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The laboratory rat emerges as a useful tool for studying the interaction between the host and its microbiome. To advance principles relevant to the human microbiome, we systematically investigated and defined a multi-tissue full lifespan microbial biogeography for healthy Fischer 344 rats. Microbial community profiling data was extracted and integrated with host transcriptomic data from the Sequencing Quality Control (SEQC) consortium. Unsupervised machine learning, Spearman’s correlation, taxonomic diversity, and abundance analyses were performed to determine and characterize the rat microbial biogeography and the identification of four inter-tissue microbial heterogeneity patterns (P1-P4). The 11 body habitats harbor a greater diversity of microbes than previously suspected. Lactic acid bacteria (LAB) abundances progressively declined in lungs from breastfeed newborn to adolescence/adult and was below detectable levels in elderly rats. LAB’s presence and levels in lungs were further evaluated by PCR in the two validation datasets. The lung, testes, thymus, kidney, adrenal, and muscle niches were found to have age-dependent alterations in microbial abundance. P1 is dominated by lung samples. P2 contains the largest sample size and is enriched for environmental species. Liver and muscle samples were mostly classified into P3. Archaea species were exclusively enriched in P4. The 357 pattern-specific microbial signatures were positively correlated with host genes in cell migration and proliferation (P1), DNA damage repair and synaptic transmissions (P2), as well as DNA transcription and cell cycle in P3. Our study established a link between metabolic properties of LAB with lung microbiota maturation and development. Breastfeeding and environmental exposure influence microbiome composition and host health and longevity. The inferred rat microbial biogeography and pattern-specific microbial signatures would be useful for microbiome therapeutic approaches to human health and good quality of life.Graphical Abstract

Increased inflammasome responses are strongly implicated in inflammatory diseases; however, their specific roles are incompletely understood. Therefore, we sought to examine the roles of nucleotide-binding oligomerization domain-like receptor (NLR) family, pyrin domain-containing 3 (NLRP3) and absent in melanoma-2 (AIM2) inflammasomes in cigarette smoke-induced inflammation in a model of experimental chronic obstructive pulmonary disease (COPD). We targeted NLRP3 with the inhibitor MCC950 given prophylactically or therapeutically and examined Aim2

ELK3 is upregulated in blood and pulmonary vascular cells of PAH patients and may play a significant role in PAH potentially through modulating BMPR2 signaling.

Hereditary Hemorrhagic Telangiectasia (HHT) is an autosomal dominant disease that causes arteriovenous vascular malformations (AVMs) in different organs, including the lung. Three genes, ENG (endoglin), ACVRL1 (ALK1) and SMAD4, all members of the TGF-β/BMPR2 signaling pathway, are responsible for over 85% of all HHT cases. However, how these loss-of-function gene mutations lead to AVMs formation and what common downstream signaling they target is unknown. Here, using a combination of siRNA-mediated gene silencing, whole transcriptomic RNA sequencing, bioinformatic analysis, transcriptomic-based drug discovery, endothelial cells functional assays and VEGF signaling analysis, andex vivoprecision cut lung slice (PCLS) cultures approach, we uncovered common downstream transcriptomic gene signatures of HHT-casing genes and identified promising drug for HHT. We found the commonly used BMPR2-signaling downstream target ID1 is not a common downstream target of all the three HHT genes knockdown in human pulmonary microvascular endothelial cells (PMVECs). We identified novel common downstream targets of all the three HHT-causing genes that were enriched for HHT-related biological process and signaling pathways. Among those downstream genes, LYVE1, GPNMB, and MC5R were strong downstream targets that could serve as a better common downstream target than ID1. Furthermore, using the common downstream upregulated genes (HHT disease signature) following HHT gene knockdown, we identified a small molecule drug, Brivanib, that reversed the HHT disease signature, and inhibited VEGF-induced ERK1/2 phosphorylation, proliferation, and angiogenesis in PMVECs and inhibited some of the upregulated HHT disease genes in PCLS. Our findings suggest that Brivanib could be an emerging new drug for HHT.

