Single nuclei RNA-seq of Ossabaw pig atherosclerotic and healthy aortae

Atherosclerosis is a major contributor to cardiovascular diseases. Well-established preclinical models that can accurately recapitulate human atherosclerosis development and progression are necessary for developing new therapeutics. Pig models are extensively used in cardiovascular research due to their physiological similarities to humans. However, their translational efficacy into clinical settings has remained limited. To ensure better translational outcomes, a deeper molecular characterization of atherosclerotic disease mechanisms in swine models is urgently required. Methods: To address this gap, we employed single nuclei transcriptomics to characterize healthy and atherosclerotic aortas in the Ossabaw pig model. We analyzed over 36,000 nuclei from aortas of 5 adult male castrated pigs kept on atherogenic and chow diets. In-depth single-nuclei transcriptomic and cell-cell communication analyses were undertaken to uncover molecular changes in swine atherosclerosis development. Comparisons to human and mouse atherosclerosis were used to establish the veracity of the Ossabaw pig in modeling human disease. Castrate male Ossabaw pigs of 12-month age were put on HF/HFru or chow diet for 9 months. Abdominal aortae were dissected and snap-frozen. Frozen tissues were processed for nuclei isolation followed by snRNA-seq protocol. Single nuclei RNA-seq was performed using 10x Next GEM Single Cell 3 GEM kit v3.1 according to the manufacturers protocol. Separate 10x genomics reactions were used for each sample. Generated libraries were sequenced on an Illumina NovaSeq with >27.5 x 10^3 reads per cell followed by de-multiplexing and mapping to the domesticated pig genome (build Sscrofa11) using CellRanger v5.0. Further analyses were performed using Seurat package v.5.0.