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Ottesen EW, Singh NN, Luo D, Kaas B, Gillette B, Seo J, Jorgensen H, Singh RN. Diverse targets of SMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy. Nucleic Acids Res 2023; 51:5948-5980. [PMID: 37026480 PMCID: PMC10325915 DOI: 10.1093/nar/gkad259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 03/13/2023] [Accepted: 03/28/2023] [Indexed: 04/08/2023] Open
Abstract
Designing an RNA-interacting molecule that displays high therapeutic efficacy while retaining specificity within a broad concentration range remains a challenging task. Risdiplam is an FDA-approved small molecule for the treatment of spinal muscular atrophy (SMA), the leading genetic cause of infant mortality. Branaplam is another small molecule which has undergone clinical trials. The therapeutic merit of both compounds is based on their ability to restore body-wide inclusion of Survival Motor Neuron 2 (SMN2) exon 7 upon oral administration. Here we compare the transcriptome-wide off-target effects of these compounds in SMA patient cells. We captured concentration-dependent compound-specific changes, including aberrant expression of genes associated with DNA replication, cell cycle, RNA metabolism, cell signaling and metabolic pathways. Both compounds triggered massive perturbations of splicing events, inducing off-target exon inclusion, exon skipping, intron retention, intron removal and alternative splice site usage. Our results of minigenes expressed in HeLa cells provide mechanistic insights into how these molecules targeted towards a single gene produce different off-target effects. We show the advantages of combined treatments with low doses of risdiplam and branaplam. Our findings are instructive for devising better dosing regimens as well as for developing the next generation of small molecule therapeutics aimed at splicing modulation.
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Affiliation(s)
- Eric W Ottesen
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Natalia N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Diou Luo
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Bailey Kaas
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Benjamin J Gillette
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Joonbae Seo
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Hannah J Jorgensen
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
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Kivrak Pfiffner F, Koller S, Ménétrey A, Graf U, Bähr L, Maspoli A, Hackenberg A, Kottke R, Gerth-Kahlert C, Berger W. Homozygosity for a Novel DOCK7 Variant Due to Segmental Uniparental Isodisomy of Chromosome 1 Associated with Early Infantile Epileptic Encephalopathy (EIEE) and Cortical Visual Impairment. Int J Mol Sci 2022; 23:ijms23137382. [PMID: 35806387 PMCID: PMC9266905 DOI: 10.3390/ijms23137382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/19/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022] Open
Abstract
Early infantile epileptic encephalopathy (EIEE) is a severe neurologic and neurodevelopmental disease that manifests in the first year of life. It shows a high degree of genetic heterogeneity, but the genetic origin is only identified in half of the cases. We report the case of a female child initially diagnosed with Leber congenital amaurosis (LCA), an early-onset retinal dystrophy due to photoreceptor cell degeneration in the retina. The first examination at 9 months of age revealed no reaction to light or objects and showed wandering eye movements. Ophthalmological examination did not show any ocular abnormalities. The patient displayed mildly dysmorphic features and a global developmental delay. Brain MRI demonstrated pontine hypo-/dysplasia. The patient developed myoclonic epileptic seizures and epileptic spasms with focal and generalized epileptiform discharges on electroencephalogram (EEG) at the age of 16 months. Genetic screening for a potentially pathogenic DNA sequence variant by whole-exome sequencing (WES) revealed a novel, conserved, homozygous frameshift variant (c.5391delA, p.(Ala1798LeufsTer59)) in exon 42 of the DOCK7 gene (NM_001271999.1). Further analysis by SNP array (Karyomapping) showed loss of heterozygosity (LOH) in four segments of chromosome 1. WES data of the parents and the index patient (trio analysis) demonstrated that chromosome 1 was exclusively inherited from the mother. Four LOH segments of chromosome 1 alternately showed isodisomy (UPiD) and heterodisomy (UPhD). In WES data, the father was a noncarrier, and the mother was heterozygous for this DOCK7 variant. The DOCK7 gene is located in 1p31.3, a region situated in one of the four isodisomic segments of chromosome 1, explaining the homozygosity seen in the affected child. Finally, Sanger sequencing confirmed maternal UPiD for the DOCK7 variant. Homozygous or compound heterozygous pathogenic variants in the DOCK7 (dedicator of cytokinesis 7) gene are associated with autosomal recessive, early infantile epileptic encephalopathy 23 (EIEE23; OMIM #615,859), a rare and heterogeneous group of neurodevelopmental disorders diagnosed during early childhood. To our knowledge, this is the first report of segmental uniparental iso- and heterodisomy of chromosome 1, leading to homozygosity of the DOCK7 frameshift variant in the affected patient.
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Affiliation(s)
- Fatma Kivrak Pfiffner
- Institute of Medical Molecular Genetics, University of Zurich, Wagistrasse 12, 8952 Schlieren, Switzerland; (F.K.P.); (S.K.); (U.G.); (L.B.); (A.M.)
| | - Samuel Koller
- Institute of Medical Molecular Genetics, University of Zurich, Wagistrasse 12, 8952 Schlieren, Switzerland; (F.K.P.); (S.K.); (U.G.); (L.B.); (A.M.)
| | - Anika Ménétrey
- Department of Pediatric Neurology, University Children’s Hospital, University of Zurich, 8032 Zurich, Switzerland; (A.M.); (A.H.)
| | - Urs Graf
- Institute of Medical Molecular Genetics, University of Zurich, Wagistrasse 12, 8952 Schlieren, Switzerland; (F.K.P.); (S.K.); (U.G.); (L.B.); (A.M.)
| | - Luzy Bähr
- Institute of Medical Molecular Genetics, University of Zurich, Wagistrasse 12, 8952 Schlieren, Switzerland; (F.K.P.); (S.K.); (U.G.); (L.B.); (A.M.)
| | - Alessandro Maspoli
- Institute of Medical Molecular Genetics, University of Zurich, Wagistrasse 12, 8952 Schlieren, Switzerland; (F.K.P.); (S.K.); (U.G.); (L.B.); (A.M.)
| | - Annette Hackenberg
- Department of Pediatric Neurology, University Children’s Hospital, University of Zurich, 8032 Zurich, Switzerland; (A.M.); (A.H.)
| | - Raimund Kottke
- Department of Diagnostic Imaging, University Children’s Hospital, University of Zurich, 8032 Zurich, Switzerland;
| | | | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, Wagistrasse 12, 8952 Schlieren, Switzerland; (F.K.P.); (S.K.); (U.G.); (L.B.); (A.M.)
- Neuroscience Center Zurich, University and ETH Zurich, 8057 Zurich, Switzerland
- Center for Integrative Human Physiology, University of Zurich, 8057 Zurich, Switzerland
- Correspondence:
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Kapoor D, Anand A, Siddiqui S, Sharma S. A novel pathogenic variant in DOCK 7 gene in an infant with dysmorphism, epileptic encephalopathy and cortical blindness. Clin Dysmorphol 2022; 31:39-41. [PMID: 34561314 DOI: 10.1097/mcd.0000000000000393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Dipti Kapoor
- Department of Pediatrics, Lady Hardinge Medical College, New Delhi
| | - Aakanksha Anand
- Department of Pediatrics, Lady Hardinge Medical College, New Delhi
| | - Shahyan Siddiqui
- Department of Neuroimaging and Intervention Radiology, STAR Institute of Neurosciences, STAR Hospitals, Hyderabad
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