Digital Spatial Profiling identifies distinct molecular signatures of vascular lesions in Pulmonary Arterial Hypertension

Idiopathic Pulmonary Arterial Hypertension (IPAH) is a severe human disease, characterized by extensive pulmonary vascular remodeling due to plexiform and obliterative lesions, media hypertrophy, and alterations of adventitia. The objective of the study was to test the hypothesis that microscopic IPAH vascular lesions express unique molecular profiles, which collectively are different from control pulmonary arteries. We used digital spatial transcriptomics to profile the genome-wide differential transcriptomic signature of key pathological lesions (plexiform, obliterative, intima+media hypertrophy, and adventitia) in IPAH lungs (n= 11) and compared these data to the intima+media and adventitia of control pulmonary artery (n=5). The IPAH lesions and pulmonary artery compartments were defined by the analyses of hematoxylin-eosin stained serial section, aided by labeling with CD31 (for endothelial cells), smooth muscle cell actin (SMA), and CD45 for inflammatory mononuclear cells, also in serial sections. Approximately 12 regions of interest (ROI) were sampled from a histological section of a paraffin-embedded block of each lung, which was selected based on the finding of enrichment for IPAH lesions or control pulmonary arteries. A total of 211 ROIs were studied with 149 ROIs representing IPAH lesions with 39 plexiform lesions, 37 obliterative lesions, 36 intima+media hypertrophy, and 37 IPAH adventitia; of 62 ROIs of control lungs, including 34 intima+media and 28 control adventitia. The ROIs were selected largely based on the histopathological identification of each type of lesion (in IPAH lungs) or control pulmonary artery compartments. The selected ROIs were then processed by the GeoMx Nanostring platform, followed by whole genome sequencing. *** FASTQ raw data files have been requested. ***