Neurogenetics最新文献

{"title":"Gene-gene interaction network analysis indicates CNTN2 is a candidate gene for idiopathic generalized epilepsy.","authors":"Zhi-Jian Lin, Jun-Wei He, Sheng-Yin Zhu, Li-Hong Xue, Jian-Feng Zheng, Li-Qin Zheng, Bi-Xia Huang, Guo-Zhang Chen, Peng-Xing Lin","doi":"10.1007/s10048-024-00748-w","DOIUrl":"10.1007/s10048-024-00748-w","url":null,"abstract":"<p><p>Twin and family studies have established the genetic contribution to idiopathic generalized epilepsy (IGE). The genetic architecture of IGE is generally complex and heterogeneous, and the majority of the genetic burden in IGE remains unsolved. We hypothesize that gene-gene interactions contribute to the complex inheritance of IGE. CNTN2 (OMIM* 615,400) variants have been identified in cases with familial adult myoclonic epilepsy and other epilepsies. To explore the gene-gene interaction network in IGE, we took the CNTN2 gene as an example and investigated its co-occurrent genetic variants in IGE cases. We performed whole-exome sequencing in 114 unrelated IGE cases and 296 healthy controls. Variants were qualified with sequencing quality, minor allele frequency, in silico prediction, genetic phenotype, and recurrent case numbers. The STRING_TOP25 gene interaction network analysis was introduced with the bait gene CNTN2 (denoted as A). The gene-gene interaction pair mode was presumed to be A + c, A + d, A + e, with a leading gene A, or A + B + f, A + B + g, A + B + h, with a double-gene A + B, or other combinations. We compared the number of gene interaction pairs between the case and control groups. We identified three pairs in the case group, CNTN2 + PTPN18, CNTN2 + CNTN1 + ANK2 + ANK3 + SNTG2, and CNTN2 + PTPRZ1, while we did not discover any pairs in the control group. The number of gene interaction pairs in the case group was much more than in the control group (p = 0.021). Taking together the genetic bioinformatics, reported epilepsy cases, and statistical evidence in the study, we supposed CNTN2 as a candidate pathogenic gene for IGE. The gene interaction network analysis might help screen candidate genes for IGE or other complex genetic disorders.</p>","PeriodicalId":56106,"journal":{"name":"Neurogenetics","volume":" ","pages":"131-139"},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140068940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DYT-THAP1: exploring gene expression in fibroblasts for potential biomarker discovery","authors":"Sokhna Haissatou Diaw, Sylvie Delcambre, Christoph Much, Fabian Ott, Vladimir S. Kostic, Agata Gajos, Alexander Münchau, Simone Zittel, Hauke Busch, Anne Grünewald, Christine Klein, Katja Lohmann","doi":"10.1007/s10048-024-00752-0","DOIUrl":"https://doi.org/10.1007/s10048-024-00752-0","url":null,"abstract":"<p>Dystonia due to pathogenic variants in the <i>THAP1</i> gene (DYT-THAP1) shows variable expressivity and reduced penetrance of ~ 50%. Since <i>THAP1</i> encodes a transcription factor, modifiers influencing this variability likely operate at the gene expression level. This study aimed to assess the transferability of differentially expressed genes (DEGs) in neuronal cells related to pathogenic variants in the <i>THAP1</i> gene, which were previously identified by transcriptome analyses. For this, we performed quantitative (qPCR) and Digital PCR (dPCR) in cultured fibroblasts. RNA was extracted from THAP1 manifesting (MMCs) and non-manifesting mutation carriers (NMCs) as well as from healthy controls. The expression profiles of ten of 14 known neuronal DEGs demonstrated differences in fibroblasts between these three groups. This included transcription factors and targets (<i>ATF4</i>, <i>CLN3</i>, <i>EIF2A, RRM1, YY1</i>), genes involved in G protein-coupled receptor signaling (<i>BDKRB2, LPAR1</i>), and a gene linked to apoptosis and DNA replication/repair (<i>CRADD</i>), which all showed higher expression levels in MMCs and NMCs than in controls. Moreover, the analysis of genes linked to neurological disorders (<i>STXBP1</i>, <i>TOR1A</i>) unveiled differences in expression patterns between MMCs and controls. Notably, the genes <i>CUEDC2</i>, <i>DRD4</i>, <i>ECH1</i>, and <i>SIX2</i> were not statistically significantly differentially expressed in fibroblast cultures. With &gt; 70% of the tested genes being DEGs also in fibroblasts, fibroblasts seem to be a suitable model for DYT-THAP1 research despite some restrictions. Furthermore, at least some of these DEGs may potentially also serve as biomarkers of DYT-THAP1 and influence its penetrance and expressivity.