown that colonization of mouse skin with the model human skin commensal Staphylococcus epidermidis is protective against subsequent excisional wound or pathogen challenge. However, less is known about concurrent skin damage and exposure to commensal microbes, despite growing interest in interventional probiotic therapy. Here, we address this open question by applying commensal skin bacteria at a high dose to abraded skin. While depletion of the skin microbiome via antibiotics delayed repair from damage, application of commensals-- including the mouse commensal Staphylococcus xylosus , three distinct isolates of S. epidermidis, and all other tested human skin commensals-- also significantly delayed barrier repair. Increased inflammation was observed within four hours of S. epidermidis exposure and persisted through day four, at which point the skin displayed a chronic-wound-like inflammatory state with increased neutrophil infiltration, increased fibroblast activity, and decreased monocyte differentiation. Transcriptomic analysis suggested that the prolonged upregulation of early canonical proliferative pathways inhibited the progression of barrier repair. These results highlight the nuanced role of members of the skin microbiome in modulating barrier integrity and indicate the need for caution in their development as probiotics.
    DOI:  https://doi.org/10.1101/2023.12.04.569980
  2. mBio. 2023 Dec 19. e0022523
    TLR4 sensing of IsdB of Staphylococcus aureus induces a proinflammatory cytokine response via the NLRP3-caspase-1 inflammasome cascade.
    Juan José Izquierdo Gonzalez, Md Faruq Hossain, Jolanda Neef, Erin E Zwack, Chih-Ming Tsai, Dina Raafat, Kevin Fechtner, Luise Herzog, Thomas P Kohler, Rabea Schlüter, Alexander Reder, Silva Holtfreter, George Y Liu, Sven Hammerschmidt, Uwe Völker, Victor J Torres, Jan Maarten van Dijl, Christopher H Lillig, Barbara M Bröker, Murty N Darisipudi.
       IMPORTANCE: The prevalence of multidrug-resistant Staphylococcus aureus is of global concern, and vaccines are urgently needed. The iron-regulated surface determinant protein B (IsdB) of S. aureus was investigated as a vaccine candidate because of its essential role in bacterial iron acquisition but failed in clinical trials despite strong immunogenicity. Here, we reveal an unexpected second function for IsdB in pathogen-host interaction: the bacterial fitness factor IsdB triggers a strong inflammatory response in innate immune cells via Toll-like receptor 4 and the inflammasome, thus acting as a novel pathogen-associated molecular pattern of S. aureus. Our discovery contributes to a better understanding of how S. aureus modulates the immune response, which is necessary for vaccine development against the sophisticated pathogen.
    Keywords:  IsdB; NLRP3 inflammasome; Staphylococcus aureus; TLR4; cytokines; innate immunity
    DOI:  https://doi.org/10.1128/mbio.00225-23
  3. mBio. 2023 Dec 18. e0257123
    Staphylococcus aureus suppresses the pentose phosphate pathway in human neutrophils via the adenosine receptor A2aR to enhance intracellular survival.
    Emilio G Vozza, Clíodhna M Daly, Sinead A O'Rourke, Hannah K Fitzgerald, Aisling Dunne, Rachel M McLoughlin.
       IMPORTANCE: Staphylococcus aureus is one of the leading causes of antimicrobial-resistant infections whose success as a pathogen is facilitated by its massive array of immune evasion tactics, including intracellular survival within critical immune cells such as neutrophils, the immune system's first line of defense. In this study, we describe a novel pathway by which intracellular S. aureus can suppress the antimicrobial capabilities of human neutrophils by using the anti-inflammatory adenosine receptor, adora2a (A2aR). We show that signaling through A2aR suppresses the pentose phosphate pathway, a metabolic pathway used to fuel the antimicrobial NADPH oxidase complex that generates reactive oxygen species (ROS). As such, neutrophils show enhanced ROS production and reduced intracellular S. aureus when treated with an A2aR inhibitor. Taken together, we identify A2aR as a potential therapeutic target for combatting intracellular S. aureus infection.
    Keywords:  A2aR; Staphylococcus aureus; adora2a; host-pathogen interactions; intracellular pathogen; metabolism; neutrophil; pentose phosphate pathway
    DOI:  https://doi.org/10.1128/mbio.02571-23
  4. Eur J Intern Med. 2023 Dec 21. pii: S0953-6205(23)00456-9. [Epub ahead of print]
    Enduring echoes: Post-infectious long-term changes in innate immunity.
    Elisabeth A Dulfer, Leo A B Joosten, Mihai G Netea.
      Upon encountering pathogens, the immune system typically responds by initiating an acute and self-limiting reaction, with symptoms subsiding after the pathogen has been cleared. However, long-term post-infectious clinical symptoms can manifest months or even years after the initial infection. 'Trained immunity', the functional reprogramming of innate immune cells through epigenetic and metabolic rewiring, has been proposed as a key concept for understanding these long-term effects. Although trained immunity can result in enhanced protection against reinfection with heterologous pathogens, it can also contribute to detrimental outcomes. Persisting and excessive inflammation can cause tissue damage and aggravate immune-mediated conditions and cardiovascular complications. On the other hand, suppression of immune cell effector functions by long-lasting epigenetic changes can result in post-infectious immune paralysis. Distinct stimuli can evoke different trained immunity programs, potentially resulting in different consequences for the host. In this review, we provide an overview of both the adaptive and maladaptive consequences of infectious diseases. We discuss how long-term immune dysregulation in patients can be addressed by tailoring host-directed interventions and identify areas of scientific and therapeutic potential to advance further.
    Keywords:  Infectious diseases; Innate immunity; Post-infectious complications; Trained immunity
    DOI:  https://doi.org/10.1016/j.ejim.2023.12.020
  5. Cell Rep. 2023 Dec 19. pii: S2211-1247(23)01619-4. [Epub ahead of print]43(1): 113607
    CpsA mediates infection of recruited lung myeloid cells by Mycobacterium tuberculosis.
    Steven J Grigsby, G V R Krishna Prasad, Joshua B Wallach, Ekansh Mittal, Fong-Fu Hsu, Dirk Schnappinger, Jennifer A Philips.
      Mycobacterium tuberculosis (Mtb) possesses an arsenal of virulence factors to evade host immunity. Previously, we showed that the Mtb protein CpsA, which protects Mtb against the host NADPH oxidase, is required in mice during the first 3 weeks of infection but is thereafter dispensable for full virulence. Using flow cytometry, we find that ΔcpsA Mtb is retained in alveolar macrophages, impaired in recruiting and disseminating into monocyte-derived cells, and more likely to be localized in airway cells than wild-type Mtb. The lungs of ΔcpsA-infected mice also have markedly fewer antigen-specific T cells, indicating a delay in adaptive immunity. Thus, we conclude that CpsA promotes dissemination of Mtb from alveolar macrophages and the airways and generation of an adaptive immune response. Our studies of ΔcpsA Mtb show that a more effective innate immune response against Mtb can be undermined by a corresponding delay in the adaptive immune response.
    Keywords:  CP: Immunology; CP: Microbiology; CpsA; NADPH oxidase; airways; alveolar macrophages; innate immunity; mycobacteria; tuberculosis
    DOI:  https://doi.org/10.1016/j.celrep.2023.113607
  6. Int J Mol Sci. 2023 Dec 10. pii: 17318. [Epub ahead of print]24(24):
    Wound Microbiota and Its Impact on Wound Healing.
    Małgorzata Zielińska, Agnieszka Pawłowska, Anna Orzeł, Luiza Sulej, Katarzyna Muzyka-Placzyńska, Arkadiusz Baran, Dagmara Filipecka-Tyczka, Paulina Pawłowska, Aleksandra Nowińska, Joanna Bogusławska, Anna Scholz.
      Wound healing is a complex process influenced by age, systemic conditions, and local factors. The wound microbiota's crucial role in this process is gaining recognition. This concise review outlines wound microbiota impacts on healing, emphasizing distinct phases like hemostasis, inflammation, and cell proliferation. Inflammatory responses, orchestrated by growth factors and cytokines, recruit neutrophils and monocytes to eliminate pathogens and debris. Notably, microbiota alterations relate to changes in wound healing dynamics. Commensal bacteria influence immune responses, keratinocyte growth, and blood vessel development. For instance, Staphylococcus epidermidis aids keratinocyte progression, while Staphylococcus aureus colonization impedes healing. Other bacteria like Group A Streptococcus spp. And Pseudomonas affect wound healing as well. Clinical applications of microbiota-based wound care are promising, with probiotics and specific bacteria like Acinetobacter baumannii aiding tissue repair through molecule secretion. Understanding microbiota influence on wound healing offers therapeutic avenues. Tailored approaches, including probiotics, prebiotics, and antibiotics, can manipulate the microbiota to enhance immune modulation, tissue repair, and inflammation control. Despite progress, critical questions linger. Determining the ideal microbiota composition for optimal wound healing, elucidating precise influence mechanisms, devising effective manipulation strategies, and comprehending the intricate interplay between the microbiota, host, and other factors require further exploration.
    Keywords:  microbiome composition; microbiota; wounds
    DOI:  https://doi.org/10.3390/ijms242417318
  7. Nat Rev Immunol. 2023 Dec 19.
    Spatial resolution of host-microbiome interactions.
    Kirsty Minton.
      
    DOI:  https://doi.org/10.1038/s41577-023-00984-5
  8. Nat Microbiol. 2023 Dec 18.
    Commensal production of a broad-spectrum and short-lived antimicrobial peptide polyene eliminates nasal Staphylococcus aureus.
    Benjamin O Torres Salazar, Taulant Dema, Nadine A Schilling, Daniela Janek, Jan Bornikoel, Anne Berscheid, Ahmed M A Elsherbini, Sophia Krauss, Simon J Jaag, Michael Lämmerhofer, Min Li, Norah Alqahtani, Malcolm J Horsburgh, Tilmann Weber, José Manuel Beltrán-Beleña, Heike Brötz-Oesterhelt, Stephanie Grond, Bernhard Krismer, Andreas Peschel.
      Antagonistic bacterial interactions often rely on antimicrobial bacteriocins, which attack only a narrow range of target bacteria. However, antimicrobials with broader activity may be advantageous. Here we identify an antimicrobial called epifadin, which is produced by nasal Staphylococcus epidermidis IVK83. It has an unprecedented architecture consisting of a non-ribosomally synthesized peptide, a polyketide component and a terminal modified amino acid moiety. Epifadin combines a wide antimicrobial target spectrum with a short life span of only a few hours. It is highly unstable under in vivo-like conditions, potentially as a means to limit collateral damage of bacterial mutualists. However, Staphylococcus aureus is eliminated by epifadin-producing S. epidermidis during co-cultivation in vitro and in vivo, indicating that epifadin-producing commensals could help prevent nasal S. aureus carriage. These insights into a microbiome-derived, previously unknown antimicrobial compound class suggest that limiting the half-life of an antimicrobial may help to balance its beneficial and detrimental activities.
    DOI:  https://doi.org/10.1038/s41564-023-01544-2
  9. Pathogens. 2023 Nov 24. pii: 1386. [Epub ahead of print]12(12):
    Current Understanding of Bacillus Calmette-Guérin-Mediated Trained Immunity and Its Perspectives for Controlling Intracellular Infections.
    Ana Carolina V S C de Araujo, Fábio Mambelli, Rodrigo O Sanches, Fábio V Marinho, Sergio C Oliveira.
      The bacillus Calmette-Guérin (BCG) is an attenuated bacterium derived from virulent Mycobacterium bovis. It is the only licensed vaccine used for preventing severe forms of tuberculosis in children. Besides its specific effects against tuberculosis, BCG administration is also associated with beneficial non-specific effects (NSEs) following heterologous stimuli in humans and mice. The NSEs from BCG could be related to both adaptive and innate immune responses. The latter is also known as trained immunity (TI), a recently described biological feature of innate cells that enables functional improvement based on metabolic and epigenetic reprogramming. Currently, the mechanisms related to BCG-mediated TI are the focus of intense research, but many gaps are still in need of elucidation. This review discusses the present understanding of TI induced by BCG, exploring signaling pathways that are crucial to a trained phenotype in hematopoietic stem cells and monocytes/macrophages lineage. It focuses on BCG-mediated TI mechanisms, including the metabolic-epigenetic axis and the inflammasome pathway in these cells against intracellular pathogens. Moreover, this study explores the TI in different immune cell types, its ability to protect against various intracellular infections, and the integration of trained innate memory with adaptive memory to shape next-generation vaccines.
