1
|
Shum C, Han SY, Thiruvahindrapuram B, Wang Z, de Rijke J, Zhang B, Sundberg M, Chen C, Buttermore ED, Makhortova N, Howe J, Sahin M, Scherer SW. Combining Off-flow, a Nextflow-coded program, and whole genome sequencing reveals unintended genetic variation in CRISPR/Cas-edited iPSCs. Comput Struct Biotechnol J 2024; 23:638-647. [PMID: 38283851 PMCID: PMC10819409 DOI: 10.1016/j.csbj.2023.12.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 01/30/2024] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas nucleases and human induced pluripotent stem cell (iPSC) technology can reveal deep insight into the genetic and molecular bases of human biology and disease. Undesired editing outcomes, both on-target (at the edited locus) and off-target (at other genomic loci) hinder the application of CRISPR-Cas nucleases. We developed Off-flow, a Nextflow-coded bioinformatic workflow that takes a specific guide sequence and Cas protein input to call four separate off-target prediction programs (CHOPCHOP, Cas-Offinder, CRISPRitz, CRISPR-Offinder) to output a comprehensive list of predicted off-target sites. We applied it to whole genome sequencing (WGS) data to investigate the occurrence of unintended effects in human iPSCs that underwent repair or insertion of disease-related variants by homology-directed repair. Off-flow identified a 3-base-pair-substitution and a mono-allelic genomic deletion at the target loci, KCNQ2, in 2 clones. Unbiased WGS analysis further identified off-target missense variants and a mono-allelic genomic deletion at the targeted locus, GNAQ, in 10 clones. On-target substitution and deletions had escaped standard PCR and Sanger sequencing analysis, while missense variants at other genomic loci were not detected by Off-flow. We used these results to filter out iPSC clones for subsequent functional experiments. Off-flow, which we make publicly available, works for human and mouse genomes currently and can be adapted for other genomes. Off-flow and WGS analysis can improve the integrity of studies using CRISPR/Cas-edited cells and animal models.
Collapse
Affiliation(s)
- Carole Shum
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sang Yeon Han
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | | | - Zhuozhi Wang
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jill de Rijke
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Benjamin Zhang
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Maria Sundberg
- Department of Neurology, FM Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Cidi Chen
- Human Neuron Core, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Nina Makhortova
- Human Neuron Core, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jennifer Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Mustafa Sahin
- Department of Neurology, FM Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephen W. Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, ON M5S 1A8, Canada
- Lead contact
| |
Collapse
|
2
|
Peyda P, Lin CH, Onwuzurike K, Black DL. The Rbfox1/LASR complex controls alternative pre-mRNA splicing by recognition of multi-part RNA regulatory modules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603345. [PMID: 39071271 PMCID: PMC11275806 DOI: 10.1101/2024.07.12.603345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The Rbfox proteins regulate alternative pre-mRNA splicing by binding to the RNA element GCAUG. In the nucleus, most of Rbfox is bound to LASR, a complex of RNA-binding proteins that recognize additional RNA motifs. However, it remains unclear how the different subunits of the Rbfox/LASR complex act together to bind RNA and regulate splicing. We used a nuclease-protection assay to map the transcriptome-wide footprints of Rbfox1/LASR on nascent cellular RNA. In addition to GCAUG, Rbfox1/LASR binds RNA containing motifs for LASR subunits hnRNPs M, H/F, C, and Matrin3. These elements are often arranged in tandem, forming multi-part modules of RNA motifs. To distinguish contact sites of Rbfox1 from the LASR subunits, we analyzed a mutant Rbfox1(F125A) that has lost RNA binding but remains associated with LASR. Rbfox1(F125A)/LASR complexes no longer interact with GCAUG but retain binding to RNA elements for LASR. Splicing analyses reveal that in addition to activating exons through adjacent GCAUG elements, Rbfox can also stimulate exons near binding sites for LASR subunits. Mini-gene experiments demonstrate that these diverse elements produce a combined regulatory effect on a target exon. These findings illuminate how a complex of RNA-binding proteins can decode combinatorial splicing regulatory signals by recognizing groups of tandem RNA elements.
Collapse
|
3
|
Kim JH, Lee BD, Park JM, Lee YM, Moon E, Suh H, Kim K, Kim YJ, Lee HJ, Oh HY. Family-based genome-wide association analysis of novelty seeking in a Korean schizophrenic population: A pilot study. Medicine (Baltimore) 2024; 103:e38694. [PMID: 38941432 DOI: 10.1097/md.0000000000038694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/30/2024] Open
Abstract
Schizophrenia (SPR) is the most devastating mental illness that causes severe deterioration in social and occupational functioning, but, the etiology remains unknown. The objective of this study is to explore the genetic underpinnings of novelty seeking behavior in schizophrenic family within the Korean population. By conducting a family-based genome-wide association study, we aim to identify potential genetic markers and variations associated with novelty seeking traits in the context of SPR. We have recruited 27 probands (with SPR) with their parents and siblings whenever possible. DNA was extracted from blood sampling of 58 individuals in 27 families and analyzed in an Illumina core exome single nucleotide polymorphism (SNP) array. A family-based association test (qFAM) was used to derive SNP association values across all chromosomes. Although none of the final 800,000 SNPs reached the genome-wide significant threshold of 8.45 × 10-7, the most significant 4 SNPs were within the 10-5 to 10-7. This study identifies genetic associations between novelty seeking behavior and SPR within families. RAPGEF5 emerges as a significant gene, along with other neuropsychiatric-related genes. Noteworthy genes like DRD4 and COMT did not show associations, possibly due to the focus on schizophrenic family. While shedding light on this complex relationship, larger studies are needed for robust conclusions and deeper mechanistic insights.
Collapse
Affiliation(s)
- Ji Hye Kim
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Byung Dae Lee
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
- Department of Psychiatry, Pusan National University College of Medicine, Kyungnam, South Korea
| | - Je Min Park
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
- Department of Psychiatry, Pusan National University College of Medicine, Kyungnam, South Korea
| | - Young Min Lee
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
- Department of Psychiatry, Pusan National University College of Medicine, Kyungnam, South Korea
| | - Eunsoo Moon
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
- Department of Psychiatry, Pusan National University College of Medicine, Kyungnam, South Korea
| | - Hwagyu Suh
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Kyungwon Kim
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Yoo Jun Kim
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Hyun Ji Lee
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Ha Young Oh
- Department of Psychiatry, Pusan National University Hospital, Busan, South Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| |
Collapse
|
4
|
Morgan AT, Amor DJ, St John MD, Scheffer IE, Hildebrand MS. Genetic architecture of childhood speech disorder: a review. Mol Psychiatry 2024; 29:1281-1292. [PMID: 38366112 PMCID: PMC11189821 DOI: 10.1038/s41380-024-02409-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 02/18/2024]
Abstract
Severe speech disorders lead to poor literacy, reduced academic attainment and negative psychosocial outcomes. As early as the 1950s, the familial nature of speech disorders was recognized, implying a genetic basis; but the molecular genetic basis remained unknown. In 2001, investigation of a large three generational family with severe speech disorder, known as childhood apraxia of speech (CAS), revealed the first causative gene; FOXP2. A long hiatus then followed for CAS candidate genes, but in the past three years, genetic analysis of cohorts ascertained for CAS have revealed over 30 causative genes. A total of 36 pathogenic variants have been identified from 122 cases across 3 cohorts in this nascent field. All genes identified have been in coding regions to date, with no apparent benefit at this stage for WGS over WES in identifying monogenic conditions associated with CAS. Hence current findings suggest a remarkable one in three children have a genetic variant that explains their CAS, with significant genetic heterogeneity emerging. Around half of the candidate genes identified are currently supported by medium (6 genes) to strong (9 genes) evidence supporting the association between the gene and CAS. Despite genetic heterogeneity; many implicated proteins functionally converge on pathways involved in chromatin modification or transcriptional regulation, opening the door to precision diagnosis and therapies. Most of the new candidate genes for CAS are associated with previously described neurodevelopmental conditions that include intellectual disability, autism and epilepsy; broadening the phenotypic spectrum to a distinctly milder presentation defined by primary speech disorder in the setting of normal intellect. Insights into the genetic bases of CAS, a severe, rare speech disorder, are yet to translate to understanding the heritability of more common, typically milder forms of speech or language impairment such as stuttering or phonological disorder. These disorders likely follow complex inheritance with polygenic contributions in many cases, rather than the monogenic patterns that underly one-third of patients with CAS. Clinical genetic testing for should now be implemented for individuals with CAS, given its high diagnostic rate, which parallels many other neurodevelopmental disorders where this testing is already standard of care. The shared mechanisms implicated by gene discovery for CAS highlight potential new targets for future precision therapies.
Collapse
Affiliation(s)
- Angela T Morgan
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.
- Speech Pathology, University of Melbourne, Melbourne, VIC, Australia.
- Speech Pathology, Royal Children's Hospital, Melbourne, VIC, Australia.
| | - David J Amor
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Miya D St John
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Speech Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Ingrid E Scheffer
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Epilepsy Research Centre, Austin Health, Melbourne, VIC, Australia
| | - Michael S Hildebrand
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Epilepsy Research Centre, Austin Health, Melbourne, VIC, Australia
| |
Collapse
|
5
|
He L, Guo H, Wang H, Zhu K, Li D, Zhang C, Ai Y, Yang JJ. Rbfox1 regulates alternative splicing of Nrcam in primary sensory neurons to mediate peripheral nerve injury-induced neuropathic pain. Neurotherapeutics 2024; 21:e00309. [PMID: 38241164 PMCID: PMC10903086 DOI: 10.1016/j.neurot.2023.e00309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 01/21/2024] Open
Abstract
The primary sensory neurons of the dorsal root ganglia (DRG) are subject to transcriptional alterations following peripheral nerve injury. These alterations are believed to play a pivotal role in the genesis of neuropathic pain. Alternative RNA splicing is a process that generates multiple transcript variants from a single gene, significantly contributing to the complexity of the transcriptome. However, little is known about the functional significance and control of alternative RNA splicing in injured DRG after spinal nerve ligation (SNL). In our study, we conducted a comprehensive transcriptome profiling and bioinformatic analysis to approach and identified a neuron-specific isoform of an RNA splicing regulator, RNA-binding Fox1 (Rbfox1, also known as A2BP1), as a crucial regulator of alternative RNA splicing in injured DRG after SNL. Notably, Rbfox1 expression is markedly reduced in injured DRG following peripheral nerve injury. Restoring this reduction effectively mitigates nociceptive hypersensitivity. Conversely, mimicking the downregulation of Rbfox1 expression generates neuropathic pain symptoms. Mechanistically, we uncovered that Rbfox1 may be a key factor influencing alternative RNA splicing of neuron-glial related cell adhesion molecule (NrCAM), a key neuronal cell adhesion molecule. In injured DRG after SNL, the downregulation of Rbfox1amplifies the insertion of exon 10 in Nrcam transcripts, leading to an increase in long Nrcam variants (L-Nrcam) and a corresponding decrease in short Nrcam variants (S-Nrcam) within injured DRG. In summary, our study supports the essential role of Rbfox1 in neuropathic pain within DRG, probably via the regulation of Nrcam splicing. These findings suggest that Rbfox1 could be a potential target for neuropathic pain therapy.
Collapse
Affiliation(s)
- Long He
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Haoyu Guo
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China; Department of Laboratory Animal Resources, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Hongwei Wang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Kuicheng Zhu
- Department of Laboratory Animal Resources, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Da Li
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Chaofan Zhang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Yanqiu Ai
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China.
| | - Jian-Jun Yang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China.
| |
Collapse
|
6
|
Kostic M, Raymond JJ, Freyre CAC, Henry B, Tumkaya T, Khlghatyan J, Dvornik J, Li J, Hsiao JS, Cheon SH, Chung J, Sun Y, Dolmetsch RE, Worringer KA, Ihry RJ. Patient Brain Organoids Identify a Link between the 16p11.2 Copy Number Variant and the RBFOX1 Gene. ACS Chem Neurosci 2023; 14:3993-4012. [PMID: 37903506 PMCID: PMC10655044 DOI: 10.1021/acschemneuro.3c00442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/14/2023] [Indexed: 11/01/2023] Open
Abstract
Copy number variants (CNVs) that delete or duplicate 30 genes within the 16p11.2 genomic region give rise to a range of neurodevelopmental phenotypes with high penetrance in humans. Despite the identification of this small region, the mechanisms by which 16p11.2 CNVs lead to disease are unclear. Relevant models, such as human cortical organoids (hCOs), are needed to understand the human-specific mechanisms of neurodevelopmental disease. We generated hCOs from 17 patients and controls, profiling 167,958 cells with single-cell RNA-sequencing analysis, which revealed neuronal-specific differential expression of genes outside the 16p11.2 region that are related to cell-cell adhesion, neuronal projection growth, and neurodevelopmental disorders. Furthermore, 16p11.2 deletion syndrome organoids exhibited reduced mRNA and protein levels of RBFOX1, a gene that can also harbor CNVs linked to neurodevelopmental phenotypes. We found that the genes previously shown to be regulated by RBFOX1 are also perturbed in organoids from patients with the 16p11.2 deletion syndrome and thus identified a novel link between independent CNVs associated with neuronal development and autism. Overall, this work suggests convergent signaling, which indicates the possibility of a common therapeutic mechanism across multiple rare neuronal diseases.