</p>","PeriodicalId":56106,"journal":{"name":"Neurogenetics","volume":"2 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140154198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Early onset epileptic and developmental encephalopathy and MOGS variants: a new diagnosis in the whole exome sequencing (WES) ERA","authors":"","doi":"10.1007/s10048-024-00754-y","DOIUrl":"https://doi.org/10.1007/s10048-024-00754-y","url":null,"abstract":"<h3>Abstract</h3> <p>Mannosyl-oligosaccharide<?tk 4?> glucosidase – congenital disorder of glycosylation (MOGS-CDG) is determined by biallelic mutations in the mannosyl-oligosaccharide glucosidase (glucosidase I) gene. MOGS-CDG is a rare disorder affecting the processing of N-Glycans (CDG type II) and is characterized by prominent neurological involvement including hypotonia, developmental delay, seizures and movement disorders. To the best of our knowledge, 30 patients with MOGS-CDG have been published so far. We described a child who is compound heterozygous for two novel variants in the <em>MOGS</em> gene. He presented Early Infantile Developmental and Epileptic Encephalopathy (EI-DEE) in the absence of other specific systemic involvement and unrevealing first-line biochemical findings. In addition to the previously described features, the patient presented a Hirschprung disease, never reported before in individuals with MOGS-CDG.<?tk 0?></p>","PeriodicalId":56106,"journal":{"name":"Neurogenetics","volume":"144 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140154054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic evidence for the suitability of Göttingen Minipigs with a rare seizure phenotype as a model for human epilepsy","authors":"Pardis Najafi, Christian Reimer, Jonathan D. Gilthorpe, Kirsten R. Jacobsen, Maja Ramløse, Nora-Fabienne Paul, Henner Simianer, Jens Tetens, Clemens Falker-Gieske","doi":"10.1007/s10048-024-00750-2","DOIUrl":"https://doi.org/10.1007/s10048-024-00750-2","url":null,"abstract":"<p>Epilepsy is a complex genetic disorder that affects about 2% of the global population. Although the frequency and severity of epileptic seizures can be reduced by a range of pharmacological interventions, there are no disease-modifying treatments for epilepsy. The development of new and more effective drugs is hindered by a lack of suitable animal models. Available rodent models may not recapitulate all key aspects of the disease. Spontaneous epileptic convulsions were observed in few Göttingen Minipigs (GMPs), which may provide a valuable alternative animal model for the characterisation of epilepsy-type diseases and for testing new treatments. We have characterised affected GMPs at the genome level and have taken advantage of primary fibroblast cultures to validate the functional impact of fixed genetic variants on the transcriptome level. We found numerous genes connected to calcium metabolism that have not been associated with epilepsy before, such as <i>ADORA2B</i>, <i>CAMK1D</i>, <i>ITPKB</i>, <i>MCOLN2</i>, <i>MYLK</i>, <i>NFATC3</i>, <i>PDGFD</i>, and <i>PHKB</i>. Our results have identified two transcription factor genes, <i>EGR3</i> and <i>HOXB6</i>, as potential key regulators of <i>CACNA1H</i>, which was previously linked to epilepsy-type disorders in humans. Our findings provide the first set of conclusive results to support the use of affected subsets of GMPs as an alternative and more reliable model system to study human epilepsy. Further neurological and pharmacological validation of the suitability of GMPs as an epilepsy model is therefore warranted.</p>","PeriodicalId":56106,"journal":{"name":"Neurogenetics","volume":"42 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139926618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation of RFC1 tandem nucleotide repeat locus in diverse neurodegenerative outcomes in an Indian cohort.","authors":"Nishu Tyagi, Bharathram Uppili, Pooja Sharma, Shaista Parveen, Sheeba Saifi, Abhinav Jain, Akhilesh Sonakar, Istaq Ahmed, Shweta Sahni, Uzma Shamim, Avni Anand, Varun Suroliya, Vivekanand Asokachandran, Achal Srivastava, Sridhar Sivasubbu, Vinod Scaria, Mohammed Faruq","doi":"10.1007/s10048-023-00736-6","DOIUrl":"10.1007/s10048-023-00736-6","url":null,"abstract":"<p><p>An intronic bi-allelic pentanucleotide repeat expansion mutation, (AAGGG)_400-2000, at AAAAG repeat locus in RFC1 gene, is known as underlying genetic cause in cases with cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS) and late-onset sporadic ataxia. Biallelic positive cases carry a common recessive risk haplotype, \"AAGA,\" spanning RFC1 gene. In this study, our aim is to find prevalence of bi-allelic (AAGGG)_exp in Indian ataxia and other neurological disorders and investigate the complexity of RFC1 repeat locus and its potential association with neurodegenerative diseases in Indian population-based cohorts. We carried out repeat number and repeat type estimation using flanking PCR and repeat primed PCR (AAAAG/AAAGG/AAGGG) in four Indian disease cohorts and healthy controls. Haplotype assessment of suspected cases was done by genotyping and confirmed by Sanger sequencing. Blood samples and consent of all the cases and detailed clinical details of positive cases were collected in collaboration with A.I.I.M.S. Furthermore, comprehension of RFC1 repeat locus and risk haplotype analysis in Indian background was performed on the NGS data of Indian healthy controls by ExpansionHunter, ExpansionHunter Denovo, and PHASE analysis, respectively. Genetic screening of RFC1-TNR locus in 1998 uncharacterized cases (SCA12: 87; uncharacterized ataxia: 1818, CMT: 93) and 564 heterogenous controls showed that the frequency of subjects with bi-allelic (AAGGG)_exp are 1.15%, < 0.05%, 2.15%, and 0% respectively. Two RFC1 positive sporadic late-onset ataxia cases, one bi-allelic (AAGGG)_exp and another, (AAAGG)_~700/(AAGGG)_exp, had recessive risk haplotype and CANVAS symptoms. Long normal alleles, 15-27, are significantly rare in ataxia cohort. In IndiGen control population (IndiGen; N = 1029), long normal repeat range, 15-27, is significantly associated with A₃G₃ and some rare repeat motifs, AGAGG, AACGG, AAGAG, and AAGGC. Risk-associated \"AAGA\" haplotype of the original pathogenic expansion of A₂G₃ was found associated with the A₃G₃ representing alleles in background population. Apart from bi-allelic (AAGGG)_exp, we report cases with a new pathogenic expansion of (AAAGG)_exp/(AAGGG)_exp in RFC1 and recessive risk haplotype. We found different repeat motifs at RFC1 TNR locus, like AAAAG, AAAGG, AAAGGG, AAAAGG, AAGAG, AACGG, AAGGC, AGAGG, and AAGGG, in Indian background population except ACAGG and (AAAGG)_n/(AAGGG)_n. Our findings will help in further understanding the role of long normal repeat size and different repeat motifs, specifically AAAGG, AAAGGG, and other rare repeat motifs, at the RFC1 locus.</p>","PeriodicalId":56106,"journal":{"name":"Neurogenetics","volume":" ","pages":"13-25"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71429522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dem-Aging: autophagy-related pathologies and the \"two faces of dementia\".","authors":"N Gammaldi, S Doccini, S Bernardi, M Marchese, M Cecchini, R Ceravolo, S Rapposelli, G M Ratto, S Rocchiccioli, F Pezzini, F M Santorelli","doi":"10.1007/s10048-023-00739-3","DOIUrl":"10.1007/s10048-023-00739-3","url":null,"abstract":"<p><p>Neuronal ceroid lipofuscinosis (NCL) is an umbrella term referring to the most frequent childhood-onset neurodegenerative diseases, which are also the main cause of childhood dementia. Although the molecular mechanisms underlying the NCLs remain elusive, evidence is increasingly pointing to shared disease pathways and common clinical features across the disease forms. The characterization of pathological mechanisms, disease modifiers, and biomarkers might facilitate the development of treatment strategies.The DEM-AGING project aims to define molecular signatures in NCL and expedite biomarker discovery with a view to identifying novel targets for monitoring disease status and progression and accelerating clinical trial readiness in this field. In this study, we fused multiomic assessments in established NCL models with similar data on the more common late-onset neurodegenerative conditions in order to test the hypothesis of shared molecular fingerprints critical to the underlying pathological mechanisms. Our aim, ultimately, is to combine data analysis, cell models, and omic strategies in an effort to trace new routes to therapies that might readily be applied in the most common forms of dementia.