Genetic-epigenetic and aging interactions at COVID- 19 host response loci in Down syndrome and mouse models

The importance of the COVID-19 pandemic, with >3M cases and >130K deaths in the USA alone, cannot beoverstated. This highly contagious and too often lethal infection with SARS-CoV-2 has both severe acuteeffects and longer-term adverse sequelae, and disease severity and death rates are strikingly higher in elderlyindividuals. Pathogenesis and host responses to COVID-19 are still very much under investigation, but initialhypotheses 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 withDown syndrome (DS; trisomy 21), and other COVID-19 relevant genes, including S100B and TMPRSS2 arealso on chromosome 21. In addition, investigators seeking drug targets have pointed out the dependence ofthe virus on the methyl donor (folate pathway; S-adenosylmethionine; SAM) status of host cells, and a group ofgenes in this pathway are triplicated in DS. From research on COVID-19 in the general population, the geneticbackground 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 3p21and 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 criticalgenetic variant. How the presence of the extra chromosome 21 in DS might affect this important locus is acritical 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 isneeded but has not yet been developed. Given these challenges, here we propose to localize COVID-19related host genomic sequences that are epigenetically regulated and altered in immune cell types from DS vseuploid individuals, to use allele-specific methylation mapping to pinpoint key regulatory elements in the 3p21COVID-19 GWAS region, and ask whether these elements are epigenetically altered in DS. We will engineerCRISPR/Cas9-mediated deletions in the differentially methylated sequences and measure the effects onmethylation patterns and regional gene expression. Building upon the progress of genetic engineering, we willdevelop an experimentally tractable mouse model to ask whether COVID-19 infections are more severe in agenetic background that accurately mimics human DS. In both the mouse model and our human biosamplesfrom DS and controls, we will quantitate the age-dependence of methylation of COVID-19 host responsegenes. These fundamental studies, to be carried out in one year, will lay a crucial groundwork for subsequentwork using biosamples from DS individuals who have been exposed to SARS-CoV-2, cohorts that are beingorganized by our colleagues under separate funding.