Collapse
Affiliation(s)
- Milos Kostic
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Joseph J. Raymond
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Christophe A. C. Freyre
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Beata Henry
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Tayfun Tumkaya
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Cambridge 02139, Massachusetts, United States
| | - Jivan Khlghatyan
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Jill Dvornik
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Jingyao Li
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Jack S. Hsiao
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Seon Hye Cheon
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Jonathan Chung
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Cambridge 02139, Massachusetts, United States
| | - Yishan Sun
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Ricardo E. Dolmetsch
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Kathleen A. Worringer
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Robert J. Ihry
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| |
Collapse
|
7
|
Sahajpal NS, Jeffrey DHF, DuPont BR, Hilton B. 17q25.3 copy number changes: association with neurodevelopmental disorders and cardiac malformation. Mol Cytogenet 2023; 16:15. [PMID: 37430334 DOI: 10.1186/s13039-023-00644-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 06/19/2023] [Indexed: 07/12/2023] Open
Abstract
Copy number variants (CNVs) have been identified as common genomic variants that play a significant role in inter-individual variability. Conversely, rare recurrent CNVs have been found to be causal for many disorders with well-established genotype-phenotype relationships. However, the phenotypic implications of rare non-recurrent CNVs remain poorly understood. Herein, we re-investigated 18,542 cases reported from chromosomal microarray at Greenwood Genetic Center from 2010 to 2022 and identified 15 cases with CNVs involving the 17q25.3 region. We report the detailed clinical features of these subjects, and compare with the cases reported in the literature to determine genotype-phenotype correlations for a subset of genes in this region. The CNVs in the 17q25.3 region were found to be rare events, with a prevalence of 0.08% (15/18542) observed in our cohort. The CNVs were dispersed across the entire 17q25.3 region with variable breakpoints and no smallest region of overlap. The subjects presented with a wide range of clinical features, with neurodevelopmental disorders (autism spectrum disorder, intellectual disability, developmental delay) being the most common features (80%), then expressive language disorder (33%), and finally cardiovascular malformations (26%). The association of CNVs involving the critical gene-rich region of 17q25.3 with neurodevelopmental disorders and cardiac malformation, implicates several genes as plausible drivers for these events.
Collapse
Affiliation(s)
| | - David H F Jeffrey
- Diagnostic Laboratories, Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - Barbara R DuPont
- Diagnostic Laboratories, Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - Benjamin Hilton
- Diagnostic Laboratories, Greenwood Genetic Center, Greenwood, SC, 29646, USA.
| |
Collapse
|
8
|
Cocco C, Manca E, Corda G, Angioni MM, Noli B, Congia M, Loy F, Isola M, Chessa E, Floris A, Lorefice L, Saba L, Mathieu A, Ferri GL, Cauli A, Piga M. Brain-reactive autoantibodies in neuropsychiatric systemic lupus erythematosus. Front Immunol 2023; 14:1157149. [PMID: 37383228 PMCID: PMC10294074 DOI: 10.3389/fimmu.2023.1157149] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/19/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction The pathogenesis of neuropsychiatric systemic lupus erythematosus (NPSLE) is widely unknown, and the role of autoantibodies is still undetermined. Methods To identify brain-reactive autoantibodies possibly related to NPSLE, immunofluorescence (IF) and transmission electron microscopy (TEM) on rat and human brains were performed. ELISA was used to reveal the presence of known circulating autoantibodies, while western blot (WB) was applied to characterize potential unknown autoantigen(s). Results We enrolled 209 subjects, including patients affected by SLE (n=69), NPSLE (n=36), Multiple Sclerosis (MS, n=22), and 82 age- and gender-matched healthy donors (HD). Autoantibody reactivity by IF was observed in almost the entire rat brain (cortex, hippocampus, and cerebellum) using sera from NPSLE and SLE patients and was virtually negative in MS and HD. NPSLE showed higher prevalence (OR 2.4; p = 0.047), intensity, and titer of brain-reactive autoantibodies than SLE patients. Most of the patient sera with brain-reactive autoantibodies (75%) also stained human brains. Double staining experiments on rat brains mixing patients' sera with antibodies directed against neuronal (NeuN) or glial markers showed autoantibody reactivity restricted to NeuN-containing neurons. Using TEM, the targets of brain-reactive autoantibodies were located in the nuclei and, to a lesser extent, in the cytoplasm and mitochondria. Given the high degree of colocalization between NeuN and brain-reactive autoantibodies, we assumed NeuN was a possible autoantigen. However, WB analysis with HEK293T cell lysates expressing or not expressing the gene encoding for NeuN protein (RIBFOX3) showed that patients' sera carrying brain-reactive autoantibodies did not recognize the NeuN corresponding band size. Among the panel of NPSLE-associated autoantibodies (e.g., anti-NR2, anti-P-ribosomal protein, antiphospholipid) investigated by ELISA assay, only the anti-β2-glycoprotein-I (aβ2GPI) IgG was exclusively found in those sera containing brain-reactive autoantibodies. Conclusion In conclusion, SLE and NPSLE patients possess brain-reactive autoantibodies but with higher frequency and titers found in NPSLE patients. Although many target antigens of brain-reactive autoantibodies are still undetermined, they likely include β2GPI.
Collapse
Affiliation(s)
- Cristina Cocco
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Elias Manca
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Giulia Corda
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Maria Maddalena Angioni
- Rheumatology Unit, University Clinic, AOU Cagliari, Cagliari, Italy
- Department of Medical Sciences and Public health, University of Cagliari, Monserrato, Italy
| | - Barbara Noli
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Mattia Congia
- Rheumatology Unit, University Clinic, AOU Cagliari, Cagliari, Italy
| | - Francesco Loy
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Michela Isola
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | | | - Alberto Floris
- Rheumatology Unit, University Clinic, AOU Cagliari, Cagliari, Italy
- Department of Medical Sciences and Public health, University of Cagliari, Monserrato, Italy
| | - Lorena Lorefice
- Multiple Sclerosis Center, Binaghi Hospital, ATS Sardegna, ASSL Cagliari, Cagliari, Italy
| | - Luca Saba
- Department of Medical Sciences and Public health, University of Cagliari, Monserrato, Italy
- Radiology Department, University Clinic, AOU Cagliari, Cagliari, Italy
| | - Alessandro Mathieu
- Department of Medical Sciences and Public health, University of Cagliari, Monserrato, Italy
| | - Gian Luca Ferri
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Alberto Cauli
- Rheumatology Unit, University Clinic, AOU Cagliari, Cagliari, Italy
- Department of Medical Sciences and Public health, University of Cagliari, Monserrato, Italy
| | - Matteo Piga
- Rheumatology Unit, University Clinic, AOU Cagliari, Cagliari, Italy
- Department of Medical Sciences and Public health, University of Cagliari, Monserrato, Italy
| |
Collapse
|
9
|
Soo CC, Brandenburg JT, Nebel A, Tollman S, Berkman L, Ramsay M, Choudhury A. Genome-wide association study of population-standardised cognitive performance phenotypes in a rural South African community. Commun Biol 2023; 6:328. [PMID: 36973338 PMCID: PMC10043003 DOI: 10.1038/s42003-023-04636-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
Cognitive function is an indicator for global physical and mental health, and cognitive impairment has been associated with poorer life outcomes and earlier mortality. A standard cognition test, adapted to a rural-dwelling African community, and the Oxford Cognition Screen-Plus were used to capture cognitive performance as five continuous traits (total cognition score, verbal episodic memory, executive function, language, and visuospatial ability) for 2,246 adults in this population of South Africans. A novel common variant, rs73485231, reached genome-wide significance for association with episodic memory using data for ~14 million markers imputed from the H3Africa genotyping array data. Window-based replication of previously implicated variants and regions of interest support the discovery of African-specific associated variants despite the small population size and low allele frequency. This African genome-wide association study identifies suggestive associations with general cognition and domain-specific cognitive pathways and lays the groundwork for further genomic studies on cognition in Africa.
Collapse
Affiliation(s)
- Cassandra C Soo
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Almut Nebel
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lisa Berkman
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Center for Population and Development Studies, Harvard University, Cambridge, MA, USA
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| |
Collapse
|
10
|
Leng X, Zhang T, Guan Y, Tang M. Genotype and phenotype analysis of epilepsy caused by ADGRV1 mutations in Chinese children. Seizure 2022; 103:108-114. [DOI: 10.1016/j.seizure.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 11/13/2022] Open
|
11
|
Fisher E, Feng J. RNA splicing regulators play critical roles in neurogenesis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1728. [PMID: 35388651 DOI: 10.1002/wrna.1728] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Alternative RNA splicing increases transcript diversity in different cell types and under varying conditions. It is executed with the help of RNA splicing regulators (RSRs), which are operationally defined as RNA-binding proteins (RBPs) that regulate alternative splicing, but not directly catalyzing the chemical reactions of splicing. By systematically searching for RBPs and manually identifying those that regulate splicing, we curated 305 RSRs in the human genome. Surprisingly, most of the RSRs are involved in neurogenesis. Among these RSRs, we focus on nine families (PTBP, NOVA, RBFOX, ELAVL, CELF, DBHS, MSI, PCBP, and MBNL) that play essential roles in the neurogenic pathway. A better understanding of their functions will provide novel insights into the role of splicing in brain development, health, and disease. This comprehensive review serves as a stepping-stone to explore the diverse and complex set of RSRs as fundamental regulators of neural development. This article is categorized under: RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Splicing Regulation/Alternative Splicing.
Collapse
Affiliation(s)
- Emily Fisher
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
- Veterans Affairs Western New York Healthcare System, Buffalo, New York, USA
| | - Jian Feng
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
- Veterans Affairs Western New York Healthcare System, Buffalo, New York, USA
| |
Collapse
|
12
|
Neuronal splicing regulator RBFOX3 mediates seizures via regulating Vamp1 expression preferentially in NPY-expressing GABAergic neurons. Proc Natl Acad Sci U S A 2022; 119:e2203632119. [PMID: 35951651 PMCID: PMC9388145 DOI: 10.1073/pnas.2203632119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Epilepsy is a common neurological disorder, which has been linked to mutations or deletions of RNA binding protein, fox-1 homolog (Caenorhabditis elegans) 3 (RBFOX3)/NeuN, a neuronal splicing regulator. However, the mechanism of seizure mediation by RBFOX3 remains unknown. Here, we show that mice with deletion of Rbfox3 in gamma-aminobutyric acid (GABA) ergic neurons exhibit spontaneous seizures and high premature mortality due to increased presynaptic release, postsynaptic potential, neuronal excitability, and synaptic transmission in hippocampal dentate gyrus granule cells (DGGCs). Attenuating early excitatory gamma-aminobutyric acid (GABA) action by administering bumetanide, an inhibitor of early GABA depolarization, rescued premature mortality. Rbfox3 deletion reduced hippocampal expression of vesicle-associated membrane protein 1 (VAMP1), a GABAergic neuron-specific presynaptic protein. Postnatal restoration of VAMP1 rescued premature mortality and neuronal excitability in DGGCs. Furthermore, Rbfox3 deletion in GABAergic neurons showed fewer neuropeptide Y (NPY)-expressing GABAergic neurons. In addition, deletion of Rbfox3 in NPY-expressing GABAergic neurons lowered intrinsic excitability and increased seizure susceptibility. Our results establish RBFOX3 as a critical regulator and possible treatment path for epilepsy.
Collapse
|
13
|
Ma R, Duan Y, Zhang L, Qi X, Zhang L, Pan S, Gao L, Wang C, Wang Y. SCN1A-Related Epilepsy: Novel Mutations and Rare Phenotypes. Front Mol Neurosci 2022; 15:826183. [PMID: 35663268 PMCID: PMC9162153 DOI: 10.3389/fnmol.2022.826183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectivesTo expand the genotypes and phenotypes of sodium voltage-gated channel alpha subunit 1 (SCN1A)-related epilepsy.MethodsWe retrospectively collected the clinical and genetic information of 22 epilepsy patients (10 males, 12 females; mean: 9.2 ± 3.9 years; 3.9–20.3 years) carrying 22 variants of SCN1A. SCN1A mutations were identified by next-generation sequencing.ResultsTwenty-two variants were identified, among which 12 have not yet been reported. The median age at seizure onset was 6 months. Sixteen patients were diagnosed with Dravet syndrome (DS), two with genetic epilepsy with febrile seizures plus [one evolved into benign epilepsy with centrotemporal spikes (BECTS)], one with focal epilepsy, one with atypical childhood epilepsy with centrotemporal spikes (ABECTS) and two with unclassified epilepsy. Fourteen patients showed a global developmental delay/intellectual disability (GDD/ID). Slow background activities were observed in one patient and epileptiform discharges were observed in 11 patients during the interictal phase.SignificanceThis study enriches the genotypes and phenotypes of SCN1A-related epilepsy. The clinical characteristics of patients with 12 previously unreported variants were described.
