RNA Sequencing – the twenty-first century stethoscope in pulmonary medicine

From Anesthesiology by Eliana Lucchinetti & Michael Zaugg

Lung atelectasis was first described by the French physician René Théophile Hyacinthe Laënnec in his iconic book entitled, De L’Auscultation Médiate; ou Traité du Diagnostic des Maladies des Poumons et du Cœur published in 1819 in Paris, where he compiled his observations of lung and heart sounds derived from the use of his newly invented stethoscope, a simple wooden tube carved by himself. Europe was recovering from the French Revolutionary and the Napoleonic Wars and was battling with poverty, famine, and tuberculosis, a mysterious, untreatable pulmonary disease, reminiscent of today’s SARS-CoV-2.

Researchers at Massachusetts General Hospital present their data exploring the molecular events related to atelectasis, a common clinical entity, by taking advantage of a translational large animal model with high fidelity to human disease. Atelectasis was induced with a bronchial blocker and thoracotomy on the left whole lung, while the right lung was ventilated in the presence or absence of systemic endotoxin infusion. Physiologic parameters were recorded, and imaging techniques were used to visualize regional aeration. After 8 h, lung tissue was collected from aerated and atelectatic lung regions and used for next generation RNA sequencing. The authors used gene set enrichment analysis, a pattern recognition tool assessing whether functionally related genes are coordinately and consistently regulated, and transcription factor prediction analysis, a tool pinpointing the transcription factors that drive the transcriptomic differences among groups, to reveal a wealth of novel findings.

Downregulated genes associated with host defense, barrier integrity, and tissue regeneration or repair were found to be overrepresented in atelectatic tissue. Systemic endotoxin was capable of upregulating the immune response in atelectatic tissue, while genes linked to alveolar-capillary barrier integrity and function remained depressed. Results from transcription factor prediction analysis were even more intriguing. The data suggested the involvement of the interferon regulatory factor family of transcription factors in endotoxin-exposed atelectasis. These transcription factors, which play pivotal roles in many aspects of the immune response, including immune cell development and differentiation, are likely involved in the enhanced response of the atelectatic tissue to systemic inflammation. In addition, the authors found defective YES-associated protein signaling in atelectasis independent of endotoxin exposure. YES-associated protein, a transcriptional coactivator of the transcriptional enhanced associate domain transcription factor family, which controls cell proliferation and stem cell functions, appears to be involved in the loss of pulmonary barrier function of the atelectatic lung.

These are important discoveries and fit very well to our current understanding where interferon-stimulated genes have been linked to severe outcomes in acute respiratory distress syndrome (ARDS) patients because of their role of predisposing to additional lung injury. Likewise, YES-associated protein signaling is known to play a major role in respiratory epithelial cell regeneration and regulation of the cytoskeleton, and it is conceivable that lack of cyclic stretch in atelectatic tissue downregulates this pathway.