The omicron variant of SARS-CoV-2: Understanding the known and living with unknowns.

The recently discovered Omicron variant of SARS-CoV-2 has rapidly burst into the public and scientific eye, being detected in more than 26 countries around the world. Given its more than 50 mutations, there is widespread concern about its public health impact, leading the World Health Organization to designate it a variant of concern. This Commentary provides a summary of current knowledge and unknowns about this viral variant as of December 2, 2021 and summarizes the key questions that need to be rapidly answered.

A Preclinical Safety Study of Thyroid Hormone Instilled into the Lungs of Healthy Rats-an Investigational Therapy for ARDS.

Acute respiratory distress syndrome (ARDS) is a severe, life-threatening form of respiratory failure characterized by pulmonary edema, inflammation, and hypoxemia due to reduced alveolar fluid clearance (AFC). Alveolar fluid clearance is required for recovery and effective gas exchange, and higher rates of AFC are associated with reduced mortality. Thyroid hormones play multiple roles in lung function, and L-3,5,3'-triiodothyronine (T3) has multiple effects on lung alveolar type II cells. T3 enhances AFC in normal adult rat lungs when administered intramuscularly and in normal or hypoxia-injured lungs when given intratracheally. The safety of a commercially available formulation of liothyronine sodium (synthetic T3) administered intratracheally was assessed in an Investigational New Drug Application-enabling toxicology study in healthy rats. Instillation of the commercial formulation of T3 without modification rapidly caused tracheal injury and often mortality. Intratracheal instillation of T3 that was reformulated and brought to a neutral pH at the maximum feasible dose of 2.73 µg T3 in 300 µl for 5 consecutive days had no clinically relevant T3-related adverse clinical, histopathologic, or clinical pathology findings. There were no unscheduled deaths that could be attributed to the reformulated T3 or control articles, no differences in the lung weights, and no macroscopic or microscopic findings considered to be related to treatment with T3. This preclinical safety study has paved the way for a phase I/II study to determine the safety and tolerability of a T3 formulation delivered into the lungs of patients with ARDS, including coronavirus disease 2019-associated ARDS, and to measure the effect on extravascular lung water in these patients. SIGNIFICANCE STATEMENT: There is growing interest in treating lung disease with thyroid hormone [triiodothyronine (T3)] in pulmonary edema and acute respiratory distress syndrome (ARDS). However, there is not any published experience on the impact of direct administration of T3 into the lung. An essential step is to determine the safety of multiple doses of T3 administered in a relevant animal species. This study enabled Food and Drug Administration approval of a phase I/II clinical trial of T3 instillation in patients with ARDS, including coronavirus disease 2019-associated ARDS (T3-ARDS ClinicalTrials.gov Identifier NCT04115514).

Acute lung injury in patients with COVID-19 infection.

During the 2020 Spring Festival in China, the outbreak of a novel coronavirus, named COVID-19 by WHO, brought on a worldwide panic. According to the clinical data of infected patients, radiologic evidence of lung edema is common and deserves clinical attention. Lung edema is a manifestation of acute lung injury (ALI) and may progress to hypoxemia and potentially acute respiratory distress syndrome (ARDS). Patients diagnosed with ARDS have poorer prognosis and potentially higher mortality. Although no effective treatment is formally approved for COVID-19 infection, support of ventilation with oxygen therapy and sometimes mechanical ventilation is often required. Treatment with systemic and/or local glucocorticoids might be helpful to alleviate the pulmonary inflammation and edema, which may decrease the development and/or consequences of ARDS. In this article, we focus on the lung edema and ALI of patients with this widely transmitted COVID-19 infection in order to provide clinical indications and potential therapeutic targets for clinicians and researchers.

Personalized training pathways for translational science trainees: Building on a framework of knowledge, skills, and abilities across the translational science spectrum.