    Keywords:  BCG; innate memory; intracellular infections; trained immunity
    DOI:  https://doi.org/10.3390/pathogens12121386
  10. Nat Commun. 2023 Dec 22. 14(1): 8525
    Epithelial SIRT6 governs IL-17A pathogenicity and drives allergic airway inflammation and remodeling.
    Jingyun Quan, Xiaoxia Wen, Guomei Su, Yu Zhong, Tong Huang, Zhilin Xiong, Jiewen Huang, Yingying Lv, Shihai Li, Shuhua Luo, Chaole Luo, Xin Cai, Xianwen Lai, Yuanyuan Xiang, Song Guo Zheng, Yiming Shao, Haitao Lin, Xiao Gao, Jing Tang, Tianwen Lai.
      Dysregulation of IL-17A is closely associated with airway inflammation and remodeling in severe asthma. However, the molecular mechanisms by which IL-17A is regulated remain unclear. Here we identify epithelial sirtuin 6 (SIRT6) as an epigenetic regulator that governs IL-17A pathogenicity in severe asthma. Mice with airway epithelial cell-specific deletion of Sirt6 are protected against allergen-induced airway inflammation and remodeling via inhibiting IL-17A-mediated inflammatory chemokines and mesenchymal reprogramming. Mechanistically, SIRT6 directly interacts with RORγt and mediates RORγt deacetylation at lysine 192 via its PPXY motifs. SIRT6 promotes RORγt recruitment to the IL-17A gene promoter and enhances its transcription. In severe asthma patients, high expression of SIRT6 positively correlates with airway remodeling and disease severity. SIRT6 inhibitor (OSS_128167) treatment significantly attenuates airway inflammation and remodeling in mice. Collectively, these results uncover a function for SIRT6 in regulating IL-17A pathogenicity in severe asthma, implicating SIRT6 as a potential therapeutic target for severe asthma.
    DOI:  https://doi.org/10.1038/s41467-023-44179-x
  11. Microbiol Immunol. 2023 Dec 17.
    HPV vaccines induce trained immunity and modulate pro-inflammatory cytokine expression in response to secondary Toll-like receptor stimulations.
    Mako Yamaguchi, Yohana S Mtali, Hitomi Sonokawa, Ken Takashima, Yoshimi Fukushima, Takahisa Kouwaki, Hiroyuki Oshiumi.
      Cervical cancer is caused mostly by human papillomavirus (HPV), and several HPV vaccines have been developed to prevent its onset. Vaccines include antigens as well as adjuvants, with adjuvants playing an important role in activating the innate immune responses necessary for inducing adaptive immunological responses. Recent research has shown the presence of trained immunity inside the innate immune system. However, trained immunity conferred by HPV vaccinations is not well understood. In this work, we explored the innate immune responses and trained immunity caused by two HPV vaccines, Cervarix and Gardasil. Cervarix includes monophosphoryl lipid A and an aluminum adjuvant, and it significantly increased the expression of IL-6 and IFN-β mRNAs in RAW264.7 cells. On the contrary, Gardasil, which only includes an aluminum adjuvant, exhibited little cytokine expression but increased the expression of TLRs. Furthermore, Cervarix significantly increased IL-1β secretion from mouse macrophages, while Gardasil only mildly induced IL-1β secretion. Interestingly, initial stimulation with Gardasil enhanced the expression of IL-6 and TNF-α mRNAs upon secondary stimulation with TLR ligands, indicating that Gardasil induced trained immunity in macrophages. Moreover, Gardasil injection into mice resulted in enhanced TNF-α production in sera following secondary TLR stimulation. Our findings suggest that HPV vaccinations have the ability to induce trained immunity that modulate TLR ligand responses.
    Keywords:  HPV; inflammation; innate immunity; trained immunity; vaccine
    DOI:  https://doi.org/10.1111/1348-0421.13108
  12. Nat Metab. 2023 Dec;5(12): 2045-2046
    Lactate helps in tissue repair by promoting efferocytosis-induced macrophage proliferation.
      
    DOI:  https://doi.org/10.1038/s42255-023-00920-w
  13. bioRxiv. 2023 Dec 06. pii: 2023.12.05.570291. [Epub ahead of print]
    Pseudomonas aeruginosa kills Staphylococcus aureus in a polyphosphate-dependent manner.
    Ritika Shah, Olivia Jankiewicz, Colton Johnson, Barry Livingston, Jan-Ulrik Dahl.
      Due to their frequent coexistence in many polymicrobial infections, including in patients with burn or chronic wounds or cystic fibrosis, recent studies have started to investigate the mechanistic details of the interaction between the opportunistic pathogens Pseudomonas aeruginosa and Staphylococcus aureus . P. aeruginosa rapidly outcompetes S. aureus under in vitro co-cultivation conditions, which is mediated by several of P. aeruginosa 's virulence factors. Here, we report that polyphosphate (polyP), an efficient stress defense system and virulence factor in P. aeruginosa , plays a role for the pathogen's ability to inhibit and kill S. aureus in a contact-independent manner. We show that P. aeruginosa cells characterized by low polyP level are less detrimental to S. aureus growth and survival while the gram-positive pathogen is significantly more compromised by the presence of P. aeruginosa cells that produce high level of polyP. We show that the polyP-dependent phenotype could be a direct effect by the biopolymer, as polyP is present in the spent media and causes significant damage to the S. aureus cell envelope. However, more likely is that polyP's effects are indirect through the regulation of one of P. aeruginosa's virulence factors, pyocyanin. We show that pyocyanin production in P. aeruginosa occurs polyP-dependent and harms S. aureus through membrane damage and the generation of reactive oxygen species, resulting in increased expression of antioxidant enzymes. In summary, our study adds a new component to the list of biomolecules that the gram-negative pathogen P. aeruginosa generates to compete with S. aureus for resources.
    IMPORTANCE: How do interactions between microorganisms shape the course of polymicrobial infections? Previous studies have provided evidence that the two opportunistic pathogens P. aeruginosa and S. aureus generate molecules that modulate their interaction with potentially significant impact on disease outcomes. Our study identified the biopolymer polyP as a new effector molecule that impacts P. aeruginosa 's interaction with S. aureus . We show that P. aeruginosa kills S. aureus in a polyP-dependent manner, which occurs primarily through the polyP-dependent production of the P. aeruginosa virulence factor pyocyanin. Our findings add a new role for polyP to an already extensive list of functions. A more in-depth understanding of how polyP influences interspecies interactions is critical, as targeting polyP synthesis in bacteria such as P. aeruginosa may have a significant impact on other microorganisms and potentially result in dynamic changes in the microbial composition.
    DOI:  https://doi.org/10.1101/2023.12.05.570291
  14. Antibiotics (Basel). 2023 Dec 04. pii: 1698. [Epub ahead of print]12(12):
    Innovative Approaches for Maintaining and Enhancing Skin Health and Managing Skin Diseases through Microbiome-Targeted Strategies.
    Khadeejeh Al-Smadi, Vania Rodrigues Leite-Silva, Newton Andreo Filho, Patricia Santos Lopes, Yousuf Mohammed.
      The skin microbiome is crucial in maintaining skin health, and its disruption is associated with various skin diseases. Prebiotics are non-digestible fibers and compounds found in certain foods that promote the activity and growth of beneficial bacteria in the gut or skin. On the other hand, live microorganisms, known as probiotics, benefit in sustaining healthy conditions when consumed in reasonable quantities. They differ from postbiotics, which are by-product compounds from bacteria that release the same effects as their parent bacteria. The human skin microbiome is vital when it comes to maintaining skin health and preventing a variety of dermatological conditions. This review explores novel strategies that use microbiome-targeted treatments to maintain and enhance overall skin health while managing various skin disorders. It is important to understand the dynamic relationship between these beneficial microorganisms and the diverse microbial communities present on the skin to create effective strategies for using probiotics on the skin. This understanding can help optimize formulations and treatment regimens for improved outcomes in skincare, particularly in developing solutions for various skin problems.
    Keywords:  microbiome; postbiotics; prebiotics; probiotics; vitiligo
    DOI:  https://doi.org/10.3390/antibiotics12121698
  15. J Endocrinol. 2023 Dec 01. pii: JOE-23-0348. [Epub ahead of print]
    Human gut microbiota and endocrinology: paradigm shift from genome to its regulation.
    Matthew T F Lamaudière, Mark C Turner, Ramesh P Arasaradnam, Igor Morozov.
      Over the last two decades, it has become clear that the human gut microbiota, a complex community of bacteria, archaea, fungi, and viruses, are a critical determinant of human health and disease. Microbiota-derived metabolites provide the host with energy, protect against pathogens, modulate immune and endocrine systems as well as the level of reactive oxygen species in the gut. It has come with no surprise that the human gut microbiota is also linked to the production, utilisation, and regulation of host hormones. This implies that the gut microbiota is capable of influencing human behaviour, appetite regulation, and metabolism as well as development and immunity. Many of the advances in the field of crosstalk between the gut microbiota and host health, disease and behaviours are generally based on DNA analyses of microbial populations and transplantation of monocultured commensal species to germ-free animals. Recent reports on the activity of the gut microbiota in gastrointestinal diseases such as IBD and CRC have highlighted two important points. Firstly, microbial DNA-based abundance does not always correlate with their level of activity and secondly, that metabolism of the complex gut microbiota is regulated by host health status, including the production and metabolism of several human hormones. In this review, we will discuss the lessons learnt from studying the activity and metabolism of the human gut microbiota in health and across gastrointestinal diseases, and how these findings can shape future research on the microbiome-gut-endocrine axis.
    DOI:  https://doi.org/10.1530/JOE-23-0348
  16. Proc Natl Acad Sci U S A. 2023 Dec 26. 120(52): e2318710120
    A distinct human cell type expressing MHCII and RORγt with dual characteristics of dendritic cells and type 3 innate lymphoid cells.
    Alina Ulezko Antonova, Silvia Lonardi, Matilde Monti, Francesco Missale, Changxu Fan, Matthew L Coates, Mattia Bugatti, Natalia Jaeger, Patrick Fernandes Rodrigues, Simone Brioschi, Tihana Trsan, José L Fachi, Khai M Nguyen, Ryan M Nunley, Daniele Moratto, Stefania Zini, Lingjia Kong, Jacques Deguine, Mark E Peeples, Ramnik J Xavier, Menna R Clatworthy, Ting Wang, Marina Cella, William Vermi, Marco Colonna.
      Recent studies have characterized various mouse antigen-presenting cells (APCs) expressing the lymphoid-lineage transcription factor RORγt (Retinoid-related orphan receptor gamma t), which exhibit distinct phenotypic features and are implicated in the induction of peripheral regulatory T cells (Tregs) and immune tolerance to microbiota and self-antigens. These APCs encompass Janus cells and Thetis cell subsets, some of which express the AutoImmune REgulator (AIRE). RORγt+ MHCII+ type 3 innate lymphoid cells (ILC3) have also been implicated in the instruction of microbiota-specific Tregs. While RORγt+ APCs have been actively investigated in mice, the identity and function of these cell subsets in humans remain elusive. Herein, we identify a rare subset of RORγt+ cells with dendritic cell (DC) features through integrated single-cell RNA sequencing and single-cell ATAC sequencing. These cells, which we term RORγt+ DC-like cells (R-DC-like), exhibit DC morphology, express the MHC class II machinery, and are distinct from all previously reported DC and ILC3 subsets, but share transcriptional and epigenetic similarities with DC2 and ILC3. We have developed procedures to isolate and expand them in vitro, enabling their functional characterization. R-DC-like cells proliferate in vitro, continue to express RORγt, and differentiate into CD1c+ DC2-like cells. They stimulate the proliferation of allogeneic T cells. The identification of human R-DC-like cells with proliferative potential and plasticity toward CD1c+ DC2-like cells will prompt further investigation into their impact on immune homeostasis, inflammation, and autoimmunity.
