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

COVID-19大流行的重要性，仅在美国就有超过300万例病例和超过13万例死亡， 言过其实。这种高度传染性和致命性的SARS-CoV-2感染，既有严重的急性 老年人的不良反应和长期不良后遗症以及疾病严重程度和死亡率明显更高 个体COVID-19的发病机制和宿主反应仍在研究中，但初步 假设包括宿主细胞因子的作用，包括促炎性IL-6和I型和III型干扰素 （IFN）和S100家族蛋白。重要的是，一组IFN途径基因在患有 唐氏综合征（DS; 21三体）和其他COVID-19相关基因，包括S100 B和TMPRSS 2， 也在21号染色体上此外，寻求药物靶点的研究人员指出， 病毒对宿主细胞的甲基供体（叶酸途径; S-腺苷甲硫氨酸; SAM）状态的影响，以及一组 该途径中的基因在DS中是三重的。根据对普通人群中COVID-19的研究， 已知受感染宿主的背景是重要的，全基因组关联研究（GWAS） 显示与染色体3 p21带单核苷酸多态性rs 11385942显著相关 和9 q34处的rs657152。在基因座3 p21处，关联信号跨越基因SLC 6A 20、LZTFL 1、CCR 9、 FYCO 1、CXCR 6和XCR 1，目前还不清楚哪一个是最重要的基因，哪一个是关键的基因。 基因变异DS中额外的21号染色体的存在如何影响这个重要的基因座是一个问题。 关键问题，我们有初步的数据表明，在这一地区的DNA甲基化的差异，在DS与 控制个人。重要的是，在DS遗传背景下精确的COVID-19小鼠模型是 需要，但尚未开发。鉴于这些挑战，我们在此建议将COVID-19本地化 在DS与DS的免疫细胞类型中表观遗传调节和改变的相关宿主基因组序列 整倍体个体，使用等位基因特异性甲基化定位来确定3 p21中的关键调控元件。 COVID-19 GWAS区域，并询问这些元素是否在DS中发生了表观遗传学改变。我们将工程师 CRISPR/Cas9介导的差异甲基化序列中的缺失，并测量对差异甲基化序列的影响。 甲基化模式和区域基因表达。在基因工程的基础上，我们将 开发一种实验上易于处理的小鼠模型，以询问COVID-19感染是否在 精确模仿人类DS的遗传背景在小鼠模型和我们的人类生物样本中 根据DS和对照，我们将量化COVID-19宿主反应甲基化的年龄依赖性 基因.这些基础研究将在一年内进行，将为今后的研究奠定重要的基础。 使用来自暴露于SARS-CoV-2的DS个体的生物样本进行工作， 由我们的同事单独出资组织。

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.