BACKGROUND: In order to conduct translational science, scientists must combine domain-specific expertise with knowledge on how to identify and cross translational hurdles, and insights on positioning discoveries for the next translational stage. Expert educators from the Clinical and Translational Science Awards (CTSA) Consortium identified 97 knowledge, skills, and abilities (KSAs) important to include in training programs for translational scientists. To assist educators and trainees to use these KSAs, a conceptual model called "Personalized Pathways" was developed that prioritizes KSAs based on trainee background, research area, or phenotype, and expertise on the research team. PURPOSE: To understand how CTSA educators prioritize specific KSAs when developing personalized training plans for different translational phenotypes and to identify areas of similarity and difference across phenotypes. METHODS: A web-based, cross-sectional survey of CTSA educators was done. For a selected phenotype, respondents recommended one of four levels of mastery for each of the 97 KSAs. Results were tabulated by frequency, weighted by importance, and divided into tertiles representing high, middle, and lower priority KSAs. Agreement across phenotypes was compared using Krippendorff's alpha. RESULTS: Ten KSAs were high training priority for Preclinical, Clinical, and Community-Engaged phenotypes. These address research methods, responsible conduct of research, team building, and communicating research results. Nine KSAs were in the next tertile for priority reflecting KSAs in biostatistics, bioinformatics, regulatory precepts, and translating implications of research findings. CONCLUSION: A smaller set of KSAs can be prioritized for training Preclinical-, Clinical-, and Community-Engaged researchers. Future work should explore this approach for other phenotypes.

Immediate impact of the COVID-19 pandemic on CTSA TL1 and KL2 training and career development.

Clinical and Translational Science Award (CTSA) TL1 trainees and KL2 scholars were surveyed to determine the immediate impact of the COVID-19 pandemic on training and career development. The most negative impact was lack of access to research facilities, clinics, and human subjects, plus for KL2 scholars lack of access to team members and need for homeschooling. TL1 trainees reported having more time to think and write. Common strategies to maintain research productivity involved time management, virtual connections with colleagues, and shifting to research activities not requiring laboratory/clinic settings. Strategies for mitigating the impact of the COVID-19 pandemic on training and career development are described.

Cardiogenic pulmonary edema: mechanisms and treatment - an intensivist's view.

PURPOSE OF REVIEW: This review summarizes current understanding of the pathophysiology of cardiogenic pulmonary edema, its causes and treatment. RECENT FINDINGS: The pathobiology and classification of pulmonary edema is more complex than the hydrostatic vs. permeability dichotomy of the past. Mechanisms of alveolar fluid clearance and factors that affect the clearance rate are under intensive study to find therapeutic strategies. Patients need early stabilization of oxygenation and ventilation, preferably with high-flow nasal cannula oxygen or noninvasive ventilation whereas the diagnostic cause is quickly sought with echocardiography and other testing. SUMMARY: Treatments must be initiated early, whereas evaluation still is occurring and requires multimodality intervention. The general treatment of cardiogenic pulmonary edema includes diuretics, possibly morphine and often nitrates. The appropriate use of newer approaches - such as, nesiritide, high-dose vasodilators, milrinone, and vasopressin receptor antagonists - needs larger clinical trials.

Developing senior leadership for clinical and translational science.

The fifth in a 5-part series on the clinical and translational sciences educational pipeline, this paper focuses on strategies for developing leadership capacity among senior faculty and administrators responsible for clinical and translational science (CTS) research. Although progression in academic rank recognizes scientific excellence in research or scholarship, neither disciplinary training nor experience alone prepare senior faculty for the leadership challenges they inevitably face. Yet these faculty are increasingly responsible for multidisciplinary teams working within complex organizations with unclear or conflicting incentives that demand innovation. In academic health centers with Clinical and Translational Science Awards (CTSAs), investing in leadership often includes career development support in the CTSA education and training pillar programs. Only a few CTSAs have taken an intentional approach to developing senior leadership capacity, however, and still fewer have focused specifically on building such capacity for current CTS leaders within the context of a growing emphasis on team science. This manuscript explains the need for senior leadership training and describes an established example of such a program, the year-long Leadership for Innovative Team Science program for senior CTS researchers at the University of Colorado. The development of the program over time, topical elements, and participant perspectives are provided.

Proteome Profiling in Lung Injury after Hematopoietic Stem Cell Transplantation.