    Keywords:  antigen presentation; dendritic cells; human; innate lymphoid cells; retinoid-related orphan receptor gamma t
    DOI:  https://doi.org/10.1073/pnas.2318710120
  17. Inflammation. 2023 Dec 20.
    IL-27 Alleviates Airway Inflammation and Airway Hyperresponsiveness in Asthmatic Mice by Targeting the CD39/ATP Axis of Dendritic Cells.
    Yifei Chen, Miaojuan Zhu, Jiahao Hu, Shaojun He, Shuhua Li, Bing Liu, Jiong Yang.
      Interleukin-27 receptor (IL-27R) is expressed in a variety of immune cells and structural cells, including dendritic cells. The mechanism of IL-27 in asthma has not been fully elucidated. This study aimed to examine whether IL-27 regulated the CD39/ATP axis of dendritic cells in asthma. Our results showed that in ovalbumin (OVA)-induced asthma mouse model, IL-27Rα-/- asthmatic mice showed increased airway resistance, increased infiltration of inflammatory cells in lung tissue, proliferation of goblet cells, enhanced expression of Muc5 AC around airway epithelium, increased total number of cells and eosinophils, increased levels of total IgE, OVA-IgE, IL-4, IL-5, IL-13 and IL-17 A, and increased expression of transcription factors GATA-3 and RORγt in lung tissue. The expression of CD39 mRNA and protein in the lung tissue of IL-27Rα-/- asthmatic mice decreased, and the expression of NLRP3, ASC and Caspase-1 in NLRP3 inflammasome components increased. The concentration of ATP was significantly increased compared with WT asthmatic mice. In vitro experiments showed that the expression of CD39 in lung dendritic cells of IL-27Rα-/- asthmatic mice decreased, while the expression of NLRP3 inflammasome components NLRP3, ASC and Caspase-1 increased. These findings indicate that IL-27 directly and indirectly regulates immunoinflammatory responses in asthma by acting on dendritic cells CD39/ATP Axis.
    Keywords:  CD39; allergic asthma; regulatory T cells.; rxtracellular ATP
    DOI:  https://doi.org/10.1007/s10753-023-01945-9
  18. bioRxiv. 2023 Dec 04. pii: 2023.12.01.569623. [Epub ahead of print]
    Innate extracellular Hsp70 inflammatory properties are mediated by the interaction of Siglec-E and LOX-1 receptors.
    Thiago J Borges, Karina Lima, Ayesha Murshid, Isadora T Lape, Yunlong Zhao, Maurício M Rigo, Benjamin J Lang, Shoib S Siddiqui, Enfu Hui, Leonardo V Riella, Cristina Bonorino, Stuart K Calderwood.
      Innate immune responses to cell damage-associated molecular patterns induce a controlled degree of inflammation, ideally avoiding the promotion of intense unwanted inflammatory adverse events. When released by damaged cells, Hsp70 can stimulate different responses that range from immune activation to immune suppression. The effects of Hsp70 are mediated through innate receptors expressed primarily by myeloid cells, such as dendritic cells (DCs). The regulatory innate receptors that bind to extracellular mouse Hsp70 (mHsp70) are not fully characterized, and neither are their potential interactions with activating innate receptors. Here, we describe that extracellular mHsp70 interacts with a receptor complex formed by inhibitory Siglec-E and activating LOX-1 on DCs. We also find that this interaction takes place within lipid microdomains, and Siglec-E acts as a negative regulator of LOX-1-mediated innate activation upon mHsp70 or oxidized LDL binding. Thus, HSP70 can both bind to and modulate the interaction of inhibitory and activating innate receptors on the cell surface. These findings add another dimension of regulatory mechanism to how self-molecules contribute to dampening of exacerbated inflammatory responses.
    DOI:  https://doi.org/10.1101/2023.12.01.569623
  19. Cancer Immunol Res. 2023 Dec 21. OF1-OF5
    A Metabolic Axis of Immune Intractability.
    Dominique C Hinshaw, Meet Patel, Lalita A Shevde.
      Immune cells in the tumor niche robustly influence disease progression. Remarkably, in cancer, developmental pathways are reenacted. Many parallels between immune regulation of embryonic development and immune regulation of tumor progression can be drawn, with evidence clearly supporting an immune-suppressive microenvironment in both situations. In these ecosystems, metabolic and bioenergetic circuits guide and regulate immune cell differentiation, plasticity, and functional properties of suppressive and inflammatory immune subsets. As such, there is an emerging pattern of intersection across the dynamic process of ontogeny and the ever-evolving tumor neighborhood. In this article, we focus on the convergence of immune programming during ontogeny and in the tumor microenvironment. Exemplifying dysregulation of Hedgehog (Hh) activity, a key player during ontogeny, we highlight a critical convergence of these fields and the metabolic axis of the nutrient sensing hexosamine biosynthetic pathway (HBP) that integrates glucose, glutamine, amino acids, acetyl CoA, and uridine-5'-triphosphate (UTP), culminating in the synthesis of UDP-GlcNAc, a metabolite that functions as a metabolic and bioenergetic sensor. We discuss an emerging pattern of immune regulation, orchestrated by O-GlcNAcylation of key transcriptional regulators, spurring suppressive activity of dysfunctional immune cells in the tumor microenvironment.
    DOI:  https://doi.org/10.1158/2326-6066.CIR-23-0433
  20. Ann Allergy Asthma Immunol. 2024 Jan;pii: S1081-1206(23)01298-X. [Epub ahead of print]132(1): 5-6
    Don't lose sleep over chronic rhinosinusitis with nasal polyps.
    Charlene Dunaway Altamirano, Marc Breidenbaugh, Larry Borish.
      
    DOI:  https://doi.org/10.1016/j.anai.2023.09.012
  21. Microbiome. 2023 Dec 20. 11(1): 277
    A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice.
    Rachel M Bleich, Chuang Li, Shan Sun, Ju-Hyun Ahn, Belgin Dogan, Cassandra J Barlogio, Christopher A Broberg, Adrienne R Franks, Emily Bulik-Sullivan, Ian M Carroll, Kenneth W Simpson, Anthony A Fodor, Janelle C Arthur.
       BACKGROUND: Inflammatory bowel disease (IBD) patients experience recurrent episodes of intestinal inflammation and often follow an unpredictable disease course. Mucosal colonization with adherent-invasive Escherichia coli (AIEC) are believed to perpetuate intestinal inflammation. However, it remains unclear if the 24-year-old AIEC in vitro definition fully predicts mucosal colonization in vivo. To fill this gap, we have developed a novel molecular barcoding approach to distinguish strain variants in the gut and have integrated this approach to explore mucosal colonization of distinct patient-derived E. coli isolates in gnotobiotic mouse models of colitis.
    RESULTS: Germ-free inflammation-susceptible interleukin-10-deficient (Il10-/-) and inflammation-resistant WT mice were colonized with a consortium of AIEC and non-AIEC strains, then given a murine fecal transplant to provide niche competition. E. coli strains isolated from human intestinal tissue were each marked with a unique molecular barcode that permits identification and quantification by barcode-targeted sequencing. 16S rRNA sequencing was used to evaluate the microbiome response to E. coli colonization. Our data reveal that specific AIEC and non-AIEC strains reproducibly colonize the intestinal mucosa of WT and Il10-/- mice. These E. coli expand in Il10-/- mice during inflammation and induce compositional dysbiosis to the microbiome in an inflammation-dependent manner. In turn, specific microbes co-evolve in inflamed mice, potentially diversifying E. coli colonization patterns. We observed no selectivity in E. coli colonization patterns in the fecal contents, indicating minimal selective pressure in this niche from host-microbe and interbacterial interactions. Because select AIEC and non-AIEC strains colonize the mucosa, this suggests the in vitro AIEC definition may not fully predict in vivo colonization potential. Further comparison of seven E. coli genomes pinpointed unique genomic features contained only in highly colonizing strains (two AIEC and two non-AIEC). Those colonization-associated features may convey metabolic advantages (e.g., iron acquisition and carbohydrate consumption) to promote efficient mucosal colonization.
    CONCLUSIONS: Our findings establish the in vivo mucosal colonizer, not necessarily AIEC, as a principal dysbiosis driver through crosstalk with host and associated microbes. Furthermore, we highlight the utility of high-throughput screens to decode the in vivo colonization dynamics of patient-derived bacteria in murine models. Video Abstract.
    Keywords:  AIEC; Adherent-invasive E. coli; Colitis; Inflammatory bowel disease; Interleukin-10-deficient mouse; Intestinal microbiota; Mucosal colonization
    DOI:  https://doi.org/10.1186/s40168-023-01710-y
  22. Sci Adv. 2023 Dec 22. 9(51): eadj1397
    NET formation is a default epigenetic program controlled by PAD4 in apoptotic neutrophils.
    Yanfang Peipei Zhu, Mary Speir, ZheHao Tan, Jamie Casey Lee, Cameron J Nowell, Alyce A Chen, Hajera Amatullah, Ari J Salinger, Carolyn J Huang, Gio Wu, Weiqi Peng, Kasra Askari, Eric Griffis, Majid Ghassemian, Jennifer Santini, Motti Gerlic, William B Kiosses, Sergio D Catz, Hal M Hoffman, Kimberly F Greco, Edie Weller, Paul R Thompson, Lai Ping Wong, Ruslan Sadreyev, Kate L Jeffrey, Ben A Croker.
      Neutrophil extracellular traps (NETs) not only counteract bacterial and fungal pathogens but can also promote thrombosis, autoimmunity, and sterile inflammation. The presence of citrullinated histones, generated by the peptidylarginine deiminase 4 (PAD4), is synonymous with NETosis and is considered independent of apoptosis. Mitochondrial- and death receptor-mediated apoptosis promote gasdermin E (GSDME)-dependent calcium mobilization and membrane permeabilization leading to histone H3 citrullination (H3Cit), nuclear DNA extrusion, and cytoplast formation. H3Cit is concentrated at the promoter in bone marrow neutrophils and redistributes in a coordinated process from promoter to intergenic and intronic regions during apoptosis. Loss of GSDME prevents nuclear and plasma membrane disruption of apoptotic neutrophils but prolongs early apoptosis-induced cellular changes to the chromatin and cytoplasmic granules. Apoptotic signaling engages PAD4 in neutrophils, establishing a cellular state that is primed for NETosis, but that occurs only upon membrane disruption by GSDME, thereby redefining the end of life for neutrophils.
    DOI:  https://doi.org/10.1126/sciadv.adj1397
  23. STAR Protoc. 2023 Dec 19. pii: S2666-1667(23)00743-8. [Epub ahead of print]5(1): 102776
    Protocol for the induction of innate immune memory in human smooth muscle cells and endothelial cells in vitro.
    Jannik Sonnenberg, Dennis Schwarz, Sina Mm Lagache, Lucia Schnack, Helena Körner, Merle Leffers, Hannah Hardege, Yuanyuan Liu, Holger Reinecke, Hannes M Findeisen, Yahya Sohrabi.
      Non-immune cells, like innate immune cells, can develop a memory-like phenotype in response to priming with microbial compounds or certain metabolites, which enables an enhanced response to a secondary unspecific stimulus. This paper describes a step-by-step protocol for the induction and analysis of trained immunity in human endothelial and smooth muscle cells. We then describe steps for cell culture with cryopreserved vascular cells, subcultivation, and induction of trained immunity. We then provide detailed procedures for downstream analysis using ELISA and qPCR. For complete details on the use and execution of this protocol, please refer to Sohrabi et al. (2020)1 and Shcnack et al.2.
    Keywords:  Cell Biology; Immunology; Molecular Biology
    DOI:  https://doi.org/10.1016/j.xpro.2023.102776
  24. Microbes Infect. 2023 Dec 20. pii: S1286-4579(23)00195-8. [Epub ahead of print] 105282
    Transcriptional Regulation of Suppressors of Cytokine Signaling During Infection with Mycobacterium tuberculosis in human THP-1-derived macrophages and in mice.
    Trisha Roy, Anuradha Seth, Hasham Shafi, D V Siva Reddy, Sunil Kumar Raman, J V U S Chakradhar, Sonia Verma, Reena Bharti, Lubna Azmi, Lipika Ray, Amit Misra.
