Rationale: The contributions of diverse cell populations in the human lung to pulmonary fibrosis pathogenesis are poorly understood. Single-cell RNA sequencing can reveal changes within individual cell populations during pulmonary fibrosis that are important for disease pathogenesis. Objectives: To determine whether single-cell RNA sequencing can reveal disease-related heterogeneity within alveolar macrophages, epithelial cells, or other cell types in lung tissue from subjects with pulmonary fibrosis compared with control subjects. Methods: We performed single-cell RNA sequencing on lung tissue obtained from eight transplant donors and eight recipients with pulmonary fibrosis and on one bronchoscopic cryobiospy sample from a patient with idiopathic pulmonary fibrosis. We validated these data using in situ RNA hybridization, immunohistochemistry, and bulk RNA-sequencing on flow-sorted cells from 22 additional subjects. Measurements and Main Results: We identified a distinct, novel population of profibrotic alveolar macrophages exclusively in patients with fibrosis. Within epithelial cells, the expression of genes involved in Wnt secretion and response was restricted to nonoverlapping cells. We identified rare cell populations including airway stem cells and senescent cells emerging during pulmonary fibrosis. We developed a web-based tool to explore these data. Conclusions: We generated a single-cell atlas of pulmonary fibrosis. Using this atlas, we demonstrated heterogeneity within alveolar macrophages and epithelial cells from subjects with pulmonary fibrosis. These results support the feasibility of discovery-based approaches using next-generation sequencing technologies to identify signaling pathways for targeting in the development of personalized therapies for patients with pulmonary fibrosis.

Some patients infected with Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) develop severe pneumonia and the acute respiratory distress syndrome (ARDS) 1 . Distinct clinical features in these patients have led to speculation that the immune response to virus in the SARS-CoV-2-infected alveolus differs from other types of pneumonia 2 . We collected bronchoalveolar lavage fluid samples from 88 patients with SARS-CoV-2-induced respiratory failure and 211 patients with known or suspected pneumonia from other pathogens and subjected them to flow cytometry and bulk transcriptomic profiling. We performed single-cell RNA-seq on 10 bronchoalveolar lavage fluid samples collected from patients with severe COVID-19 within 48 hours of intubation. In the majority of patients with SARS-CoV-2 infection, the alveolar space was persistently enriched in T cells and monocytes. Bulk and single-cell transcriptomic profiling suggested that SARS-CoV-2 infects alveolar macrophages, which in turn respond by producing T cell chemoattractants. These T cells produce interferon-gamma to induce inflammatory cytokine release from alveolar macrophages and further promote T cell activation. Collectively, our results suggest that SARS-CoV-2 causes a slowly-unfolding, spatially limited alveolitis in which alveolar macrophages harboring SARS-CoV-2 and T cells form a positive feedback loop that drives persistent alveolar inflammation.

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Transbronchial lung biopsy with a cryoprobe, or cryobiopsy, is a promising new bronchoscopic biopsy technique capable of obtaining larger and better-preserved samples than previously possible using traditional biopsy forceps. Over two dozen case series and several small randomized trials are now available describing experiences with this technique, largely for the diagnosis of diffuse parenchymal lung disease (DPLD), in which the reported diagnostic yield is typically 70% to 80%. Cryobiopsy technique varies widely between centers and this predominantly single center-based retrospective literature heterogeneously defines diagnostic yield and complications, limiting the degree to which this technique can be compared between centers or to surgical lung biopsy (SLB). This review explores the broad range of cryobiopsy techniques currently in use, their rationale, the current state of the literature, and suggestions for the direction of future study into this promising but unproven procedure.

BACKGROUND: The role of tracheostomy during the coronavirus disease 2019 (COVID-19) pandemic remains unknown. The goal of this consensus statement is to examine the current evidence for performing tracheostomy in patients with respiratory failure from COVID-19 and offer guidance to physicians on the preparation, timing, and technique while minimizing the risk of infection to health care workers (HCWs). METHODS: A panel including intensivists and interventional pulmonologists from three professional societies representing 13 institutions with experience in managing patients with COVID-19 across a spectrum of health-care environments developed key clinical questions addressing specific topics on tracheostomy in COVID-19. A systematic review of the literature and an established modified Delphi consensus methodology were applied to provide a reliable evidence-based consensus statement and expert panel report. RESULTS: Eight key questions, corresponding to 14 decision points, were rated by the panel. The results were aggregated, resulting in eight main recommendations and five additional remarks intended to guide health-care providers in the decision-making process pertinent to tracheostomy in patients with COVID-19-related respiratory failure. CONCLUSION: This panel suggests performing tracheostomy in patients expected to require prolonged mechanical ventilation. A specific timing of tracheostomy cannot be recommended. There is no evidence for routine repeat reverse transcription polymerase chain reaction testing in patients with confirmed COVID-19 evaluated for tracheostomy. To reduce the risk of infection in HCWs, we recommend performing the procedure using techniques that minimize aerosolization while wearing enhanced personal protective equipment. The recommendations presented in this statement may change as more experience is gained during this pandemic.

Background: Thoracentesis is commonly performed to evaluate pleural effusions. Many medications (warfarin, heparin, clopidogrel) or physiological factors (elevated International Normalized Ratio [INR], thrombocytopenia, uremia) increase the risk for bleeding. Frequently these medications are withheld or transfusions are performed to normalize physiological parameters before a procedure. The safety of performing thoracentesis without correction of these bleeding risks has not been prospectively evaluated.

Background Of the 1.5 million people diagnosed with pleural effusion annually in the U.S., approximately 178,000 undergo thoracentesis. While it is known that malignant pleural effusion portends a poor prognosis, mortality of patients with nonmalignant effusions has not been well studied. Methods This prospective cohort study evaluated 308 patients undergoing thoracentesis. Chart review was performed to obtain baseline characteristics. The etiology of the effusions was determined using standardized criteria. Mortality was determined at 30-days and 1-year. Results 247 unilateral and 61 bilateral thoracenteses were performed. Malignant effusion had the highest 30-day (37%) and 1 year (77%) mortality. There was substantial patient 30-day and 1-year mortality with effusions due to multiple benign etiologies (29% and 55%), CHF (22% and 53%), and renal failure (14% and 57%). Patients with bilateral pleural effusion, relative to unilateral, were associated with higher risk of death at 30 days and 1 year (17% versus 47%; HR 2.58 CI [1.44–4.63] and 36% versus 69%; HR 2.32 CI [1.55–3.48]). Conclusions Patients undergoing thoracentesis for pleural effusion have high short and long-term mortality. Patients with malignant effusion had the highest mortality followed by multiple benign etiologies, CHF and renal failure. Bilateral pleural effusion is distinctly associated with high mortality.

We report the first multicenter study to date confirming the feasibility and utility of EBUS-TBNA in the pediatric population. Due to the low overall procedural risk of EBUS-TBNA, it should be considered as a potential first line diagnostic option for children presenting with mediastinal or hilar abnormalities but further prospective studies are needed.