TWAS-based translational genomics approach identifies IL10RB as the top candidate gene for COVID-19 host susceptibility and severity. TWAS-based translational genomics approach identifies IL10RB as the top candidate gene for COVID-19 host susceptibility and severity

Recent efforts have identified genetic loci that are associated with coronavirus disease 2019 (COVID-19) infection rates and disease outcome severity. Translating these genetic findings into druggable genes that regulate COVID-19 host susceptibility is a critical next step. Using a translational genomics approach that integrates COVID-19 genetic susceptibility variants, multi-tissue genetically regulated gene expression (GReX) and perturbagen signatures, we identify IL10RB as the top key regulator of COVID-19 host susceptibility. In a series of validation steps we show that predicted GReX up-regulation of IL10RB and higher IL10RB expression in COVID-19 patient blood is associated with worse COVID-19 outcomes, and that in vitro IL10RB overexpression is associated with increased viral load and activation of disease-relevant molecular pathways. Overall design: 3 samples each matching the following conditions/treatments (48 total): NPCs;CoV+;CRISPRa;IL10RB-1 gRNA NPCs;CoV+;CRISPRa;IL10RB-2 gRNA NPCs;CoV+;CRISPRa;IL10RB-3 gRNA NPCs;CoV+;CRISPRa;IL10RB-4 gRNA NPCs;CoV+;CRISPRa;Scramble gRNA NPCs;CoV+;shRNA;IFNAR2 shRNA NPCs;CoV+;shRNA;IL10RB shRNA NPCs;CoV+;shRNA;Scramble shRNA NPCs;CoV-;CRISPRa;IL10RB-1 gRNA NPCs;CoV-;CRISPRa;IL10RB-2 gRNA NPCs;CoV-;CRISPRa;IL10RB-3 gRNA NPCs;CoV-;CRISPRa;IL10RB-4 gRNA NPCs;CoV-;CRISPRa;Scramble gRNA NPCs;CoV-;shRNA;IFNAR2 shRNA NPCs;CoV-;shRNA;IL10RB shRNA NPCs;CoV-;shRNA;Scramble shRNA

已有研究通过相关工作鉴定出与2019冠状病毒病（COVID-19）感染率及疾病严重程度结局相关的遗传位点。将这些遗传学发现转化为调控COVID-19宿主易感性的可成药基因，是后续研究的关键方向。本研究采用整合了COVID-19遗传易感性变异、多组织遗传调控基因表达（genetically regulated gene expression, GReX）及扰动特征（perturbagen signatures）的转化基因组学方法，鉴定出IL10RB是调控COVID-19宿主易感性的首要关键调节因子。通过一系列验证实验，本研究证实：IL10RB的预测性GReX上调及COVID-19患者血液中IL10RB的高表达，均与更差的COVID-19结局相关；且体外实验中IL10RB过表达与病毒载量升高及疾病相关分子通路的激活存在关联。
实验整体设计：共设置48个样本，每种条件/处理组均设置3个生物学重复，具体分组如下：
1. 神经前体细胞（neural progenitor cells, NPCs）；冠状病毒感染阳性（CoV+）；CRISPR激活（CRISPRa）；IL10RB-1向导RNA（guide RNA, gRNA）
2. 神经前体细胞（NPCs）；CoV+；CRISPRa；IL10RB-2 gRNA
3. 神经前体细胞（NPCs）；CoV+；CRISPRa；IL10RB-3 gRNA
4. 神经前体细胞（NPCs）；CoV+；CRISPRa；IL10RB-4 gRNA
5. 神经前体细胞（NPCs）；CoV+；CRISPRa；阴性对照gRNA（Scramble gRNA）
6. 神经前体细胞（NPCs）；CoV+；短发夹RNA（short hairpin RNA, shRNA）；IFNAR2 shRNA
7. 神经前体细胞（NPCs）；CoV+；shRNA；IL10RB shRNA
8. 神经前体细胞（NPCs）；CoV+；shRNA；阴性对照shRNA（Scramble shRNA）
9. 神经前体细胞（NPCs）；冠状病毒感染阴性（CoV-）；CRISPRa；IL10RB-1 gRNA
10. 神经前体细胞（NPCs）；CoV-；CRISPRa；IL10RB-2 gRNA
11. 神经前体细胞（NPCs）；CoV-；CRISPRa；IL10RB-3 gRNA
12. 神经前体细胞（NPCs）；CoV-；CRISPRa；IL10RB-4 gRNA
13. 神经前体细胞（NPCs）；CoV-；CRISPRa；Scramble gRNA
14. 神经前体细胞（NPCs）；CoV-；shRNA；IFNAR2 shRNA
15. 神经前体细胞（NPCs）；CoV-；shRNA；IL10RB shRNA
16. 神经前体细胞（NPCs）；CoV-；shRNA；Scramble shRNA