Systems and Chemical Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
Rwanda Biomedical Centre, Kigali, Rwanda.
PLoS One. 2022 Aug 8;17(8):e0271870. doi: 10.1371/journal.pone.0271870. eCollection 2022.
Proteome profile changes post-severe acute respiratory syndrome coronavirus 2 (post-SARS-CoV-2) infection in different body sites of humans remains an active scientific investigation whose solutions stand a chance of providing more information on what constitutes SARS-CoV-2 pathogenesis. While proteomics has been used to understand SARS-CoV-2 pathogenesis, there are limited data about the status of proteome profile in different human body sites infected by the SARS-CoV-2 virus. To bridge this gap, our study aims to characterize the proteins secreted in urine, bronchoalveolar lavage fluid (BALF), gargle solution, and nasopharyngeal samples and assess the proteome differences in these body samples collected from SARS-CoV-2-positive patients. We downloaded publicly available proteomic data from (https://www.ebi.ac.uk/pride/). The data we downloaded had the following identifiers: (i) PXD019423, n = 3 from Charles Tanford Protein Center in Germany. (ii) IPX0002166000, n = 15 from Beijing Proteome Research Centre, China. (iii) IPX0002429000, n = 5 from Huazhong University of Science and Technology, China, and (iv) PXD022889, n = 18 from Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA. MaxQuant was used for the human peptide spectral matching using human and SARS-CoV-2 proteome database which we downloaded from the UniProt database (access date 13th October 2021). The individuals infected with SARS-CoV-2 viruses displayed a different proteome diversity from the different body sites we investigated. Overally, we identified 1809 proteins across the four sample types we compared. Urine and BALF samples had significantly more abundant SARS-CoV-2 proteins than the other body sites we compared. Urine samples had 257(33.7%) unique proteins, followed by nasopharyngeal with 250(32.8%) unique proteins. Gargle solution and BALF had 38(5%) and 73(9.6%) unique proteins respectively. Urine, gargle solution, nasopharyngeal, and bronchoalveolar lavage fluid samples have different protein diversity in individuals infected with SARS-CoV-2. Moreover, our data also demonstrated that a given body site is characterized by a unique set of proteins in SARS-CoV-2 seropositive individuals.
严重急性呼吸综合征冠状病毒 2 （SARS-CoV-2）感染后不同人体部位的蛋白质组谱变化仍然是一个活跃的科学研究领域，其解决方案有可能提供更多关于 SARS-CoV-2 发病机制的信息。尽管蛋白质组学已被用于了解 SARS-CoV-2 的发病机制，但关于 SARS-CoV-2 病毒感染的不同人体部位蛋白质组谱的状态的数据有限。为了弥补这一空白，我们的研究旨在描述从 SARS-CoV-2 阳性患者采集的尿液、支气管肺泡灌洗液（BALF）、漱口液和鼻咽样本中分泌的蛋白质，并评估这些样本中的蛋白质组差异。我们从（https://www.ebi.ac.uk/pride/）下载了公开可用的蛋白质组学数据。我们下载的数据具有以下标识符：（i）来自德国 Charles Tanford 蛋白质中心的 PXD019423，n = 3。（ii）来自中国北京蛋白质组研究中心的 IPX0002166000，n = 15。（iii）来自中国华中科技大学的 IPX0002429000，n = 5。（iv）来自美国明尼苏达州罗切斯特市 Mayo 诊所的 Department of Laboratory Medicine and Pathology 的 PXD022889，n = 18。MaxQuant 用于使用我们从 UniProt 数据库（访问日期为 2021 年 10 月 13 日）下载的人类和 SARS-CoV-2 蛋白质组数据库对人类肽谱进行匹配。感染 SARS-CoV-2 病毒的个体与我们研究的不同身体部位显示出不同的蛋白质组多样性。总体而言，我们在四个比较样本类型中鉴定出 1809 种蛋白质。与我们比较的其他身体部位相比，尿液和 BALF 样本中 SARS-CoV-2 蛋白的丰度明显更高。尿液样本中有 257（33.7%）种独特蛋白质，其次是鼻咽样本，有 250（32.8%）种独特蛋白质。漱口液和 BALF 分别有 38（5%）和 73（9.6%）种独特蛋白质。感染 SARS-CoV-2 的个体的尿液、漱口液、鼻咽和支气管肺泡灌洗液样本具有不同的蛋白质多样性。此外，我们的数据还表明，在 SARS-CoV-2 血清阳性个体中，特定身体部位的特征是一组独特的蛋白质。
