Cystic fibrosis patient-derived bronchial organoids unveil druggable pathways against Mycobacterium abscessus infection.

Mycobacterium abscessus (Mabs) drives life-shortening mortality in cystic fibrosis (CF) patients, primarily because of its resistance to chemotherapeutic agents. Both our knowledge on and models to investigate the host and bacterial determinants that drive Mabs pathology in CF patients remain rudimentary. Here, we evaluated whether the lung organoid technology from CF patients is appropriate for modelling Mabs infection and whether antioxidant treatment is a candidate therapeutic approach in the context of CF disease. We derived airway organoids (AOs) from lung biopsy of a CF patient and characterized these AO by assessing CF transmembrane conductance regulator (CFTR) function, mucus and reactive oxygen species (ROS) production, lipid peroxidation, and cell death. We microinjected smooth (S-) or rough (R-)Mabs in the lumen of AOs to evaluate its fitness, responses of AOs to infection, and treatment efficacy by colony forming unit assay, qPCR and microscopy. We show that CF patient-derived AOs exhibited low residual CFTR function, enhanced mucus accumulation, and increased oxidative stress, lipid peroxidation, and cell death at basal state. While in AOs, S Mabs formed biofilm, R Mabs formed cord serpentines and displayed a higher virulence. S and R Mabs replicated more efficiently in CF AOs than in AOs derived from healthy lung. Pharmacological activation of antioxidant pathways resulted in better control of Mabs growth. In conclusion, we have established CF patient-derived AOs as a suitable human system to decipher mechanisms of CF-enhanced respiratory infection by Mabs and confirmed antioxidant approaches as a potential host-directed strategy to improve Mabs infection control.

Lung Function Reserve and Physical Function in Healthy Older Adults: Findings from BLSA

Forced Expiratory Volume in 1-second (FEV1) that falls below the lower limit of normal (LLN) is a well-established correlate of functional limitation and disability. However, less is known about the functional implications of gradations of lung function above the LLN. We examined the cross-sectional association between gradations of healthy lung function and usual gait speed, reported walking ability, and fast 400m walk performance in 750 persons (50.7% men) aged 55-95 free from respiratory disease and mobility limitations, participating in the Baltimore Longitudinal Study of Aging (BLSA). The 2012 Global Lung Initiative (GLI) reference equations were used to calculate FEV1 Z-scores, with healthy lung function categorized as follows: -1.6 < Z ≤ -1.0 (pre-clinical), -1.0 < Z ≤ -0.3 (low normal), -0.3 < Z ≤ 0.3 (normal), 0.3 < Z ≤ 1.0 (high-normal), and Z > 1.0 (high). Associations between gradations of healthy lung function and physical function were evaluated using multivariate linear regression, adjusting for age, sex, height, weight, and waist circumference. Compared to the ‘pre-clinical’ category, the difference in 400m walk time was 0.71 (p>.05), -6.60 (p>.05), -12.21 (p<0.05), and -15.52 (p<0.01) seconds for the ‘low normal’, ‘normal’, ‘high-normal’, and ‘high’ categories, respectively. No associations between gradations of healthy lung function and normal gait speed or walking ability were found (p>0.05). Higher levels of lung function reserve are associated with better 400m walking performance, thus efforts to promote and/or reduce loss of lung function reserve may help individuals maintain high functional capacity in later life.

Well-Designed Studies are Needed to Assess Adverse Effects on Healthy Lung Function after Long-Term Face Masks Usage

Face coverings, especially cloth masks, were the critical personal protective equipment during the COVID-19 pandemic. The advantages of such masks were well understood and widely used across the world. With this idea in mind, we have reviewed the available data and literature to identify whether masks exert an untoward effect on lung function in otherwise healthy persons. Interestingly enough, we have found no well-designed studies to assess whether masks have an unintended negative consequence on healthy lung function. Moreover, we are also aware that there could exist a differential impact of facial coverings depending on the type of masks exposed to. In addition, there could also be some ethical challenges in order to implement these cohort studies. We are recommending the need for thorough evaluations of long term mask utilization.

Local Defence System in Healthy Lungs

Background: The respiratory system is one of the main entrance gates for infection. The aim of this work was to compare the appearance of specific mucosal pro-inflammatory and common anti-microbial defence factors in healthy lung tissue, from an ontogenetic point of view. Materials and methods: Healthy lung tissues were collected from 15 patients (three females and 12 males) in the age range from 18 to 86. Immunohistochemistry to human β defensin 2 (HBD-2), human β defensin 3 (HBD-3), human β defensin 4 (HBD-4), cathelicidine (LL-37) and interleukine 17A (IL-17A) were performed. Results: The lung tissue material contained bronchial and lung parenchyma material in which no histological changes, connected with the inflammatory process, were detected. During the study, various statistically significant differences were detected in immunoreactive expression between different factors in all lung tissue structures. Conclusion: All healthy lung structures, but especially the cartilage, alveolar epithelium and the alveolar macrophages, are the main locations for the baseline synthesis of antimicrobial proteins and IL-17A. Cartilage shows high functional plasticity of this structure, including significant antimicrobial activity and participation in local lung protection response. Interrelated changes between antimicrobial proteins in different tissue confirm baseline synergistical cooperation of all these factors in healthy lung host defence.