      Mycobacterium tuberculosis (Mtb) infection leads to upregulation of Suppressors of Cytokine signaling (SOCS) expression in host macrophages (Mϕ). SOCS proteins inhibit cytokine signaling by negatively regulating JAK/STAT. We investigated this host-pathogen dialectic at the level of transcription. We used phorbol-differentiated THP-1 Mϕ infected with Mtb to investigate preferential upregulation of some SOCS isoforms that are known to inhibit signaling by IFN-γ, IL-12, and IL-6. We examined time kinetics of likely transcription factors and signaling molecules upstream of SOCS transcription, and survival of intracellular Mtb following SOCS upregulation. Our results suggest a plausible mechanism that involves PGE2 secretion during infection to induce the PKA/CREB axis, culminating in nuclear translocation of C/EBPβ to induce expression of SOCS1. Mtb-infected Mϕ secreted IL-10, suggesting a mechanism of induction of STAT3, which may subsequently induce SOCS3. We provide evidence of temporal variation in SOCS isoform exspression and decay. Small-interfering RNA-mediated knockdown of SOCS1 and SOCS3 restored the pro-inflammatory milieu and reduced Mtb viability. In mice infected with Mtb, SOCS isoforms persisted across Days 28- 87 post infection. Our results suggest that differential temporal regulation of SOCS isoforms by Mtb drives the host immune response towards a phenotype that facilitates the pathogen's survival.
    Keywords:  Mycobacterium tuberculosis H37Rv; SOCS1; SOCS3; host-pathogen interaction; time kinetics; transcription factors
    DOI:  https://doi.org/10.1016/j.micinf.2023.105282
  25. Mol Neurodegener. 2023 Dec 16. 18(1): 95
    Translational profiling identifies sex-specific metabolic and epigenetic reprogramming of cortical microglia/macrophages in APPPS1-21 mice with an antibiotic-perturbed-microbiome.
    Shabana M Shaik, Yajun Cao, Joseph V Gogola, Hemraj B Dodiya, Xulun Zhang, Hejer Boutej, Weinong Han, Jasna Kriz, Sangram S Sisodia.
       BACKGROUND: Microglia, the brain-resident macrophages perform immune surveillance and engage with pathological processes resulting in phenotype changes necessary for maintaining homeostasis. In preceding studies, we showed that antibiotic-induced perturbations of the gut microbiome of APPPS1-21 mice resulted in significant attenuation in Aβ amyloidosis and altered microglial phenotypes that are specific to male mice. The molecular events underlying microglial phenotypic transitions remain unclear. Here, by generating 'APPPS1-21-CD11br' reporter mice, we investigated the translational state of microglial/macrophage ribosomes during their phenotypic transition and in a sex-specific manner.
    METHODS: Six groups of mice that included WT-CD11br, antibiotic (ABX) or vehicle-treated APPPS1-21-CD11br males and females were sacrificed at 7-weeks of age (n = 15/group) and used for immunoprecipitation of microglial/macrophage polysomes from cortical homogenates using anti-FLAG antibody. Liquid chromatography coupled to tandem mass spectrometry and label-free quantification was used to identify newly synthesized peptides isolated from polysomes.
    RESULTS: We show that ABX-treatment leads to decreased Aβ levels in male APPPS1-21-CD11br mice with no significant changes in females. We identified microglial/macrophage polypeptides involved in mitochondrial dysfunction and altered calcium signaling that are associated with Aβ-induced oxidative stress. Notably, female mice also showed downregulation of newly-synthesized ribosomal proteins. Furthermore, male mice showed an increase in newly-synthesized polypeptides involved in FcγR-mediated phagocytosis, while females showed an increase in newly-synthesized polypeptides responsible for actin organization associated with microglial activation. Next, we show that ABX-treatment resulted in substantial remodeling of the epigenetic landscape, leading to a metabolic shift that accommodates the increased bioenergetic and biosynthetic demands associated with microglial polarization in a sex-specific manner. While microglia in ABX-treated male mice exhibited a metabolic shift towards a neuroprotective phenotype that promotes Aβ clearance, microglia in ABX-treated female mice exhibited loss of energy homeostasis due to persistent mitochondrial dysfunction and impaired lysosomal clearance that was associated with inflammatory phenotypes.
    CONCLUSIONS: Our studies provide the first snapshot of the translational state of microglial/macrophage cells in a mouse model of Aβ amyloidosis that was subject to ABX treatment. ABX-mediated changes resulted in metabolic reprogramming of microglial phenotypes to modulate immune responses and amyloid clearance in a sex-specific manner. This microglial plasticity to support neuro-energetic homeostasis for its function based on sex paves the path for therapeutic modulation of immunometabolism for neurodegeneration.
    Keywords:  Alzheimer’s disease; Epigenetics; Inflammation; Macrophage; Metabolism; Microbiome; Microglia; Proteomics; Sex; Translating ribosome affinity purification
    DOI:  https://doi.org/10.1186/s13024-023-00668-7
  26. Int J Mol Sci. 2023 Dec 18. pii: 17583. [Epub ahead of print]24(24):
    How Neutrophils Shape the Immune Response: Reassessing Their Multifaceted Role in Health and Disease.
    Areez Shafqat, Jibran Ahmad Khan, Aghiad Yahya Alkachem, Homaira Sabur, Khaled Alkattan, Ahmed Yaqinuddin, Garwin Kim Sing.
      Neutrophils are the most abundant of the circulating immune cells and are the first to be recruited to sites of inflammation. Neutrophils are a heterogeneous group of immune cells from which are derived extracellular traps (NETs), reactive oxygen species, cytokines, chemokines, immunomodulatory factors, and alarmins that regulate the recruitment and phenotypes of neutrophils, macrophages, dendritic cells, T cells, and B cells. In addition, cytokine-stimulated neutrophils can express class II major histocompatibility complex and the internal machinery necessary for successful antigen presentation to memory CD4+ T cells. This may be relevant in the context of vaccine memory. Neutrophils thus emerge as orchestrators of immune responses that play a key role in determining the outcome of infections, vaccine efficacy, and chronic diseases like autoimmunity and cancer. This review aims to provide a synthesis of current evidence as regards the role of these functions of neutrophils in homeostasis and disease.
    Keywords:  COVID-19; adaptive immunity; antigen-presenting cells; autoimmunity; neutrophil extracellular traps; neutrophils; tumor microenvironment
    DOI:  https://doi.org/10.3390/ijms242417583
  27. Cell. 2023 Dec 13. pii: S0092-8674(23)01317-X. [Epub ahead of print]
    Time-resolved single-cell transcriptomics defines immune trajectories in glioblastoma.
    Daniel Kirschenbaum, Ken Xie, Florian Ingelfinger, Yonatan Katzenelenbogen, Kathleen Abadie, Thomas Look, Fadi Sheban, Truong San Phan, Baoguo Li, Pascale Zwicky, Ido Yofe, Eyal David, Kfir Mazuz, Jinchao Hou, Yun Chen, Hila Shaim, Mayra Shanley, Soeren Becker, Jiawen Qian, Marco Colonna, Florent Ginhoux, Katayoun Rezvani, Fabian J Theis, Nir Yosef, Tobias Weiss, Assaf Weiner, Ido Amit.
      Deciphering the cell-state transitions underlying immune adaptation across time is fundamental for advancing biology. Empirical in vivo genomic technologies that capture cellular dynamics are currently lacking. We present Zman-seq, a single-cell technology recording transcriptomic dynamics across time by introducing time stamps into circulating immune cells, tracking them in tissues for days. Applying Zman-seq resolved cell-state and molecular trajectories of the dysfunctional immune microenvironment in glioblastoma. Within 24 hours of tumor infiltration, cytotoxic natural killer cells transitioned to a dysfunctional program regulated by TGFB1 signaling. Infiltrating monocytes differentiated into immunosuppressive macrophages, characterized by the upregulation of suppressive myeloid checkpoints Trem2, Il18bp, and Arg1, over 36 to 48 hours. Treatment with an antagonistic anti-TREM2 antibody reshaped the tumor microenvironment by redirecting the monocyte trajectory toward pro-inflammatory macrophages. Zman-seq is a broadly applicable technology, enabling empirical measurements of differentiation trajectories, which can enhance the development of more efficacious immunotherapies.
    Keywords:  cancer; computational biology; dynamics; glioblastoma; immunology; immunotherapy; single-cell biology; systems immunology; temporal transcriptomics; tumor-associated-macrophages
    DOI:  https://doi.org/10.1016/j.cell.2023.11.032
  28. Metabolites. 2023 Dec 05. pii: 1184. [Epub ahead of print]13(12):
    From Mother to Infant, from Placenta to Gut: Understanding Varied Microbiome Profiles in Neonates.
    Riadh Cheddadi, Venkata Yeramilli, Colin Martin.
      The field of human microbiome and gut microbial diversity research has witnessed a profound transformation, driven by advances in omics technologies. These advancements have unveiled essential connections between microbiome alterations and severe conditions, prompting the development of new frameworks through epidemiological studies. Traditionally, it was believed that each individual harbored unique microbial communities acquired early in life, evolving over the course of their lifetime, with little acknowledgment of any prenatal microbial development, but recent research challenges this belief. The neonatal microbiome's onset, influenced by factors like delivery mode and maternal health, remains a subject of intense debate, hinting at potential intrauterine microbial processes. In-depth research reveals associations between microbiome profiles and specific health outcomes, ranging from obesity to neurodevelopmental disorders. Understanding these diverse microbiome profiles is essential for unraveling the intricate relationships between the microbiome and health outcomes.
    Keywords:  animal models; maternal influence; maternal microbiome; metabolites; microbiome transfer; neonatal microbiome; omics; pregnancy
    DOI:  https://doi.org/10.3390/metabo13121184
  29. Tissue Eng Regen Med. 2023 Dec 19.
    An Organotypic Human Lymph Node Model Reveals the Importance of Fibroblastic Reticular Cells for Dendritic Cell Function.
    Andrew I Morrison, Aleksandra M Mikula, Sander W Spiekstra, Michael de Kok, Alsya J Affandi, Henk P Roest, Luc J W van der Laan, Charlotte M de Winde, Jasper J Koning, Susan Gibbs, Reina E Mebius.
       BACKGROUND: Human lymph node (HuLN) models have emerged with invaluable potential for immunological research and therapeutic application given their fundamental role in human health and disease. While fibroblastic reticular cells (FRCs) are instrumental to HuLN functioning, their inclusion and recognition of importance for organotypic in vitro lymphoid models remain limited.
    METHODS: Here, we established an in vitro three-dimensional (3D) model in a collagen-fibrin hydrogel with primary FRCs and a dendritic cell (DC) cell line (MUTZ-3 DC). To study and characterise the cellular interactions seen in this 3D FRC-DC organotypic model compared to the native HuLN; flow cytometry, immunohistochemistry, immunofluorescence and cytokine/chemokine analysis were performed.
    RESULTS: FRCs were pivotal for survival, proliferation and localisation of MUTZ-3 DCs. Additionally, we found that CD1a expression was absent on MUTZ-3 DCs that developed in the presence of FRCs during cytokine-induced MUTZ-3 DC differentiation, which was also seen with primary monocyte-derived DCs (moDCs). This phenotype resembled HuLN-resident DCs, which we detected in primary HuLNs, and these CD1a- MUTZ-3 DCs induced T cell proliferation within a mixed leukocyte reaction (MLR), indicating a functional DC status. FRCs expressed podoplanin (PDPN), CD90 (Thy-1), CD146 (MCAM) and Gremlin-1, thereby resembling the DC supporting stromal cell subset identified in HuLNs.
    CONCLUSION: This 3D FRC-DC organotypic model highlights the influence and importance of FRCs for DC functioning in a more realistic HuLN microenvironment. As such, this work provides a starting point for the development of an in vitro HuLN.
    Keywords:  Dendritic cells; Fibroblastic reticular cells; Human immunology; Lymph nodes; Organotypic models
    DOI:  https://doi.org/10.1007/s13770-023-00609-x
  30. Inflamm Res. 2023 Dec 23.
    Salmonella spvC gene suppresses macrophage/neutrophil antibacterial defense mediated by gasdermin D.
    Liting Zhou, Yuanyuan Li, Jiayi You, Chaoyi Wu, Lingli Zuo, Yilin Chen, Li Kang, Zhengyu Zhou, Rui Huang, Shuyan Wu.
