Unraveling the Cellular Landscape of Abdominal Aortic Aneurysm Using High-Resolution Spatial Transcriptomics:
We used Sequence-Scope (Seq-Scope), which can generate ultra-high definition images of sequence-based molecular signatures resolved at a submicrometer scale, for profiling spatial transcriptome associated with abdominal aortic aneurysm Experimental Methods: Seq-Scope experiment is divided into two consecutive sequencing steps: 1st-Seq and 2nd-Seq. 1st-Seq of Seq-Scope starts with the solid-phase amplification of a single-stranded synthetic oligonucleotide library using an Illumina sequencing-by-synthesis (SBS) platform. 2nd-Seq of Seq-scope begins with overlaying the tissue section slice onto the HDMI-array.    Computational Methods: Tissue boundaries are detected by using a custom python code to draw a smoothed density plot to visualize the density of HiSeq reads in a given XY space of each tile. Digital gene expression (DGE) matrices are  generate using STAR/STARsolo 2.7.5c with Gene,GeneFull, Velocyto, and polyAtrimming options.  Data binning is performed by dividing the imaging space into 100 µm2 square grid with 10 µm simple side or 25 µm2 square grid with 5 µm side and collapsing all HDMI-UMI information into one barcode. Binned DGE matrix was analyzed in the Seurat v4 package for clustering analysis. Overall design: Sixteen-week-old Apoe -/- male mice fed a normal diet were subcutaneously implanted minipumps to delivery AngII (1,000ng/ml, 5 mice) or saline (5 mice) for 4 weeks. No significant difference was found in body weight, TC, and TG between the two groups at 4 weeks after minipump implantation. The extraluminal diameters were significantly increased in AngII group, in which 3 mice developed AAA (60% incidence). The fresh frozen suprarenal abdominal aortas from 3 AAAs and 3 normal controls were pair-embedded in OCT and cut into 10 µm sections. A total of 20 aortic sections (10 normal aortic sections and 10 aneurysmal sections) were attached onto HDMI-array slide for histological staining, library preparation and sequencing.