AAV gene therapy for hereditary spastic paraplegia type 50: a phase 1 trial in a single patient

Abstract

There are more than 10,000 individual rare diseases and most are without therapy. Personalized genetic therapy represents one promising approach for their treatment. We present a road map for individualized treatment of an ultra-rare disease by establishing a gene replacement therapy developed for a single patient with hereditary spastic paraplegia type 50 (SPG50). Through a multicenter collaboration, an adeno-associated virus-based gene therapy product carrying the AP4M1 gene was created and successfully administered intrathecally to a 4-year-old patient within 3 years of diagnosis as part of a single-patient phase 1 trial. Primary endpoints were safety and tolerability, and secondary endpoints evaluated efficacy. At 12 months after dosing, the therapy was well tolerated. No serious adverse events were observed, with minor events, including transient neutropenia and Clostridioides difficile gastroenteritis, experienced but resolved. Preliminary efficacy measures suggest a stabilization of the disease course. Longer follow-up is needed to confirm the safety and provide additional insights on the efficacy of the therapy. Overall, this report supports the safety of gene therapy for SPG50 and provides insights into precision therapy development for rare diseases. Clinical trial registration: NCT06069687 .

Fig. 1. Development and implementation of individual gene therapy for SPG50.

a, Timeline of the development of SPG50 gene therapy, from patient diagnosis through patient dosing, with key milestones highlighted. Note that the entire process, from diagnosis to dosing, took approximately 2.5 years. UTSW, University of Texas Southwestern; FDA, Food and Drug Administration; IND, investigational new drug; GLP, Good Laboratory Practice; NHP, nonhuman primate; Tox, toxicology; CTA, clinical trial application; COA, certificate of analysis. b, Outline of the single-patient clinical trial. The schematic depicts the postdosing safety and efficacy monitoring time points, along with the immunosuppression protocol. The comprehensive immunosuppression program was implemented to attempt to minimize the innate and adaptive immune responses and to promote tolerance to the gene therapy product. ‘GT’ indicates the gene therapy dosing. MRI of the brain and spine (with and without contrast) was done at baseline and at 3, 6 and 12 months after dosing. CSF analysis included cell count, protein concentration, oligoclonal bands and cytokine analysis. Exploratory tests included measurement of the AAV9 neutralizing antibody titer, serum cytokine analysis and ELISpot assay. Safety laboratory tests (‘safety labs’) included complete blood count with differential, erythrocyte sedimentation rate, C-reactive protein, liver function tests (alanine aminotransferase, aspartate aminotransferase, γ-glutamyl transferase, alkaline phosphatase), blood urea nitrogen/creatinine, urinalysis, electrocardiography and cardiac safety panel (troponin, pro-B-type natriuretic peptide, creatine kinase isotype MB). IV MethylPred, intravenous methylprednisolone.

Fig. 2. Safety and efficacy (Bayley Scale of Infant Development) in the SPG50 single-patient therapy trial.

a, Enumeration of the adverse events reported in the clinical trial over the 1 year after dosing (IP, investigational product). No serious adverse events were observed. The patient experienced transient, asymptomatic neutropenia noted at 6 days after dosing. This resolved without intervention by day 13 after dosing. There was a prolonged episode of abdominal symptoms that included emesis, diarrhea, vomiting and abdominal pain. This episode prompted extensive evaluation, with the ultimate conclusion that the symptoms were due to side effects of tacrolimus plus C. difficile (C-diff) infection. b, Graphical representation of the longitudinal results of the Bayley Scale of Infant and Toddler Development, fourth edition. From 6 months after dosing, there were consistent increases in scores for all domains except expressive communication. This mirrors what was qualitatively observed by both the family and the examination team. c, Presentation of the longitudinal raw data from the Bayley scale (visualized graphically in b). Of note, the baseline and 3-month studies were complicated by challenges with the patient’s tolerance of the test. d, Scores from the motor skills submodule of the Vineland Adaptive Behavior Scale. Improvements were noted in both fine and gross motor performance.

Extended Data Fig. 1. Schematic of the investigational product.