Collapse
|
14
|
Disrupted in schizophrenia 1 regulates ectopic neurogenesis in the mouse hilus after pilocarpine-induced status epilepticus. Neuroscience 2022; 494:69-81. [DOI: 10.1016/j.neuroscience.2022.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 05/01/2022] [Accepted: 05/06/2022] [Indexed: 11/20/2022]
|
15
|
Ghrelin Regulates Expression of the Transcription Factor Pax6 in Hypoxic Brain Progenitor Cells and Neurons. Cells 2022; 11:cells11050782. [PMID: 35269403 PMCID: PMC8909042 DOI: 10.3390/cells11050782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 12/04/2022] Open
Abstract
The nature of brain impairment after hypoxia is complex and recovery harnesses different mechanisms, including neuroprotection and neurogenesis. Experimental evidence suggests that hypoxia may trigger neurogenesis postnatally by influencing the expression of a variety of transcription factors. However, the existing data are controversial. As a proof-of-principle, we subjected cultured cerebral cortex neurons, cerebellar granule neurons and organotypic cerebral cortex slices from rat brains to hypoxia and treated these cultures with the hormone ghrelin, which is well-known for its neuroprotective functions. We found that hypoxia elevated the expression levels and stimulated nuclear translocation of ghrelin’s receptor GHSR1 in the cultured neurons and the acute organotypic slices, whereas ghrelin treatment reduced the receptor expression to normoxic levels. GHSR1 expression was also increased in cerebral cortex neurons of mice with induced experimental stroke. Additional quantitative analyses of immunostainings for neuronal proliferation and differentiation markers revealed that hypoxia stimulated the proliferation of neuronal progenitors, whereas ghrelin application during the phase of recovery from hypoxia counteracted these effects. At the mechanistic level, we provide a link between the described post-ischemic phenomena and the expression of the transcription factor Pax6, an important regulator of neural progenitor cell fate. In contrast to the neurogenic niches in the brain where hypoxia is known to increase Pax6 expression, the levels of the transcription factor in cultured hypoxic cerebral cortex cells were downregulated. Moreover, the application of ghrelin to hypoxic neurons normalised the expression levels of these factors. Our findings suggest that ghrelin stimulates neurogenic factors for the protection of neurons in a GHSR1-dependent manner in non-neurogenic brain areas such as the cerebral cortex after exposure to hypoxia.
Collapse
|
16
|
Munoz-Ballester C, Mahmutovic D, Rafiqzad Y, Korot A, Robel S. Mild Traumatic Brain Injury-Induced Disruption of the Blood-Brain Barrier Triggers an Atypical Neuronal Response. Front Cell Neurosci 2022; 16:821885. [PMID: 35250487 PMCID: PMC8894613 DOI: 10.3389/fncel.2022.821885] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/17/2022] [Indexed: 12/03/2022] Open
Abstract
Mild TBI (mTBI), which affects 75% of TBI survivors or more than 50 million people worldwide each year, can lead to consequences including sleep disturbances, cognitive impairment, mood swings, and post-traumatic epilepsy in a subset of patients. To interrupt the progression of these comorbidities, identifying early pathological events is key. Recent studies have shown that microbleeds, caused by mechanical impact, persist for months after mTBI and are correlated to worse mTBI outcomes. However, the impact of mTBI-induced blood-brain barrier damage on neurons is yet to be revealed. We used a well-characterized mouse model of mTBI that presents with frequent and widespread but size-restricted damage to the blood-brain barrier to assess how neurons respond to exposure of blood-borne factors in this pathological context. We used immunohistochemistry and histology to assess the expression of neuronal proteins in excitatory and inhibitory neurons after mTBI. We observed that the expression of NeuN, Parvalbumin, and CamKII was lost within minutes in areas with blood-brain barrier disruption. Yet, the neurons remained alive and could be detected using a fluorescent Nissl staining even 6 months later. A similar phenotype was observed after exposure of neurons to blood-borne factors due to endothelial cell ablation in the absence of a mechanical impact, suggesting that entrance of blood-borne factors into the brain is sufficient to induce the neuronal atypical response. Changes in postsynaptic spines were observed indicative of functional changes. Thus, this study demonstrates That exposure of neurons to blood-borne factors causes a rapid and sustained loss of neuronal proteins and changes in spine morphology in the absence of neurodegeneration, a finding that is likely relevant to many neuropathologies.
Collapse
Affiliation(s)
- Carmen Munoz-Ballester
- Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, United States
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Dzenis Mahmutovic
- Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, United States
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Yusuf Rafiqzad
- Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, United States
- School of Neuroscience, Virginia Tech Carilion, Blacksburg, VA, United States
| | - Alia Korot
- Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, United States
- Kenyon College, Gambier, OH, United States
| | - Stefanie Robel
- Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, United States
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- School of Neuroscience, Virginia Tech Carilion, Blacksburg, VA, United States
| |
Collapse
|
17
|
Whole-exome sequencing with targeted analysis and epilepsy after acute symptomatic neonatal seizures. Pediatr Res 2022; 91:896-902. [PMID: 33846556 PMCID: PMC9064802 DOI: 10.1038/s41390-021-01509-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 02/02/2021] [Accepted: 03/18/2021] [Indexed: 02/02/2023]
Abstract
BACKGROUND The contribution of pathogenic gene variants with development of epilepsy after acute symptomatic neonatal seizures is not known. METHODS Case-control study of 20 trios in children with a history of acute symptomatic neonatal seizures: 10 with and 10 without post-neonatal epilepsy. We performed whole-exome sequencing (WES) and identified pathogenic de novo, transmitted, and non-transmitted variants from established and candidate epilepsy association genes and correlated prevalence of these variants with epilepsy outcomes. We performed a sensitivity analysis with genes associated with coronary artery disease (CAD). We analyzed variants throughout the exome to evaluate for differential enrichment of functional properties using exploratory KEGG searches. RESULTS Querying 200 established and candidate epilepsy genes, pathogenic variants were identified in 5 children with post-neonatal epilepsy yet in only 1 child without subsequent epilepsy. There was no difference in the number of trios with non-transmitted pathogenic variants in epilepsy or CAD genes. An exploratory KEGG analysis demonstrated a relative enrichment in cell death pathways in children without subsequent epilepsy. CONCLUSIONS In this pilot study, children with epilepsy after acute symptomatic neonatal seizures had a higher prevalence of coding variants with a targeted epilepsy gene sequencing analysis compared to those patients without subsequent epilepsy. IMPACT We performed whole-exome sequencing (WES) in 20 trios, including 10 children with epilepsy and 10 without epilepsy, both after acute symptomatic neonatal seizures. Children with post-neonatal epilepsy had a higher burden of pathogenic variants in epilepsy-associated genes compared to those without post-neonatal epilepsy. Future studies evaluating this association may lead to a better understanding of the risk of epilepsy after acute symptomatic neonatal seizures and elucidate molecular pathways that are dysregulated after brain injury and implicated in epileptogenesis.
Collapse
|
18
|
Jiang Y, Fu X, Zhang Y, Wang SF, Zhu H, Wang WK, Zhang L, Wu P, Wong CCL, Li J, Ma J, Guan JS, Huang Y, Hui J. Rett syndrome linked to defects in forming the MeCP2/Rbfox/LASR complex in mouse models. Nat Commun 2021; 12:5767. [PMID: 34599184 PMCID: PMC8486766 DOI: 10.1038/s41467-021-26084-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/13/2021] [Indexed: 01/01/2023] Open
Abstract
Rett syndrome (RTT) is a severe neurological disorder and a leading cause of intellectual disability in young females. RTT is mainly caused by mutations found in the X-linked gene encoding methyl-CpG binding protein 2 (MeCP2). Despite extensive studies, the molecular mechanism underlying RTT pathogenesis is still poorly understood. Here, we report MeCP2 as a key subunit of a higher-order multiunit protein complex Rbfox/LASR. Defective MeCP2 in RTT mouse models disrupts the assembly of the MeCP2/Rbfox/LASR complex, leading to reduced binding of Rbfox proteins to target pre-mRNAs and aberrant splicing of Nrxns and Nlgn1 critical for synaptic plasticity. We further show that MeCP2 disease mutants display defective condensate properties and fail to promote phase-separated condensates with Rbfox proteins in vitro and in cultured cells. These data link an impaired function of MeCP2 with disease mutation in splicing control to its defective properties in mediating the higher-order assembly of the MeCP2/Rbfox/LASR complex. MeCP2 mutations can cause Rett syndrome, a severe childhood neurological disorder. Here the authors show that MeCP2 mediates the higher-order assembly of a large splicing complex Rbfox/LASR, which is disrupted in the mouse models of Rett syndrome.
Collapse
Affiliation(s)
- Yan Jiang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Xing Fu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, 201602, Shanghai, China
| | - Yuhan Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China.,Department of General Surgery, Shanghai Key Laboratory of Biliary Tract Disease Research, State Key Laboratory of Oncogenes and Related Genes, Xinhua Hospital, Shanghai Jiao Tong University, 200092, Shanghai, China
| | - Shen-Fei Wang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Hong Zhu
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Wei-Kang Wang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Lin Zhang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Ping Wu
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 201210, Shanghai, China
| | - Catherine C L Wong
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 201210, Shanghai, China.,Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, School of Basic Medical Sciences, Peking University, 100191, Beijing, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Ji-Song Guan
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.,Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Ying Huang
- Department of General Surgery, Shanghai Key Laboratory of Biliary Tract Disease Research, State Key Laboratory of Oncogenes and Related Genes, Xinhua Hospital, Shanghai Jiao Tong University, 200092, Shanghai, China.
| | - Jingyi Hui
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China.
| |
Collapse
|
19
|
Kos MZ, Carless MA, Blondell L, Leland MM, Knape KD, Göring HHH, Szabó CÁ. Whole Genome Sequence Data From Captive Baboons Implicate RBFOX1 in Epileptic Seizure Risk. Front Genet 2021; 12:714282. [PMID: 34490042 PMCID: PMC8417722 DOI: 10.3389/fgene.2021.714282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/27/2021] [Indexed: 01/18/2023] Open
Abstract
In this study, we investigate the genetic determinants that underlie epilepsy in a captive baboon pedigree and evaluate the potential suitability of this non-human primate model for understanding the genetic etiology of human epilepsy. Archived whole-genome sequence data were analyzed using both a candidate gene approach that targeted variants in baboon homologs of 19 genes (n = 20,881 SNPs) previously implicated in genetic generalized epilepsy (GGE) and a more agnostic approach that examined protein-altering mutations genome-wide as assessed by snpEff (n = 36,169). Measured genotype association tests for baboon cases of epileptic seizure were performed using SOLAR, as well as gene set enrichment analyses (GSEA) and protein–protein interaction (PPI) network construction of top association hits genome-wide (p < 0.01; n = 441 genes). The maximum likelihood estimate of heritability for epileptic seizure in the pedigreed baboon sample is 0.76 (SE = 0.77; p = 0.07). Among candidate genes for GGE, a significant association was detected for an intronic SNP in RBFOX1 (p = 5.92 × 10–6; adjusted p = 0.016). For protein-altering variants, no genome-wide significant results were observed for epilepsy status. However, GSEA revealed significant positive enrichment for genes involved in the extracellular matrix structure (ECM; FDR = 0.0072) and collagen formation (FDR = 0.017), which was reflected in a major PPI network cluster. This preliminary study highlights the potential role of RBFOX1 in the epileptic baboon, a protein involved in transcriptomic regulation of multiple epilepsy candidate genes in humans and itself previously implicated in human epilepsy, both focal and generalized. Moreover, protein-damaging variants from across the genome exhibit a pattern of association that links collagen-containing ECM to epilepsy risk. These findings suggest a shared genetic etiology between baboon and human forms of GGE and lay the foundation for follow-up research.
Collapse
Affiliation(s)
- Mark Z Kos
- Department of Human Genetics, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Edinburg, TX, United States
| | - Melanie A Carless
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States.,Brain Health Consortium, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Lucy Blondell
- Department of Human Genetics, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Edinburg, TX, United States
| | - M Michelle Leland
- Laboratory Animal Research, UT Health San Antonio, San Antonio, TX, United States
| | - Koyle D Knape
- Department of Neurology, UT Health San Antonio, San Antonio, TX, United States
| | - Harald H H Göring
- Department of Human Genetics, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Edinburg, TX, United States
| | - Charles Ákos Szabó
- Department of Neurology, UT Health San Antonio, San Antonio, TX, United States.,South Texas Comprehensive Epilepsy Center, San Antonio, TX, United States
| |
Collapse
|
20
|
Tascón-Arcila J, Rojas-Jiménez S, Cornejo-Sánchez D, Gómez-Builes P, Ucroz-Benavides A, Holguín BM, Restrepo-Arbeláez D, Gómez-Castillo C, Solarte-Mia R, Cornejo-Ochoa W, Pineda-Trujillo N. Differential Clinical Features in Colombian Patients With Rolandic Epilepsy and Suggestion of Unlikely Association With GRIN2A, RBFOX1, or RBFOX3 Gene Variants. J Child Neurol 2021; 36:875-882. [PMID: 34039076 DOI: 10.1177/08830738211015017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PURPOSE Our purpose was to describe the phenotypic features and test for association of genes GRIN2A, RBFOX1 and RBFOX3 with rolandic epilepsy in patients from Colombia. METHODS Thirty patients were enrolled. A structured interview was applied. In addition, saliva samples were collected from the patients and their parents. One polymorphism in each of GRIN2A, RBFOX1 and RBFOX3 genes was tested. RESULTS The average age at onset was 5.3 years. Almost half the sample presented prolonged seizures (>5 minutes); although the majority of the patients presented their seizures only while asleep, over a quarter presented them only while awake. The most frequent comorbidity was the presence of symptoms compatible with attention-deficit hyperactivity disorder (ADHD). Personal history of febrile seizures and parasomnias were equally frequent (20%). Family history of any type of epilepsy was reported in 80% of the patients, followed by migraine (73.3%) and poor academic performance (63.3%). About half the sample reported sleepwalking in parents or sibs. Most patients had received pharmacologic treatment. We found no association of rolandic epilepsy with the single nucleotide polymorphisms tested. CONCLUSIONS Our rolandic epilepsy cohort presents clinical features clearly different from other cohorts. For instance, age at onset is much earlier in our set of patients, and personal and family history of febrile seizures as well as parasomnias are highly prevalent in our sample. No association of rolandic epilepsy with variants at the 3 genes tested was found. This lack of association may reflect the high genetic heterogeneity of the epilepsies.