       OBJECTIVE: Salmonella enterica serovar Typhimurium (S. Typhimurium) is a representative model organism for investigating host-pathogen interactions. It was reported that S. Typhimurium spvC gene alleviated intestinal inflammation to aggravate systemic infection, while the precise mechanisms remain unclear. In this study, the influence of spvC on the antibacterial defense of macrophage/neutrophil mediated by gasdermin D (GSDMD) was investigated.
    METHODS: Mouse macrophage-like cell lines J774A.1 and RAW264.7, neutrophil-like cells derived from HL-60 cells (human promyletic leukemia cell lines) were infected with S. Typhimurium wild type, spvC deletion and complemented strains. Cell death was evaluated by LDH release and Annexin V-FITC/PI staining. Macrophage pyroptosis and neutrophil NETosis were detected by western blotting, live cell imaging and ELISA. Flow cytometry was used to assess the impact of spvC on macrophage-neutrophil cooperation in macrophage (dTHP-1)-neutrophil (dHL-60) co-culture model pretreated with GSDMD inhibitor disulfiram. Wild-type and Gsdmd-/- C57BL/6J mice were utilized for in vivo assay. The degree of phagocytes infiltration and inflammation were analyzed by immunofluorescence and transmission electron microscopy.
    RESULTS: Here we find that spvC inhibits pyroptosis in macrophages via Caspase-1/Caspase-11 dependent canonical and non-canonical pathways, and restrains neutrophil extracellular traps extrusion in GSDMD-dependent manner. Moreover, spvC could ameliorate macrophages/neutrophils infiltration and cooperation in the inflammatory response mediated by GSDMD to combat Salmonella infection.
    CONCLUSIONS: Our findings highlight the antibacterial activity of GSDMD in phagocytes and reveal a novel pathogenic mechanism employed by spvC to counteract this host defense, which may shed new light on designing effective therapeutics to control S. Typhimurium infection.
    Keywords:  Gasdermin D; Macrophage; Neutrophil; Salmonella spvC
    DOI:  https://doi.org/10.1007/s00011-023-01818-9
  31. J Immunol. 2023 Dec 20. pii: ji2300256. [Epub ahead of print]
    A Bacterial and Ganglioside-based Nanoparticle Initiates Reprogramming of Macrophages and Promotes Antitumor Phenotypes.
    Rydell Alvarez-Arzola, Liliana Oliver, Michelle M Messmer, Danielle Y F Twum, Kelvin P Lee, Jason B Muhitch, Circe Mesa, Scott I Abrams.
      Macrophages represent the most abundant immune component of the tumor microenvironment and often exhibit protumorigenic (M2-like) phenotypes that contribute to disease progression. Despite their generally accepted protumorigenic role, macrophages can also display tumoricidal (or M1-like) behavior, revealing that macrophages can be functionally reprogrammed, depending on the cues received within the tumor microenvironment. Moreover, such plasticity may be achieved by pharmacologic or biologic interventions. To that end, we previously demonstrated that a novel immunomodulator termed the "very small size particle" (VSSP) facilitates maturation of dendritic cells and differentiation of myeloid-derived suppressor cells to APCs with reduced suppressive activity in cancer models. VSSP was further shown to act in the bone marrow to drive the differentiation of progenitors toward monocytes, macrophages, and dendritic cells during emergency myelopoiesis. However, the underlying mechanisms for VSSP-driven alterations in myeloid differentiation and function remained unclear. In this study, in mouse models, we focused on macrophages and tested the hypothesis that VSSP drives macrophages toward M1-like functional states via IRF8- and PU.1-dependent mechanisms. We further hypothesized that such VSSP-mediated actions would be accompanied by enhanced antitumor responses. Overall, we showed that (1) VSSP drives naive or M2-derived macrophages to M1-like states, (2) the M1-like state induced by VSSP occurs via IRF8- and PU.1-dependent mechanisms, and (3) single-agent VSSP induces an antitumor response that is accompanied by alterations in the intratumoral myeloid compartment. These results provide a deeper mechanistic underpinning of VSSP and strengthen its use to drive M1-like responses in host defense, including cancer.
    DOI:  https://doi.org/10.4049/jimmunol.2300256
  32. Sci Immunol. 2023 Dec 15. 8(90): eadf9988
    Early human lung immune cell development and its role in epithelial cell fate.
    Josephine L Barnes, Masahiro Yoshida, Peng He, Kaylee B Worlock, Rik G H Lindeboom, Chenqu Suo, J Patrick Pett, Anna Wilbrey-Clark, Emma Dann, Lira Mamanova, Laura Richardson, Krzysztof Polanski, Adam Pennycuick, Jessica Allen-Hyttinen, Iván T Herczeg, Romina Arzili, Robert E Hynds, Vitor H Teixeira, Muzlifah Haniffa, Kyungtae Lim, Dawei Sun, Emma L Rawlins, Amanda J Oliver, Paul A Lyons, John C Marioni, Christiana Ruhrberg, Zewen Kelvin Tuong, Menna R Clatworthy, James L Reading, Sam M Janes, Sarah A Teichmann, Kerstin B Meyer, Marko Z Nikolić.
      Studies of human lung development have focused on epithelial and mesenchymal cell types and function, but much less is known about the developing lung immune cells, even though the airways are a major site of mucosal immunity after birth. An unanswered question is whether tissue-resident immune cells play a role in shaping the tissue as it develops in utero. Here, we profiled human embryonic and fetal lung immune cells using scRNA-seq, smFISH, and immunohistochemistry. At the embryonic stage, we observed an early wave of innate immune cells, including innate lymphoid cells, natural killer cells, myeloid cells, and lineage progenitors. By the canalicular stage, we detected naive T lymphocytes expressing high levels of cytotoxicity genes and the presence of mature B lymphocytes, including B-1 cells. Our analysis suggests that fetal lungs provide a niche for full B cell maturation. Given the presence and diversity of immune cells during development, we also investigated their possible effect on epithelial maturation. We found that IL-1β drives epithelial progenitor exit from self-renewal and differentiation to basal cells in vitro. In vivo, IL-1β-producing myeloid cells were found throughout the lung and adjacent to epithelial tips, suggesting that immune cells may direct human lung epithelial development.
    DOI:  https://doi.org/10.1126/sciimmunol.adf9988
  33. Cell Rep. 2023 Nov 28. pii: 113345. [Epub ahead of print]42(11):
    CD115+ monocytes protect microbially experienced mice against E. coli-induced sepsis.
    Matthew D Martin, Cara Skon-Hegg, Caleb Y Kim, Julie Xu, Tamara A Kucaba, Whitney Swanson, Mark J Pierson, Jesse W Williams, Vladimir P Badovinac, Steven S Shen, Molly A Ingersoll, Thomas S Griffith.
      Uropathogenic E. coli (UPEC) is a primary organism responsible for urinary tract infections and a common cause of sepsis. Microbially experienced laboratory mice, generated by cohousing with pet store mice, exhibit increased morbidity and mortality to polymicrobial sepsis or lipopolysaccharide challenge. By contrast, cohoused mice display significant resistance, compared with specific pathogen-free mice, to a monomicrobial sepsis model using UPEC. CD115+ monocytes mediate protection in the cohoused mice, as depletion of these cells leads to increased mortality and UPEC pathogen burden. Further study of the cohoused mice reveals increased TNF-α production by monocytes, a skewing toward Ly6ChiCD115+ "classical" monocytes, and enhanced egress of Ly6ChiCD115+ monocytes from the bone marrow. Analysis of cohoused bone marrow also finds increased frequency and number of myeloid multipotent progenitor cells. These results show that a history of microbial exposure impacts innate immunity in mice, which can have important implications for the preclinical study of sepsis.
    DOI:  https://doi.org/10.1016/j.celrep.2023.113345
  34. Nat Rev Mol Cell Biol. 2023 Dec 18.
    A guide to cell death pathways.
    Junying Yuan, Dimitry Ofengeim.
      Regulated cell death mediated by dedicated molecular machines, known as programmed cell death, plays important roles in health and disease. Apoptosis, necroptosis and pyroptosis are three such programmed cell death modalities. The caspase family of cysteine proteases serve as key regulators of programmed cell death. During apoptosis, a cascade of caspase activation mediates signal transduction and cellular destruction, whereas pyroptosis occurs when activated caspases cleave gasdermins, which can then form pores in the plasma membrane. Necroptosis, a form of caspase-independent programmed necrosis mediated by RIPK3 and MLKL, is inhibited by caspase-8-mediated cleavage of RIPK1. Disruption of cellular homeostatic mechanisms that are essential for cell survival, such as normal ionic and redox balance and lysosomal flux, can also induce cell death without invoking programmed cell death mechanisms. Excitotoxicity, ferroptosis and lysosomal cell death are examples of such cell death modes. In this Review, we provide an overview of the major cell death mechanisms, highlighting the latest insights into their complex regulation and execution, and their relevance to human diseases.
    DOI:  https://doi.org/10.1038/s41580-023-00689-6
  35. Front Immunol. 2023 ;14 1328484
    The multi-faceted role of NADPH in regulating inflammation in activated myeloid cells.
    Kenneth K Y Ting, Jenny Jongstra-Bilen, Myron I Cybulsky.
      Recent advances in the immunometabolism field have demonstrated the importance of metabolites in fine-tuning the inflammatory responses in myeloid cells. Cofactors, which are metabolites comprised of inorganic ions and organic molecules, may tightly or loosely bind to distinct sites of enzymes to catalyze a specific reaction. Since many enzymes that mediate inflammatory and anti-inflammatory processes require the same cofactors to function, this raises the possibility that under conditions where the abundance of these cofactors is limited, inflammatory and anti-inflammatory enzymes must compete with each other for the consumption of cofactors. Thus, this competition may reflect a naturally evolved mechanism to efficiently co-regulate inflammatory versus anti-inflammatory pathways, fine-tuning the extent of an inflammatory response. The role of NADPH, the reduced form of nicotinamide adenine dinucleotide phosphate (NADP+), in mediating inflammatory and anti-inflammatory responses in activated myeloid cells has been well-established in the past decades. However, how the dynamic of NADPH consumption mediates the co-regulation between individual inflammatory and anti-inflammatory pathways is only beginning to be appreciated. In this review, we will summarize the established roles of NADPH in supporting inflammatory and anti-inflammatory pathways, as well as highlight how the competition for NADPH consumption by these opposing pathways fine-tunes the inflammatory response in activated myeloid cells.
    Keywords:  LPS (lipopolysaccharide); NADPH; cofactor coordination; cofactors; dendritic cells; immunometabolism; macrophages; myeloid cells
    DOI:  https://doi.org/10.3389/fimmu.2023.1328484
  36. Am J Physiol Endocrinol Metab. 2023 Dec 20.
    Monocyte immunometabolic reprogramming in human pregnancy: contribution of trophoblast cells.
    Fátima Merech, Soledad Gori, Guillermina Calo, Vanesa Hauk, Daniel Paparini, Daiana Rios, Brenda Lara, Luciana Doga, Luciana D'Eramo, Aldo Squassi, Rossana Ramhorst, Rafael J Argüello, Claudia Pérez Leirós, Daiana Vota.
      Immunometabolism research is uncovering the relationship between metabolic features and immune cell functions in physiological and pathological conditions. Normal pregnancy entails a fine immune and metabolic regulation of the maternal-fetal interaction to assist the energetic demands of the fetus with immune homeostasis maintenance. Here, we determined the immunometabolic status of monocytes of pregnant women compared to non-pregnant controls and its impact on monocyte antiinflammatory functions such as efferocytosis. Monocytes from pregnant women (16-20 weeks) and non-pregnant age-matched controls were studied. Single cell-based metabolic assays using freshly isolated monocytes from both groups were carried out in parallel with functional assays ex vivo to evaluate monocyte efferocytic capacity. On the other hand, various in vitro metabolic assays with human monocytes or monocyte-derived macrophages were designed to explore the effect of trophoblast cells in the profiles observed. We found that pregnancy alters monocyte metabolism and function. An increased glucose dependency and enhanced efferocytosis were detected in monocytes from pregnant women at resting states, compared to non-pregnant controls. Furthermore, monocytes display a reduced glycolytic response when stimulated with LPS. The metabolic profiling of monocytes at this stage of pregnancy was comparable with the immunometabolic phenotypes of human monocytes treated in vitro with human first trimester trophoblast cell conditioned media. These findings suggest that immunometabolic mechanisms are involved in the functional shaping of monocytes during pregnancy with a contribution of trophoblast cells. Results provide new clues for future hypotheses regarding pregnancies complicated by metabolic disorders.