Human, codon optimized AP4M1 (hAP4M1opt) with a bGH poly A tail was encapsulated into self-complementary (sc) AAV9. AP4M1 expression was governed by a ubiquitous promoter (UsP = JeT promoter with intron). See Chen et al., 2023, Journal of Clinical Investigation.

Extended Data Fig. 2. ELISpot assay reveals lack of immune response to AP4M1.

(a) ELISpot to show IFN-y T-cell Responses toward AAV9. As expected, there is clear evidence of an immune response against AAV9. (b) ELISpot to show IFN-y T-cell Responses toward AP4M1. No significant response against AP4M1 was identified. (c) Positive control ELISpot used to confirm that the success of the assay. Multiple two-tailed t-tests were conducted to assess for significant differences between treatment responses and negative controls. *P-values were adjusted for multiple comparisons using the two-stage linear step-up method of Benjamini, Krieger, and Yekutieli (FDR = 5%).

Extended Data Fig. 3. Safety lab trends during the 12 months post dosing.

(a-d) Presented are the main safety laboratory studies, AST (a), ALT (b), GGT (c), and neutrophils (d), from baseline to 12 months post- dosing. Normative values for age are highlighted in gray. There was a single instance of neutropenia at day 7 post- dosing (0.8×109/L). ALT and GGT values were consistently outside of the normal range, but never reached a clinically meaningful increased level, and remained < 2-fold above normal limits.

Extended Data Fig. 4. Listing of laboratory studies performed during the study.

Laboratory values obtained are listed from baseline through the first 12 months of the study. Abnormal values (i.e. values outside the normal range) are highlighted in bold. Normative values, when available, are listed in the left most column.

Extended Data Fig. 5. Listing of laboratory studies performed during the study (continued).

Laboratory values obtained are listed from baseline through the first 12 months of the study. Abnormal values (i.e. values outside the normal range) are highlighted in bold. Normative values, when available, are listed in the left most column.

Extended Data Fig. 6. Sensory nerve analyses performed during the study.

Standard nerve conduction studies were performed at baseline and then at 3 weeks, 3 months, 6 months, and 12 months. Presented are the data for the 5 sensory nerves that were studied. Values were within the normal range at all time points. Intriguingly, amplitudes increased post-dosing, suggesting, if anything, improvements in sensory nerve function. Of note, NCS was also performed on the Tibial motor nerve, and all values were within normal limits (data not shown).

Extended Data Fig. 7. Scores of the Tardieu and modified Ashworth scales for the upper limbs.

Scores from two measures of joint spasticity, the Tardieu and modified Ashworth scales. Existing natural history suggests worsening of spasticity in SPG50 over a 12-month period. We observed stabilization of scores on both scales, with no clear worsening. However, the patient poorly tolerated both outcome measures, resulting in missing data points at essentially all time points. Tardieu scale values are 0 = no resistance to passive movement, 1 = slight resistance, 2 = clear ‘catch’, interrupting passive movement, 3 = clonus ( < 10 seconds), 4 = sustained clonus. Ashworth scale values are 0 = no increase in tone, 1 = slight increase in tone, 1 + = slight increase in tone, catch/release through range of motion, 2 = marked increase in tone, 3 = marked increase in tone AND passive movement difficult, 4 = fixed contracture.

Extended Data Fig. 8. Scores of the Tardieu and modified Ashworth scales for the lower limbs.

Scores for the lower limbs for the Tardieu and Ashworth scales. Score values are presented in Extended Data Figure 7.

Extended Data Fig. 9. Vineland Adaptive Behavior Scale (version 2).

Results from the Vineland adaptive behavior scale, parent reported. Substantial gains were noted in both gross and fine motor skills (from baseline of 48 composite to 57 at 12 months post dosing). Small declines in scores were noted in adaptive behavior. This may be related in part to non-Melpida related side effects, including prolonged gastroenteritis and abdominal pain secondary to tacrolimus, as well as social impacts of immune suppression (such as prolonged absence from school).

Extended Data Fig. 10. AP4M1 vector structure and sequence.

Melpida consists of a vector containing codon optimized AP4M1 and surrounding sequences (UsP promoter and bGH polyA tail) inserted between truncated AAV2 ITR sequences and encapsulated in AAV9. (a) Schematic of the vector structure. (b) Sequence of the vector.