Collapse
Affiliation(s)
- José Tascón-Arcila
- Grupo Mapeo Genético, Departamento de Pediatría, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Sara Rojas-Jiménez
- Grupo Mapeo Genético, Departamento de Pediatría, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Diana Cornejo-Sánchez
- Grupo Mapeo Genético, Departamento de Pediatría, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Paola Gómez-Builes
- Grupo Mapeo Genético, Departamento de Pediatría, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Andrea Ucroz-Benavides
- Grupo Mapeo Genético, Departamento de Pediatría, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Blear-Maria Holguín
- Grupo Mapeo Genético, Departamento de Pediatría, Universidad de Antioquia UdeA, Medellín, Colombia
| | | | - Christhian Gómez-Castillo
- Sección de Neuropediatria, IPS Universitaria, 27983Universidad de Antioquia UdeA, Medellín, Colombia
| | - Rodrigo Solarte-Mia
- Laboratorio de Correlación Electroclínica, CECLAB. IPS Universitaria, Universidad de Antioquia UdeA, Medellín, Colombia
| | - William Cornejo-Ochoa
- PEDIACIENCIAS, Departamento de Pediatría, Facultad de Medicina, 27983Universidad de Antioquia UdeA, Medellín, Colombia
| | - Nicolas Pineda-Trujillo
- Grupo Mapeo Genético, Departamento de Pediatría, Universidad de Antioquia UdeA, Medellín, Colombia
| |
Collapse
|
21
|
Abstract
Autism is a common and complex neurologic disorder whose scientific underpinnings have begun to be established in the past decade. The essence of this breakthrough has been a focus on families, where genetic analyses are strongest, versus large-scale, case-control studies. Autism genetics has progressed in parallel with technology, from analyses of copy number variation to whole-exome sequencing (WES) and whole-genome sequencing (WGS). Gene mutations causing complete loss of function account for perhaps one-third of cases, largely detected through WES. This limitation has increased interest in understanding the regulatory variants of genes that contribute in more subtle ways to the disorder. Strategies combining biochemical analysis of gene regulation, WGS analysis of the noncoding genome, and machine learning have begun to succeed. The emerging picture is that careful control of the amounts of transcription, mRNA, and proteins made by key brain genes-stoichiometry-plays a critical role in defining the clinical features of autism.
Collapse
Affiliation(s)
- Robert B Darnell
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA;
| |
Collapse
|
22
|
Liu Z, Ye X, Zhang J, Wu B, Dong S, Gao P. Biallelic ADGRV1 variants are associated with Rolandic epilepsy. Neurol Sci 2021; 43:1365-1374. [PMID: 34160719 DOI: 10.1007/s10072-021-05403-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/10/2021] [Indexed: 01/28/2023]
Abstract
OBJECTIVE Rolandic epilepsy (RE) is among the most common focal epilepsies in childhood. For the majority of patients with RE and atypical RE (ARE), the etiology remains elusive. We thus screened patients with RE/ARE in order to detect disease-causing variants.. METHODS A trios-based whole-exome sequencing approach was performed in a cohort of 28 patients with RE/ARE. Clinical data and EEGs were reviewed. Variants were validated by Sanger sequencing. RESULTS Two compound heterozygous missense variants p.Val272Ile/p.Asn3028Ser and p.Ala3657Val/p.Met4419Val of ADGRV1 were identified in two unrelated familial cases of RE/ARE. All the variants were in the calcium exchanger β domain and were suggested to be damaging by at least one web-based prediction tool. These variants are not present or are present at a very low minor allele frequency in the gnomAD database. Previously, biallelic ADGRV1 variants (p.Gly2756Arg and p.Glu4410Lys) have been observed in RE, consistent with the observation in this study and supporting the association between ADGRV1 variants and RE. Additionally, a de novo mutation, p.Asp668Asn, in GRIN2B was identified in a sporadic case of ARE, and a missense variant, p.Asn1551Ser, in RyR2 was identified in a family with RE with incomplete penetrance. These genes are all calcium homeostasis associated genes, suggesting the potential effect of calcium homeostasis in RE/ARE. CONCLUSIONS The results from the present study suggest that the genes ADGRV1, GRIN2B, and RyR2 are associated with RE/ARE. These data link defects in neuronal intracellular calcium homeostasis to RE/ARE pathogenesis implicating that these defects plays an important role in the development of these conditions.
Collapse
Affiliation(s)
- Zhigang Liu
- Department of Pediatrics, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, 11 Renminxi Road 11, Foshan, 528000, Guangdong, China.,The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Xingguang Ye
- Department of Pediatrics, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, 11 Renminxi Road 11, Foshan, 528000, Guangdong, China
| | - Jieyan Zhang
- Department of Pediatrics, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, 11 Renminxi Road 11, Foshan, 528000, Guangdong, China
| | - Benze Wu
- Department of Pediatrics, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, 11 Renminxi Road 11, Foshan, 528000, Guangdong, China
| | - Shiwei Dong
- Department of Pediatrics, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, 11 Renminxi Road 11, Foshan, 528000, Guangdong, China
| | - Pingming Gao
- Department of Pediatrics, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, 11 Renminxi Road 11, Foshan, 528000, Guangdong, China. .,The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.
| |
Collapse
|
23
|
Gu L, Kwong JM, Caprioli J, Piri N. Loss of Rbfox1 Does Not Affect Survival of Retinal Ganglion Cells Injured by Optic Nerve Crush. Front Neurosci 2021; 15:687690. [PMID: 34108862 PMCID: PMC8180555 DOI: 10.3389/fnins.2021.687690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
Rbfox1 is a multifunctional RNA binding protein that regulates alternative splicing, transcription, mRNA stability and translation. Its roles in neurogenesis and neuronal functions are well established. Recent studies also implicate Rbfox1 in the regulation of gene networks that support cell survival during stress. We have earlier characterized the expression of Rbfox1 in amacrine and retinal ganglion cells (RGCs) and showed that deletion of Rbfox1 in adult animals results in depth perception deficiency. The current study investigates the effect of Rbfox1 downregulation on survival of RGCs injured by optic nerve crush (ONC). Seven days after ONC, animals sustained severe degeneration of RGC axons in the optic nerve and significant loss of RGC somas. Semi-quantitative grading of optic nerve damage in control + ONC, control + tamoxifen + ONC, and Rbfox1 -/- + ONC groups ranged from 4.6 to 4.8 on a scale of 1 (normal; no degenerated axons were noted) to 5 (total degeneration; all axons showed degenerated organelles, axonal content, and myelin sheath), indicating a severe degeneration. Among these three ONC groups, no statistical significance was observed when any two groups were compared. The number of RGC somas were quantitatively analyzed in superior, inferior, nasal and temporal retinal quadrants at 0.5, 1, and 1.5 mm from the center of the optic disc. The average RGC densities (cells/mm2) were: control 6,438 ± 1,203; control + ONC 2,779 ± 573; control + tamoxifen 6,163 ± 861; control + tamoxifen + ONC 2,573 ± 555; Rbfox1 -/- 6,437 ± 893; and Rbfox1 -/- + ONC 2,537 ± 526. The RGC loss in control + ONC, control + tamoxifen + ONC and Rbfox1 -/- + ONC was 57% (P = 1.44954E-42), 58% (P = 1.37543E-57) and 61% (P = 5.552E-59) compared to RGC numbers in the relevant uninjured groups, respectively. No statistically significant difference was observed between any two groups of uninjured animals or between any two ONC groups. Our data indicate that Rbfox1-mediated pathways have no effect on survival of RGCs injured by ONC.
Collapse
Affiliation(s)
- Lei Gu
- Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jacky M Kwong
- Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Joseph Caprioli
- Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States.,Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Natik Piri
- Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States.,Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, United States
| |
Collapse
|
24
|
Duan Y, Leng X, Liu C, Qi X, Zhang L, Tan W, Zhang X, Wang Y. The Correlation of ELP4-PAX6 With Rolandic Spike Sources in Idiopathic Rolandic Epilepsy Syndromes. Front Neurol 2021; 12:643964. [PMID: 33897599 PMCID: PMC8064626 DOI: 10.3389/fneur.2021.643964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 02/26/2021] [Indexed: 12/04/2022] Open
Abstract
Objective: To study the single nucleotide polymorphism rs662702 of ELP4-PAX6 in patients with idiopathic rolandic epilepsy syndromes (IRES) in China and explore the relationship between the distribution of rolandic spike sources and the single nucleotide polymorphism rs662702 in ELP4-PAX6. Methods: First, clinical information was obtained from patients diagnosed with IRES. Next, the single nucleotide polymorphism rs662702 of ELP4 was analyzed by using the Sanger method. Resting-state magnetoencephalography data were collected from 17 patients. We analyzed the epileptic spike sources using the single equivalent current dipole (SECD) model and determined the spike distributions across the whole brain. Finally, Fisher's test was performed to assess the correlation between the single nucleotide polymorphism rs662702 of ELP4-PAX6 and rolandic spike sources. Results: ELP4 rs662702 T alleles were found in 10.7% of IRES patients and occurred four times more frequently in these patients than in the healthy controls. TT homozygosity was found in one IRES patient (1.3%), while no TT homozygosity was found in the healthy control group. The IRES rolandic spike sources were unilateral in sixteen patients (94.1%) and were mainly located in the anterior central gyrus (58.8%). The spike source of patients without the ELP4 rs662702 T allele was correlated with the central region (p < 0.05). The rolandic spikes sources were significant correlated with the non-central gyrus (frontal and temporal lobes) in patients with the ELP4 rs662702 T allele (p < 0.05). Conclusion: The rolandic spike sources of the IRES patients with the ELP4 rs662702 T allele were significantly associated with the non-central gyrus, including the frontal and temporal lobes. Our study confirmed for the first time in vivo that ELP4 rs662702 T allele overexpression is correlated with the rolandic spike distribution in patients with IRES and provides important insights into how genetic abnormalities can lead to brain dysfunction and into the precise targeting of abnormal discharge sources in the brain.
Collapse
Affiliation(s)
- Yiran Duan
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Xuerong Leng
- Department of Pediatrics, Xuanwu Hospital Capital Medical University, Beijing, China
| | - Chunyan Liu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Xiaohong Qi
- Department of Pediatrics, Xuanwu Hospital Capital Medical University, Beijing, China
| | - Liping Zhang
- Department of Pediatrics, Xuanwu Hospital Capital Medical University, Beijing, China
| | - Wenjun Tan
- Key Laboratory of Intelligent Computing in Medical Image, Northeastern University, Ministry of Education, Shenyang, China
| | - Xiating Zhang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yuping Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Neuromodulation, Capital Medical University, Beijing, China.,Center of Epilepsy, Beijing Institute for Brain Disorders, Capital Medical University, Beijing, China
| |
Collapse
|
25
|
The effect of Rbfox2 modulation on retinal transcriptome and visual function. Sci Rep 2020; 10:19683. [PMID: 33184471 PMCID: PMC7665016 DOI: 10.1038/s41598-020-76879-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/02/2020] [Indexed: 01/07/2023] Open
Abstract
Rbfox proteins regulate alternative splicing, mRNA stability and translation. These proteins are involved in neurogenesis and have been associated with various neurological conditions. Here, we analyzed Rbfox2 expression in adult and developing mouse retinas and the effect of its downregulation on visual function and retinal transcriptome. In adult rodents, Rbfox2 is expressed in all retinal ganglion cell (RGC) subtypes, horizontal cells, as well as GABAergic amacrine cells (ACs). Among GABAergic AC subtypes, Rbfox2 was colocalized with cholinergic starburst ACs, NPY (neuropeptide Y)- and EBF1 (early B-cell factor 1)-positive ACs. In differentiating retinal cells, Rbfox2 expression was observed as early as E12 and, unlike Rbfox1, which changes its subcellular localization from cytoplasmic to predominantly nuclear at around P0, Rbfox2 remains nuclear throughout retinal development. Rbfox2 knockout in adult animals had no detectable effect on retinal gross morphology. However, the visual cliff test revealed a significant abnormality in the depth perception of Rbfox2-deficient animals. Gene set enrichment analysis identified genes regulating the RNA metabolic process as a top enriched class of genes in Rbfox2-deficient retinas. Pathway analysis of the top 100 differentially expressed genes has identified Rbfox2-regulated genes associated with circadian rhythm and entrainment, glutamatergic/cholinergic/dopaminergic synaptic function, calcium and PI3K-AKT signaling.
Collapse
|
26
|
Hansen TF, Møller RS. The impact of low-risk genetic variants in self-limited epilepsy with centrotemporal spikes aka Rolandic epilepsy. EBioMedicine 2020; 58:102896. [PMID: 32702638 PMCID: PMC7374607 DOI: 10.1016/j.ebiom.2020.102896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 01/05/2023] Open
Affiliation(s)
- Thomas F Hansen
- Danish Headache Center, Department of Neurology, Rigshospitalet Glostrup, Valdemar Hansens vej 1-23, 2600 Glostrup, Denmark; Center for Protein Research, Copenhagen University, Copenhagen, Denmark.
