A recombinant AAV vector has been generated to carry the codon-optimized acid alpha-glucosidase (coGAA) gene expressed from a human desmin enhancer/promoter (DES). The proposed clinical trial is a within-participant, double-blind, randomized, phase I controlled study evaluating the toxicology, biodistribution and potential activity of re-administration of rAAV9-DES-hGAA injected intramuscularly into the TA. Nine participants (18 to 50-years old) who reside within the United States with Late-Onset Pompe Disease (LOPD) will be included. The goal of the immune modulation strategy is to ablate B-cells (Rituximab and Sirolimus) prior to the initial exposure to the study agent in one leg and the subsequent exposure of the same vector to the contralateral leg after four months. At each study agent dosing, the contralateral leg will receive excipient. Patients will act as their own controls. Repeated measures, at baseline and during the following 3 months after each injection, will assess the safety, biochemical and functional impact of the vector.

Enrolling in this study will entail participating in 18 months of study-related visits. Patients will be asked to come to the Clinical and Translational Research Building at the University of Florida for a series of onsite study visits.

All the visits will be performed as outpatient procedures at the Clinical Research Center (CRC) and at other facilities at the University of Florida. Overnight observation will not be needed, however, patients will be asked to stay overnight in a hotel near the University of Florida. During the first 4 months after each injection, patients will be asked to perform outpatient laboratory work at a laboratory facility convenient for them.

In addition, during this study patients will be asked to take medications that will modulate the ability of their immune system to react against foreign agents including the gene transfer agent. The purpose of these medications is to improve the activity of the GAA within the body. Patients will receive a Rituximab injection 21 days prior to the first injection of the study agent and 7 days before each injection of the study agent and the day of the first injection. Rituximab will be delivered by infusion that may last 2-6 hours. Patients will need to take another medication (Sirolimus) every day starting 7 days before the first injection of the study agent until four months after the second injection of the study agent.

The following discusses what will occur at each visit:

Baseline Baseline Evaluation and first Rituximab infusion - Day -22/-21/-20

• Medical history: Patients will be asked to complete a questionnaire about his/her medical history.
• Physical exam: The study doctor will perform a general physical exam to evaluate patients physical health.
• Blood and urine tests: These tests will be used for evaluating the safety of the gene transfer agent.
• Electrocardiogram (ECG): This test will measure the electrical activity of patient's heart to see if it is working properly.
• Quantitative Muscle Testing (QMT): This test finds out how strong the patient's leg muscles are.
• 10 Meter Walk Test: Patients will be instructed to walk a set distance (10 meters); time will be measured while patient walks the set distance and the distance covered will be divided by the time it took to walk that distance.
• Gait analysis: Gait will be tested with Gait Mat II, which will record the spatial and temporal parameters of his/her walk such as cadence, speed and distance between your feet.
• Magnetic Resonance Imaging (MRI) and Spectroscopy (MRS): MRI and MRS testing will be done inside a large magnet that lets the study doctors measure the size and health of the patient's muscles. These tests are done at the same time. MRI and MRS testing will require the patient to stay very still for up to an hour.
• Magnetic stimulation of the common fibular nerve: The common fibular nerve, which is the nerve that controls the injected muscle, will be stimulated with a magnetic field to test the impact of the gene transfer agent to the nervous system.
• The patient will receive the first Rituximab infusion. It might last between 2 and 6 hours.

Rituximab infusion - Day -6

• The patient will receive the 2nd Rituximab infusion 7 days before the gene transfer agent. It might last between 2 and 6 hours.

• Patient will begin Rapamycin.

  1st Injection - Day 0/1

• The patient will receive the 3rd Rituximab infusion the day before the gene transfer agent. It might last between 2 and 6 hours.

• Patient will receive the gene transfer agent in 1 injection (a total of about 1 teaspoon) into the tibialis anterior (TA) muscle of one leg. The other leg will receive a pharmacologically inactive solution. An ultrasound will be used to detect the proper location of injection. A photograph of the injection at the injection site may be taken. If the patient agrees to this, he/she will be asked to sign a consent form for this procedure.

On day 1, blood tests will be done.

Outpatient lab work - Day 3/7/15/30/60

• Blood and urine tests

Onsite visit - Day 89/90

• Medical history
• Physical Exam
• Blood and urine tests
• Quantitative Muscle Testing (QMT)
• 10 Meter Walk Test
• Gait analysis
• Magnetic Resonance Imaging (MRI) and Spectroscopy (MRS)
• Muscle Biopsy: Tissue samples obtained will be used for evaluation of muscle glycogen and GAA activity in the injected muscle.
• Magnetic stimulation of the common fibular nerve

Rituximab infusion - Day 114

• The patient will receive the 4th Rituximab infusion, it might last between 2-6 hours.

  2nd Injection - Day 121/122

• The patient will receive the second gene transfer agent injection in the leg that previously received the inactive solution. The leg that previously received the study agent will receive the inactive solution. The injection procedure and the amount of study agent injected will be the same as the first injection.

On day 122, blood tests will be done.

Outpatient lab work - Day 124/128/135/150/180

• Blood and urine tests

Onsite visit - Day 209/210

• Medical History
• Physical Exam
• Blood and urine tests
• Quantitative Muscle Testing (QMT)
• 10 Meter Walk Test
• Gait analysis
• Magnetic Resonance Imaging (MRI) and Spectroscopy (MRS)
• Muscle Biopsy
• Magnetic stimulation of the common fibular nerve

Onsite visit - Day 365

• Medical history
• Physical exam
• Quantitative Muscle Testing (QMT)
• 10 Meter Walk Test
• Blood and urine tests

Onsite visit - Day 520

• Medical history
• Physical exam
• Quantitative Muscle Testing (QMT)
• 10 Meter Walk Test
• Blood and urine tests

Inclusion Criteria:

• Male or female subjects 18 to 50-years old
• Have a diagnosis of Pompe disease, as defined by protein assay AND/OR DNA sequence of the acid alpha-glucosidase gene, AND clinical symptoms of the disease
• Have residual ability to complete the 10 meter walk test
• Willing to discontinue aspirin, aspirin-containing products and other drugs that may alter platelet function, 7 days prior to dosing, resuming 24 hours after the dose has been administered
• Consistently taking enzyme replacement therapy (ERT) or remain off ERT from baseline until Day 520
• United States residents only.

Exclusion Criteria:

• Be pregnant or nursing, and if the subject is of child bearing potential they should use contraception until the end of the study
• Have required oral or systemic corticosteroids within the last 15 days prior to baseline screening
• Have a platelet count less than 75,000/mm^3
• Have an INR greater than 1.3
• Have seronegative to AAV9 capsid protein (neutralizing Ab titers <1:5 and total binding Ab titer <50 U/ml)
• Have transaminases and alkaline phosphatase more than ten times the upper limit of normal at screening or Day-1
• Have bilirubin and gamma-glutamyl transpeptidase greater than 2 times the upper limit of normal at screening or Day -1
• Have any chronic liver disease (aside from hepatic dysfunction related to Pompe disease) such as hepatitis B and C and cirrhosis
• Be currently, or within the past 30 days, participating in any other research protocol involving investigational agents or therapies
• Have history of platelet dysfunction, evidence of abnormal platelet function at screening, or history of recent use of drugs that may alter platelet function, which the subject is unable/unwilling to discontinue for study agent administration
• Have received gene transfer agents within the past 6 months
• Have any medical condition or circumstance for which an MRI evaluation is contraindicated
• Have any other concurrent condition that, in the opinion of the investigator, would make the subject unsuitable for the study
• Inconsistent with use of ERT.