Oral Presentation International Congress on Neuronal Ceroid Lipofuscinoses 2025

Patient-derived retinal, cortical and neuromuscular junction organoids reveal tissue-specific pathomechanisms in CLN3 Batten disease (127770)

Mirta ML Sousa 1 , Xiaolin Lin 1 , Ingrid Åmellem 1 , Jørn-Ove Schølberg 1 , Borghild H Farsund 1 , María Cámara-Quílez 1 , Niklas N Andersen 1 , Aleksandr Ianovski 1 , Mingyi Yang 2 , Animesh Sharma 3 , Davi M Fonseca 3 , Vidar L Saasen 1 , Karin Garten 1 , Nan T Skogaker 1 , Wei Wang 1 , Ingrid Helland 4 , Jing Ye 1 , Magnar Bjørås 1 5
  1. Norwegian University of Science and Technology (NTNU), Trondheim, SøR-TRøNDELAG, Norway
  2. Department of Medical Biochemistry, Oslo University Hospital , Oslo, Norway
  3. Proteomics and Modomics Experimental Core Facility (PROMEC), NTNU, Trondheim, Sør-Trøndelag, Norway
  4. The Pediatric Department of Neuroscience at Rikshospitalet, Oslo University Hospital , Oslo, Norway
  5. Department of Microbiology, Oslo University Hospital, Oslo, Norway

CLN3 Batten disease is the most common childhood neurodegenerative disorder, caused by a 1 kb deletion in the CLN3 gene, leading to progressive vision loss, cognitive decline, and premature death1. To investigate disease mechanisms, we developed retinal, cortical, and neuromuscular junction organoids from CLN3 patient-derived iPSCs2,3,4. Retinal organoids collected at early (Day 7) and advanced (Day 50) stages revealed reduced populations of immature photoreceptors and ganglion cells, alongside increased retinal and forebrain progenitors, indicating delayed development. Single-cell RNA sequencing and proteomics showed impaired mitochondrial function and neurotransmitter signaling. Electron microscopy revealed accumulation of membrane-like storage material, and immunohistochemistry confirmed buildup of Subunit c of mitochondrial ATPase (SCMAS) and LAMP1, particularly in photoreceptors. Cortical organoids also exhibited impaired development, as shown by phase contrast imaging and immunohistochemical analyses. Single-cell RNA sequencing revealed upregulation of genes involved in cilium assembly and movement, extracellular matrix remodeling, lipid and transmembrane transport, and G-protein coupled receptor signaling. In contrast, genes related to axon guidance, synaptic transmission, and nervous system development were downregulated. Early neural progenitors showed elevated stress and defense responses, suggesting early cellular dysfunction. Our group also generated the first CLN3 patient-derived neuromuscular junction organoid (NMOs) model. While healthy NMOs recapitulated neuromuscular junction (NMJ) morphology and cell diversity, only 20–50% of CLN3 NMOs progressed beyond early development. These patient-derived NMOs exhibited reduced NMJ formation, impaired myogenesis, and defective glial cell development—mirroring findings in Cln3Δex7/8 mice5. This highlights their relevance for studying NMJ dysfunction in CLN3 disease. Proteomic analyses of cortical organoids and NMOs at multiple developmental stages will also be performed to further elucidate molecular alterations over time. Together, these organoid models reveal shared and tissue-specific molecular disruptions in CLN3 disease and provide a powerful platform for dissecting disease mechanisms and evaluating therapeutic strategies in CLN3 Batten disease.

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