The genetic landscape and classification of infantile epileptic spasms syndrome requiring surgery due to suspected focal brain malformations.Brain communications • September 12, 2024
Matthew Coleman, Min Wang, Penny Snell, Wei Lee, Colleen D'arcy, Cristina Mignone, Kate Pope, Greta Gillies, Wirginia Maixner, Alison Wray, A Harvey, Cas Simons, Richard Leventer, Sarah E Stephenson, Paul Lockhart, Katherine Howell
Infantile epileptic spasms syndrome is a severe epilepsy of infancy that is often associated with focal malformations of cortical development. This study aimed to elucidate the genetic landscape and histopathologic aetiologies of infantile epileptic spasms syndrome due to focal malformations of cortical development requiring surgery. Fifty-nine children with a history of infantile epileptic spasms syndrome and focal malformations of cortical development on MRI were studied. Genetic testing of resected brain tissue was performed by high-coverage targeted panel sequencing or exome sequencing. Histopathology and MRI were reviewed, and integrated clinico-pathological diagnoses were established. A genetic diagnosis was achieved in 47 children (80% of cohort). Germline pathogenic variants were identified in 27/59 (46%) children, in TSC2 (x19), DEPDC5 (x2), CDKL5 (x2), NPRL3 (x1), FGFR1 (x1), TSC1 (x1), and one child with both a TUBB2A/TUBB2B deletion and a pathogenic variant in COL4A1 (x1). Pathogenic brain somatic variants were identified in 21/59 (36%) children, in SLC35A2 (x9), PIK3CA (x3), AKT3 (x2), TSC2 (x2), MTOR (x2), OFD1 (x1), TSC1 (x1) and DEPDC5 (x1). One child had 'two-hit' diagnosis, with both germline and somatic pathogenic DEPDC5 variants in trans. Multimodal data integration resulted in clinical diagnostic reclassifications in 24% of children, emphasizing the importance of combining genetic, histopathologic and imaging findings. Mammalian target of rapamycin pathway variants were identified in most children with tuberous sclerosis or focal cortical dysplasia type II. All nine children with somatic SLC35A2 variants in brain were reclassified to mild malformation of cortical development with oligodendroglial hyperplasia in epilepsy. Somatic mosaicism was a major cause of focal cortical dysplasia type II/hemimegalencephaly (81%) and mild malformation of cortical development with oligodendroglial hyperplasia (100%). The genetic landscape of infantile epileptic spasms syndrome due to focal malformations comprises germline and somatic variants in a range of genes, with mTORopathies and SLC35A2-related mild malformation of cortical development with oligodendroglial hyperplasia being the major causes. Multimodal data integration incorporating genetic data aids in optimizing diagnostic pathways and can guide surgical decision-making and inform future research and therapeutic interventions.
Saturation genome editing of RNU4-2 reveals distinct dominant and recessive neurodevelopmental disorders.MedRxiv : The Preprint Server For Health Sciences • April 29, 2025
Joachim De Jonghe, Hyung Kim, Ayanfeoluwa Adedeji, Elsa LeitĂŁo, Ruebena Dawes, Yuyang Chen, Alexander Blakes, Cas Simons, Rocio Rius, Javeria Alvi, Florence Amblard, Christina Austin Tse, Sarah Baer, Elsa Balton, Pierre Blanc, Daniel Calame, Charles Coutton, Chloe Cunningham, Nitsuh Dargie, Katrina Dipple, Haowei Du, Salima El Chehadeh, Ian Glass, Joseph Gleeson, Olivier Grunewald, Paul Gueguen, Radu Harbuz, Marie-line Jacquemont, Richard Leventer, Pierre Marijon, Olfa Messaoud, Tipu Sultan, Christel Thauvin, Catherine Vincent Delorme, Elif Yilmaz Gulec, Julien Thevenon, Rodrigo Mendez, Daniel Macarthur, Christel Depienne, Caroline Nava, Nicola Whiffin, Gregory Findlay
Recently, de novo variants in an 18 nucleotide region in the centre of RNU4-2 were shown to cause ReNU syndrome, a syndromic neurodevelopmental disorder (NDD) that is predicted to affect tens of thousands of individuals worldwide 1,2 . RNU4-2 is a non-protein-coding gene that is transcribed into the U4 small nuclear RNA (snRNA) component of the major spliceosome 3 . ReNU syndrome variants disrupt spliceosome function and alter 5' splice site selection 1,4 . Here, we performed saturation genome editing (SGE) of RNU4-2 to identify the functional and clinical impact of variants across the entire gene. The resulting SGE function scores, derived from variants' effects on cell fitness, discriminate ReNU syndrome variants from those observed in the population and dramatically outperform in silico variant effect prediction. Using these data, we redefine the ReNU syndrome critical region at single nucleotide resolution, resolve variant pathogenicity for variants of uncertain significance, and show that SGE function scores delineate variants by phenotypic severity. Further, we identify variants impacting function in regions of RNU4-2 that are critical for interactions with other spliceosome components. We show that these variants cause a novel recessive NDD that is clinically distinct from ReNU syndrome. Together, this work defines the landscape of variant function across RNU4-2 , providing critical insights for both diagnosis and therapeutic development.