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Filadelfia, Kolonivej 1, 4293 Dianalund, Denmark; Department of Regional Health Services, University of Southern Denmark, Odense, Denmark.
| |
Collapse
|
27
|
Shi XY, Wang G, Li T, Li Z, Leo P, Liu Z, Wu G, Zhu H, Zhang Y, Li D, Gao L, Yang L, Wang W, Liao J, Wang J, Zhou S, Wang H, Li X, Gao J, Zhang L, Shu X, Li D, Li Y, Chen C, Zhang X, Partida GC, Lundberg M, Reutens D, Bartlett P, Brown MA, Zou LP, Xu H. Identification of susceptibility variants to benign childhood epilepsy with centro-temporal spikes (BECTS) in Chinese Han population. EBioMedicine 2020; 57:102840. [PMID: 32580138 PMCID: PMC7317238 DOI: 10.1016/j.ebiom.2020.102840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/11/2020] [Accepted: 06/02/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Benign Childhood Epilepsy with Centro-temporal Spikes (BECTS) is the most common form of idiopathic epilepsy in children, accounting for up to 23% of pediatric epilepsy. The pathogenesis of BECTS is unknown, but it is thought that genetic factors play a role in susceptibility to the disease. METHODS To investigate the role of common genetic variants in BECTS pathogenesis, a 2-stage genome-wide association study (GWAS) was performed in 1,800 Chinese Han BECTS patients, and 7,090 healthy controls. Genetic findings were used in a Mendelian Randomization study in the UK Biobank dataset to investigate the potential role of smoking in BECTS. FINDINGS Definitive evidence of a role for common-variant heritability was demonstrated, with heritability of BECTS of >10% observed even with conservative disease prevalence assumptions. Although no individual locus achieved genome-wide significance, twelve loci achieved suggestive evidence of association (5 × 10-8<P<10-5). Using combined genetic and brain tissue gene expression data analyzed by Summary-data-based Mendelian Randomization (SMR), causative association of BECTS was demonstrated with SNP rs1948 and the CHRNA5 t3603436 transcript (Peqtl = 2·10 × 10-12, Psmr = 7·9 × 10-5). This finding indicates rs1948 is significantly associated with BECTS through effects on expression of CHRNA5 in brain tissue. The identification of novel loci suggests involvements of KALRN and the CHRNA5-A3-B4 cluster in BECTS. Using a generalized SMR approach we demonstrate that maternal smoking around birth is significantly associated with increased risk of BECTS (odds ratio = 3·90, P = 0·0099). INTERPRETATION This study shows that BECTS risk is at least partially heritable and due to common genetic variants. Additionally, we demonstrate that BECTS risk is substantially increased by maternal smoking around birth.
Collapse
Affiliation(s)
- Xiu-Yu Shi
- Department of Pediatrics, Chinese PLA General Hospital, 28 Fuxing Road, Haidian district, Beijing, China
| | - Geng Wang
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China; University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia
| | - Ting Li
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zhixiu Li
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Brisbane, Australia
| | - Paul Leo
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Brisbane, Australia
| | - Zhisheng Liu
- Department of Neurology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science & Technology Wuhan, Hubei, China
| | - Gefei Wu
- Department of Neurology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science & Technology Wuhan, Hubei, China
| | - Hongmin Zhu
- Department of Neurology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science & Technology Wuhan, Hubei, China
| | - Yuqin Zhang
- Department of Neurology, Tian Jin Children's hospital, 238 Longyan road, Beichen district, Tianjin, China
| | - Dong Li
- Department of Neurology, Tian Jin Children's hospital, 238 Longyan road, Beichen district, Tianjin, China
| | - Li Gao
- Department of Pediatrics, Henan Provincial People's Hospital, 7 Weiwu Road, Jinshui District, Zhengzhou, Henan Province, China
| | - Liu Yang
- Department of Pediatrics, Henan Provincial People's Hospital, 7 Weiwu Road, Jinshui District, Zhengzhou, Henan Province, China
| | - Wei Wang
- Department of Neurology, Harbin Children's Hospital, 57 YouYi Road, DaoLi District, Harbin, Heilongjiang Province, China
| | - Jianxiang Liao
- Department of Neurology, Shenzhen Children's Hospital, 7019 Yitian Road Futian, Shenzhen, Guangdong Province, China
| | - Jiwen Wang
- Department of Neurology, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, 1678 Dongfang Road, New Pudong district, Shanghai, China
| | - Shuizhen Zhou
- Department of Neurology, Children's Hospital of Fudan University, 399 Wanyuan Road, Minhang District, Shanghai, China
| | - Hua Wang
- Department of Pediatric Neurology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, Shenyang, Liaoning Province, China
| | - Xiaojing Li
- Department of Neurology, Guangzhou Women and Children's Medical Center, 9 Jinsui Road, Tianhe district, Guangzhou, Guangdong Province, China
| | - Jingyun Gao
- Department of Pediatric Neurology, Hebei Tangshan City maternal and child health care hospital,14 South Jianhe Road, Tangshan, Hebei Province, China
| | - Li Zhang
- Department of Pediatrics, Linyi People's Hospital, 130 Yizhou Road, Lanshan, Linyi, Shandong Province, China
| | - Xiaomei Shu
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical College, 149 Dalian Road, Zunyi, Guizhou Province, China
| | - Dan Li
- Department of Pediatrics, the Second affiliated Hospital of Xi'an Jiaotong University, 157 Xiwu Road, Xi'an, Shaanxi Province, China
| | - Yan Li
- Department of Neurology, Children's Hospital Affiliated to Soochow University, 92 Zhongnan Street, Suzhou, Jiangsu Province, China
| | - Chunhong Chen
- Department of Neurology, Beijing Children's Hospital, 56 South Lishi Road, Xicheng District, Beijing, China
| | - Xiuju Zhang
- Department of Pediatrics, Xingtai People's Hospital,16 Hongxing Street, Xingtai, Hebei Province, China
| | - Gabriel Cuellar Partida
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia
| | - Mischa Lundberg
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia
| | - David Reutens
- Centre for Advanced Imaging, University of Queensland, Brisbane, Australia
| | - Perry Bartlett
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Matthew A Brown
- Guy's & St Thomas' NHS Foundation Trust and King's College London, NIHR Biomedical Research Centre, London, England United Kingdom.
| | - Li-Ping Zou
- Department of Pediatrics, Chinese PLA General Hospital, 28 Fuxing Road, Haidian district, Beijing, China; Center of Epilepsy, Beijing Institute for Brain Disorders, Beijing, China.
| | - Huji Xu
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China; Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
28
|
Li ML, Tang H, Shao Y, Wang MS, Xu HB, Wang S, Irwin DM, Adeola AC, Zeng T, Chen L, Li Y, Wu DD. Evolution and transition of expression trajectory during human brain development. BMC Evol Biol 2020; 20:72. [PMID: 32576137 PMCID: PMC7310562 DOI: 10.1186/s12862-020-01633-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 05/26/2020] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The remarkable abilities of the human brain are distinctive features that set us apart from other animals. However, our understanding of how the brain has changed in the human lineage remains incomplete, but is essential for understanding cognition, behavior, and brain disorders in humans. Here, we compared the expression trajectory in brain development between humans and rhesus macaques (Macaca mulatta) to explore their divergent transcriptome profiles. RESULTS Results showed that brain development could be divided into two stages, with a demarcation date in a range between 25 and 26 postconception weeks (PCW) for humans and 17-23PCWfor rhesus macaques, rather than birth time that have been widely used as a uniform demarcation time of neurodevelopment across species. Dynamic network biomarker (DNB) analysis revealed that the two demarcation dates were transition phases during brain development, after which the brain transcriptome profiles underwent critical transitions characterized by highly fluctuating DNB molecules. We also found that changes between early and later brain developmental stages (as defined by the demarcation points) were substantially greater in the human brain than in the macaque brain. To explore the molecular mechanism underlying prolonged timing during early human brain development, we carried out expression heterochrony tests. Results demonstrated that compared to macaques, more heterochronic genes exhibited neoteny during early human brain development, consistent with the delayed demarcation time in the human lineage, and proving that neoteny in human brain development could be traced to the prenatal period. We further constructed transcriptional networks to explore the profile of early human brain development and identified the hub gene RBFOX1 as playing an important role in regulating early brain development. We also found RBFOX1 evolved rapidly in its non-coding regions, indicating that this gene played an important role in human brain evolution. Our findings provide evidence that RBFOX1 is a likely key hub gene in early human brain development and evolution. CONCLUSIONS By comparing gene expression profiles between humans and macaques, we found divergent expression trajectories between the two species, which deepens our understanding of the evolution of the human brain.
Collapse
Affiliation(s)
- Ming-Li Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Hui Tang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Hai-Bo Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - David M Irwin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, Ontario, M5G 2C4, Canada
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Tao Zeng
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Luonan Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, 310024, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
| | - Yan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resource, Yunnan University, Kunming, 650091, Yunnan, China.
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
| |
Collapse
|
29
|
Casanovas S, Schlichtholz L, Mühlbauer S, Dewi S, Schüle M, Strand D, Strand S, Zografidou L, Winter J. Rbfox1 Is Expressed in the Mouse Brain in the Form of Multiple Transcript Variants and Contains Functional E Boxes in Its Alternative Promoters. Front Mol Neurosci 2020; 13:66. [PMID: 32431595 PMCID: PMC7214753 DOI: 10.3389/fnmol.2020.00066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 04/06/2020] [Indexed: 01/25/2023] Open
Abstract
The RNA-binding protein RBFOX1 is an important regulator of neuron development and neuronal excitability. Rbfox1 is a dosage-sensitive gene and in both mice and humans, decreased expression of Rbfox1 has been linked to neurodevelopmental disorders. Alternative promoters drive expression of Rbfox1 transcript isoforms that encode an identical protein. The tissue- and developmental stage-specific expression of these isoforms, as well as the underlying regulatory mechanisms, are, however, unclear. Here, we set out to capture all of the Rbfox1 transcript isoforms and identify transcriptional mechanisms that regulate brain-specific Rbfox1 expression. Isoform sequencing identified multiple alternative Rbfox1 transcript variants in the mouse cerebral cortex, including transcripts with novel first exons, alternatively spliced exons and 3′-truncations. Quantitative RT-PCR determined the expression of the alternative first exons in the developing cerebral cortex and different subregions of the juvenile brain. Alternative first exons were found to be highly stage- and subregion specific in their expression patterns suggesting that they fulfill specific functions during cortex development and in different brain regions. Using reporter assays we found that the promoter regions of the two first exons E1B and E1C/E1C.1 contain several functional E-boxes. Together, we provide an extensive picture of Rbfox1 isoform expression. We further identified important regulatory mechanisms that drive neuron-specific Rbfox1 expression. Thus, our study forms the basis for further research into the mechanisms that ensure physiological Rbfox1 expression in the brain. It also helps to understand why, in patients with neurodevelopmental disorders deletion of individual RBFOX1 transcript isoforms could affect brain function.
Collapse
Affiliation(s)
- Sonia Casanovas
- Institute of Human Genetics, University Medical Center Mainz, Mainz, Germany.,Focus Program of Translational Neurosciences, University Medical Center Mainz, Mainz, Germany
| | - Laura Schlichtholz
- Institute of Human Genetics, University Medical Center Mainz, Mainz, Germany.,Focus Program of Translational Neurosciences, University Medical Center Mainz, Mainz, Germany
| | - Sophia Mühlbauer
- Institute of Human Genetics, University Medical Center Mainz, Mainz, Germany
| | - Sri Dewi
- Institute of Human Genetics, University Medical Center Mainz, Mainz, Germany
| | - Martin Schüle
- Institute of Human Genetics, University Medical Center Mainz, Mainz, Germany
| | - Dennis Strand
- First Department of Internal Medicine, University Medical Center Mainz, Mainz, Germany
| | - Susanne Strand
- First Department of Internal Medicine, University Medical Center Mainz, Mainz, Germany
| | - Lea Zografidou
- Institute of Human Genetics, University Medical Center Mainz, Mainz, Germany
| | - Jennifer Winter
- Institute of Human Genetics, University Medical Center Mainz, Mainz, Germany.,Focus Program of Translational Neurosciences, University Medical Center Mainz, Mainz, Germany.,German Resilience Centre, University Medical Center Mainz, Mainz, Germany
| |
Collapse
|
30
|
Price KM, Wigg KG, Feng Y, Blokland K, Wilkinson M, He G, Kerr EN, Carter TC, Guger SL, Lovett MW, Strug LJ, Barr CL. Genome-wide association study of word reading: Overlap with risk genes for neurodevelopmental disorders. GENES BRAIN AND BEHAVIOR 2020; 19:e12648. [PMID: 32108986 DOI: 10.1111/gbb.12648] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 01/28/2020] [Accepted: 02/24/2020] [Indexed: 12/12/2022]
Abstract
Reading disabilities (RD) are the most common neurocognitive disorder, affecting 5% to 17% of children in North America. These children often have comorbid neurodevelopmental/psychiatric disorders, such as attention deficit/hyperactivity disorder (ADHD). The genetics of RD and their overlap with other disorders is incompletely understood. To contribute to this, we performed a genome-wide association study (GWAS) for word reading. Then, using summary statistics from neurodevelopmental/psychiatric disorders, we computed polygenic risk scores (PRS) and used them to predict reading ability in our samples. This enabled us to test the shared aetiology between RD and other disorders. The GWAS consisted of 5.3 million single nucleotide polymorphisms (SNPs) and two samples; a family-based sample recruited for reading difficulties in Toronto (n = 624) and a population-based sample recruited in Philadelphia [Philadelphia Neurodevelopmental Cohort (PNC)] (n = 4430). The Toronto sample SNP-based analysis identified suggestive SNPs (P ~ 5 × 10-7 ) in the ARHGAP23 gene, which is implicated in neuronal migration/axon pathfinding. The PNC gene-based analysis identified significant associations (P < 2.72 × 10-6 ) for LINC00935 and CCNT1, located in the region of the KANSL2/CCNT1/LINC00935/SNORA2B/SNORA34/MIR4701/ADCY6 genes on chromosome 12q, with near significant SNP-based analysis. PRS identified significant overlap between word reading and intelligence (R2 = 0.18, P = 7.25 × 10-181 ), word reading and educational attainment (R2 = 0.07, P = 4.91 × 10-48 ) and word reading and ADHD (R2 = 0.02, P = 8.70 × 10-6 ; threshold for significance = 7.14 × 10-3 ). Overlap was also found between RD and autism spectrum disorder (ASD) as top-ranked genes were previously implicated in autism by rare and copy number variant analyses. These findings support shared risk between word reading, cognitive measures, educational outcomes and neurodevelopmental disorders, including ASD.
