Figure 6.

AAV Liver Gene Therapy Largely Normalizes Transcriptome in Muscle

(A and B) 9-month-old mice were injected with an AAV8-secGAA (secGAA-Gaa^−/−) vector at a dose of 2 × 10¹² vg/kg. Gaa^+/+ (PBS-Gaa^+/+) and Gaa^−/− (PBS-Gaa^−/−) mice, injected with PBS, served as controls in the study. Animals were followed for 9 months after treatment (n = 3/4 per cohort). (A) Gene expression in quadriceps muscle tissue from PBS-Gaa^−/−, PBS-Gaa^+/+, and secGAA-Gaa^−/− mice was analyzed by RNA sequencing. The expression profiles of 2,864 genes, detected as differentially expressed in any of the three possible pairwise contrasts (Figure S4B), were assigned to clusters using k-means. Three metaclusters, containing genes in which their expression levels had been fully rescued (FR; 23.3%, 666 genes), partially rescued (PR; 51.3%, 1,470 genes), or not rescued (NR; 25.4%, 728 genes) by the expression of secGAA in the Gaa^−/− background, were defined by combining gene clusters with complementary expression profiles. Normalized expression counts, averaged for each condition and scaled for each gene, are represented on the y axis. Gray lines represent the expression profile of individual genes. Black lines represent average expression profiles for each of the combined clusters. (B) Significant associations in 9 of total 41 canonical pathways were found for the three metacluster gene lists (FR, PR, and NR) after Ingenuity Pathway Analysis (IPA) enrichment analyses. Bar plots represent Fisher’s test p values for nine of the pathways and the three metaclusters. Red lines indicate the significance threshold (p < 0.05). Results for the remaining 33 pathways are presented in Figure S6.