APBD is an adult-onset glycogen storage disease (GSD IV) caused by mutations in the glycogen branching enzyme (GBE1) gene. It is characterized by abnormally branched glycogen aggregates, known as polyglucosan bodies (PBs), which disrupt normal cellular function in neurons and skeletal muscle. We conducted an IND-enabling pre-clinical study using an AAV9 vector encoding human GBE1, driven by a ubiquitous promoter and delivered intrathecally in APBD model mice(GBE1ys/ys). We observed dose-dependent improvements in both histological and functional parameters. We screened for diagnostic and treatment-responsive biomarkers in this large cohort. Glycogen breakdown products(glucans) were found to be elevated in the urine of GBE1ys/ys mice and rescued by gene therapy. Based on these findings, we established the first biorepository for APBD and validated urine glucans, including Glc4, as biomarkers in APBD patients. Glc4 levels correlated with disease severity, supporting their clinical utility. These results advance gene therapy development and biomarker translation for APBD.