CO-ResNet: Optimized ResNet model for COVID-19 diagnosis from X-ray images

This paper focuses on the application of deep learning (DL) based model in the analysis of novel coronavirus disease (COVID-19) from X-ray images. The novelty of this work is in the development of a new DL algorithm termed as optimized residual network (CO-ResNet) for COVID-19. The proposed CO-ResNet is developed by applying hyperparameter tuning to the conventional ResNet 101. CO-ResNet is applied to a novel dataset of 5,935 X-ray images retrieved from two publicly available datasets. By utilizing resizing, augmentation and normalization and testing different epochs our CO-ResNet was optimized for detecting COVID-19 versus pneumonia with normal healthy lung controls. Different evaluation metrics such as the classification accuracy, F1 score, recall, precision, area under the receiver operating characteristics curve (AUC) are used. Our proposed CO-ResNet obtains consistently best performance in the multi-level data classification problem, including health lung, pneumonia affected lung and COVID-19 affected lung samples. In the experimental evaluation, the detection rate accuracy in discerning COVID-19 is 98.74%, and for healthy normal lungs, pneumonia affected lungs are 92.08% and 91.32% respectively for our CO-ResNet with ResNet101 backbone. Further, our model obtained accuracy values of 83.68% and 82% for healthy normal lungs and pneumonia affected lungs with ResNet152 backbone. Experimental results indicate the potential usage of our new DL driven model for classification of COVID-19 and pneumonia.

Novel computational analysis of large transcriptome datasets identifies sets of genes distinguishing chronic obstructive pulmonary disease from healthy lung samples

Chronic obstructive pulmonary disease (COPD) kills over three million people worldwide every year. Despite its high global impact, the knowledge about the underlying molecular mechanisms is still limited. In this study, we aimed to extend the available knowledge by identifying a small set of COPD-associated genes. We analysed different publicly available gene expression datasets containing whole lung tissue (WLT) and airway epithelium (AE) samples from over 400 human subjects for differentially expressed genes (DEGs). We reduced the resulting sets of 436 and 663 DEGs using a novel computational approach that utilises a random depth-first search to identify genes which improve the distinction between COPD patients and controls along the first principle component of the data. Our method identified small sets of 10 and 15 genes in the WLT and AE, respectively. These sets of genes significantly (p < 10–20) distinguish COPD patients from controls with high fidelity. The final sets revealed novel genes like cysteine rich protein 1 (CRIP1) or secretoglobin family 3A member 2 (SCGB3A2) that may underlie fundamental molecular mechanisms of COPD in these tissues.

Novel TNIP2 and TRAF2 Variants Are Implicated in the Pathogenesis of Pulmonary Arterial Hypertension

Background: Pulmonary arterial hypertension (PAH) is a rare disease characterized by pulmonary vascular remodeling and right heart failure. Specific genetic variants increase the incidence of PAH in carriers with a family history of PAH, those who suffer from certain medical conditions, and even those with no apparent risk factors. Inflammation and immune dysregulation are related to vascular remodeling in PAH, but whether genetic susceptibility modifies the PAH immune response is unclear. TNIP2 and TRAF2 encode for immunomodulatory proteins that regulate NF-κB activation, a transcription factor complex associated with inflammation and vascular remodeling in PAH.Methods: Two unrelated families with PAH cases underwent whole-exome sequencing (WES). A custom pipeline for variant prioritization was carried out to obtain candidate variants. To determine the impact of TNIP2 and TRAF2 in cell proliferation, we performed an MTS [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium] assay on healthy lung pericytes transfected with siRNA specific for each gene. To measure the effect of loss of TNIP2 and TRAF2 on NF-kappa-beta (NF-κB) activity, we measured levels of Phospho-p65-NF-κB in siRNA-transfected pericytes using western immunoblotting.Results: We discovered a novel missense variant in the TNIP2 gene in two affected individuals from the same family. The two patients had a complex form of PAH with interatrial communication and scleroderma. In the second family, WES of the proband with PAH and primary biliary cirrhosis revealed a de novo protein-truncating variant in the TRAF2. The knockdown of TNIP2 and TRAF2 increased NF-κB activity in healthy lung pericytes, which correlated with a significant increase in proliferation over 24 h.Conclusions: We have identified two rare novel variants in TNIP2 and TRAF2 using WES. We speculate that loss of function in these genes promotes pulmonary vascular remodeling by allowing overactivation of the NF-κB signaling activity. Our findings support a role for WES in helping identify novel genetic variants associated with dysfunctional immune response in PAH.

Determination of initial airtightness after anatomical laser segmentectomy in an ex vivo model

If a pulmonary pathology can be removed by anatomical segmentectomy, the need for lobectomy is obviated. The procedure is considered oncologically equivalent and saves healthy lung tissue. In every segmentectomy, lung parenchyma must be transected in the intersegmental plane. Using an ex vivo model based on porcine lung, three transection techniques (monopolar cutter + suture, stapler, and Nd:YAG laser) are to be compared with respect to their initial airtightness. At an inspiratory ventilation pressure of 25 mbar, all three preparations were airtight. Upon further increase in ventilation pressure up to 40 mbar, the laser group performed best in terms of airtightness. Since thanks to its use of a laser fibre, this technique is particularly suitable for minimally invasive surgery; it should be further evaluated clinically for this indication in the future.