Pulmonary complications due to infection and idiopathic pneumonia syndrome (IPS), a noninfectious lung injury in hematopoietic stem cell transplant (HSCT) recipients, are frequent causes of transplantation-related mortality and morbidity. Our objective was to characterize the global bronchoalveolar lavage fluid (BALF) protein expression of IPS to identify proteins and pathways that differentiate IPS from infectious lung injury after HSCT. We studied 30 BALF samples from patients who developed lung injury within 180 days of HSCT or cellular therapy transfusion (natural killer cell transfusion). Adult subjects were classified as having IPS or infectious lung injury by the criteria outlined in the 2011 American Thoracic Society statement. BALF was depleted of hemoglobin and 14 high-abundance proteins, treated with trypsin, and labeled with isobaric tagging for relative and absolute quantification (iTRAQ) 8-plex reagent for two-dimensional capillary liquid chromatography (LC) and data dependent peptide tandem mass spectrometry (MS) on an Orbitrap Velos system in higher-energy collision-induced dissociation activation mode. Protein identification employed a target-decoy strategy using ProteinPilot within Galaxy P. The relative protein abundance was determined with reference to a global internal standard consisting of pooled BALF from patients with respiratory failure and no history of HSCT. A variance weighted t-test controlling for a false discovery rate of ≤5% was used to identify proteins that showed differential expression between IPS and infectious lung injury. The biological relevance of these proteins was determined by using gene ontology enrichment analysis and Ingenuity Pathway Analysis. We characterized 12 IPS and 18 infectious lung injury BALF samples. In the 5 iTRAQ LC-MS/MS experiments 845, 735, 532, 615, and 594 proteins were identified for a total of 1125 unique proteins and 368 common proteins across all 5 LC-MS/MS experiments. When comparing IPS to infectious lung injury, 96 proteins were differentially expressed. Gene ontology enrichment analysis showed that these proteins participate in biological processes involved in the development of lung injury after HSCT. These include acute phase response signaling, complement system, coagulation system, liver X receptor (LXR)/retinoid X receptor (RXR), and farsenoid X receptor (FXR)/RXR modulation. We identified 2 canonical pathways modulated by TNF-α, FXR/RXR activation, and IL2 signaling in macrophages. The proteins also mapped to blood coagulation, fibrinolysis, and wound healing-processes that participate in organ repair. Cell movement was identified as significantly over-represented by proteins with differential expression between IPS and infection. In conclusion, the BALF protein expression in IPS differed significantly from infectious lung injury in HSCT recipients. These differences provide insights into mechanisms that are activated in lung injury in HSCT recipients and suggest potential therapeutic targets to augment lung repair.

Hypoxia: an unusual cause with specific treatment.

Hypoxia is a well-recognized consequence of venous admixture resulting from right to left intracardiac shunting. Right to left shunting is usually associated with high pulmonary artery pressure or alteration in the direction of blood flow due to an anatomical abnormality of the thorax. Surgical or percutaneous closure remains controversial; however it is performed frequently for patients presenting with clinical sequela presumed to be resulting from paradoxical embolization secondary to right to left shunting. We report two patients with hypoxia and dyspnea due to right to left shunting through a patent foramen ovale (PFO) and venous admixture in the absence of elevated pulmonary artery pressures or other predisposing conditions like pneumonectomy or diaphragmatic weakness. Percutaneous closures of the PFOs with the self-centering Amplatzer device resulted in resolution of hypoxia and symptoms related to it.

Proteomic profiles in acute respiratory distress syndrome differentiates survivors from non-survivors.

Acute Respiratory Distress Syndrome (ARDS) continues to have a high mortality. Currently, there are no biomarkers that provide reliable prognostic information to guide clinical management or stratify risk among clinical trial participants. The objective of this study was to probe the bronchoalveolar lavage fluid (BALF) proteome to identify proteins that differentiate survivors from non-survivors of ARDS. Patients were divided into early-phase (1 to 7 days) and late-phase (8 to 35 days) groups based on time after initiation of mechanical ventilation for ARDS (Day 1). Isobaric tags for absolute and relative quantitation (iTRAQ) with LC MS/MS was performed on pooled BALF enriched for medium and low abundance proteins from early-phase survivors (n = 7), early-phase non-survivors (n = 8), and late-phase survivors (n = 7). Of the 724 proteins identified at a global false discovery rate of 1%, quantitative information was available for 499. In early-phase ARDS, proteins more abundant in survivors mapped to ontologies indicating a coordinated compensatory response to injury and stress. These included coagulation and fibrinolysis; immune system activation; and cation and iron homeostasis. Proteins more abundant in early-phase non-survivors participate in carbohydrate catabolism and collagen synthesis, with no activation of compensatory responses. The compensatory immune activation and ion homeostatic response seen in early-phase survivors transitioned to cell migration and actin filament based processes in late-phase survivors, revealing dynamic changes in the BALF proteome as the lung heals. Early phase proteins differentiating survivors from non-survivors are candidate biomarkers for predicting survival in ARDS.

Application of clinical proteomics in acute respiratory distress syndrome.

