Proteome Characterictics of Endotracheal Tube Washes from COVID-19 ICU Patients: Assessing the Host Response and Understanding the Pathways Involved in Generation of Severe Disease

ABSTRACT

RATIONALE There is a great need to understand the pathogenesis of COVID-19, to predict the host responses to COVID-19 infection, and to efficiently assess clinical trial data for effectiveness. Data describing the sequence and predictability of progression of COVID-19 lung disease are not available, nor are biomarkers available to estimate lung damage. Using a proteomic approach, we measured the composition of tracheal aspirate of intubated COVID-19 positive subject and compared to COVID-19 negative ARDS subjects. METHODS EndoTracheal Tube (ETT) washes from critically ill 20 COVID-19+ patients and from 13 COVID19 negative ARDS patients were obtained from UNC COVID-19 Biospecimens Core. This BSL2+ facility obtained ICU samples and treated them with 8M urea to sterilize pathogens and solubilize the samples. Samples were normalized by total biomolecular concentration by SEC-MALLS dRI and prepared with filter aided sample preparation for mass spectrometry based label free quantiative proteome analyses. Proteins were quantified using Scaffold software (normalized total precursor intensity). Unpaired, non-parametric, Mann-Whitney test was performed in GraphPad Prism 9.0.0. RESULTS More than 1,200 proteins were identified. Of these, 209 were unique to COVID-19 samples. Of 823 proteins common to disease controls, the level of 32 proteins were decreased, and 10 proteins incresased in the in COVID-19 samples comparing to non-COVID controls (p value <0.05). Proteins significantly reduced in COVID-19 were mostly in the innate immune category including SFTPA1, BPIB1, PIGRS, and ezrin. Acute-phase proteins (alpha 1 acid glycoprotein 1, prothrombin), proteins related to iron homeostasis (serotransferrin, hemopexin), and complement pathway proteins (Complement C9 and vitronectin) were significantly increased in the COVID-19 lung. Pathways analysis indicated that acute phase signalling and LXR/RXR pathway were activated, while the glycolysis I pathway was inhibited in the COVID-19 group CONCLUSIONS These data reveal several important aspects of COVID-19-induced lung injury 1) TNF-alpha and/or IL-6 pathways are involved;2) the pulmonary epithelia are severely injured as acute phase serum components including albumin and serotransferrin, are excessively leaking into the lung from serum;3) Activation of LXR/RXR pathways in the macrophages and the inhibition of glycolysis pathway could be an important pathological outcome of the severe form of COVID-19. These data help elucidate cell-type-specific host responses and identify these pathways and their roles in generation of disease sequelae useful in the development of new therapies to reduce virus-relate injury and/or improve resolution of injury.