Saturation genome editing of RNU4-2 reveals distinct dominant and recessive neurodevelopmental disorders.MedRxiv : The Preprint Server For Health Sciences • April 29, 2025
Joachim De Jonghe, Hyung Kim, Ayanfeoluwa Adedeji, Elsa LeitĂŁo, Ruebena Dawes, Yuyang Chen, Alexander Blakes, Cas Simons, Rocio Rius, Javeria Alvi, Florence Amblard, Christina Austin Tse, Sarah Baer, Elsa Balton, Pierre Blanc, Daniel Calame, Charles Coutton, Chloe Cunningham, Nitsuh Dargie, Katrina Dipple, Haowei Du, Salima El Chehadeh, Ian Glass, Joseph Gleeson, Olivier Grunewald, Paul Gueguen, Radu Harbuz, Marie-line Jacquemont, Richard Leventer, Pierre Marijon, Olfa Messaoud, Tipu Sultan, Christel Thauvin, Catherine Vincent Delorme, Elif Gulec, Julien Thevenon, Rodrigo Mendez, Daniel Macarthur, Christel Depienne, Caroline Nava, Nicola Whiffin, Gregory Findlay
Recently, de novo variants in an 18 nucleotide region in the centre of RNU4-2 were shown to cause ReNU syndrome, a syndromic neurodevelopmental disorder (NDD) that is predicted to affect tens of thousands of individuals worldwide1,2. RNU4-2 is a non-protein-coding gene that is transcribed into the U4 small nuclear RNA (snRNA) component of the major spliceosome3. ReNU syndrome variants disrupt spliceosome function and alter 5' splice site selection1,4. Here, we performed saturation genome editing (SGE) of RNU4-2 to identify the functional and clinical impact of variants across the entire gene. The resulting SGE function scores, derived from variants' effects on cell fitness, discriminate ReNU syndrome variants from those observed in the population and dramatically outperform in silico variant effect prediction. Using these data, we redefine the ReNU syndrome critical region at single nucleotide resolution, resolve variant pathogenicity for variants of uncertain significance, and show that SGE function scores delineate variants by phenotypic severity. Further, we identify variants impacting function in regions of RNU4-2 that are critical for interactions with other spliceosome components. We show that these variants cause a novel recessive NDD that is clinically distinct from ReNU syndrome. Together, this work defines the landscape of variant function across RNU4-2, providing critical insights for both diagnosis and therapeutic development.
ILAE genetic literacy series: Focal cortical dysplasia.Epileptic Disorders : International Epilepsy Journal With Videotape • July 24, 2024
Emma Macdonald Laurs, Richard Leventer
Focal cortical dysplasia (FCD) is a common cause of drug-resistant focal epilepsy in children and young adults and is often surgically remediable. The genetics of FCD are increasingly understood due to the ability to perform genomic testing including deep sequencing of resected FCD tissue specimens. There is clear evidence that FCD type II occurs secondary to both germline and somatic mTOR pathway variants, while emerging literature supports the role of SLC35A2, a glycosylation gene, in mild malformation of cortical development with oligodendroglial hyperplasia and epilepsy (MOGHE). Herein, we provide a review of FCDs focusing on their clinical phenotypes, genetic basis, and management considerations when performing genetic testing in this patient group.
Slc35a2 mosaic knockout impacts cortical development, dendritic arborisation, and neuronal firing.Neurobiology Of Disease • June 07, 2024
James Spyrou, Khaing Aung, Hannah Vanyai, Richard Leventer, Snezana Maljevic, Paul Lockhart, Katherine Howell, Christopher Reid
Mild malformation of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE) is an important cause of drug-resistant epilepsy. A significant subset of individuals diagnosed with MOGHE display somatic mosaicism for loss-of-function variants in SLC35A2, which encodes the UDP-galactose transporter. We developed a mouse model to investigate how disruption of this transporter leads to a malformation of cortical development. We used in utero electroporation and CRISPR/Cas9 to knockout Slc35a2 in a subset of layer 2/3 cortical neuronal progenitors in the developing brains of male and female fetal mice to model mosaic expression. Mosaic Slc35a2 knockout was verified through next-generation sequencing and immunohistochemistry of GFP-labelled transfected cells. Histology of brain tissue in mosaic Slc35a2 knockout mice revealed the presence of upper layer-derived cortical neurons in the white matter. Reconstruction of single filled neurons identified altered dendritic arborisation with Slc35a2 knockout neurons having increased complexity. Whole-cell electrophysiological recordings revealed that Slc35a2 knockout neurons display reduced action potential firing, increased afterhyperpolarisation duration and reduced burst-firing when compared with control neurons. Mosaic Slc35a2 knockout mice also exhibited significantly increased epileptiform spiking and increased locomotor activity. We successfully generated a mouse model of mosaic Slc35a2 deficiency, which recapitulates features of the human phenotype, including impaired neuronal migration. We show that knockout in layer 2/3 cortical neuron progenitors is sufficient to disrupt neuronal excitability, increase epileptiform activity and cause hyperactivity in mosaic mice. Our mouse model provides an opportunity to further investigate the disease mechanisms that contribute to MOGHE and facilitate the development of precision therapies.