</p>","PeriodicalId":56106,"journal":{"name":"Neurogenetics","volume":" ","pages":"39-46"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138812648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lethal variant in the C2A domain may cause severe SYT1-associated neurodevelopmental disorder in the newborns.","authors":"Wendi Huang, Ying Yang, Fengyu Che, Haibin Wu, Ying Ma, Yujuan Zhao","doi":"10.1007/s10048-023-00738-4","DOIUrl":"10.1007/s10048-023-00738-4","url":null,"abstract":"<p><p>Synaptotagmin-1 (SYT1) plays a pivotal role in regulating presynaptic processes, including neurotransmitter release. SYT1 variants perturb synaptic vesicle endocytosis and exocytosis, resulting in a series of neurodevelopmental disorders defined as Baker-Gordon syndrome. Herein, we report the case of a newborn with dysmorphic facial appearance, severe hypotonia, poor feeding, gastroesophageal reflux, and an inability to eat and breathe, diagnosed with Baker-Gordon syndrome. A retrospective search was performed on a newborn with Baker-Gordon syndrome. Medical charts were reviewed, with focus on the clinical presentation, diagnostic process, and treatment outcomes. Whole-genome high-throughput DNA sequencing was performed to identify genetic variants. Whole-exome sequencing identified the likely pathogenic variant as SYT1 C.551 T > C(p.V184A). Sanger sequencing results indicated that this variant was a de novo mutation in a conservative site located in the C2A domain of the protein. The patient died at 57 days old because of severe feeding and breathing problems. Our findings of a novel lethal variant in the C2A domain of SYT1 in the youngest patient diagnosed infantile Baker-Gordon syndrome who presented with the most severe hypotonia reported to date expands the spectrum of SYT1- associated neurodevelopmental disorders.</p>","PeriodicalId":56106,"journal":{"name":"Neurogenetics","volume":" ","pages":"27-31"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71489384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Two novel cases of biallelic SMPD4 variants with brain structural abnormalities.","authors":"Shintaro Aoki, Kazuki Watanabe, Mitsuhiro Kato, Yukihiko Konishi, Kazuo Kubota, Emiko Kobayashi, Mitsuko Nakashima, Hirotomo Saitsu","doi":"10.1007/s10048-023-00737-5","DOIUrl":"10.1007/s10048-023-00737-5","url":null,"abstract":"<p><p>Sphingomyelin phosphodiesterase 4 (SMPD4) encodes a member of the Mg²⁺-dependent, neutral sphingomyelinase family that catalyzes the hydrolysis of the phosphodiester bond of sphingomyelin to form phosphorylcholine and ceramide. Recent studies have revealed that biallelic loss-of-function variants of SMPD4 cause syndromic neurodevelopmental disorders characterized by microcephaly, congenital arthrogryposis, and structural brain anomalies. In this study, three novel loss-of-function SMPD4 variants were identified using exome sequencing (ES) in two independent patients with developmental delays, microcephaly, seizures, and brain structural abnormalities. Patient 1 had a homozygous c.740_741del, p.(Val247Glufs*21) variant and showed profound intellectual disability, hepatomegaly, a simplified gyral pattern, and a thin corpus callosum without congenital dysmorphic features. Patient 2 had a compound heterozygous nonsense c.2124_2125del, p.(Phe709*) variant and splice site c.1188+2dup variant. RNA analysis revealed that the c.1188+2dup variant caused exon 13 skipping, leading to a frameshift (p.Ala406Ser*6). In vitro transcription analysis using minigene system suggested that mRNA transcribed from mutant allele may be degraded by nonsense-mediated mRNA decay system. He exhibited diverse manifestations, including growth defects, muscle hypotonia, respiratory distress, arthrogryposis, insulin-dependent diabetes mellitus, sensorineural hearing loss, facial dysmorphism, and various brain abnormalities, including cerebral atrophy, hypomyelination, and cerebellar hypoplasia. Here, we review previous literatures and discuss the phenotypic diversity of SMPD4-related disorders.</p>","PeriodicalId":56106,"journal":{"name":"Neurogenetics","volume":" ","pages":"3-11"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50163891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Retraction Note: Clinical characterization of familial 1p36.3 microduplication.","authors":"Junping Jiao, Yuping Wang, Yue Hou, Chao Gao, Huimin Shi, Shujuan Tian","doi":"10.1007/s10048-023-00735-7","DOIUrl":"10.1007/s10048-023-00735-7","url":null,"abstract":"","PeriodicalId":56106,"journal":{"name":"Neurogenetics","volume":" ","pages":"49"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10891255/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41164279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New Editors-in-Chief and future directions: a glimpse into the evolving future of Neurogenetics.","authors":"Geraldine Zimmer-Bensch","doi":"10.1007/s10048-023-00740-w","DOIUrl":"10.1007/s10048-023-00740-w","url":null,"abstract":"","PeriodicalId":56106,"journal":{"name":"Neurogenetics","volume":" ","pages":"1-2"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10891218/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139076042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}