A 3D iPSC retina model reveals non-cell-autonomous and non-neuronal mechanism of photoreceptor degeneration in a lysosomal storage disorder.

Han, J.; Foley, N.; Dalvi, S.; Tang, J. A. H.; Chatterjee, A.; Kumar, L. K.; Galloway, C. A.; Singh, K.; Subedi, Y.; Ling, K.; Heffer, A.; LIbby, R. T.; Benoit, D. S. W.; Cook, A. L.; Bonilha, V. L.; Gullapalli, V.; Schuchman, E.; Hunter, J. J.; Singh, R.

doi:10.1101/2025.07.10.664233

bioRxiv · 10.1101/2025.07.10.664233

A 3D iPSC retina model reveals non-cell-autonomous and non-neuronal mechanism of photoreceptor degeneration in a lysosomal storage disorder.

Han, J.·Foley, N.·Dalvi, S.·Tang, J. A. H.·Chatterjee, A.·Kumar, L. K.·Galloway, C. A.·Singh, K.·Subedi, Y.·Ling, K.·Heffer, A.·LIbby, R. T.·Benoit, D. S. W.·Cook, A. L.·Bonilha, V. L.·Gullapalli, V.·Schuchman, E.·Hunter, J. J.·Singh, R.

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Abstract

Disruption of photoreceptor-retinal pigment epithelium (RPE) interface with loss of photoreceptor outer segments (POSs) in the retina is a pathological hallmark of several neurodegenerative and retinal diseases including lysosomal storage disorders like CLN3 disease. However, the retina is a functional composite in vivo; and in vitro stem cell models of retina that enable investigation of the photoreceptor-RPE interface in healthy and diseased retina are lacking. Here, we developed a 3D human pluripotent stem cell (hPSC)-derived retina model to investigate the photoreceptor-RPE interface in healthy and disease tissue. Using this 3D hPSC retina model, we demonstrated that the most common disease causing CLN3 mutation (CLN3{Delta}ex7-8) leads to reduced levels of acid ceramidase (AC) and consequently altered sphingolipid metabolism and signaling and POS loss in CLN3 disease. Consistent with the 3D hPSC retina model, altered sphingolipid metabolism and signaling coincided with POS loss in a large animal model of CLN3 disease, CLN3 miniswine. Therapeutically, recombinant human acid ceramidase (rhAC) targeted both altered sphingolipid metabolism and retina degeneration in the CLN3 hPSC retina model and the CLN3 miniswine eye. These findings demonstrate a proof-of-concept that rhAC can rescue disease phenotype in a large animal model of CLN3 disease and suggest that rhAC could be a therapeutic approach for CLN3 disease. One Sentence SummaryAcid ceramidase deficiency and consequently altered sphingolipid signaling promotes disease phenotype(s) in a lysosomal storage disorder, CLN3 disease.

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Han, J., Foley, N., Dalvi, S., Tang, J. A. H., Chatterjee, A., Kumar, L. K., Galloway, C. A., Singh, K., Subedi, Y., Ling, K., Heffer, A., LIbby, R. T., Benoit, D. S. W., Cook, A. L., Bonilha, V. L., Gullapalli, V., Schuchman, E., Hunter, J. J., Singh, R.. 2025-07-15. A 3D iPSC retina model reveals non-cell-autonomous and non-neuronal mechanism of photoreceptor degeneration in a lysosomal storage disorder.. https://doi.org/10.1101/2025.07.10.664233

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