Spatial transcriptomics of in vivo invasive trancheobronchitis biopsies obtained from patients with influenza-associated pulmonary aspergillosis or COVID-19-associated pulmonary aspergillosis. Spatial transcriptomics of in vivo invasive trancheobronchitis biopsies obtained from patients with influenza-associated pulmonary aspergillosis or COVID-19-associated pulmonary aspergillosis

To assess whether transcriptional differences exist in the epithelial tissue and the inflammatory infiltrate of invasive Aspergillus tracheobronchitis in patients with severe influenza or severe COVID-19, we performed GeoMx spatial transcriptomics on four biopsy samples in total: two of patients with influenza-associated pulmonary aspergillosis (IAPA) and two of patients with COVID-19-associated pulmonary aspergillosis (CAPA). Several regions of interest (ROIs) were delineated in each biopsy sample, and transcriptomic data was derived of each of these ROIs using GeoMx with a whole transcriptome atlas with SARS-CoV-2 spike-in. Overall design: Four in vivo tracheobronchial biopsies of invasive Aspergillus tracheobronchitis were obtained from patients with IAPA (n=2) and CAPA (n=2). ROIs were selected in epithelial tissue and in the (subepithelial) inflammatory infiltrate.

为明确重症流感或重症新型冠状病毒肺炎（COVID-19）患者所患侵袭性曲霉性气管支气管炎的上皮组织与炎性浸润灶是否存在转录组差异，本研究对总计4份活检标本开展GeoMx空间转录组学（GeoMx spatial transcriptomics）检测：其中2份标本取自流感相关肺曲霉病（influenza-associated pulmonary aspergillosis, IAPA）患者，另外2份取自新冠相关肺曲霉病（COVID-19-associated pulmonary aspergillosis, CAPA）患者。
每份活检标本均划定多个感兴趣区域（regions of interest, ROIs），并基于搭载SARS-CoV-2刺突基因外参的全转录组图谱，通过GeoMx平台获取各ROIs的转录组数据。
整体实验设计：本研究从IAPA（n=2）及CAPA（n=2）患者体内获取4份侵袭性曲霉性气管支气管炎活体气管支气管活检标本，在每份标本的上皮组织及（上皮下）炎性浸润灶中选取感兴趣区域（ROIs）。