概要: Understanding SARS-CoV-2 immune pathology is critical for the development of effective vaccines and treatments. Here, we employed unbiased serial whole-blood transcriptome profiling by weighted gene network correlation analysis (WGCNA) at pre-specified timepoints of infection to understand SARS-CoV-2-related immune alterations in a cohort of rhesus macaques (RMs) and African green monkeys (AGMs) presenting with varying degrees of pulmonary pathology. We found that the bulk of transcriptional changes occurred at day 3 post-infection and normalized to pre-infection levels by 3 weeks. There was evidence of coordination of transcriptional networks in blood (defined by WGCNA) and the nasopharyngeal SARS-CoV-2 burden as well as the absolute monocyte count. Pathway analysis of gene modules revealed prominent regulation of type I and type II interferon stimulated genes (ISGs) in both RMs and AGMs, with the latter species exhibiting a greater breadth of ISG upregulation. Notably, pathways relating to neutrophil degranulation were enriched in blood of SARS-CoV-2 infected AGMs, but not RMs. Our results elude to hallmark similarities as well as differences in the RM and AGM acute response to SARS-CoV-2 infection, and may help guide the selection of particular NHP species in modeling aspects of COVID-19 disease outcome.
项目整体设计: Examination of gene networks regulated in response to SARS-CoV-2 in rhesus macaques and African green monkeys.
Total RNA samples were quantitated using Qubit RNA HS Assay kit (Invitrogen Q32855). A RIN for each sample was determined by running 1ul on an Agilent 4150 TapeStation using RNA Screen Tapes (Agilent 5067-5576). 1-2 ug of each sample were treated with Baseline Zero DNase (Epicentre, DB0711K) for 30 minutes at 37°C. DNase was inactivated by adding 2ul 10X Stop solution and following a 10 minute incubation at 65°C. The Total RNAs were then purified using Agencourt RNAClean XP magnetic beads by following the manufactory recommendation (Beckman Coulter Life Sciences).
建库方案:
10 ng of each sample were used to make SMART-Seq libraries following the SMART-Seq Stranded Kit User Manual (Takara Bio). Briefly, cDNAs were first generated from all total RNA fragments after RNA fragmentation. Addition of Illumina adapters and indexes and then library purification were followed. Final library amplification and purification were performed after enzymatically removing ribosomal fragments originating from rRNA molecules by using probes specific to mammalian rRNA.
Libraries were quantitated using Qubit DNA HS Assay kit (Molecular Probes Life Technologies, Q32854). Average size of each library was determined by running each sample on Agilent 4150 TapeStation using D1000 Screen Tapes. (Agilent 5067-5582). Each library was diluted to 4nM in DNase RNase free ultrapure water (Invitrogen 10977-015). All libraries were pooled at a concentration of 4nM before denaturing with 0.2 N NaOH for 5 min at RT. The libraries were neutralized using 0.2 N Tris-HCl, pH 7 before being diluted to 20pM in HT1 buffer (Illumina).
测序信息
分子类型:
polyA(+) RNA
库的片段类型:
PAIRED
库的链类型:
Forward
测序平台:
ILLUMINA
测序仪型号:
Illumina NextSeq 550
链特异性:
Specific
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文章
Similarities and Differences in the Acute-Phase Response to SARS-CoV-2 in Rhesus Macaques and African Green Monkeys.
Frontiers in immunology . 2021-10-06 [PMID:
34691074]