Single-cell transcriptomics reveals distinct cell response between acute and chronic pulmonary infection of Pseudomonas aeruginosa

A vasculature-resident innate lymphoid cell population in mouse lungs

Tissue-resident immune cells such as innate lymphoid cells (ILC) are known to reside in the parenchymal compartments of tissues and modulate local immune protection. Here we use intravascular cell labeling, parabiosis and multiplex 3D imaging to identify a population of group 3 ILCs in mice that are present within the intravascular space of lung blood vessels (vILC3). vILC3s are distributed broadly in alveolar capillary beds from which inhaled pathogens enter the lung parenchyma. By contrast, conventional ILC3s in tissue parenchyma are enriched in lymphoid clusters in proximity to large veins. In a mouse model of pneumonia, Pseudomonas aeruginosa infection results in rapid vILC3 expansion and production of chemokines including CCL4. Blocking CCL4 in vivo attenuates neutrophil recruitment to the lung at the early stage of infection, resulting in prolonged inflammation and delayed bacterial clearance. Our findings thus define the intravascular space as a site of ILC residence in mice, and reveal a unique immune cell population that interfaces with tissue alarmins and the circulating immune system for timely host defense.

Nanobody-Targeted Conditional Antimicrobial Therapeutics

Conditional therapeutics that rely on disease microenvironment-specific triggers for activation are a promising strategy to improve therapeutic cargos. Among the investigated triggers, protease activity is used most often because of its dysregulation in several diseases. How to optimally fine-tune protease activation for different therapeutic cargos remains a challenge. Here, we designed nanobody-targeted conditional antimicrobial therapeutics to deliver a model therapeutic peptide and protein to the site of bacterial infection. We explored several parameters that influence proteolytic activation. We report the use of targeting nanobodies to enhance the activation of therapeutics that are otherwise activated inefficiently despite extensive optimization of the cleavable linker. Specifically, the pairing of Ly6G/C or ADAM10-targeting nanobodies with ADAM10-cleavable linkers improved activation via proximity-enabled reactivity. This study demonstrates a distinct role of active targeting in conditional therapeutic activation. More broadly, this optimization framework provides a guideline for the development of conditional therapeutics to treat various diseases in which protease activity is dysregulated.

Exploring the dynamic responses of group 3 innate lymphoid cells at different times in response to LPS challenge

Group 3 innate lymphoid cells (ILC3s) have clear roles in regulating mucosal immunity and tissue homeostasis in the intestine, though the immunological functions in lungs remain unclear. This study aimed to demonstrate the dynamic responses of ILC3s to acute inflammation upon LPS challenge. Microarray data and single-cell RNA sequencing (scRNA-seq) data obtained from the GEO database were combined to analyze the function of ILC3 subset, confirmed by flow cytometry assay and qRT-PCR. The gene enrichment analysis of intersected genes identified between microarray data in bacterial pneumonia and single-cell RNA sequencing of intestinal ILC3s were closely related to TNF-alpha effects on cytokine activity, cell motility and apoptosis pathway, indicating the possibility of intestinal ILC3s migration to the lung. Furthermore, the cellular landscapes of ILC3s in lung and intestine at different times after pulmonary infection exhibited varied ILC3 statuses. ILC3s in lung expanded a lot at 48 h while intestinal ILC3s decreased at 72 h response to LPS challenge, with higher expression of marked genes related to TNF-alpha effects on cytokine activity, cell motility and apoptosis pathway. The main findings in our study may serve as valuable resources for understanding the roles that ILC3s play upon LPS challenge, which may offer opportunities for translating ILC3s as therapeutic targets to regulate LPS-induced pulmonary inflammation.

Outer membrane vesicle contributes to the Pseudomonas aeruginosa resistance to antimicrobial peptides in the acidic airway of bronchiectasis patients

Pseudomonas aeruginosa is the predominant pathogen causing chronic infection in the airway of patients with bronchiectasis (BE), a chronic respiratory disease with high prevalence worldwide. Environmental factors are vital for bacterial successful colonization. Here, with sputa and bronchoalveolar lavage fluids, we determined that the concentration of airway antimicrobial peptide LL-37 and lactate was elevated in BE patients, especially in those infected with P. aeruginosa. The in vitro antibacterial assay revealed the bactericidal activity of LL-37 against the clinical P. aeruginosa isolates, which were dampened in the acidic condition. P. aeruginosa production of outer membrane vesicles (OMVs) enhanced in the lactate-adjusted acidic condition. Transcriptomic analysis suggested that OMVs induce the hyperproduction of the chemical compound 2-heptyl-4-quinolone (HHQ) in the bacterial population, which was verified by high-performance liquid chromatography. The positively charged HHQ interfered with the binding of LL-37 to bacterial cell membrane, potentiating the P. aeruginosa resistance to LL-37. To our knowledge, this is a new resistance mechanism of P. aeruginosa against antimicrobial peptides and may provide theoretical support for the development of new antibacterial therapies.

