RNA Sequencing of WT Aged Vehicle vs. HPBCD Infarcts

We systematically characterized the transcriptomes of stroke infarcts in vehicle- and HPβCD-treated aged (18-month-old) mice by performing bulk RNA-Seq on infarcted brain tissue collected 7 weeks after distal middle cerebral artery occlusion + hypoxia (DH) stroke. The DE analysis revealed 991 upregulated genes and 1,876 downregulated genes. HPβCD treatment upregulated intracellular cholesterol transporters, lipoproteins, and lipoprotein receptors, such as Npc1, Npc2, Apoe, Trem2, Abca1, Vldlr, and Hdlbp, and downregulated Ffar1, Lrpb1, and Dgkb. These alterations in lipid metabolism suggest that HPβCD aids in the restoration of lipid homeostasis by 7 weeks after stroke. In addition, the DE analysis revealed a downregulation of genes involved in chemotaxis, including Cx3cr1, Cxcl5, and Ccr6, and innate and adaptive immune responses, including Mmd2, Mzb1, Btla, Jchain, and Igkv5-48. Correspondingly, there was an upregulation of anti-inflammatory genes, such as Tgfb1, Tgfb2, P2ry2, and Il18bp. Next, we performed genome-wide expression analysis of the RNA-Seq data using GSEA, which revealed significant enrichment of various biological processes in infarcts of HPβCD-treated aged mice, including (i) collagen formation, (ii) regulation of angiogenesis, (iii) lipid catabolic process, (iv) regulation of autophagy, and (v) regulation of apoptotic process. These results indicate that HPβCD treatment promotes lipid metabolism and angiogenesis and dampens chronic inflammation in infarcts of aged mice at 7 weeks after stroke. Bulk RNA sequencing was performed on chronic stroke infarcts of vehicle- and HPBCD-treated aged mice to assess transcriptional changes that occur following repeated subcutaneous administration of HPBCD.