The COVIDome Explorer researcher portal

Abstract

COVID-19 pathology involves dysregulation of diverse molecular, cellular, and physiological processes. To expedite integrated and collaborative COVID-19 research, we completed multi-omics analysis of hospitalized COVID-19 patients including matched analysis of the whole blood transcriptome, plasma proteomics with two complementary platforms, cytokine profiling, plasma and red blood cell metabolomics, deep immune cell phenotyping by mass cytometry, and clinical data annotation. We refer to this multidimensional dataset as the COVIDome. We then created the COVIDome Explorer, an online researcher portal where the data can be analyzed and visualized in real-time. We illustrate here the use of the COVIDome dataset through a multi-omics analysis of biosignatures associated with C-reactive protein (CRP), an established marker of poor prognosis in COVID-19, revealing associations between CRP levels and damage-associated molecular patterns, depletion of protective serpins, and mitochondrial metabolism dysregulation. We expect that the COVIDome Explorer will rapidly accelerate data sharing, hypothesis testing, and discoveries worldwide.

The Impact of Age and BMI on the VWF/ADAMTS13 Axis and Simultaneous Thrombin and Plasmin Generation in Hospitalized COVID-19 Patients

“…COVID-19 infected patients are at greater risk for venous and arterial thrombosis, particularly once the severity of disease requires intensive care (5,(28)(29)(30). Several studies identify important links between metabolic and protein changes that indicate up-regulated coagulation linked to inflammation and complement and offer unique insight into the relevant changes in COVID-19 coagulation omics (31)(32)(33). However, to our knowledge, no study has specifically focused on VWF/ADAMTS13 axis changes of coagulation combined with thrombin and plasmin generation in COVID-19 (−) or COVID-19 (+) patient cohorts at the time of hospital presentation and admission.…”

Integrating 3D genomic and epigenomic data to enhance target gene discovery and drug repurposing in transcriptome-wide association studies

“…7d ). Circulating RBBP5 was independently identified as positively correlated with C-reactive protein, an established marker of poor prognosis in COVID 63 . TFR2 encodes transferrin receptor 2 and is involved in iron transport.…”

Generation and Export of Red Blood Cell ATP in Health and Disease

“…The subsequent rush to biobank samples for molecular phenotyping has been unprecedented. Plasma and serum, which are easy to obtain, were the focus of dozens, if not hundreds, of 'omic (e.g., metabolomics and proteomics) studies of COVID-19 disease, including mass spectrometry-based proteomics and metabolomics (Chen et al, 2020;D'Alessandro et al, 2020;Hou et al, 2020;Messner et al, 2020;Shen et al, 2020;Thomas et al, 2020b;Zecha et al, 2020;Aggarwal et al, 2021;Overmyer et al, 2021;Sindelar et al, 2021;Sullivan et al, 2021). Changes in metabolite and protein expression are now well-correlated with COVID-19 severity, and this approach may facilitate the identification of diagnostic and prognostic markers of disease, yield mechanistic insight and reveal potential therapeutic targets.…”