EBioMedicine (Apr 2021)

Epigenome-wide association study of COVID-19 severity with respiratory failure

  • Manuel Castro de Moura,
  • Veronica Davalos,
  • Laura Planas-Serra,
  • Damiana Alvarez-Errico,
  • Carles Arribas,
  • Montserrat Ruiz,
  • Sergio Aguilera-Albesa,
  • Jesús Troya,
  • Juan Valencia-Ramos,
  • Valentina Vélez-Santamaria,
  • Agustí Rodríguez-Palmero,
  • Judit Villar-Garcia,
  • Juan P. Horcajada,
  • Sergiu Albu,
  • Carlos Casasnovas,
  • Anna Rull,
  • Laia Reverte,
  • Beatriz Dietl,
  • David Dalmau,
  • Maria J. Arranz,
  • Laia Llucià-Carol,
  • Anna M. Planas,
  • Jordi Pérez-Tur,
  • Israel Fernandez-Cadenas,
  • Paula Villares,
  • Jair Tenorio,
  • Roger Colobran,
  • Andrea Martin-Nalda,
  • Pere Soler-Palacin,
  • Francesc Vidal,
  • Aurora Pujol,
  • Manel Esteller

Journal volume & issue
Vol. 66
p. 103339

Abstract

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Background: Patients infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the coronavirus disease 2019 (COVID-19), exhibit a wide spectrum of disease behaviour. Since DNA methylation has been implicated in the regulation of viral infections and the immune system, we performed an epigenome-wide association study (EWAS) to identify candidate loci regulated by this epigenetic mark that could be involved in the onset of COVID-19 in patients without comorbidities. Methods: Peripheral blood samples were obtained from 407 confirmed COVID-19 patients ≤ 61 years of age and without comorbidities, 194 (47.7%) of whom had mild symptomatology that did not involve hospitalization and 213 (52.3%) had a severe clinical course that required respiratory support. The set of cases was divided into discovery (n = 207) and validation (n = 200) cohorts, balanced for age and sex of individuals. We analysed the DNA methylation status of 850,000 CpG sites in these patients. Findings: The DNA methylation status of 44 CpG sites was associated with the clinical severity of COVID-19. Of these loci, 23 (52.3%) were located in 20 annotated coding genes. These genes, such as the inflammasome component Absent in Melanoma 2 (AIM2) and the Major Histocompatibility Complex, class I C (HLA-C) candidates, were mainly involved in the response of interferon to viral infection. We used the EWAS-identified sites to establish a DNA methylation signature (EPICOVID) that is associated with the severity of the disease. Interpretation: We identified DNA methylation sites as epigenetic susceptibility loci for respiratory failure in COVID-19 patients. These candidate biomarkers, combined with other clinical, cellular and genetic factors, could be useful in the clinical stratification and management of patients infected with the SARS-CoV-2. Funding: The Unstoppable campaign of the Josep Carreras Leukaemia Foundation, the Cellex Foundation and the CERCA Programme/Generalitat de Catalunya.

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