Nutraceuticals have emerged as potential compounds to attenuate the COVID-19 complications. Precisely, these food additives strengthen the overall COVID treatment and enhance the immunity of a person. Such compounds have been used at a large scale, in almost every household due to their better affordability and easy access. Therefore, current research is focused on developing newer advanced formulations from potential drug candidates including nutraceuticals with desirable properties viz, affordability, ease of availability, ease of administration, stability under room temperature, and potentially longer shelf-lives. As such, various nutraceutical-based products such as compounds could be promising agents for effectively managing COVID-19 symptoms and complications. Most importantly, regular consumption of such nutraceuticals has been shown to boost the immune system and prevent viral infections. Nutraceuticals such as vitamins, amino acids, flavonoids like curcumin, and probiotics have been studied for their role in the prevention of COVID-19 symptoms such as fever, pain, malaise, and dry cough. In this review, we have critically reviewed the potential of various nutraceutical-based therapeutics for the management of COVID-19. We searched the information relevant to our topic from search engines such as PubMed and Scopus using COVID-19, nutraceuticals, probiotics, and vitamins as a keyword. Any scientific literature published in a language other than English was excluded. PRACTICAL APPLICATIONS: Nutraceuticals possess both nutritional values and medicinal properties. They can aid in the prevention and treatment of diseases, as well as promote physical health and the immune system, normalizing body functions, and improving longevity. Recently, nutraceuticals such as probiotics, vitamins, polyunsaturated fatty acids, trace minerals, and medicinal plants have attracted considerable attention and are widely regarded as potential alternatives to current therapeutic options for the effective management of various diseases, including COVID-19.

This study shows that the long non-coding RNA RGMB-AS1 is upregulated in the blood and pulmonary vascular cells of PAH patient and that it regulates BMPR2 signaling. Inhibiting RGMB-AS1 increases BMPR2 signaling and improves pulmonary vascular cell function.

Extrachromosomal DNA (ecDNA) is often found in cancerous cells, and numerous scientific investigations have already shown that ecDNA-mediated oncogene amplification which contributes to cancer therapy resistance. This ecDNA is found to be essential for enhancing gene transcription and resistance to chemotherapeutic drugs, as well as promoting tumor heterogeneity and reversing tumor phenotypes, suggesting that it plays a key role in carcinogenesis. The ecDNA induces tumors to become hostile which results in a lower survival rate and chemotherapy tolerance. It also holds the potential as a target for treatment or diagnostic procedure of tumors. The review describes the properties and origins of ecDNA, as well as how it affects carcinogenesis, its function in cancer etiology and progression, and its therapeutic value. Propagation of oncogenes and resistance genes situated in extra-chromosomal DNA has been discovered to become one of the primary causes of intra-tumor genetic heterogeneity and may result in a threshold of probable evolutionary adaptation in many investigations.

BACKGROUND: Asthma and chronic obstructive pulmonary disease (COPD) are common chronic respiratory diseases, and some patients have overlapping disease features, termed asthma-COPD overlap (ACO). Patients characterized with ACO have increased disease severity; however, the mechanisms driving this have not been widely studied. OBJECTIVES: This study sought to characterize the phenotypic and transcriptomic features of experimental ACO in mice induced by chronic house dust mite antigen and cigarette smoke exposure. METHODS: Female BALB/c mice were chronically exposed to house dust mite antigen for 11 weeks to induce experimental asthma, cigarette smoke for 8 weeks to induce experimental COPD, or both concurrently to induce experimental ACO. Lung inflammation, structural changes, and lung function were assessed. RNA-sequencing was performed on separated airway and parenchyma lung tissues to assess transcriptional changes. Validation of a novel upstream driver SPI1 in experimental ACO was assessed using the pharmacological SPI1 inhibitor, DB2313. RESULTS: Experimental ACO recapitulated features of both asthma and COPD, with mixed pulmonary eosinophilic/neutrophilic inflammation, small airway collagen deposition, and increased airway hyperresponsiveness. Transcriptomic analysis identified common and distinct dysregulated gene clusters in airway and parenchyma samples in experimental asthma, COPD, and ACO. Upstream driver analysis revealed increased expression of the transcription factor Spi1. Pharmacological inhibition of SPI1 using DB2313, reduced airway remodeling and airway hyperresponsiveness in experimental ACO. CONCLUSIONS: A new experimental model of ACO featuring chronic dual exposures to house dust mite and cigarette smoke mimics key disease features observed in patients with ACO and revealed novel disease mechanisms, including upregulation of SPI1, that are amenable to therapy.