Single-cell transcriptome atlas revealed bronchoalveolar immune features related to disease severity in pediatric Mycoplasma pneumoniae pneumonia

The mechanisms underlying protective immunity in mild Mycoplasma pneumoniae pneumonia (MPP) and the pathogenesis of severe MPP, characterized by dysregulated immune responses, remain unclear. Here, we performed single-cell RNA sequencing (scRNA-seq) to profile bronchoalveolar lavage fluid (BALF) samples from 13 healthy donors and 24 hospitalized pediatric patients with MPP, covering both mild and severe cases. Severe MPP patients exhibited high levels of exhausted T cells and M1-like macrophages, with the exhaustion of T cells attributed to persistent type I interferon signaling and inadequate assistance from CD4+ T cells. Significant cell-cell interactions between exhausted T cells and programmed death-ligand 1+ (PD-L1+) macrophages were detected in severe patients, potentially mediated through inhibitor molecules (e.g., PD1) and their receptors (e.g., PD-L1), as well as human leukocyte antigen class I molecules and their receptors (e.g., KLRC1/D2), resulting in the dysfunction of anti-MP immune responses. Mild MPP patients were featured by an increased abundance of neutrophils, coupled with enhanced activation, contributing to protective immunity. Together, our study provides a detailed characterization of the BALF immune landscape in MPP patients, revealing distinct immune characteristics between mild and severe cases, which offers a valuable resource for understanding MPP immunopathogenesis and formulating effective therapeutic strategies.

Glucocorticoids in lung cancer: Navigating the balance between immunosuppression and therapeutic efficacy

Glucocorticoids (GCs), a class of hormones secreted by the adrenal glands, are released into the bloodstream to maintain homeostasis and modulate responses to various stressors. These hormones function by binding to the widely expressed GC receptor (GR), thereby regulating a wide range of pathophysiological processes, especially in metabolism and immunity. The role of GCs in the tumor immune microenvironment (TIME) of lung cancer (LC) has been a focal point of research. As immunosuppressive agents, GCs exert a crucial impact on the occurrence, progression, and treatment of LC. In the TIME of LC, GCs act as a constantly swinging pendulum, simultaneously offering tumor-suppressive properties while diminishing the efficacy of immune-based therapies. The present study reviews the role and mechanisms of GCs in the TIME of LC.

Lung microbiome: new insights into the pathogenesis of respiratory diseases

The lungs were long thought to be sterile until technical advances uncovered the presence of the lung microbial community. The microbiome of healthy lungs is mainly derived from the upper respiratory tract (URT) microbiome but also has its own characteristic flora. The selection mechanisms in the lung, including clearance by coughing, pulmonary macrophages, the oscillation of respiratory cilia, and bacterial inhibition by alveolar surfactant, keep the microbiome transient and mobile, which is different from the microbiome in other organs. The pulmonary bacteriome has been intensively studied recently, but relatively little research has focused on the mycobiome and virome. This up-to-date review retrospectively summarizes the lung microbiome's history, composition, and function. We focus on the interaction of the lung microbiome with the oropharynx and gut microbiome and emphasize the role it plays in the innate and adaptive immune responses. More importantly, we focus on multiple respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD), fibrosis, bronchiectasis, and pneumonia. The impact of the lung microbiome on coronavirus disease 2019 (COVID-19) and lung cancer has also been comprehensively studied. Furthermore, by summarizing the therapeutic potential of the lung microbiome in lung diseases and examining the shortcomings of the field, we propose an outlook of the direction of lung microbiome research.

Biofilm formation: mechanistic insights and therapeutic targets

Biofilms are complex multicellular communities formed by bacteria, and their extracellular polymeric substances are observed as surface-attached or non-surface-attached aggregates. Many types of bacterial species found in living hosts or environments can form biofilms. These include pathogenic bacteria such as Pseudomonas, which can act as persistent infectious hosts and are responsible for a wide range of chronic diseases as well as the emergence of antibiotic resistance, thereby making them difficult to eliminate. Pseudomonas aeruginosa has emerged as a model organism for studying biofilm formation. In addition, other Pseudomonas utilize biofilm formation in plant colonization and environmental persistence. Biofilms are effective in aiding bacterial colonization, enhancing bacterial resistance to antimicrobial substances and host immune responses, and facilitating cell‒cell signalling exchanges between community bacteria. The lack of antibiotics targeting biofilms in the drug discovery process indicates the need to design new biofilm inhibitors as antimicrobial drugs using various strategies and targeting different stages of biofilm formation. Growing strategies that have been developed to combat biofilm formation include targeting bacterial enzymes, as well as those involved in the quorum sensing and adhesion pathways. In this review, with Pseudomonas as the primary subject of study, we review and discuss the mechanisms of bacterial biofilm formation and current therapeutic approaches, emphasizing the clinical issues associated with biofilm infections and focusing on current and emerging antibiotic biofilm strategies.