Collapse
Affiliation(s)
- Kaitlyn M Price
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Karen G Wigg
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Yu Feng
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Kirsten Blokland
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Margaret Wilkinson
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gengming He
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elizabeth N Kerr
- Department of Psychology, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Tasha-Cate Carter
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.,Holland Bloorview Rehabilitation Hospital, Toronto, Ontario, Canada
| | - Sharon L Guger
- Department of Psychology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maureen W Lovett
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Lisa J Strug
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Cathy L Barr
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
31
|
Al-Eitan LN, Alghamdi MA, Tarkhan AH, Al-Qarqaz FA. Genome-Wide CpG Island Methylation Profiles of Cutaneous Skin with and without HPV Infection. Int J Mol Sci 2019; 20:E4822. [PMID: 31569353 PMCID: PMC6801420 DOI: 10.3390/ijms20194822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/15/2022] Open
Abstract
HPV infection is one of the most commonly transmitted diseases among the global population. While it can be asymptomatic, non-genital HPV infection often gives rise to cutaneous warts, which are benign growths arising from the epidermal layer of the skin. This study aimed to produce a global analysis of the ways in which cutaneous wart formation affected the CpG island methylome. The Infinium MethylationEPIC BeadChip microarray was utilized in order to quantitatively interrogate CpG island methylation in genomic DNA extracted from 24 paired wart and normal skin samples. Differential methylation analysis was carried out by means of assigning a combined rank score using RnBeads. The 1000 top-ranking CpG islands were then subject to Locus Overlap Analysis (LOLA) for enrichment of genomic ranges, while signaling pathway analysis was carried out on the top 100 differentially methylated CpG islands. Differential methylation analysis illustrated that the most differentially methylated CpG islands in warts lay within the ITGB5, DTNB, RBFOX3, SLC6A9, and C2orf27A genes. In addition, the most enriched genomic region sets in warts were Sheffield's tissue-clustered DNase hypersensitive sites, ENCODE's segmentation and transcription factor binding sites, codex sites, and the epigenome sites from cistrome. Lastly, signaling pathway analysis showed that the GRB2, GNB1, NTRK1, AXIN1, and SKI genes were the most common regulators of the genes associated with the top 100 most differentially methylated CpG islands in warts. Our study shows that HPV-induced cutaneous warts have a clear CpG island methylation profile that sets them apart from normal skin. Such a finding could account for the temporary nature of warts and the capacity for individuals to undergo clinical remission.
Collapse
Affiliation(s)
- Laith N Al-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan.
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Mansour A Alghamdi
- Department of Human Anatomy, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia.
| | - Amneh H Tarkhan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Firas A Al-Qarqaz
- Department of Internal Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan.
- Division of Dermatology, Department of Internal Medicine, King Abdullah University Hospital Jordan University of Science and Technology, Irbid 22110, Jordan.
| |
Collapse
|
32
|
Rbfox1 Regulates Synaptic Transmission through the Inhibitory Neuron-Specific vSNARE Vamp1. Neuron 2019; 98:127-141.e7. [PMID: 29621484 DOI: 10.1016/j.neuron.2018.03.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 01/08/2018] [Accepted: 03/05/2018] [Indexed: 12/19/2022]
Abstract
Dysfunction of the neuronal RNA binding protein RBFOX1 has been linked to epilepsy and autism spectrum disorders. Rbfox1 loss in mice leads to neuronal hyper-excitability and seizures, but the physiological basis for this is unknown. We identify the vSNARE protein Vamp1 as a major Rbfox1 target. Vamp1 is strongly downregulated in Rbfox1 Nes-cKO mice due to loss of 3' UTR binding by RBFOX1. Cytoplasmic Rbfox1 stimulates Vamp1 expression in part by blocking microRNA-9. We find that Vamp1 is specifically expressed in inhibitory neurons, and that both Vamp1 knockdown and Rbfox1 loss lead to decreased inhibitory synaptic transmission and E/I imbalance. Re-expression of Vamp1 selectively within interneurons rescues the electrophysiological changes in the Rbfox1 cKO, indicating that Vamp1 loss is a major contributor to the Rbfox1 Nes-cKO phenotype. The regulation of interneuron-specific Vamp1 by Rbfox1 provides a paradigm for broadly expressed RNA-binding proteins performing specialized functions in defined neuronal subtypes.
Collapse
|
33
|
Tacke M, Rupp N, Gerstl L, Heinen F, Vill K, Bonfert M, Neubauer BA, Bast T, Borggraefe I. Benign epilepsy with centrotemporal spikes: Correlating spike frequency and neuropsychology. Acta Neurol Scand 2018; 138:475-481. [PMID: 30259965 DOI: 10.1111/ane.13015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 08/10/2018] [Indexed: 12/22/2022]
Abstract
OBJECTIVES Neuropsychological sequelae are a feature of benign epilepsy with centrotemporal spikes (BECTS) in children. A correlation between the frequency of interictal EEG discharges and the cognitive as well as behavioral profile of the patients has been suspected but not proven. MATERIALS AND METHODS Children with BECTS that had not yet been treated were included into a randomized controlled trial. In the initial visit, EEGs were recorded. The frequency of interictal discharges was quantified. Correlations between the discharge frequency and the performance in a neuropsychological test battery were examined. RESULTS The cognitive test results were within or slightly above normal range (Culture-free intelligence test: 99.4%-confidence interval [CI]: [50.3, 59.9], test standardized to a population mean of 50). Parent-reported behavioral abnormalities were statistically significantly increased (CBCL total score CI: [51.9, 61.9], population mean as above). Correlations between the frequency of interictal epileptic discharges and the test results could not be identified (lowest encountered P-value: 0.034, not significant after correction for multiple testing). CONCLUSION The data do not support the hypothesis that the frequency of the interictal EEG discharges influences the neurocognitive performance or behavioral parameters of children with BECTS.
Collapse
Affiliation(s)
- Moritz Tacke
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics; University of Munich; Munich Germany
| | - Nina Rupp
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics; University of Munich; Munich Germany
| | - Lucia Gerstl
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics; University of Munich; Munich Germany
| | - Florian Heinen
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics; University of Munich; Munich Germany
| | - Katharina Vill
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics; University of Munich; Munich Germany
| | - Michaela Bonfert
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics; University of Munich; Munich Germany
| | - Bernd Axel Neubauer
- Department of Neuropediatrics; Justus-Liebig-University of Giessen; Giessen Germany
- Children's Hospital; Rosenheim Germany
| | - Thomas Bast
- Kork Epilepsy Center; Kehl-Kork Germany
- Medical Faculty of the University of Freiburg; Freiburg Germany
| | - Ingo Borggraefe
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics; University of Munich; Munich Germany
- Epilepsy Center; University of Munich; Munich Germany
| | | |
Collapse
|
34
|
Kumar J, Solaiman A, Mahakkanukrauh P, Mohamed R, Das S. Sleep Related Epilepsy and Pharmacotherapy: An Insight. Front Pharmacol 2018; 9:1088. [PMID: 30319421 PMCID: PMC6171479 DOI: 10.3389/fphar.2018.01088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/07/2018] [Indexed: 01/26/2023] Open
Abstract
In the last several decades, sleep-related epilepsy has drawn considerable attention among epileptologists and neuroscientists in the interest of new paradigms of the disease etiology, pathogenesis and management. Sleep-related epilepsy is nocturnal seizures that manifest solely during the sleep state. Sleep comprises two distinct stages i.e., non-rapid eye movement (NREM) and rapid eye movement (REM) that alternate every 90 min with NREM preceding REM. Current findings indicate that the sleep-related epilepsy manifests predominantly during the synchronized stages of sleep; NREM over REM stage. Sleep related hypermotor epilepsy (SHE), benign partial epilepsy with centrotemporal spikes or benign rolandic epilepsy (BECTS), and Panayiotopoulos Syndrome (PS) are three of the most frequently implicated epilepsies occurring during the sleep state. Although some familial types are described, others are seemingly sporadic occurrences. In the present review, we aim to discuss the predominance of sleep-related epilepsy during NREM, established familial links to the pathogenesis of SHE, BECTS and PS, and highlight the present available pharmacotherapy options.
Collapse
Affiliation(s)
- Jaya Kumar
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Amro Solaiman
- Department of Anatomy, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Pasuk Mahakkanukrauh
- Department of Anatomy, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Excellence Centre in Forensic Osteology Research Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Rashidi Mohamed
- Department of Familty Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Srijit Das
- Department of Anatomy, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| |
Collapse
|
35
|
Benign epilepsy with centrotemporal spikes - Current concepts of diagnosis and treatment. Neurol Neurochir Pol 2018; 52:677-689. [PMID: 30219586 DOI: 10.1016/j.pjnns.2018.08.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/29/2018] [Accepted: 08/30/2018] [Indexed: 11/21/2022]
Abstract
Benign epilepsy with centrotemporal spikes (BECTS) is the most common focal epilepsy of the childhood and also one of the best known. It has a proclivity to start at a particular age and remit spontaneously before adolescence. Majority of patients may avoid long-term treatment, because of the mild course and very good outcome. Only few patients may present cognitive deficits if the proper treatment is not implied. BECTS is a part of heterogeneous group of syndromes that consists of Landau-Kleffner Syndrome (LKS), Continuous Spike-and-Wave during Sleep (CSWS) and Atypical benign partial epilepsy (ABPE). These syndromes may be also a result of various trajectories that BECTS may evolve to. Disease is suggested to have genetic origins, as some patients have relatives with different types of epilepsy. The discovery of the pathogenic mechanism of the disease and implementation of targeted therapy belong to the main challenges in the treatment of these patients.
Collapse
|
36
|
Gu L, Bok D, Yu F, Caprioli J, Piri N. Downregulation of splicing regulator RBFOX1 compromises visual depth perception. PLoS One 2018; 13:e0200417. [PMID: 30001398 PMCID: PMC6042722 DOI: 10.1371/journal.pone.0200417] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/26/2018] [Indexed: 02/05/2023] Open
Abstract
Rbfox1 is a splicing regulator that has been associated with various neurological conditions such as autism spectrum disorder, mental retardation, epilepsy, attention-deficit/hyperactivity disorder and schizophrenia. We show that in adult rodent retinas, Rbfox1 is expressed in all types of retinal ganglion cells (RGCs) and in certain subsets of amacrine cells (ACs), within the inner nuclear (INL) and ganglion cell (GCL) layers. In the INL, all Rbfox1-positive cells were colocalized with GABAergic ACs, however not all GABAergic ACs were immunostained for Rbfox1. In the GCL, a vast majority of GABAergic dACs were Rbfox1-immunopositive. Furthermore, all cholinergic starburst ACs (SACs) in the INL (type a) and in the GCL (type b) were Rbfox1 positive. The expression of Rbfox1 in the retina significantly overlapped with expression of Rbfox2, another member of Rbfox family of proteins. Rbfox2, in addition to RGCs and ACs, was also expressed in horizontal cells. In developing retinas at E12 and E15, Rbfox1 is localized to the cytoplasm of differentiating RGCs and ACs. Between P0 and P5, Rbfox1 subcellular localization switched from cytoplasmic to predominantly nuclear. Downregulation of Rbfox1 in adult Rbfox1loxP/loxP mice had no detectable effect on retinal gross morphology. However, the visual cliff test revealed marked abnormalities of depth perception of these animals. RNA sequencing of retinal transcriptomes of control and Rbfox1 knockout animals identified a number of Rbfox1-regulated genes that are involved in establishing neuronal circuits and synaptic transmission, including Vamp1, Vamp2, Snap25, Trak2, and Slc1A7, suggesting the role of Rbfox1 in facilitating synaptic communications between ACs and RGCs.