Maternal iron deficiency occurs in 40–50% of all pregnancies and is associated with an increased risk of respiratory disease and asthma in children. We used murine models to examine the effects of lower iron status during pregnancy on lung function, inflammation and structure, as well as its contribution to increased severity of asthma in the offspring. A low iron diet during pregnancy impairs lung function, increases airway inflammation, and alters lung structure in the absence and presence of experimental asthma. A low iron diet during pregnancy further increases these major disease features in offspring with experimental asthma. Importantly, a low iron diet increases neutrophilic inflammation, which is indicative of more severe disease, in asthma. Together, our data demonstrate that lower dietary iron and systemic deficiency during pregnancy can lead to physiological, immunological and anatomical changes in the lungs and airways of offspring that predispose to greater susceptibility to respiratory disease. These findings suggest that correcting iron deficiency in pregnancy using iron supplements may play an important role in preventing or reducing the severity of respiratory disease in offspring. They also highlight the utility of experimental models for understanding how iron status in pregnancy affects disease outcomes in offspring and provide a means for testing the efficacy of different iron supplements for preventing disease.

Objective: Indiscriminate use of antibiotics in poultry farms increases the chance of antibiotic-resistant and ESBL producing bacteria in Bangladesh. Therefore, the study was undertaken to detect the extended-spectrum β-lactamase (ESBL) producing Escherichia coli (E. coli) in chickens. Materials and methods: A total of 60 cloacal swab samples (20 from commercial layer, 20 from commercial broiler, and 20 from commercial Sonali chickens) were collected from the Rajshahi district of Bangladesh. The E. coli was isolated from these samples and identified based on cultural, staining, and biochemical characteristics. The disk diffusion method was used to assay the antibiotic-resistant/sensitivity patterns of the isolated E. coli. Phenotypic detection of ESBL producing E. coli was also done. Results: The prevalence of E. coli in chickens was 61.67% in the Rajshahi district of Bangladesh, where the prevalence was 60%, 60%, and 65% in a commercial layer, commercial broiler, and commercial Sonali chickens, respectively. The antibiotic sensitivity assay of E. coli isolated from commercial layer chickens showed 100%, 80%, 50%, 40%, and 40% resistant to amoxicillin, tetracycline, cefotaxime, ciprofloxacin, and ceftazidime, respectively. E. coli isolated from commercial broiler chickens showed 100%, 100%, 60%, 50%, and 40% resistant to amoxicillin, tetracycline, cefotaxime, ceftazidime, and ciprofloxacin, respectively. E. coli isolated from commercial Sonali chickens showed 90%, 70%, 50%, 50%, and 40% resistant to amoxicillin, tetracycline, cefotaxime, ciprofloxacin, and ceftazidime, respectively. In phenotypic detection, the overall prevalence of ESBL producing E. coli was 43.33%, where 40%, 50%, and 40% in the commercial layer, commercial broiler, and commercial Sonali chickens, respectively in the Rajshahi district of Bangladesh. Conclusion: These results indicated that chickens are a potential reservoir for ESBL producing E. coli and their antibiotic resistances are obviously significant. These findings will help us to make a proper guideline for the treatment, prevention, and control of E. coli prevalent in chickens in Bangladesh