Acute Respiratory Distress Syndrome (ARDS) is a devastating cause of hypoxic respiratory failure, which continues to have high mortality. It is expected that a comprehensive systems- level approach will identify global and complex changes that contribute to the development of ARDS and subsequent repair of the damaged lung. In the last decade, powerful genome-wide analytical and informatics tools have been developed, that have provided valuable insights into the mechanisms of complex diseases such as ARDS. These tools include the rapid and precise measure of gene expression at the proteomic level. This article reviews the contemporary proteomics platforms that are available for comprehensive studies in ARDS. The challenges of various biofluids that could be investigated and some of the studies performed are also discussed.

Protein expression profile of rat type two alveolar epithelial cells during hyperoxic stress and recovery.

In rodent model systems, the sequential changes in lung morphology resulting from hyperoxic injury are well characterized and are similar to changes in human acute respiratory distress syndrome. In the injured lung, alveolar type two (AT2) epithelial cells play a critical role in restoring the normal alveolar structure. Thus characterizing the changes in AT2 cells will provide insights into the mechanisms underpinning the recovery from lung injury. We applied an unbiased systems-level proteomics approach to elucidate molecular mechanisms contributing to lung repair in a rat hyperoxic lung injury model. AT2 cells were isolated from rat lungs at predetermined intervals during hyperoxic injury and recovery. Protein expression profiles were determined by using iTRAQ with tandem mass spectrometry. Of the 959 distinct proteins identified, 183 significantly changed in abundance during the injury-recovery cycle. Gene ontology enrichment analysis identified cell cycle, cell differentiation, cell metabolism, ion homeostasis, programmed cell death, ubiquitination, and cell migration to be significantly enriched by these proteins. Gene set enrichment analysis of data acquired during lung repair revealed differential expression of gene sets that control multicellular organismal development, systems development, organ development, and chemical homeostasis. More detailed analysis identified activity in two regulatory pathways, JNK and miR 374. A novel short time-series expression miner algorithm identified protein clusters with coherent changes during injury and repair. We concluded that coherent changes occur in the AT2 cell proteome in response to hyperoxic stress. These findings offer guidance regarding the specific molecular mechanisms governing repair of the injured lung.

Src kinase integrates PI3K/Akt and MAPK/ERK1/2 pathways in T3-induced Na-K-ATPase activity in adult rat alveolar cells.

We previously reported that the 3,5,3'-triiodo-L-thyronine (T3)-induced increase of Na-K-ATPase activity in rat alveolar epithelial cells (AECs) required activation of Src kinase, PI3K, and MAPK/ERK1/2. In the present study, we assessed the role of Akt in Na-K-ATPase activity and the interaction between the PI3K and MAPK in response to T3 by using MP48 cells, inhibitors, and constitutively active mutants in the MP48 (alveolar type II-like) cell line. The Akt inhibitor VIII blocked T3-induced increases in Na-K-ATPase activity and amount of plasma membrane Na-K-ATPase protein. The Akt inhibitor VIII also abolished the increase in Na-K-ATPase activity induced by constitutively active mutants of either Src kinase or PI3K. Moreover, constitutively active mutants of Akt increased Na-K-ATPase activity in the absence of T3. Thus activation of Akt was required for T3-induced Na-K-ATPase activity in AECs and is sufficient in the absence of T3. Inhibitors of Src kinase (PP1), PI3K (wortmannin), and ERK1/2 (U0126) all blocked the T3-induced Na-K-ATPase activity. PP1 blocked the activation of PI3K and also ERK1/2 by T3, whereas U0126 did not prevent T3 activation of Src kinase or PI3K activity. Wortmannin did not significantly alter T3-increased MAPK/ERK1/2 activity, suggesting that T3-activated PI3K/Akt and MAPK/ERK1/2 pathways acted downstream of the Src kinase. Furthermore, in the absence of T3, a constitutively active mutant of Src kinase increased activities of Na-K-ATPase, PI3K, and MAPK/ERK1/2. A constitutively active mutant of PI3K enhanced Na-K-ATPase activity but did not alter the MAPK/ERK1/2 activity significantly. In summary, in adult rat AECs T3-stimulated Src kinase activity can activate both PI3K/Akt and MAPK/ERK1/2, and activation of Akt is necessary for T3-induced Na-K-ATPase activity.

Forging a critical alliance: Addressing the research needs of the United States critical illness and injury community.

