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. 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.