Background Obesity is a risk factor for asthma, and obese asthmatic individuals are more likely to have severe, steroid-insensitive disease. How obesity affects the pathogenesis and severity of asthma is poorly understood. Roles for increased inflammasome-mediated neutrophilic responses, type 2 immunity, and eosinophilic inflammation have been described. Objective We investigated how obesity affects the pathogenesis and severity of asthma and identified effective therapies for obesity-associated disease. Methods We assessed associations between body mass index and inflammasome responses with type 2 (T2) immune responses in the sputum of 25 subjects with asthma. Functional roles for NLR family, pyrin domain–containing (NLRP) 3 inflammasome and T2 cytokine responses in driving key features of disease were examined in experimental high-fat diet–induced obesity and asthma. Results Body mass index and inflammasome responses positively correlated with increased IL-5 and IL-13 expression as well as C-C chemokine receptor type 3 expression in the sputum of subjects with asthma. High-fat diet–induced obesity resulted in steroid-insensitive airway hyperresponsiveness in both the presence and absence of experimental asthma. High-fat diet–induced obesity was also associated with increased NLRP3 inflammasome responses and eosinophilic inflammation in airway tissue, but not lumen, in experimental asthma. Inhibition of NLRP3 inflammasome responses reduced steroid-insensitive airway hyperresponsiveness but had no effect on IL-5 or IL-13 responses in experimental asthma. Depletion of IL-5 and IL-13 reduced obesity-induced NLRP3 inflammasome responses and steroid-insensitive airway hyperresponsiveness in experimental asthma. Conclusion We found a relationship between T2 cytokine and NLRP3 inflammasome responses in obesity-associated asthma, highlighting the potential utility of T2 cytokine–targeted biologics and inflammasome inhibitors.

Introduction: Severe, steroid-resistant (SSR) asthma is the major unmet need in asthma management and obese asthmatics are more likely to have therapy-resistant disease. Recent studies strongly implicate a role for NLRP3 inflammasome responses in driving obesity-associated AHR, however, these studies did not assess its role in steroid resistance or therapeutic modulation in obesity-associated, SSR asthma. Aims and Objectives: To elucidate the role of NLRP3 inflammasome responses in obesity-associated, SSR asthma. Methods: We developed and characterised a novel murine model of high-fat diet (HFD)-induced, obesity-associated, SSR allergic airways disease (SSR AAD) and assessed the effects of steroid treatment. We also assessed the roles and potential for targeting the NLRP3 inflammasome, and IL-5/IL-13 responses, in our model of HFD-induced, obesity-associated, SSR AAD. Results: HFD administration results in increased weight gain and adiposity; and the development of steroid-resistant AHR. Interestingly, HFD-induced obesity results in increased levels of NLRP3 in the airways and caspase-1 activation in the lung, that are suppressed by treatment with the NLRP3 inflammasome-specific inhibitor, MCC950. Furthermore, combinatorial treatment with anti-IL-5 and anti-IL-13 neutralising antibodies suppresses airway NLRP3 inflammasome responses and steroid-resistant AHR in our model. Conclusions: Our study highlights an unrecognised role for HFD-induced, obesity-associated, NLRP3 inflammasome responses in steroid-resistant AHR. Furthermore, we identify a novel role for IL-5 and IL-13 responses upstream of the NLRP3 inflammasome in the development of obesity-associated, SSR asthma.

Transportin 3 (TNPO3) is a member of the importin-ß superfamily proteins. Despite numerous studies, the exact molecular mechanism of TNPO3 in retroviral infection is still controversial. Here, we provide evidence for the role and mechanism of TNPO3 in the replication of prototype foamy virus (PFV). Our findings revealed that PFV infection was reduced 2-fold by knockdown (KD) of TNPO3. However, late stage of viral replication including transcription, translation, viral assembly, and release was not influenced. The differential cellular localization of PFV integrase (IN) in KD cells pinpointed a remarkable reduction of viral replication at the nuclear import step. We also found that TNPO3 interacted with PFV IN but not with Gag, suggesting that IN-TNPO3 interaction is important for nuclear import of PFV pre-integration complex. Our report enlightens the mechanism of PFV interaction with TNPO3 and support ongoing research on PFV as a promising safe vector for gene therapy.

