Pulmonary Immune Cell-microbiome Interactions in the Healthy Lung

The coronavirus disease 2019 pandemic, caused by severe acute respiratory syndrome coronavirus 2, has brought with it several studies on the local pulmonary immune system, which was until very recently largely a terra incognita. With these new methods, apparently fundamental aspects of lung disease have been uncovered, including pulmonary hyper inflammation. However, very little is currently known about the composition of the normal immune cell population in the human lung, including its interplay with the pulmonary microbiome, that is, the commensal microbiota of interacting bacteria and fungi that reside within the healthy lung

Overall design: In 50 patients (25 males, 25 females), intubated for elective surgery in general anaesthesia, an endotracheal aspirate and BAL fluid (BALF) from separate lung segments will be obtained. Furthermore, an oral and nasal swab and blood samples will be collected. This will be done immediately after intubation.

The following is obtained from the patient's electronic health record: diagnosis codes and medication (type and dosage), smoking history (current/previous/never smoker; pack years), type of operation; furthermore, the health record is screened for any exclusion criteria

Blood samples are drawn from the patient's peripheral venous catheter (inserted for clinical purposes) immediately before BALF collection.

Bronchoscopy with BALF collection: This procedure is performed in a standardized fashion according to current clinical guidelines. Immediately prior to the procedure, an oral swab, nasal swab and an endotracheal aspirate (ETA) are obtained. FIO2 is then increased to 1.0, and the bronchoscopy procedure is performed using a disposable videoscope with an outer diameter of 5.0 mm). Three successive 50-ml aliquots of prewarmed (37°C) isotonic saline are instilled in the medial segment of the right middle lobe, aspirated immediately with low negative suction pressure (\< 100 cm H2O), and pooled into a sterile glass container on ice to obtain a BALF specimen.

Afterwards a mini-BAL is performed in the upper and lower lobe of the right lung with a single installation of 20 ml isotonic saline in each lobe with immediately aspiration into a sterile container.

Measurements: The composition of the immune cell population, as well as the function and differentiation of various cell lines will be investigated by single-cell RNA sequencing (scRNA-seq) on selected immune cells from BALF, ETA, and blood, and this will be supplemented by bulk RNA sequencing with sample barcoding and multiplexing, giving a detailed expression pattern of all samples.

The composition microbiome in BALF, ETA, and oral swabs will be assessed by targeted amplicon sequencing of the hyper-variable regions 1 through 3 of the 16S subunit of ribosomal RNA gene for bacteria.

Statistical analyses: will be performed using R statistical software version 4.1.1 (R Project for Statistical Computing) within RStudio statistical software version 1.4.1717 (RStudio), and p\<0.05 considered statistically significant. Inspection of normality and variance homogeneity will be done by creating qq-plots and histograms. The statistical inference tools SPIEC-EASI and HeatMaps will be used, and based on correlational analyses, principal component analyses, including non-hierarchal cluster analysis, will be applied to identify traits.

• Cell differential counts and cytomorphological analyses of BALF [Time frame: Day 0 (subsequent to study inclusion)]
• Trans-compartmental fluxes [Time frame: Day 0 (subsequent to study inclusion)]
• Auto-antibodies against tI-IFNs in blood [Time frame: Day 0 (subsequent to study inclusion)]
• White blood cells counts [Time frame: Day 0 (subsequent to study inclusion)]
• Cytokines [Time frame: Day 0 (subsequent to study inclusion)]
• Number and characterizations of respiratory pathogens [Time frame: Day 0 (subsequent to study inclusion)]
• Number and characterizations of microorganisms [Time frame: Up to 12 weeks]