    Keywords:  Early pregnancy; Glucose metabolism; Immunometabolism; Monocytes; Trophoblast soluble factors
    DOI:  https://doi.org/10.1152/ajpendo.00357.2023
  37. Crit Rev Microbiol. 2023 Dec 23. 1-25
    Group A Streptococcus adaptation to diverse niches: lessons from transcriptomic studies.
    Lionel Schiavolin, Geoffrey Deneubourg, Jenny Steinmetz, Pierre R Smeesters, Anne Botteaux.
      Group A Streptococcus (GAS) is a major human pathogen, causing diseases ranging from mild superficial infections of the skin and pharyngeal epithelium to severe systemic and invasive diseases. Moreover, post infection auto-immune sequelae arise by a yet not fully understood mechanism. The ability of GAS to cause a wide variety of infections is linked to the expression of a large set of virulence factors and their transcriptional regulation in response to various physiological environments. The use of transcriptomics, among others -omics technologies, in addition to traditional molecular methods, has led to a better understanding of GAS pathogenesis and host adaptation mechanisms. This review focusing on bacterial transcriptomic provides new insight into gene-expression patterns in vitro, ex vivo and in vivo with an emphasis on metabolic shifts, virulence genes expression and transcriptional regulators role.
    Keywords:  Gene expression; Streptococcus pyogenes; host–pathogen interaction; niche adaptation
    DOI:  https://doi.org/10.1080/1040841X.2023.2294905
  38. Clin Transl Med. 2023 Dec;13(12): e1507
    Single-cell immune profiling reveals markers of emergency myelopoiesis that distinguish severe from mild respiratory syncytial virus disease in infants.
    RESCEU Investigators
      Whereas most infants infected with respiratory syncytial virus (RSV) show no or only mild symptoms, an estimated 3 million children under five are hospitalized annually due to RSV disease. This study aimed to investigate biological mechanisms and associated biomarkers underlying RSV disease heterogeneity in young infants, enabling the potential to objectively categorize RSV-infected infants according to their medical needs. Immunophenotypic and functional profiling demonstrated the emergence of immature and progenitor-like neutrophils, proliferative monocytes (HLA-DRLow , Ki67+), impaired antigen-presenting function, downregulation of T cell response and low abundance of HLA-DRLow B cells in severe RSV disease. HLA-DRLow monocytes were found as a hallmark of RSV-infected infants requiring hospitalization. Complementary transcriptomics identified genes associated with disease severity and pointed to the emergency myelopoiesis response. These results shed new light on mechanisms underlying the pathogenesis and development of severe RSV disease and identified potential new candidate biomarkers for patient stratification.
    DOI:  https://doi.org/10.1002/ctm2.1507
  39. Cell Mol Immunol. 2023 Dec 20.
    The RNA m6A demethylase ALKBH5 drives emergency granulopoiesis and neutrophil mobilization by upregulating G-CSFR expression.
    Yang Liu, Renjie Song, Zhike Lu, Lu Zhao, Xinyi Zhan, Yini Li, Xuetao Cao.
      Emergency granulopoiesis and neutrophil mobilization that can be triggered by granulocyte colony-stimulating factor (G-CSF) through its receptor G-CSFR are essential for antibacterial innate defense. However, the epigenetic modifiers crucial for intrinsically regulating G-CSFR expression and the antibacterial response of neutrophils remain largely unclear. N6-methyladenosine (m6A) RNA modification and the related demethylase alkB homolog 5 (ALKBH5) are key epigenetic regulators of immunity and inflammation, but their roles in neutrophil production and mobilization are still unknown. We used cecal ligation and puncture (CLP)-induced polymicrobial sepsis to model systemic bacterial infection, and we report that ALKBH5 is required for emergency granulopoiesis and neutrophil mobilization. ALKBH5 depletion significantly impaired the production of immature neutrophils in the bone marrow of septic mice. In addition, Alkbh5-deficient septic mice exhibited higher retention of mature neutrophils in the bone marrow and defective neutrophil release into the circulation, which led to fewer neutrophils at the infection site than in their wild-type littermates. During bacterial infection, ALKBH5 imprinted production- and mobilization-promoting transcriptome signatures in both mouse and human neutrophils. Mechanistically, ALKBH5 erased m6A methylation on the CSF3R mRNA to increase the mRNA stability and protein expression of G-CSFR, consequently upregulating cell surface G-CSFR expression and downstream STAT3 signaling in neutrophils. The RIP-qPCR results confirmed the direct binding of ALKBH5 to the CSF3R mRNA, and the binding strength declined upon bacterial infection, accounting for the decrease in G-CSFR expression on bacteria-infected neutrophils. Considering these results collectively, we define a new role of ALKBH5 in intrinsically driving neutrophil production and mobilization through m6A demethylation-dependent posttranscriptional regulation, indicating that m6A RNA modification in neutrophils is a potential target for treating bacterial infections and neutropenia.
    Keywords:  ALKBH5; Emergency granulopoiesis; G-CSF receptor; Neutrophil mobilization; m6A RNA modification
    DOI:  https://doi.org/10.1038/s41423-023-01115-9
  40. Antibiotics (Basel). 2023 Dec 14. pii: 1732. [Epub ahead of print]12(12):
    Gut-Antimicrobial Peptides: Synergistic Co-Evolution with Antibiotics to Combat Multi-Antibiotic Resistance.
    Piyush Baindara, Santi M Mandal.
      Due to huge diversity and dynamic competition, the human gut microbiome produces a diverse array of antimicrobial peptides (AMPs) that play an important role in human health. The gut microbiome has an important role in maintaining gut homeostasis by the AMPs and by interacting with other human organs via established connections such as the gut-lung, and gut-brain axis. Additionally, gut AMPs play a synergistic role with other gut microbiota and antimicrobials to maintain gut homeostasis by fighting against multi-antibiotic resistance (MAR) bacteria. Further, conventional antibiotics intake creates a synergistic evolutionary pressure for gut AMPs, where antibiotics and gut AMPs fight synergistically against MAR. Overall, gut AMPs are evolving under a complex and highly synergistic co-evolutionary pressure created by the various interactions between gut microbiota, gut AMPs, and antibiotics; however, the complete mechanism is not well understood. The current review explores the synergistic action of gut AMPs and antibiotics along with possibilities to fight against MAR bacteria.
    Keywords:  co-evolution; gut microbiota; gut peptides; multi-antibiotic resistance
    DOI:  https://doi.org/10.3390/antibiotics12121732
  41. J Biol Chem. 2023 Dec 14. pii: S0021-9258(23)02594-2. [Epub ahead of print] 105566
    CTRP6 promotes the macrophage inflammatory response, and its deficiency attenuates LPS-induced inflammation.
    Cheng Xu, Dylan C Sarver, Xia Lei, Ageline Sahagun, Jun Zhong, Chan Hyun Na, Assaf Rudich, G William Wong.
      Macrophages play critical roles in inflammation and tissue homeostasis, and their functions are regulated by various autocrine, paracrine, and endocrine factors. We have previously shown that CTRP6, a secreted protein of the C1q family, targets both adipocytes and macrophages to promote obesity-linked inflammation. However, the gene programs and signaling pathways directly regulated by CTRP6 in macrophages remain unknown. Here, we combine transcriptomic and phosphoproteomic analyses to show that CTRP6 activates inflammatory gene programs and signaling pathways in mouse bone marrow-derived macrophages (BMDMs). Treatment of BMDMs with CTRP6 upregulated proinflammatory, and suppressed the anti-inflammatory, gene expression. We also showed that CTRP6 activates p44/42-MAPK, p38-MAPK, and NF-κB signaling pathways to promote inflammatory cytokine secretion from BMDMs, and that pharmacologic inhibition of these signaling pathways markedly attenuated the effects of CTRP6. Pretreatment of BMDMs with CTRP6 also sensitized and potentiated the BMDMs response to LPS-induced inflammatory signaling and cytokine secretion. Consistent with the metabolic phenotype of proinflammatory macrophages, CTRP6 treatment induced a shift toward aerobic glycolysis and lactate production, reduced oxidative metabolism, and elevated mitochondrial ROS production in BMDMs. Importantly, in accordance with our in vitro findings, BMDMs from CTRP6-deficient mice were less inflammatory at baseline and showed a marked suppression of LPS-induced inflammatory gene expression and cytokine secretion. Finally, loss of CTRP6 in mice also dampened LPS-induced inflammation and hypothermia. Collectively, our findings suggest that CTRP6 regulates and primes the macrophage response to inflammatory stimuli and thus may have a role in modulating tissue inflammatory tone in different physiological and disease contexts.
    Keywords:  CTRP; LPS; inflammation; macrophage; phosphoproteomics; signaling; transcriptomics
    DOI:  https://doi.org/10.1016/j.jbc.2023.105566
  42. Nat Commun. 2023 Dec 21. 14(1): 8507
    Distinct gene expression signatures comparing latent tuberculosis infection with different routes of Bacillus Calmette-Guérin vaccination.
    Richard F Silver, Mei Xia, Chad E Storer, Jessica R Jarvela, Michelle C Moyer, Azra Blazevic, David A Stoeckel, Erin K Rakey, Jan M Tennant, Johannes B Goll, Richard D Head, Daniel F Hoft.
      Tuberculosis remains an international health threat partly because of limited protection from pulmonary tuberculosis provided by standard intradermal vaccination with Bacillus of Calmette and Guérin (BCG); this may reflect the inability of intradermal vaccination to optimally induce pulmonary immunity. In contrast, respiratory Mycobacterium tuberculosis infection usually results in the immune-mediated bacillary containment of latent tuberculosis infection (LTBI). Here we present RNA-Seq-based assessments of systemic and pulmonary immune cells from LTBI participants and recipients of intradermal and oral BCG. LTBI individuals uniquely display ongoing immune activation and robust CD4 T cell recall responses in blood and lung. Intradermal BCG is associated with robust systemic immunity but only limited pulmonary immunity. Conversely, oral BCG induces limited systemic immunity but distinct pulmonary responses including enhanced inflammasome activation potentially associated with mucosal-associated invariant T cells. Further, IL-9 is identified as a component of systemic immunity in LTBI and intradermal BCG, and pulmonary immunity following oral BCG.
    DOI:  https://doi.org/10.1038/s41467-023-44136-8
  43. Adv Healthc Mater. 2023 Dec 20. e2302835
    Extracellular Proteins Isolated from L. acidophilus as an Osteomicrobiological Therapeutic Agent to Reduce Pathogenic Biofilm Formation, Regulate Chronic Inflammation, and Augment Bone Formation In Vitro.
    Abinaya Sindu Pugazhendhi, Anouska Seal, Megan Hughes, Udit Kumar, Elayaraja Kolanthai, Fei Wei, Jonathan D Schwartzman, Melanie J Coathup.
      Periprosthetic joint infection (PJI) is a challenging complication that can occur following joint replacement surgery. Efficacious strategies to prevent and treat PJI and its recurrence remain elusive, and a novel resolution is urgently needed. Commensal bacteria within the gut microbiota convey beneficial effects by contributing to a defense strategy named "colonization resistance" thereby preventing pathogenic infection and overgrowth along the intestinal surface. This blueprint may be applicable to PJI. Here, the aim was to investigate Lactobacillus acidophilus spp. and primarily, isolated extracellular-derived L. acidophilus proteins (LaEPs) on PJI relevant S. aureus, MRSA, and E. coli planktonic growth and biofilm formation in vitro. The effect of LaEPs on cultured RAW264.7 macrophages and osteogenic, and adipogenic hBMSC differentiation was also analyzed. Data show electrostatically-induced probiotic-pathogen species co-aggregation and pathogenic growth inhibition together with LaEP-induced biofilm prevention. LaEPs activated macrophages priming them for enhanced microbial phagocytosis via cathepsin K, reduced lipopolysaccharide-induced DNA damage and RANKL expression, and promoted a reparative M2 macrophage morphology when under chronic inflammatory conditions. Our data also show LaEPs significantly augmented bone deposition while abating adipogenesis thus holding promise as a potential multimodal therapeutic strategy. Proteomic analyses highlight high abundance of lysyl endopeptidase, urocanate reductase, uridylate kinase, large ribosomal subunit protein bL12, and polyketide synthase. Further in vivo analyses are warranted to elucidate their role in the prevention and treatment of PJIs. This article is protected by copyright. All rights reserved.