Introduction: Steroid-resistant (SR) asthma represents a significant clinical and economic burden. The mechanisms which drive SR asthma are unknown, but respiratory infections have been implicated in the development of disease. Infections increase oxidative stress in the lung and SR asthma is associated with defective antioxidant responses and increased oxidative stress. Hypotheses: Respiratory infections induce changes in the asthmatic airway that increase oxidative stress and contribute to dysregulated antioxidant responses which play a crucial role in the development of SR asthma. Aim: To determine the effects of antioxidant therapy on oxidative stress, inflammation and airways hyper-responsiveness (AHR) in a murine model of Chlamydia -induced SR asthma. Methods: Oxidative stress was measured in our established model of Chlamydia -induced SR allergic airways disease (AAD) using 3-nitrotyrosine and 8-isoprostane assays. The effects of treatment with vitamin E or an NRF2 activator on oxidative stress, inflammation and AHR in SRAAD were assessed compared to dexamethasone (DEX). Results: We show that oxidative stress responses are increased in Chlamydia -induced SRAAD compared to controls with steroid-sensitive AAD. Oxidative stress responses in SRAAD are not affected by DEX. Vitamin E treatment alone reduces oxidative stress and, when combined with DEX, suppresses oxidative stress, inflammation and AHR, in SRAAD. Treatment with the NRF2 activator suppresses all features of SRAAD in the absence of DEX. Conclusions: SRAAD is associated with increased oxidative stress that are resistant to steroids. Our findings suggest that antioxidant therapy may be appropriate for SR asthma especially when combined with steroid therapy.

CO2 produced by systemic cellular respiration is hydrated into carbonic acid (H2CO3) that dissociates into H+ and HCO3−. These are transported in the plasma to the lungs where HCO3− is converted back into H2CO3 and CO2 that are expelled through breathing. Evidence suggests that dysfunction of the mechanisms that govern these processes may result in the development of respiratory acidosis (RA) and the cardinal features of severe, steroid-resistant (SSR) asthma. Reduced lung function, which occurs in SSR asthma, impairs removal of volatile H2CO3 and CO2, resulting in acid accumulation and increased arterial PaCO2. Patients with severe asthma often develop complications from increased PaCO2, which skews the PaCO2/HCO3− ratio resulting in increased H+ concentration and reduced pH. We developed three mouse models of respiratory infection and ovalbumin-induced SSR allergic airways disease (SSRAAD) that are highly representative of SSR asthma in humans. We used these models to show a role for impaired homeostatic acid-base balance in SSR asthma. All three infections suppress the induction of the expression of the chloride (Cl−)/HCO− pump, Slc26a4, in the airway mucosa in AAD. Importantly, SSRAAD is associated with increased levels of free H+ ions in bronchoalveolar lavage fluid. Administration of Slc26a4-specific siRNA in steroid-sensitive AAD, which mimics the effect of decreased Slc26a4 responses in SSRAAD, induced RA and steroid-resistant airway inflammation and AHR. Importantly, treatment of RA with NaHCO3 during infection-induced SSRAAD suppressed steroid-resistant AHR. Thus, we have identified a previously unrecognised role for deficient Slc26a4 responses that result in the development of RA and the pathogenesis of SSRAAD.

Altered iron levels and/or dysregulated iron homeostasis have been associated with a number of lung diseases, however, the mechanisms that underpin these associations, and whether iron plays a role in the pathogenesis of disease, are yet to be fully elucidated. In this study, systemic and pulmonary iron and lung structure and function were assessed in transferrin receptor (TFR)2 mutant and wild-type (WT) BALB/c mice fed a high-iron diet (containing 2% carbonyl iron) compared to normal diet controls, respectively. The effects of increased iron loading on murine models of ovalbumin- and house dust mite-induced allergic airways disease (AAD) were also assessed. Excess iron accumulation was observed in the lungs in both the genetic and diet-induced models of iron overloading. Increased iron levels in the lung were associated with emphysema-like alveolar enlargement, small airways collagen deposition, alterations in baseline lung function and increased airways hyper-responsiveness (AHR). Increased iron loading also resulted in altered type 1, 2 and 17 cytokine production, increased eosinophilic inflammation and severe, steroid-resistant AHR in AAD. Interestingly, AAD also results in altered systemic and pulmonary iron levels and iron regulatory molecule expression. These data show that increased iron levels in the lung results in emphysema and airways fibrosis that corresponds with reduced lung function. We also show that lung disease may be closely associated with changes in iron homeostasis. These models will be used to characterize the interplay between iron and immunity in the pathogenesis of lung disease and determine the therapeutic effectiveness of correcting dysregulated iron homeostasis for the treatment of lung disease.