The importance of the COVID-19 pandemic, with >3M cases and >130K deaths in the USA alone, cannot be overstated. This highly contagious and too often lethal infection with SARS-CoV-2 has both severe acute effects and longer-term adverse sequelae, and disease severity and death rates are strikingly higher in elderly individuals. Pathogenesis and host responses to COVID-19 are still very much under investigation, but initial hypotheses include roles for host cytokines, including pro-inflammatory IL-6 and Type I and III interferons (IFNs), and S100-family proteins. Importantly, a group of IFN pathway genes are triplicated in people with Down syndrome (DS; trisomy 21), and other COVID-19 relevant genes, including S100B and TMPRSS2 are also on chromosome 21. In addition, investigators seeking drug targets have pointed out the dependence of the virus on the methyl donor (folate pathway; S-adenosylmethionine; SAM) status of host cells, and a group of genes in this pathway are triplicated in DS. From research on COVID-19 in the general population, the genetic background of the infected host is known to be important, with a Genome Wide Association Study (GWAS) revealing significant associations with single nucleotide polymorphism rs11385942 in chromosome band 3p21 and rs657152 at 9q34. At locus 3p21, the association signal spans the genes SLC6A20, LZTFL1, CCR9, FYCO1, CXCR6 and XCR1, and it is not yet clear which is the most important gene, and which is the critical genetic variant. How the presence of the extra chromosome 21 in DS might affect this important locus is a critical issue, and we have preliminary data pointing to differences in DNA methylation in this region in DS vs. control individuals. Importantly, an accurate mouse model of COVID-19 in the DS genetic background is needed but has not yet been developed. Given these challenges, here we propose to localize COVID-19 related host genomic sequences that are epigenetically regulated and altered in immune cell types from DS vs euploid individuals, to use allele-specific methylation mapping to pinpoint key regulatory elements in the 3p21 COVID-19 GWAS region, and ask whether these elements are epigenetically altered in DS. We will engineer CRISPR/Cas9-mediated deletions in the differentially methylated sequences and measure the effects on methylation patterns and regional gene expression. Building upon the progress of genetic engineering, we will develop an experimentally tractable mouse model to ask whether COVID-19 infections are more severe in a genetic background that accurately mimics human DS. In both the mouse model and our human biosamples from DS and controls, we will quantitate the age-dependence of methylation of COVID-19 host response genes. These fundamental studies, to be carried out in one year, will lay a crucial groundwork for subsequent work using biosamples from DS individuals who have been exposed to SARS-CoV-2, cohorts that are being organized by our colleagues under separate funding.

Given the major importance of the COVID-19 pandemic, with >3M cases and >130K deaths in the USA alone, and potential vulnerability of people with Down syndrome (DS; trisomy 21), we propose here to elucidate biological, genetic and epigenetic factors that can influence the response to SARS-CoV-2 in people with DS. We will map DNA methylation patterns and assess gene expression in chromosomal regions that are genetically and biologically linked to the COVID-19 host response, comparing these patterns in immune system cells from people with DS to those in age-matched control individuals, we will engineer CRISPR/Cas9-mediated deletions in the strongest differentially methylated sequences and measure effects on gene expression, we will develop an accurate and experimentally tractable mouse model of COVID-19 in DS, and quantitate age-dependence of methylation of the host response genes both in humans and in this well controlled model system. We expect our findings to lead to improved clinical and public health management of COVID-19 both in DS and in the general population.