Cell-free DNA maps COVID-19 tissue injury and risk of death and can cause tissue injury
Temesgen E. Andargie, Naoko Tsuji, Fayaz Seifuddin, Moon Kyoo Jang, Peter S.T. Yuen, Hyesik Kong, Ilker Tunc, Komudi Singh, Ananth Charya, Kenneth Wilkins, Steven Nathan, Andrea Cox, Mehdi Pirooznia, Robert A. Star, Sean Agbor-Enoh
Temesgen E. Andargie, Naoko Tsuji, Fayaz Seifuddin, Moon Kyoo Jang, Peter S.T. Yuen, Hyesik Kong, Ilker Tunc, Komudi Singh, Ananth Charya, Kenneth Wilkins, Steven Nathan, Andrea Cox, Mehdi Pirooznia, Robert A. Star, Sean Agbor-Enoh
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Clinical Research and Public Health COVID-19 Inflammation

Cell-free DNA maps COVID-19 tissue injury and risk of death and can cause tissue injury

Abstract

INTRODUCTION The clinical course of coronavirus 2019 (COVID-19) is heterogeneous, ranging from mild to severe multiorgan failure and death. In this study, we analyzed cell-free DNA (cfDNA) as a biomarker of injury to define the sources of tissue injury that contribute to such different trajectories.METHODS We conducted a multicenter prospective cohort study to enroll patients with COVID-19 and collect plasma samples. Plasma cfDNA was subject to bisulfite sequencing. A library of tissue-specific DNA methylation signatures was used to analyze sequence reads to quantitate cfDNA from different tissue types. We then determined the correlation of tissue-specific cfDNA measures to COVID-19 outcomes. Similar analyses were performed for healthy controls and a comparator group of patients with respiratory syncytial virus and influenza.RESULTS We found markedly elevated levels and divergent tissue sources of cfDNA in COVID-19 patients compared with patients who had influenza and/or respiratory syncytial virus and with healthy controls. The major sources of cfDNA in COVID-19 were hematopoietic cells, vascular endothelium, hepatocytes, adipocytes, kidney, heart, and lung. cfDNA levels positively correlated with COVID-19 disease severity, C-reactive protein, and D-dimer. cfDNA profile at admission identified patients who subsequently required intensive care or died during hospitalization. Furthermore, the increased cfDNA in COVID-19 patients generated excessive mitochondrial ROS (mtROS) in renal tubular cells in a concentration-dependent manner. This mtROS production was inhibited by a TLR9-specific antagonist.CONCLUSION cfDNA maps tissue injury that predicts COVID-19 outcomes and may mechanistically propagate COVID-19–induced tissue injury.FUNDING Intramural Targeted Anti–COVID-19 grant, NIH.

Authors

Temesgen E. Andargie, Naoko Tsuji, Fayaz Seifuddin, Moon Kyoo Jang, Peter S.T. Yuen, Hyesik Kong, Ilker Tunc, Komudi Singh, Ananth Charya, Kenneth Wilkins, Steven Nathan, Andrea Cox, Mehdi Pirooznia, Robert A. Star, Sean Agbor-Enoh

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Figure 1

Flow diagram showing patient selection and experiments.

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Flow diagram showing patient selection and experiments. Out of 85 enroll...
Out of 85 enrolled patients with COVID-19 (67 hospitalized and 18 nonhospitalized), 6 hospitalized patients were excluded from analysis for absence of admission samples. Total ncfDNA and mtcfDNA were quantified from all study subjects via digital droplet PCR (ddPCR). A subset of hospitalized patients (n = 50: 30 ICU and 20 non-ICU) were subjected to whole genome bisulfite sequencing (WGBS). Among the 32 healthy controls enrolled, ddPCR and WGBS were performed in 31 and 19 healthy controls, respectively. All the patients with influenza or RSV were subjected to ddPCR and WGBS.