Collapse
Affiliation(s)
- Lei Gu
- Department of Ophthalmology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Dean Bok
- Department of Ophthalmology, University of California, Los Angeles, Los Angeles, CA, United States of America
- Department of Neurobiology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Fei Yu
- Department of Ophthalmology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Joseph Caprioli
- Department of Ophthalmology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Natik Piri
- Department of Ophthalmology, University of California, Los Angeles, Los Angeles, CA, United States of America
| |
Collapse
|
37
|
Addis L, Sproviero W, Thomas SV, Caraballo RH, Newhouse SJ, Gomez K, Hughes E, Kinali M, McCormick D, Hannan S, Cossu S, Taylor J, Akman CI, Wolf SM, Mandelbaum DE, Gupta R, van der Spek RA, Pruna D, Pal DK. Identification of new risk factors for rolandic epilepsy: CNV at Xp22.31 and alterations at cholinergic synapses. J Med Genet 2018; 55:607-616. [PMID: 29789371 PMCID: PMC6119347 DOI: 10.1136/jmedgenet-2018-105319] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/18/2018] [Accepted: 04/28/2018] [Indexed: 12/25/2022]
Abstract
Background Rolandic epilepsy (RE) is the most common genetic childhood epilepsy, consisting of focal, nocturnal seizures and frequent neurodevelopmental impairments in speech, language, literacy and attention. A complex genetic aetiology is presumed in most, with monogenic mutations in GRIN2A accounting for >5% of cases. Objective To identify rare, causal CNV in patients with RE. Methods We used high-density SNP arrays to analyse the presence of rare CNVs in 186 patients with RE from the UK, the USA, Sardinia, Argentina and Kerala, India. Results We identified 84 patients with one or more rare CNVs, and, within this group, 14 (7.5%) with recurrent risk factor CNVs and 15 (8.0%) with likely pathogenic CNVs. Nine patients carried recurrent hotspot CNVs including at 16p13.11 and 1p36, with the most striking finding that four individuals (three from Sardinia) carried a duplication, and one a deletion, at Xp22.31. Five patients with RE carried a rare CNV that disrupted genes associated with other epilepsies (KCTD7, ARHGEF15, CACNA2D1, GRIN2A and ARHGEF4), and 17 cases carried CNVs that disrupted genes associated with other neurological conditions or that are involved in neuronal signalling/development. Network analysis of disrupted genes with high brain expression identified significant enrichment in pathways of the cholinergic synapse, guanine-exchange factor activation and the mammalian target of rapamycin. Conclusion Our results provide a CNV profile of an ethnically diverse cohort of patients with RE, uncovering new areas of research focus, and emphasise the importance of studying non-western European populations in oligogenic disorders to uncover a full picture of risk variation.
Collapse
Affiliation(s)
- Laura Addis
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK.,Neuroscience Discovery Research, Eli Lilly and Company, Surrey, UK
| | - William Sproviero
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Sanjeev V Thomas
- Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, Kerala, India
| | - Roberto H Caraballo
- Department of Neurology, Hospital de Pediatría Prof. Dr. J.P. Garrahan, Combate de los Pozos 1881, Buenos Aires, Argentina
| | - Stephen J Newhouse
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.,NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust, Bethlem Royal Hospital, Beckenham, UK.,Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London, UK
| | - Kumudini Gomez
- Department of Paediatrics, University Hospital Lewisham, Lewisham and Greenwich NHS Trust, London, UK
| | - Elaine Hughes
- Department of Paediatric Neurosciences, Evelina London Children's Hospital, St Thomas' Hospital, London, UK
| | - Maria Kinali
- Department of Paediatric Neurology, Chelsea and Westminster Hospital, London, UK
| | - David McCormick
- Department of Paediatric Neurosciences, Evelina London Children's Hospital, St Thomas' Hospital, London, UK
| | - Siobhan Hannan
- Department of Paediatric Neurology, Chelsea and Westminster Hospital, London, UK
| | - Silvia Cossu
- Neurosurgery Unit, Neuroscience and Neurorehabilitation Department, Bambino Gesù Children Hospital, Rome, Italy.,Neurology Unit, Pediatric Hospital A. Cao, Brotzu Hospital Trust, Cagliari, Italy
| | | | - Cigdem I Akman
- Division of Pediatric Neurology, College of Physicians and Surgeons of Columbia University, New York City, New York, USA
| | - Steven M Wolf
- Department of Neurology, Mount Sinai Health System, New York City, New York, USA
| | - David E Mandelbaum
- Departments of Pediatrics, Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Rajesh Gupta
- Department of Paediatrics, Tunbridge Wells Hospital, Pembury, UK
| | - Rick A van der Spek
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dario Pruna
- Neurology Unit, Pediatric Hospital A. Cao, Brotzu Hospital Trust, Cagliari, Italy
| | - Deb K Pal
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| |
Collapse
|
38
|
Lesca G. Aspetti genetici delle epilessie. Neurologia 2018. [DOI: 10.1016/s1634-7072(18)41286-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
39
|
Lin YS, Kuo KT, Chen SK, Huang HS. RBFOX3/NeuN is dispensable for visual function. PLoS One 2018; 13:e0192355. [PMID: 29401485 PMCID: PMC5798780 DOI: 10.1371/journal.pone.0192355] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/22/2018] [Indexed: 11/19/2022] Open
Abstract
RBFOX3/NeuN is a neuronal splicing regulator involved in neural circuitry balance, as well as neurogenesis and synaptogenesis. Rbfox3 is expressed in neurons; however, in the retina, expression is restricted to cells in the ganglion cell layer and some cells of the inner nuclear layer. Rbfox3 is expressed in a layer-specific manner in the retina, which implies a functional role, however, the role of RBFOX3 in the retina is unknown. Rbfox3 homozygous knockout (Rbfox3-/-) mice exhibit deficits in visual learning; therefore, understanding the role of RBFOX3 in the retina is critical for interpreting behavioral results. We found Rbfox3 expression was developmentally regulated in the retina and specifically expressed in ganglion cells, amacrine cells and horizontal cells of the retina. We demonstrate deletion of Rbfox3 resulted in a reduction in the thickness of the inner plexiform layer of the retina, where synapses are formed. Number of ganglion cells and amacrine cells is normal with loss of Rbfox3. Innervation of retinal ganglion cells into their targeted brain regions is normal in Rbfox3-/- mice. Importantly, Rbfox3-/- mice displayed normal non-image and image forming functions. Taken together, our results suggest RBFOX3 is dispensable for visual function.
Collapse
Affiliation(s)
- Yi-Sian Lin
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Kuan-Ting Kuo
- Department of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shih-Kuo Chen
- Department of Life Science, College of Life Science, National Taiwan University, Taipei, Taiwan
- Neurodevelopmental Club in Taiwan, Taipei, Taiwan
| | - Hsien-Sung Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
- Neurodevelopmental Club in Taiwan, Taipei, Taiwan
| |
Collapse
|
40
|
Bobbili DR, Lal D, May P, Reinthaler EM, Jabbari K, Thiele H, Nothnagel M, Jurkowski W, Feucht M, Nürnberg P, Lerche H, Zimprich F, Krause R, Neubauer BA, Reinthaler EM, Zimprich F, Feucht M, Steinböck H, Neophytou B, Geldner J, Gruber-Sedlmayr U, Haberlandt E, Ronen GM, Altmüller J, Lal D, Nürnberg P, Sander T, Thiele H, Krause R, May P, Balling R, Lerche H, Neubauer BA. Exome-wide analysis of mutational burden in patients with typical and atypical Rolandic epilepsy. Eur J Hum Genet 2018; 26:258-264. [PMID: 29358611 DOI: 10.1038/s41431-017-0034-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 09/27/2017] [Accepted: 10/06/2017] [Indexed: 12/30/2022] Open
Abstract
Rolandic epilepsy (RE) is the most common focal epilepsy in childhood. To date no hypothesis-free exome-wide mutational screen has been conducted for RE and atypical RE (ARE). Here we report on whole-exome sequencing of 194 unrelated patients with RE/ARE and 567 ethnically matched population controls. We identified an exome-wide significantly enriched burden for deleterious and loss-of-function variants only for the established RE/ARE gene GRIN2A. The statistical significance of the enrichment disappeared after removing ARE patients. For several disease-related gene-sets, an odds ratio >1 was detected for loss-of-function variants.
Collapse
Affiliation(s)
- Dheeraj R Bobbili
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Dennis Lal
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.,Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Eva M Reinthaler
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Kamel Jabbari
- Cologne Biocenter, Institute for Genetics, University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Wiktor Jurkowski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.,The Genome Analysis Centre, Norwich, UK
| | - Martha Feucht
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Roland Krause
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - Bernd A Neubauer
- Department of Neuropediatrics, Medical Faculty University Giessen, Giessen, Germany.
| | - Eva M Reinthaler
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Martha Feucht
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090, Vienna, Austria
| | - Hannelore Steinböck
- Private Practice for Pediatrics, St. Anna Children's Hospital, 1150, Vienna, Austria
| | | | - Julia Geldner
- Department of Pediatrics, Hospital SMZ Süd Kaiser-Franz-Josef, 1100, Vienna, Austria
| | | | - Edda Haberlandt
- Department of Pediatrics, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Gabriel M Ronen
- Department of Pediatrics, McMaster University, Hamilton, L8N3Z5, ON, Canada
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Dennis Lal
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Thomas Sander
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Roland Krause
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Bernd A Neubauer
- Department of Neuropediatrics, Medical Faculty University Giessen, Giessen, Germany
| | | |
Collapse
|
41
|
Choi S, Kim YE, Kim JW, Cho N, Cheon S, Kim KK. Rbfox family proteins make the homo- and hetero-oligomeric complexes. Biochem Biophys Res Commun 2018; 495:1022-1027. [PMID: 29170129 DOI: 10.1016/j.bbrc.2017.11.128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 11/19/2017] [Indexed: 12/17/2022]
Abstract
Rbfox family of proteins that consists of Rbfox1, Rbfox2, and Rbfox3 in mammals regulates alternative pre-mRNA splicing in various tissues via direct binding to their RNA binding element. Although many studies have indicated the splicing activity of each member of the Rbfox family, the interactions of Rbfox family proteins are largely unknown. Here, we have investigated interactions among Rbfox family proteins. Co-immunoprecipitation (Co-IP) and GST-pull down assays confirmed that Rbfox proteins form homo and hetero complexes. Moreover, in vivo crosslinking using disuccinimidyl suberate treatment indicated that the Rbfox proteins form a dimer which then assembles with other proteins to form a large multiprotein complex. Duolink in situ proximity ligation (PLA) assay revealed that neuron specific Rbfox3 protein interacts with other Rbfox family proteins. This study is the first to provide an evidence that Rbfox family proteins form homo- and hetero-oligomeric complexes in vivo.
Collapse
Affiliation(s)
- Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Yong-Eun Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jae Whan Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Seonghye Cheon
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea.
| |
Collapse
|
42
|
Reble E, Dineen A, Barr CL. The contribution of alternative splicing to genetic risk for psychiatric disorders. GENES BRAIN AND BEHAVIOR 2017; 17:e12430. [PMID: 29052934 DOI: 10.1111/gbb.12430] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 09/25/2017] [Accepted: 10/12/2017] [Indexed: 12/12/2022]
Abstract
A genetic contribution to psychiatric disorders has clearly been established and genome-wide association studies now provide the location of risk genes and genetic variants associated with risk. However, the mechanism by which these genes and variants contribute to psychiatric disorders is mostly undetermined. This is in part because non-synonymous protein coding changes cannot explain the majority of variants associated with complex genetic traits. Based on this, it is predicted that these variants are causing gene expression changes, including changes to alternative splicing. Genetic changes influencing alternative splicing have been identified as risk factors in Mendelian disorders; however, currently there is a paucity of research on the role of alternative splicing in complex traits. This stems partly from the difficulty of predicting the role of genetic variation in splicing. Alterations to canonical splice site sequences, nucleotides adjacent to splice junctions, and exonic and intronic splicing regulatory sequences can influence splice site choice. Recent studies have identified global changes in alternatively spliced transcripts in brain tissues, some of which correlate with altered levels of splicing trans factors. Disease-associated variants have also been found to affect cis-acting splicing regulatory sequences and alter the ratio of alternatively spliced transcripts. These findings are reviewed here, as well as the current datasets and resources available to study alternative splicing in psychiatric disorders. Identifying and understanding risk variants that cause alternative splicing is critical to understanding the mechanisms of risk as well as to pave the way for new therapeutic options.
Collapse
Affiliation(s)
- E Reble
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - A Dineen
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - C L Barr
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
43
|
Deriziotis P, Fisher SE. Speech and Language: Translating the Genome. Trends Genet 2017; 33:642-656. [DOI: 10.1016/j.tig.2017.07.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 01/30/2023]
|
44
|
Ying Y, Wang XJ, Vuong CK, Lin CH, Damianov A, Black DL. Splicing Activation by Rbfox Requires Self-Aggregation through Its Tyrosine-Rich Domain. Cell 2017; 170:312-323.e10. [PMID: 28708999 DOI: 10.1016/j.cell.2017.06.022] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 03/31/2017] [Accepted: 06/14/2017] [Indexed: 10/19/2022]
Abstract
Proteins of the Rbfox family act with a complex of proteins called the Large Assembly of Splicing Regulators (LASR). We find that Rbfox interacts with LASR via its C-terminal domain (CTD), and this domain is essential for its splicing activity. In addition to LASR recruitment, a low-complexity (LC) sequence within the CTD contains repeated tyrosines that mediate higher-order assembly of Rbfox/LASR and are required for splicing activation by Rbfox. This sequence spontaneously aggregates in solution to form fibrous structures and hydrogels, suggesting an assembly similar to the insoluble cellular inclusions formed by FUS and other proteins in neurologic disease. Unlike the pathological aggregates, we find that assembly of the Rbfox CTD plays an essential role in its normal splicing function. Rather than simple recruitment of individual regulators to a target exon, alternative splicing choices also depend on the higher-order assembly of these regulators within the nucleus.
