AAV2/9-Mediated Gene Therapy for SPLIS Treatment

Background

Sphingosine-1-phosphate lyase insufficiency syndrome (SPLIS) is a rare metabolic disorder discovered in 2017 and caused by inactivating mutations in SGPL1. SGPL1 encodes sphingosine-1-phosphate lyase (SPL), the final enzyme of sphingolipid metabolism. SPLIS is representative of a new family of atypical, non-lysosomal disorders of sphingolipid metabolism recently recognized through next-generation sequencing diagnostic testing. Researchers from the Department of Pediatrics at the University of California San Francisco (UCSF) estimate the worldwide SPLIS prevalence is 11,000; prevalence is likely to increase as variants of unknown significance are confirmed experimentally to cause loss-of-function.

SPLIS causes steroid-resistant nephrotic syndrome and glomerulosclerosis. Kidney involvement characteristically progresses rapidly to end-stage renal disease, often accompanied by adrenal insufficiency, neurological defects, lymphopenia, ichthyosis, and failure to thrive. SPLIS has a wide phenotypic spectrum. However, the onset of SPLIS nephropathy by the first birthday is associated with a 70% mortality by age five. Kidney transplantation may be lifesaving in SPLIS. Currently, there is no targeted therapy for SPLIS.

Technology Overview

To address this urgent unmet medical need, researchers from the Department of Pediatrics at UCSF are developing adeno-associated virus-mediated SGPL1 gene therapy (AAV-SPL) as a potentially life-saving treatment that addresses the root cause of SPLIS. Beyond the treatment of SPLIS children, AAV-SPL could have broader therapeutic implications in the context of other atypical sphingolipid disorders, fibrotic conditions, and kidney diseases.

AAV-SPL is designed to express a functional SPL protein in SPLIS patient target tissues, thereby addressing the root cause of SPLIS. This is accomplished by delivering an AAV2/9 vector that expresses human SGPL1. Despite AAV9’s poor kidney targeting profile, AAV-SPL afforded dramatic improvement in the survival of Sgpl1 knockout mice which model SPLIS. A second-generation AAV-SPL packaged in a novel-engineered AAV capsid exhibits markedly improved kidney bioavailability and potency.

SPL catalyzes the irreversible cleavage of the bioactive lipid sphingosine-1-phosphate (S1P), which plays an important role in pro-fibrogenic cytokine signaling. SPLIS nephropathy is a fibrotic condition, likely caused by aberrant S1P signaling. UCSF scientists reasoned that AAV-SPL could have therapeutic activity in other fibrotic diseases. They have now established proof-of-concept for AAV-SPL’s efficacy in the bleomycin mouse model of pulmonary fibrosis and are developing AAV-SPL for this expansion indication.

UCSF scientists identified the first SPL-encoding gene in a yeast genetic screen in the 1990s. She subsequently identified SPL-encoding genes from invertebrates, mice, and man, characterizing mutant phenotypes and revealing SPL to be an essential enzyme. In 2017, UCSF researchers discovered SPLIS. They are developing SPLIS therapeutics, SPLIS biomarkers, and have developed novel mouse models of SPLIS for preclinical testing and investigation of SPLIS pathophysiology. In collaboration with SPLIS patients, scientists established a SPLIS advocacy group and will host the inaugural SPLIS meeting in 2023. UCSF researcher provided the first calculation of worldwide SPLIS prevalence, established a SPLIS plasma and fibroblast biobank, and is planning to generate SPLIS iPSCs for research. They are preparing to conduct the first prospective SPLIS natural history study, create the first SPLIS specialty clinic, perform the first SPLIS patient journey survey, and further develop AAV-SPL gene therapy.

Stage of Development

Preclinical proof of concept validation of AAV-SPL has been established in in vivo mouse models of SPLIS and pulmonary fibrosis. Optimization studies are underway prior to undertaking GLP toxicology/PK studies.

The efficacy of AAV-SPL in SPLIS was demonstrated in a proof-of-concept study using a robust knockout mouse model in which AAV-SPL was given intravenously in the first days of life. The treatment extended survival from 3 weeks to 6-11 months and prevented serious sequelae of the condition.

Benefits

• SPL is a pyridoxal 5’-phosphate-dependent intracellular enzyme that catalyzes the cleavage of the terminal sphingolipid metabolite S1P into two products (hexadecenal and ethanolamine phosphate). This step is the only way sphingolipids can be degraded. SPL inactivation causes disease manifestations by a combination of aberrant S1P signaling, accumulation of upstream cytotoxic sphingolipids, and loss of SPL products. Therefore, treatment with S1P receptor modulators is unlikely to address all manifestations of the disease. For example, SPL product deficiency has been implicated in the neurological consequences of SPLIS. Ceramide accumulation is involved in ichthyosis, etc. In UCSF scientists’ experience, S1P receptor modulators do not extend the survival of Sgpl1 KO mice.
• The only reported targeted therapy available for SPLIS patients is supplementation with vitamin B6 (the enzyme’s cofactor). In some SPLIS cases in which patients harbor missense mutations, cofactor supplementation may affect disease biomarkers or even disease endpoints. However, this is limited to a minority of patients and is not a universal solution, as a stable protein must be expressed for cofactor supplementation to work.

Applications

• Sphingosine-1-phosphate lyase insufficiency syndrome (SPLIS).
• Idiopathic pulmonary fibrosis.
• Pulmonary fibrosis secondary to coronavirus infection (COVID).
• Fibrotic conditions of the kidney.
• Fibrotic conditions of the liver.
• Fibrotic conditions of the heart or skeletal muscle.

Opportunity

The Department of Pediatrics at UCSF anticipates incorporating in the coming year to further develop and commercialize AAV-SPL. It will be very helpful to receive industry support such as mentorship, investment, and potential co-development opportunities including manufacturing, pivotal toxicology studies, and clinical investigation. In addition, a sincere appreciation for any effort to advocate and raise awareness about the SPLIS indication.