Dynamic Cellular Proteome Remodeling during SARS-CoV‑2 Infection. Identification of Plasma Protein Readouts

The outbreak of COVID-19, led to an ongoing pandemic
with devastating
consequences for the global economy and human health. With the global
spread of SARS-CoV-2, multidisciplinary initiatives were launched
to explore new diagnostic, therapeutic, and vaccination strategies.
From this perspective, proteomics could help to understand the mechanisms
associated with SARS-CoV-2 infection and to identify new therapeutic
options. A TMT-based quantitative proteomics and phosphoproteomics
analysis was performed to study the proteome remodeling of human lung
alveolar cells expressing human ACE2 (A549-ACE2) after infection with
SARS-CoV-2. Detectability and the prognostic value of selected proteins
was analyzed by targeted PRM. A total of 6802 proteins and 6428 phospho-sites
were identified in A549-ACE2 cells after infection with SARS-CoV-2.
The differential proteins here identified revealed that A549-ACE2
cells undergo a time-dependent regulation of essential processes,
delineating the precise intervention of the cellular machinery by
the viral proteins. From this mechanistic background and by applying
machine learning modeling, 29 differential proteins were selected
and detected in the serum of COVID-19 patients, 14 of which showed
promising prognostic capacity. Targeting these proteins and the protein
kinases responsible for the reported phosphorylation changes may provide
efficient alternative strategies for the clinical management of COVID-19.

新型冠状病毒肺炎（COVID-19）的暴发引发了持续蔓延的全球大流行，对全球经济与人类健康造成了毁灭性影响。随着严重急性呼吸综合征冠状病毒2（SARS-CoV-2）在全球范围内扩散，多学科研究项目纷纷启动，以探索新型诊断、治疗及疫苗研发策略。在此研究背景下，蛋白质组学（proteomics）有助于阐明SARS-CoV-2感染相关的分子机制，并发掘全新的治疗方案。本研究采用基于串联质量标签（Tandem Mass Tag, TMT）的定量蛋白质组学与磷酸化蛋白质组学分析方法，对表达人血管紧张素转换酶2（Angiotensin-converting enzyme 2, ACE2）的人肺肺泡细胞（A549-ACE2）在感染SARS-CoV-2后的蛋白质组重塑情况进行了研究。通过靶向平行反应监测（Parallel Reaction Monitoring, PRM）技术，对筛选得到的蛋白质的可检测性及预后价值展开分析。在感染SARS-CoV-2后的A549-ACE2细胞中，共计鉴定到6802种蛋白质与6428个磷酸化位点。本研究鉴定得到的差异表达蛋白显示，A549-ACE2细胞的核心生命过程呈现时间依赖性调控模式，清晰展现了病毒蛋白对宿主细胞生理机制的精准干预。基于这一机制研究基础，并结合机器学习建模分析，研究人员筛选出29种差异蛋白，并在新型冠状病毒肺炎患者的血清中检测到了这些蛋白，其中14种展现出良好的预后应用潜力。靶向此类蛋白以及介导上述磷酸化修饰变化的蛋白激酶，可为新型冠状病毒肺炎的临床管理提供高效的替代治疗策略。