Abnormal expression of splicing regulators RBFOX and NOVA is associated with aberrant splicing patterns at the Neurexin-3 gene in a monogenic autism spectrum disorder

Forti, P. K. K.; Depieri, L. L.; Hernandes, B. B.; Bueno, J. G. R.; Vercosa, G. D.; Vasconcelos, I. C.; Bengtson, M. H.; Carazzolle, M. F.; Camargo, A. P.; Papes, F.

doi:10.1101/2025.10.02.680092

bioRxiv · 10.1101/2025.10.02.680092

Abnormal expression of splicing regulators RBFOX and NOVA is associated with aberrant splicing patterns at the Neurexin-3 gene in a monogenic autism spectrum disorder

Forti, P. K. K.·Depieri, L. L.·Hernandes, B. B.·Bueno, J. G. R.·Vercosa, G. D.·Vasconcelos, I. C.·Bengtson, M. H.·Carazzolle, M. F.·Camargo, A. P.·Papes, F.

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Abstract

Autism spectrum disorders are diseases characterized by a combination of cognitive, behavioral and neurological symptoms. A complex interplay between environmental factors and a multitude of genetic determinants, most of them composed of low-risk variants, impose difficulties in understanding the molecular and cellular underpinnings of these conditions. In some cases, autistic patients have been shown to display alterations in splicing patterns of several genes, but the extent to which this phenomenon is common in the context of these multifactorial disorders is unknown, nor is it known if monogenic cases of autism also display dysregulation of splicing. Moreover, very few studies have investigated the causal links between splicing alterations in specific genes and the phenotypic characteristics of the neural tissue in autism patients. In this study, we have focused on a monogenic type of autism caused by haploinsufficiency of the Transcription Factor 4 gene, known as Pitt-Hopkins Syndrome. We show that neurons and organoids derived from patients with this disease have altered expression of splicing regulators in the NOVA and RBFOX families, accompanied by aberrant splicing patterns in a substantial number of genes involved in neural tissue development and synapse organization. We focused on a gene encoding a member of the Neurexin Family, the splicing of which normally leads to the production of transcript variants coding for both transmembrane and secreted protein isoforms. In Pitt-Hopkins Syndrome neurons, we detected an aberrant splicing pattern that results in lower expression of the secreted isoform and its corresponding transcript, a phenomenon that may explain why the neural tissue in these patients have decreased electrical activity through impaired synapse organization. Our data shed light on the role splicing regulation plays in a monogenic type of autism.

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Forti, P. K. K., Depieri, L. L., Hernandes, B. B., Bueno, J. G. R., Vercosa, G. D., Vasconcelos, I. C., Bengtson, M. H., Carazzolle, M. F., Camargo, A. P., Papes, F.. 2025-10-03. Abnormal expression of splicing regulators RBFOX and NOVA is associated with aberrant splicing patterns at the Neurexin-3 gene in a monogenic autism spectrum disorder. https://doi.org/10.1101/2025.10.02.680092

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