    Keywords:  Implant infection; Lactobacillus; adipogenesis; bone; gut microbiota; inflammation; osteogenesis
    DOI:  https://doi.org/10.1002/adhm.202302835
  44. Nat Rev Genet. 2023 Dec 15.
    Spatial resolution of host-microbiome interactions.
    Kirsty Minton.
      
    DOI:  https://doi.org/10.1038/s41576-023-00687-6
  45. J Invest Dermatol. 2023 Dec 20. pii: S0022-202X(23)03190-1. [Epub ahead of print]
    CD69 is indispensable for the development of functional local immune memory in murine contact hypersensitivity.
    Shuichi Nakai, Miki Kume, Yutaka Matsumura, Hanako Koguchi-Yoshioka, Shoichi Matsuda, Manabu Fujimoto, Rei Watanabe.
      Local immune memory develops at the site of antigen exposure and facilitates a rapid and strong local adaptive defense upon re-exposure. Resident memory T cells (TRM) play a role in local immune memory, and their cell-surface molecules CD69 and CD103 promote their tissue residency. However, the contribution of these molecules to skin immune memory remains unclear. Here, by inducing CHS in CD69-deficient (CD69KO) and CD103-deficient mice, where different degrees of TRM contribution are observed by repeated challenges on the right ear and a single challenge on the left ear, we found that the deficiency of CD69 but not CD103, leads to impaired CHS upon repeated antigen challenges, even although TRM-like CD8 T cells developed at the challenged site of CD69KO. CHS responses in both ears were diminished in CD69KO by FTY720 or CD8 neutralization, suggesting that CHS in CD69KO is ascribed to circulating CD8 T cells and that the developed TRM-like CD8 T cells do not behave as TRM. The infiltration of macrophages was reduced in the re-challenged site of CD69KO, along with the downregulation of Cxcl1 and Cxcl2. Thus, CD69 is considered essential for an effective recall response, involving the development of functional TRM and the recruitment of macrophages.
    Keywords:  contact hypersensitivity; local immune memory; resident memory T cells
    DOI:  https://doi.org/10.1016/j.jid.2023.11.015
  46. Elife. 2023 Dec 21. pii: e86269. [Epub ahead of print]12
    Apoptosis recognition receptors regulate skin tissue repair in mice.
    Olivia Justynski, Kate Bridges, Will Krause, Maria Fernanda Forni, Quan M Phan, Teresa Sandoval-Schaefer, Kristyn Carter, Diane E King, Henry C Hsia, Michael I Gazes, Steven D Vyce, Ryan R Driskell, Kathryn Miller-Jensen, Valerie Horsley.
      Apoptosis and clearance of apoptotic cells via efferocytosis are evolutionarily conserved processes that drive tissue repair. However, the mechanisms by which recognition and clearance of apoptotic cells regulate repair are not fully understood. Here, we use single-cell RNA sequencing to provide a map of the cellular dynamics during early inflammation in mouse skin wounds. We find that apoptotic pathways and efferocytosis receptors are elevated in fibroblasts and immune cells, including resident Lyve1+ macrophages, during inflammation. Interestingly, human diabetic foot wounds upregulate mRNAs for efferocytosis pathway genes and display altered efferocytosis signaling via the receptor Axl and its ligand Gas6. During early inflammation in mouse wounds, we detect upregulation of Axl in dendritic cells and fibroblasts via TLR3-independent mechanisms. Inhibition studies in vivo in mice reveal that Axl signaling is required for wound repair but is dispensable for efferocytosis. By contrast, inhibition of another efferocytosis receptor, Timd4, in mouse wounds decreases efferocytosis and abrogates wound repair. These data highlight the distinct mechanisms by which apoptotic cell detection coordinates tissue repair and provides potential therapeutic targets for chronic wounds in diabetic patients.
    Keywords:  apoptosis; cell biology; efferocytosis; human; immunology; inflammation; mouse; repair; skin; wound healing
    DOI:  https://doi.org/10.7554/eLife.86269
  47. Cancers (Basel). 2023 Dec 12. pii: 5810. [Epub ahead of print]15(24):
    Experimental Modeling of Host-Bacterial Interactions in Head and Neck Squamous Cell Carcinoma.
    Ogoegbunam Okolo, Emily Honzel, William R Britton, Victoria X Yu, Samuel Flashner, Cecilia Martin, Hiroshi Nakagawa, Anuraag S Parikh.
      The microscopic species colonizing the human body, collectively referred to as the microbiome, play a crucial role in the maintenance of tissue homeostasis, immunity, and the development of disease. There is evidence to suggest associations between alterations in the microbiome and the development of head and neck squamous cell carcinomas (HNSCC). The use of two-dimensional (2D) modeling systems has made significant strides in uncovering the role of microbes in carcinogenesis; however, direct mechanistic links remain in their infancy. Patient-derived three-dimensional (3D) HNSCC organoid and organotypic models have recently been described. Compared to 2D models, 3D organoid culture systems effectively capture the genetic and epigenetic features of parent tissue in a patient-specific manner and may offer a more nuanced understanding of the role of host-microbe responses in carcinogenesis. This review provides a topical literature review assessing the current state of the field investigating the role of the microbiome in HNSCC; including in vivo and in vitro modeling methods that may be used to characterize microbiome-epithelial interactions.
    Keywords:  3D organoids; head and neck squamous cell carcinoma; in vitro modeling; microbiome; organotypic culture systems
    DOI:  https://doi.org/10.3390/cancers15245810
  48. Cell Rep. 2023 Dec 15. pii: S2211-1247(23)01593-0. [Epub ahead of print]42(12): 113581
    The tetrapeptide sequence of IL-18 and IL-1β regulates their recruitment and activation by inflammatory caspases.
    Patrick M Exconde, Claudia Hernandez-Chavez, Christopher M Bourne, Rachel M Richards, Mark B Bray, Jan L Lopez, Tamanna Srivastava, Marisa S Egan, Jenna Zhang, William Yoo, Sunny Shin, Bohdana M Discher, Cornelius Y Taabazuing.
      Inflammasomes are multiprotein signaling complexes that activate the innate immune system. Canonical inflammasomes recruit and activate caspase-1, which then cleaves and activates IL-1β and IL-18, as well as gasdermin D (GSDMD) to induce pyroptosis. In contrast, non-canonical inflammasomes, caspases-4/-5 (CASP4/5) in humans and caspase-11 (CASP11) in mice, are known to cleave GSDMD, but their role in direct processing of other substrates besides GSDMD has remained unknown. Here, we show that CASP4/5 but not CASP11 can directly cleave and activate IL-18. However, CASP4/5/11 can all cleave IL-1β to generate a 27-kDa fragment that deactivates IL-1β signaling. Mechanistically, we demonstrate that the sequence identity of the tetrapeptide sequence adjacent to the caspase cleavage site regulates IL-18 and IL-1β recruitment and activation. Altogether, we have identified new substrates of the non-canonical inflammasomes and reveal key mechanistic details regulating inflammation that may aid in developing new therapeutics for immune-related disorders.
    Keywords:  CP: Immunology; IL-18; IL-1β; caspase-1; caspase-11; caspase-4; caspase-5; cytokines; inflammasomes; pyroptosis
    DOI:  https://doi.org/10.1016/j.celrep.2023.113581
  49. Cell Metab. 2023 Dec 12. pii: S1550-4131(23)00460-6. [Epub ahead of print]
    Nutrient inputs and social metabolic control of T cell fate.
    Zachary A Bacigalupa, Madelyn D Landis, Jeffrey C Rathmell.
      Cells in multicellular organisms experience diverse neighbors, signals, and evolving physical environments that drive functional and metabolic demands. To maintain proper development and homeostasis while avoiding inappropriate cell proliferation or death, individual cells interact with their neighbors via "social" cues to share and partition available nutrients. Metabolic signals also contribute to cell fate by providing biochemical links between cell-extrinsic signals and available resources. In addition to metabolic checkpoints that sense nutrients and directly supply molecular intermediates for biosynthetic pathways, many metabolites directly signal or provide the basis for post-translational modifications of target proteins and chromatin. In this review, we survey the landscape of T cell nutrient sensing and metabolic signaling that supports proper immunity while avoiding immunodeficiency or autoimmunity. The integration of cell-extrinsic microenvironmental cues with cell-intrinsic metabolic signaling provides a social metabolic control model to integrate cell signaling, metabolism, and fate.
    Keywords:  T cells; epigenetics; immunometabolism; metabolic signaling; social control model
    DOI:  https://doi.org/10.1016/j.cmet.2023.12.009
  50. Int J Mol Sci. 2023 Dec 18. pii: 17620. [Epub ahead of print]24(24):
    How Can Imbalance in Oral Microbiota and Immune Response Lead to Dental Implant Problems?
    Mansur Rahnama-Hezavah, Paulina Mertowska, Sebastian Mertowski, Julia Skiba, Karol Krawiec, Michał Łobacz, Ewelina Grywalska.
      Dental implantology is one of the most dynamically developing fields of dentistry, which, despite developing clinical knowledge and new technologies, is still associated with many complications that may lead to the loss of the implant or the development of the disease, including peri-implantitis. One of the reasons for this condition may be the fact that dental implants cannot yield a proper osseointegration process due to the development of oral microbiota dysbiosis and the accompanying inflammation caused by immunological imbalance. This study aims to present current knowledge as to the impact of oral microflora dysbiosis and deregulation of the immune system on the course of failures observed in dental implantology. Evidence points to a strong correlation between these biological disturbances and implant complications, often stemming from improper osseointegration, pathogenic biofilms on implants, as well as an exacerbated inflammatory response. Technological enhancements in implant design may mitigate pathogen colonization and inflammation, underscoring implant success rates.
    Keywords:  dental implantology failures; dental implants; dysbiosis; immune system; microbiota; osseointegration
    DOI:  https://doi.org/10.3390/ijms242417620
  51. Nephrol Dial Transplant. 2023 Dec 19. pii: gfad266. [Epub ahead of print]
    Neutrophils - Biology and Diversity.
    TRR332 consortium
      Neutrophils, the most abundant white blood cells in the human circulation, play crucial roles in various diseases, including kidney disease. Traditionally viewed as short-lived pro-inflammatory phagocytes that release reactive oxygen species, cytokines and neutrophil extracellular traps, recent studies have revealed their complexity and heterogeneity, thereby challenging this perception. Neutrophils are now recognized as transcriptionally active cells capable of proliferation and reverse migration, displaying phenotypic and functional heterogeneity. They respond to a wide range of signals and deploy various cargo to influence the activity of other cells in the circulation and in tissues. They can regulate the behavior of multiple immune cell types, exhibit innate immune memory, and contribute to both acute and chronic inflammatory responses while also promoting inflammation resolution in a context-dependent manner. Here, we explore the origin and heterogeneity of neutrophils, their functional diversity, and the cues that regulate their effector functions. We also examine their emerging role in infectious and non-infectious diseases with a particular emphasis on kidney disease. Understanding the complex behavior of neutrophils during tissue injury and inflammation may provide novel insights, thereby paving the way for potential therapeutic strategies to manage acute and chronic conditions. By deciphering their multifaceted role, targeted interventions can be developed to address the intricacies of neutrophil-mediated immune responses and improve disease outcomes.
    Keywords:  autoimmunity; cardiovascular disease; infection; kidney disease; neutrophils
    DOI:  https://doi.org/10.1093/ndt/gfad266
  52. PLoS Comput Biol. 2023 Dec;19(12): e1011705
    Statistical prediction of microbial metabolic traits from genomes.
    Zeqian Li, Ahmed Selim, Seppe Kuehn.