Collapse
Affiliation(s)
- Yi Ying
- Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xiao-Jun Wang
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Celine K Vuong
- Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Andrey Damianov
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
45
|
Pérez-Palma E, Helbig I, Klein KM, Anttila V, Horn H, Reinthaler EM, Gormley P, Ganna A, Byrnes A, Pernhorst K, Toliat MR, Saarentaus E, Howrigan DP, Hoffman P, Miquel JF, De Ferrari GV, Nürnberg P, Lerche H, Zimprich F, Neubauer BA, Becker AJ, Rosenow F, Perucca E, Zara F, Weber YG, Lal D. Heterogeneous contribution of microdeletions in the development of common generalised and focal epilepsies. J Med Genet 2017; 54:598-606. [PMID: 28756411 PMCID: PMC5574393 DOI: 10.1136/jmedgenet-2016-104495] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 06/21/2017] [Accepted: 06/26/2017] [Indexed: 11/27/2022]
Abstract
Background Microdeletions are known to confer risk to epilepsy, particularly at genomic rearrangement ‘hotspot’ loci. However, microdeletion burden not overlapping these regions or within different epilepsy subtypes has not been ascertained. Objective To decipher the role of microdeletions outside hotspots loci and risk assessment by epilepsy subtype. Methods We assessed the burden, frequency and genomic content of rare, large microdeletions found in a previously published cohort of 1366 patients with genetic generalised epilepsy (GGE) in addition to two sets of additional unpublished genome-wide microdeletions found in 281 patients with rolandic epilepsy (RE) and 807 patients with adult focal epilepsy (AFE), totalling 2454 cases. Microdeletions were assessed in a combined and subtype-specific approaches against 6746 controls. Results When hotspots are considered, we detected an enrichment of microdeletions in the combined epilepsy analysis (adjusted p=1.06×10−6,OR 1.89, 95% CI 1.51 to 2.35). Epilepsy subtype-specific analyses showed that hotspot microdeletions in the GGE subgroup contribute most of the overall signal (adjusted p=9.79×10−12, OR 7.45, 95% CI 4.20–13.5). Outside hotspots , microdeletions were enriched in the GGE cohort for neurodevelopmental genes (adjusted p=9.13×10−3,OR 2.85, 95% CI 1.62–4.94). No additional signal was observed for RE and AFE. Still, gene-content analysis identified known (NRXN1, RBFOX1 and PCDH7) and novel (LOC102723362) candidate genes across epilepsy subtypes that were not deleted in controls. Conclusions Our results show a heterogeneous effect of recurrent and non-recurrent microdeletions as part of the genetic architecture of GGE and a minor contribution in the aetiology of RE and AFE.
Collapse
Affiliation(s)
- Eduardo Pérez-Palma
- Faculty of Biological Sciences and Medicine, Center for Biomedical Research, Universidad Andres Bello, Santiago, Chile.,Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Ingo Helbig
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Kiel, Germany.,Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Karl Martin Klein
- Department of Neurology, Epilepsy Center Frankfurt Rhine-Main, Center of Neurology and Neurosurgery, University Hospital, Goethe-University Frankfurt, Frankfurt, Germany.,Department of Neurology, Epilepsy Center Hessen, University Hospitals Giessen & Marburg, and University of Marburg, Marburg, Germany
| | - Verneri Anttila
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Heiko Horn
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Padhraig Gormley
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Andrea Ganna
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Andrea Byrnes
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Mohammad R Toliat
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Elmo Saarentaus
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel P Howrigan
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Per Hoffman
- Division of Medical Genetics Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Juan Francisco Miquel
- Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Giancarlo V De Ferrari
- Faculty of Biological Sciences and Medicine, Center for Biomedical Research, Universidad Andres Bello, Santiago, Chile
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research,University of Tübingen, Tübingen, Germany
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Bern A Neubauer
- Department of Neuropediatrics, University Medical Center Giessen and Marburg, Giessen, Germany
| | - Albert J Becker
- Department of Neuropathology, University of Bonn, Bonn, Germany
| | - Felix Rosenow
- Department of Neurology, Epilepsy Center Frankfurt Rhine-Main, Center of Neurology and Neurosurgery, University Hospital, Goethe-University Frankfurt, Frankfurt, Germany.,Department of Neurology, Epilepsy Center Hessen, University Hospitals Giessen & Marburg, and University of Marburg, Marburg, Germany
| | - Emilio Perucca
- C. Mondino National Neurological Institute, Pavia, Italy.,Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy
| | - Federico Zara
- Laboratory of Neurogenetics, Neuromuscular Disease Unit, Genova, Italy
| | - Yvonne G Weber
- Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Dennis Lal
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany.,Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
46
|
Uemori T, Toda K, Seki T. Seizure severity-dependent selective vulnerability of the granule cell layer and aberrant neurogenesis in the rat hippocampus. Hippocampus 2017; 27:1054-1068. [PMID: 28608989 DOI: 10.1002/hipo.22752] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 06/07/2017] [Accepted: 06/08/2017] [Indexed: 12/20/2022]
Abstract
The pilocarpine-induced status epilepticus rodent model has been commonly used to analyze the mechanisms of human temporal lobe epilepsy. Recent studies using this model have demonstrated that epileptic seizures lead to increased adult neurogenesis of the dentate granule cells, and cause abnormal cellular organization in dentate neuronal circuits. In this study, we examined these structural changes in rats with seizures of varying severity. In rats with frequent severe seizures, we found a clear loss of Prox1 and NeuN expression in the dentate granule cell layer (GCL), which was confined mainly to the suprapyramidal blade of the GCL at the septal and middle regions of the septotemporal axis of the hippocampus. In the damaged suprapyramidal region, the number of immature neurons in the subgranular zone was markedly reduced. In contrast, in rats with less frequent severe seizures, there was almost no loss of Prox1 and NeuN expression, and the number of immature neurons was increased. In rats with no or slight loss of Prox1 expression in the GCL, ectopic immature neurons were detected in the molecular layer of the suprapyramidal blade in addition to the hilus, and formed chainlike aggregated structures along the blood vessels up to the hippocampal fissure, suggesting that newly generated neurons migrate at least partially along blood vessels to the hippocampal fissure. These results suggest that seizures of different severity cause different effects on GCL damage, neurogenesis, and the migration of new neurons, and that these structural changes are selective to subdivisions of the GCL and the septotemporal axis of the hippocampus.
Collapse
Affiliation(s)
- Takeshi Uemori
- Department of Histology and Neuroanatomy, Tokyo Medical University, Tokyo, Japan
| | - Keiko Toda
- Department of Histology and Neuroanatomy, Tokyo Medical University, Tokyo, Japan
| | - Tatsunori Seki
- Department of Histology and Neuroanatomy, Tokyo Medical University, Tokyo, Japan
| |
Collapse
|
47
|
Xiong W, Zhou D. Progress in unraveling the genetic etiology of rolandic epilepsy. Seizure 2017; 47:99-104. [PMID: 28351718 DOI: 10.1016/j.seizure.2017.02.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 02/05/2023] Open
Abstract
Rolandic epilepsy (RE), or benign epilepsy of childhood with centrotemporal spikes (BECT), is the most frequent idiopathic partial epilepsy syndrome of childhood, where the "idiopathic" implies a genetic predisposition. Although RE has long been presumed to have a genetic component, clinical and genetic studies have shown a complex inheritance pattern. Furthermore, the underlying major genetic influence in RE has been challenged by recent reports of twin studies. Meanwhile, many genes or loci have been shown to be associated the RE/atypical RE (ARE) spectrum, with a higher frequency of causative variants in ARE. However, a full understanding of the genetic basis in the more common forms of the RE spectrum remains elusive.
Collapse
Affiliation(s)
- Weixi Xiong
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Dong Zhou
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China.
| |
Collapse
|
48
|
Chen T, Giri M, Xia Z, Subedi YN, Li Y. Genetic and epigenetic mechanisms of epilepsy: a review. Neuropsychiatr Dis Treat 2017; 13:1841-1859. [PMID: 28761347 PMCID: PMC5516882 DOI: 10.2147/ndt.s142032] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Epilepsy is a common episodic neurological disorder or condition characterized by recurrent epileptic seizures, and genetics seems to play a key role in its etiology. Early linkage studies have localized multiple loci that may harbor susceptibility genes to epilepsy, and mutational analyses have detected a number of mutations involved in both ion channel and nonion channel genes in patients with idiopathic epilepsy. Genome-wide studies of epilepsy have found copy number variants at 2q24.2-q24.3, 7q11.22, 15q11.2-q13.3, and 16p13.11-p13.2, some of which disrupt multiple genes, such as NRXN1, AUTS2, NLGN1, CNTNAP2, GRIN2A, PRRT2, NIPA2, and BMP5, implicated for neurodevelopmental disorders, including intellectual disability and autism. Unfortunately, only a few common genetic variants have been associated with epilepsy. Recent exome-sequencing studies have found some genetic mutations, most of which are located in nonion channel genes such as the LGI1, PRRT2, EFHC1, PRICKLE, RBFOX1, and DEPDC5 and in probands with rare forms of familial epilepsy, and some of these genes are involved with the neurodevelopment. Since epigenetics plays a role in neuronal function from embryogenesis and early brain development to tissue-specific gene expression, epigenetic regulation may contribute to the genetic mechanism of neurodevelopment through which a gene and the environment interacting with each other affect the development of epilepsy. This review focused on the analytic tools used to identify epilepsy and then provided a summary of recent linkage and association findings, indicating the existence of novel genes on several chromosomes for further understanding of the biology of epilepsy.
Collapse
Affiliation(s)
- Tian Chen
- Department of Health Management Center, Chongqing Three Gorges Central Hospital, Chongqing, People's Republic of China
| | - Mohan Giri
- National Center for Rheumatic Diseases, Ratopul, Gaushala, Kathmandu, Nepal
| | - Zhenyi Xia
- Department of Thoracic Surgery, Chongqing Three Gorges Central Hospital, Chongqing, People's Republic of China
| | - Yadu Nanda Subedi
- National Center for Rheumatic Diseases, Ratopul, Gaushala, Kathmandu, Nepal
| | - Yan Li
- Department of Health Management Center, Chongqing Three Gorges Central Hospital, Chongqing, People's Republic of China
| |
Collapse
|
49
|
Damianov A, Ying Y, Lin CH, Lee JA, Tran D, Vashisht AA, Bahrami-Samani E, Xing Y, Martin KC, Wohlschlegel JA, Black DL. Rbfox Proteins Regulate Splicing as Part of a Large Multiprotein Complex LASR. Cell 2016; 165:606-19. [PMID: 27104978 DOI: 10.1016/j.cell.2016.03.040] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 12/18/2015] [Accepted: 03/22/2016] [Indexed: 12/11/2022]
Abstract
Rbfox proteins control alternative splicing and posttranscriptional regulation in mammalian brain and are implicated in neurological disease. These proteins recognize the RNA sequence (U)GCAUG, but their structures and diverse roles imply a variety of protein-protein interactions. We find that nuclear Rbfox proteins are bound within a large assembly of splicing regulators (LASR), a multimeric complex containing the proteins hnRNP M, hnRNP H, hnRNP C, Matrin3, NF110/NFAR-2, NF45, and DDX5, all approximately equimolar to Rbfox. We show that splicing repression mediated by hnRNP M is stimulated by Rbfox. Virtually all the intron-bound Rbfox is associated with LASR, and hnRNP M motifs are enriched adjacent to Rbfox crosslinking sites in vivo. These findings demonstrate that Rbfox proteins bind RNA with a defined set of cofactors and affect a broader set of exons than previously recognized. The function of this multimeric LASR complex has implications for deciphering the regulatory codes controlling splicing networks.
Collapse
Affiliation(s)
- Andrey Damianov
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yi Ying
- Molecular Biology Interdepartmental Ph.D. Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ji-Ann Lee
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Diana Tran
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ajay A Vashisht
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Emad Bahrami-Samani
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yi Xing
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kelsey C Martin
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
50
|
Conboy JG. Developmental regulation of RNA processing by Rbfox proteins. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27748060 DOI: 10.1002/wrna.1398] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/17/2016] [Accepted: 08/27/2016] [Indexed: 12/15/2022]
Abstract
The Rbfox genes encode an ancient family of sequence-specific RNA binding proteins (RBPs) that are critical developmental regulators in multiple tissues including skeletal muscle, cardiac muscle, and brain. The hallmark of Rbfox proteins is a single high-affinity RRM domain, highly conserved from insects to humans, that binds preferentially to UGCAUG motifs at diverse regulatory sites in pre-mRNA introns, mRNA 3'UTRs, and pre-miRNAs hairpin structures. Versatile regulatory circuits operate on Rbfox pre-mRNA and mRNA to ensure proper expression of Rbfox1 protein isoforms, which then act on the broader transcriptome to regulate alternative splicing networks, mRNA stability and translation, and microRNA processing. Complex Rbfox expression is encoded in large genes encompassing multiple promoters and alternative splicing options that govern spatiotemporal expression of structurally distinct and tissue-specific protein isoforms with different classes of RNA targets. Nuclear Rbfox1 is a candidate master regulator that binds intronic UGCAUG elements to impact splicing efficiency of target alternative exons, many in transcripts for other splicing regulators. Tissue-specificity of Rbfox-mediated alternative splicing is executed by combinatorial regulation through the integrated activity of Rbfox proteins and synergistic or antagonistic splicing factors. Studies in animal models show that Rbfox1-related genes are critical for diverse developmental processes including germ cell differentiation and memory in Drosophila, neuronal migration and function in mouse brain, myoblast fusion and skeletal muscle function, and normal heart function. Finally, genetic and biochemical evidence suggest that aberrations in Rbfox-regulated circuitry are risk factors for multiple human disorders, especially neurodevelopmental disorders including epilepsy and autism, and cardiac hypertrophy. WIREs RNA 2017, 8:e1398. doi: 10.1002/wrna.1398 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- John G Conboy
- Biological Systems and Engineering Division Lawrence Berkeley National Laboratory Berkeley, CA 94720, USA
| |
Collapse
|