OBJECTIVE: Discuss the research needs of the critical illness and injury communities in the United States. DATA SOURCES: Workshop session held during the 5 National Institutes of Health Symposium on the Functional Genomics of Critical Illness and Injury (November 15, 2007). STUDY SELECTION: The current clinical research infrastructure misses opportunities for synergy and does not address many important needs. In addition, it remains challenging to rapidly and properly implement system-wide changes based upon reproducible evidence from clinical research. DATA EXTRACTION: Author presentations, panel discussion, attendee feedback. DATA SYNTHESIS: The critical illness and injury research communities seek better communication and interaction, both of which will improve the breadth and quality of acute care research. Success in meeting these needs should come from cooperative and strategic actions that favor collaboration, standardization of protocols, and strong leadership. An alliance framed on common goals will foster collaboration among experts to better promote clinical trials within the critically ill or injured patient population. CONCLUSIONS: The U.S. Critical Illness and Injury Trials Group was funded to create a clinical research framework that can reduce the barriers to investigation using an investigator-initiated, evidence-driven, inclusive approach that has proven successful elsewhere. This alliance will provide an annual venue for systematic review and strategic planning that will include framing the research agenda, raising awareness for the value of acute care research, gathering and promoting best practices, and bolstering the critical care workforce.

Triiodo-L-thyronine rapidly stimulates alveolar fluid clearance in normal and hyperoxia-injured lungs.

RATIONALE: Edema fluid resorption is critical for gas exchange and requires active epithelial ion transport by Na, K-ATPase and other ion transport proteins. OBJECTIVES: In this study, we sought to determine if alveolar fluid clearance (AFC) is stimulated by 3,3',5 triiodo-L-thyronine (T(3)). METHODS: AFC was measured in in situ ventilated lungs and ex vivo isolated lungs by instilling isosmolar 5% bovine serum albumin solution with fluorescein-labeled albumin tracer and measuring the change in fluorescein isothiocyanate-albumin concentration over time. MEASUREMENTS AND MAIN RESULTS: Systemic treatment with intraperitoneal injections of T(3) for 3 consecutive days increased AFC by 52.7% compared with phosphate-buffered saline-injected control rats. Membranes prepared from alveolar epithelial cells from T(3)-treated rats had higher Na, K-ATPase hydrolytic activity. T(3) (10(-6) M), but not reverse T(3) (3,3',5' triiodo-L-thyronine), applied to the alveolar space increased AFC by 31.8% within 1.5 hours. A 61.5% increase in AFC also occurred by airspace instillation of T(3) in ex vivo isolated lungs, suggesting a direct effect of T(3) on the alveolar epithelium. Exposure of rats to an oxygen concentration of greater than 95% for 60 hours increased wet-to-dry lung weights and decreased AFC, whereas the expression of thyroid receptor was not markedly changed. Airspace T(3) rapidly restored the AFC in rat lungs with hyperoxia-induced lung injury. CONCLUSIONS: Airspace T(3) rapidly stimulates AFC by direct effects on the alveolar epithelium in rat lungs with and without lung injury.

T3 increases Na-K-ATPase activity via a MAPK/ERK1/2-dependent pathway in rat adult alveolar epithelial cells.

Thyroid hormone (T3) increases Na-K-ATPase activity in rat adult alveolar type II cells via a PI3K-dependent pathway. In these cells, dopamine and beta-adrenergic agonists can stimulate Na-K-ATPase activity through either PI3K or MAPK pathways. We assessed the role of the MAPK pathway in the stimulation of Na-K-ATPase by T3. In the adult rat alveolar type II-like cell line MP48, T3 enhanced MAPK/ERK1/2 activity in a dose-dependent manner. Increased ERK1/2 phosphorylation was observed within 5 min, peaked at 20 min, and then decreased. Two MEK1/2 inhibitors, U0126 and PD-98059, each abolished the T3-induced increase in the quantity of Na-K-ATPase alpha(1)-subunit plasma membrane protein and Na-K-ATPase activity. T3 also increased the phosphorylation of MAPK/p38; however, SB-203580, a specific inhibitor of MAPK/p38 activity, did not prevent the T3-induced Na-K-ATPase activity. SP-600125, a specific inhibitor of the MAPK/JNK pathway, also did not block the T3-induced Na-K-ATPase activity. Phorbol 12-myristate 13-acetate (PMA) significantly increased ERK1/2 phosphorylation and Na-K-ATPase activity. The PMA-induced Na-K-ATPase activity was inhibited by U0126. These data indicate that activation of MAPK-ERK1/2 was required for the T3-induced increase in Na-K-ATPase activity in addition to the requirement for the PI3K pathway.