      The metabolic activity of microbial communities is central to their role in biogeochemical cycles, human health, and biotechnology. Despite the abundance of sequencing data characterizing these consortia, it remains a serious challenge to predict microbial metabolic traits from sequencing data alone. Here we culture 96 bacterial isolates individually and assay their ability to grow on 10 distinct compounds as a sole carbon source. Using these data as well as two existing datasets, we show that statistical approaches can accurately predict bacterial carbon utilization traits from genomes. First, we show that classifiers trained on gene content can accurately predict bacterial carbon utilization phenotypes by encoding phylogenetic information. These models substantially outperform predictions made by constraint-based metabolic models automatically constructed from genomes. This result solidifies our current knowledge about the strong connection between phylogeny and metabolic traits. However, phylogeny-based predictions fail to predict traits for taxa that are phylogenetically distant from any strains in the training set. To overcome this we train improved models on gene presence/absence to predict carbon utilization traits from gene content. We show that models that predict carbon utilization traits from gene presence/absence can generalize to taxa that are phylogenetically distant from the training set either by exploiting biochemical information for feature selection or by having sufficiently large datasets. In the latter case, we provide evidence that a statistical approach can identify putatively mechanistic genes involved in metabolic traits. Our study demonstrates the potential power for predicting microbial phenotypes from genotypes using statistical approaches.
    DOI:  https://doi.org/10.1371/journal.pcbi.1011705
  53. Microbiol Mol Biol Rev. 2023 Dec 21. e0012722
    Understanding the gut microbiota by considering human evolution: a story of fire, cereals, cooking, molecular ingenuity, and functional cooperation.
    Gerald W Tannock.
      SUMMARYThe microbial community inhabiting the human colon, referred to as the gut microbiota, is mostly composed of bacterial species that, through extensive metabolic networking, degrade and ferment components of food and human secretions. The taxonomic composition of the microbiota has been extensively investigated in metagenomic studies that have also revealed details of molecular processes by which common components of the human diet are metabolized by specific members of the microbiota. Most studies of the gut microbiota aim to detect deviations in microbiota composition in patients relative to controls in the hope of showing that some diseases and conditions are due to or exacerbated by alterations to the gut microbiota. The aim of this review is to consider the gut microbiota in relation to the evolution of Homo sapiens which was heavily influenced by the consumption of a nutrient-dense non-arboreal diet, limited gut storage capacity, and acquisition of skills relating to mastering fire, cooking, and cultivation of cereal crops. The review delves into the past to gain an appreciation of what is important in the present. A holistic view of "healthy" microbiota function is proposed based on the evolutionary pathway shared by humans and gut microbes.
    Keywords:  bacterial consortia; cereals; gut microbiota; hemicelluloses; human evolution; microbiome; non-starch polysaccharides; starch
    DOI:  https://doi.org/10.1128/mmbr.00127-22
  54. Clin Immunol. 2023 Dec 17. pii: S1521-6616(23)00636-8. [Epub ahead of print]258 109872
    Lactobacillus rhamnosus (LR) ameliorates pulmonary and extrapulmonary acute respiratory distress syndrome (ARDS) via targeting neutrophils.
    Leena Sapra, Chaman Saini, Sneha Das, Pradyumna K Mishra, Anurag Singh, Asit R Mridha, Pardeep K Yadav, Rupesh K Srivastava.
      Pulmonary and extrapulmonary acute respiratory distress syndrome (ARDS) is a life-threatening respiratory failure associated with high mortality. Despite progress in our understanding of the pathological mechanism causing the crippling illness, there are currently no targeted pharmaceutical treatments available for it. Recent discoveries have emphasized the existence of a potential nexus between gut and lung health fueling novel approaches including probiotics for the treatment of ARDS. We thus investigated the prophylactic-potential of Lactobacillus rhamnosus-(LR) in lipopolysaccharide (LPS)-induced pulmonary and cecal ligation puncture (CLP) induced extrapulmonary ARDS mice. Our in-vivo findings revealed that pretreatment with LR significantly ameliorated vascular-permeability (edema) of the lungs via modulating the neutrophils along with significantly reducing the expression of inflammatory-cytokines in the BALF, lungs and serum in both pulmonary and extrapulmonary mice-models. Interestingly, our ex-vivo immunofluorescence and flow cytometric data suggested that mechanistically LR via short chain fatty acids (butyrate being the most potent and efficient in ameliorating the pathophysiology of both pulmonary and extra-pulmonary ARDS) targets the phagocytic and neutrophils extracellular traps (NETs) releasing potential of neutrophils. Moreover, our in-vivo data further corroborated our ex-vivo findings and suggested that butyrate exhibits enhanced potential in ameliorating the pathophysiology of ARDS via reducing the infiltration of neutrophils into the lungs. Altogether, our study establishes the prophylactic role of LR and its associated metabolites in the prevention and management of both pulmonary and extrapulmonary ARDS via targeting neutrophils.
    Keywords:  Acute lung injury (ALI); Acute respiratory distress syndrome (ARDS); Butyrate; Caecum ligation puncture (CLP); Innate immune system; Lactobacillus rhamnosus (LR); Lipopolysaccharide (LPS); Neutrophils; Probiotics; Short chain fatty acids (SCFA)
    DOI:  https://doi.org/10.1016/j.clim.2023.109872
  55. Sci Adv. 2023 Dec 22. 9(51): eadm8715
    Neutrophils only die twice.
    Fernando W Souza, Edward A Miao.
      After apoptotic cell death begins neutrophils initiate NETosis, a second cell death program.
    DOI:  https://doi.org/10.1126/sciadv.adm8715
  56. Microorganisms. 2023 Dec 12. pii: 2969. [Epub ahead of print]11(12):
    The Pneumococcal Protein SufC Binds to Host Plasminogen and Promotes Its Conversion into Plasmin.
    Yoshihito Yasui, Satoru Hirayama, Takumi Hiyoshi, Toshihito Isono, Hisanori Domon, Tomoki Maekawa, Koichi Tabeta, Yutaka Terao.
      Streptococcus pneumoniae causes otitis media, sinusitis, and serious diseases such as pneumonia and bacteremia. However, the in vivo dynamics of S. pneumoniae infections and disease severity are not fully understood. In this study, we investigated pneumococcal proteins detected in the bronchoalveolar lavage fluid of an S. pneumoniae-infected mouse, which were assumed to be expressed during infection. Analysis of three proteins with unknown infection-related functions revealed that recombinant Fe-S cluster assembly ATP-binding protein (SufC) binds to the host plasminogen and promotes its conversion into plasmin. SufC was detected in the bacterial cell-surface protein fraction, but it had no extracellular secretory signal. This study suggests that S. pneumoniae releases SufC extracellularly through LytA-dependent autolysis, binding to the bacterial cell surface and host plasminogen and promoting its conversion into plasmin. The recruitment of plasmin by S. pneumoniae is considered useful for bacterial survival and spread, and SufC is suggested to facilitate this process.
    Keywords:  Streptococcus pneumoniae; SufC; autolysin; plasmin; plasminogen
    DOI:  https://doi.org/10.3390/microorganisms11122969
  57. J Clin Microbiol. 2023 Dec 19. e0113323
    Effects of clinically achievable pulmonary antibiotic concentrations on the recovery of bacteria: in vitro comparison of the BioFire FILMARRAY Pneumonia Panel versus conventional culture methods in bronchoalveolar lavage fluid.
    Andrew J Fratoni, Amity L Roberts, David P Nicolau, Joseph L Kuti.
      Empiric antibiotics may affect bacterial pathogen recovery using conventional culture methods (CCMs), while PCR-based diagnostics are likely less affected. Herein, we conducted an in vitro study of bronchoalveolar lavage fluid (BAL) inoculated with bacteria and clinically relevant antibiotic concentrations to compare the recovery between the BioFire FILMARRAY Pneumonia Panel (Pn Panel) and CCMs. Remnant clinical BAL specimens were inoculated to ~105 cfu/mL using 12 clinical isolates. Isolates consisted of one wild-type (WT) and one or more resistant strains of: Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, and Staphylococcus aureus. Piperacillin-tazobactam, cefepime, meropenem, levofloxacin, or vancomycin was added to achieve pulmonary epithelial lining fluid peak and trough concentrations. Post-exposure cfu/mL was quantified by CCMs and simultaneously tested by the PN Panel for identification and semi-quantitative genetic copies/mL. CCM results were categorized as significant growth (SG) (≥1 × 104), no significant growth (NSG) (≥1 × 103, <1 × 104), or no growth (NG) (<1 × 103). The PN Panel accurately identified all isolates, resistance genes, and reported ≥106 genetic copies/mL regardless of antibiotic exposure. The CCM also identified all S. aureus strains exposed to vancomycin. For WT Gram-negative isolates exposed to antibiotics, SG, NSG, and NG were observed in 7/52 (13%), 18/52 (35%), and 27/52 (52%) of CCM experiments, respectively. For resistant Gram-negatives isolates, SG, NSG, and NG were observed in 62/88 (70%), 17/88 (19%), and 9/88 (10%), respectively. These in vitro data demonstrate that the PN Panel is able to identify Gram-negative pathogens in the presence of clinically significant antibiotic concentrations when CCM may not.
    Keywords:  Acinetobacter baumannii; Escherichia coli; Klebsiella pneumoniae; Pseudomonas aeruginosa; Staphylococcus aureus; antimicrobial resistance; hospital-acquired pneumonia; ventilator-associated pneumonia
    DOI:  https://doi.org/10.1128/jcm.01133-23
  58. Methods Mol Biol. 2024 ;2749 109-121
    Culturing and Differentiation of Patient-Derived Ectocervical Epithelial Stem Cells Using Air-Liquid Interphase and Matrigel Scaffold.
    Rajendra Kumar Gurumurthy, Naveen Kumar, Cindrilla Chumduri.
      The ectocervix acts as a multilayered defense barrier, protecting the female reproductive system from external pathogens and supporting fertility and pregnancy. To understand the complex cellular and molecular mechanisms of cervical biology and disease, reliable in vitro models are vital. We present an efficient method to isolate and cultivate epithelial stem cells from ectocervical tissue biopsies. This method combines enzymatic digestion, mechanical dissociation, and selective culturing to obtain pure ectocervical epithelial cells for further investigation. The protocol accommodates both 2D stem cell monolayer and advanced 3D culture systems, such as air-liquid interface and Matrigel scaffolds, using a defined media cocktail, making it highly versatile. The primary ectocervical epithelial cells retain their native characteristics, enabling the exploration of ectocervical epithelial tissue behavior and pathology. This chapter provides step-by-step guidelines for setting up 2D and 3D cultures, facilitating adoption across different laboratories, and advancing cervical biology and disease research.
    Keywords:  2D culture; 3D culture; Air-liquid interface (ALI); Cell isolation; Cervical tissue biopsies; Ectocervix; Epithelial cells; Organoids; Primary cell culture
    DOI:  https://doi.org/10.1007/978-1-0716-3609-1_11
  59. Nat Commun. 2023 Dec 21. 14(1): 8497
    The Mycobacterium tuberculosis methyltransferase Rv2067c manipulates host epigenetic programming to promote its own survival.
    Prakruti R Singh, Venkatareddy Dadireddy, Shubha Udupa, Shashwath Malli Kalladi, Somnath Shee, Sanjeev Khosla, Raju S Rajmani, Amit Singh, Suryanarayanarao Ramakumar, Valakunja Nagaraja.
      Mycobacterium tuberculosis has evolved several mechanisms to counter host defense arsenals for its proliferation. Here we report that M. tuberculosis employs a multi-pronged approach to modify host epigenetic machinery for its survival. It secretes methyltransferase (MTase) Rv2067c into macrophages, trimethylating histone H3K79 in a non-nucleosomal context. Rv2067c downregulates host MTase DOT1L, decreasing DOT1L-mediated nucleosomally added H3K79me3 mark on pro-inflammatory response genes. Consequent inhibition of caspase-8-dependent apoptosis and enhancement of RIPK3-mediated necrosis results in increased pathogenesis. In parallel, Rv2067c enhances the expression of SESTRIN3, NLRC3, and TMTC1, enabling the pathogen to overcome host inflammatory and oxidative responses. We provide the structural basis for differential methylation of H3K79 by Rv2067c and DOT1L. The structures of Rv2067c and DOT1L explain how their action on H3K79 is spatially and temporally separated, enabling Rv2067c to effectively intercept the host epigenetic circuit and downstream signaling.
    DOI:  https://doi.org/10.1038/s41467-023-43940-6
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