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Scala M, Tomati V, Ferla M, Lena M, Cohen JS, Fatemi A, Brokamp E, Bican A, Phillips JA, Koziura ME, Nicouleau M, Rio M, Siquier K, Boddaert N, Musante I, Tamburro S, Baldassari S, Iacomino M, Scudieri P, Rosenfeld JA, Bellus G, Reed S, Al Saif H, Russo RS, Walsh MB, Cantagrel V, Crunk A, Gustincich S, Ruggiero SM, Fitzgerald MP, Helbig I, Striano P, Severino M, Salpietro V, Pedemonte N, Zara F. De novo variants in DENND5B cause a neurodevelopmental disorder. Am J Hum Genet 2024; 111:529-543. [PMID: 38387458 PMCID: PMC10940048 DOI: 10.1016/j.ajhg.2024.02.001] [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: 08/31/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024] Open
Abstract
The Rab family of guanosine triphosphatases (GTPases) includes key regulators of intracellular transport and membrane trafficking targeting specific steps in exocytic, endocytic, and recycling pathways. DENND5B (Rab6-interacting Protein 1B-like protein, R6IP1B) is the longest isoform of DENND5, an evolutionarily conserved DENN domain-containing guanine nucleotide exchange factor (GEF) that is highly expressed in the brain. Through exome sequencing and international matchmaking platforms, we identified five de novo variants in DENND5B in a cohort of five unrelated individuals with neurodevelopmental phenotypes featuring cognitive impairment, dysmorphism, abnormal behavior, variable epilepsy, white matter abnormalities, and cortical gyration defects. We used biochemical assays and confocal microscopy to assess the impact of DENND5B variants on protein accumulation and distribution. Then, exploiting fluorescent lipid cargoes coupled to high-content imaging and analysis in living cells, we investigated whether DENND5B variants affected the dynamics of vesicle-mediated intracellular transport of specific cargoes. We further generated an in silico model to investigate the consequences of DENND5B variants on the DENND5B-RAB39A interaction. Biochemical analysis showed decreased protein levels of DENND5B mutants in various cell types. Functional investigation of DENND5B variants revealed defective intracellular vesicle trafficking, with significant impairment of lipid uptake and distribution. Although none of the variants affected the DENND5B-RAB39A interface, all were predicted to disrupt protein folding. Overall, our findings indicate that DENND5B variants perturb intracellular membrane trafficking pathways and cause a complex neurodevelopmental syndrome with variable epilepsy and white matter involvement.
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Affiliation(s)
- Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy; UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
| | - Valeria Tomati
- UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
| | - Matteo Ferla
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
| | - Mariateresa Lena
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Julie S Cohen
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ali Fatemi
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elly Brokamp
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anna Bican
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John A Phillips
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mary E Koziura
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michael Nicouleau
- Université Paris Cité, Imagine Institute, Developmental Brain Disorders Laboratory, INSERM UMR 1163, 75015 Paris, France
| | - Marlene Rio
- Université Paris Cité, Imagine Institute, Developmental Brain Disorders Laboratory, INSERM UMR 1163, 75015 Paris, France; Service de Génétique, Necker Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Pairs, Paris, France
| | - Karine Siquier
- Université Paris Cité, Imagine Institute, Developmental Brain Disorders Laboratory, INSERM UMR 1163, 75015 Paris, France
| | - Nathalie Boddaert
- Département de Radiologie Pédiatrique, INSERM UMR 1163 and INSERM U1000, AP-HP, Hôpital Necker-Enfants Malades, Paris, France
| | - Ilaria Musante
- UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
| | | | | | | | - Paolo Scudieri
- UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics Laboratories, Houston, TX, USA
| | - Gary Bellus
- Clinical Genetics, Geisinger Medical Center, Danville, PA 17822, USA
| | - Sara Reed
- Clinical Genetics, Geisinger Medical Center, Danville, PA 17822, USA
| | - Hind Al Saif
- Department of Human and Molecular Genetics, Division of Clinical Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | | | - Matthew B Walsh
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Vincent Cantagrel
- Université Paris Cité, Imagine Institute, Developmental Brain Disorders Laboratory, INSERM UMR 1163, 75015 Paris, France
| | | | - Stefano Gustincich
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Sarah M Ruggiero
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mark P Fitzgerald
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | | | - Vincenzo Salpietro
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | | | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
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2
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Bashiri FA, AlSheikh R, Hamad MH, Alsheikh H, Alsheikh RA, Kentab A, AlTheeb N, Alghamdi M. Genotype-Phenotype Analysis of Children with Epilepsy Referred for Whole-Exome Sequencing at a Tertiary Care University Hospital. CHILDREN (BASEL, SWITZERLAND) 2023; 10:1334. [PMID: 37628333 PMCID: PMC10453392 DOI: 10.3390/children10081334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023]
Abstract
BACKGROUND Despite the high consanguinity rates, data on genetic epilepsy in Saudi Arabia is limited. The objective of the current study was to characterize genetic mutations associated with epilepsy in pediatric patients and describe their phenotypic presentations. METHODS A retrospective chart review was conducted among children presented with epilepsy in one center in Saudi Arabia between 2015 and 2018. Only those who had undergone genetic testing were included. RESULTS A total of 45 patients had positive whole-exome sequencing (WES) genetic testing with 37 mutations. Six mutations (SCN1A, DENND5A, KCNQ2, ACY1, SCN2A, and PCDH19) were repeated in 15 patients, with largely heterogeneous phenotypic presentations in patients with the same mutation. Several mutations are reported for the first time in Saudi Arabia. The median age at epilepsy onset was four months. Consanguineous parents and family history of epilepsy were frequent (31.8% and 33.3%, respectively). Developmental delay (44.4%), cognitive delay (42.2%), language delay (40.0%), behavioral features (28.9%), and microcephaly (20.0%) were frequent presentations. At initial diagnosis, 68.9% of EEG and 48.9% of brain MRI were abnormal. The most currently used antiseizure medications (ASMs) were levetiracetam (48.9%), topiramate (28.9%), and valproic acid (20.0%). Approximately 60% of the patients were controlled with (47.6%) or without (11.9%) ASMs, and three (7.1%) patients died. CONCLUSIONS Multiple mutations among children with epilepsy are reported in one hospital in Saudi Arabia, with the majority reported for the first time. The current findings highlight the importance of doing genetic testing for the evaluation of childhood epilepsy.
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Affiliation(s)
- Fahad A. Bashiri
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia; (A.K.); (M.A.)
- Division of Pediatric Neurology, Department of Pediatrics, King Saud University Medical City, Riyadh 11461, Saudi Arabia; (M.H.H.); (H.A.)
| | - Rawan AlSheikh
- Division of Pediatric Neurology, Department of Pediatrics, King Saud Medical City, Riyadh 11461, Saudi Arabia; (R.A.); (R.A.A.)
| | - Muddathir H. Hamad
- Division of Pediatric Neurology, Department of Pediatrics, King Saud University Medical City, Riyadh 11461, Saudi Arabia; (M.H.H.); (H.A.)
| | - Hamad Alsheikh
- Division of Pediatric Neurology, Department of Pediatrics, King Saud University Medical City, Riyadh 11461, Saudi Arabia; (M.H.H.); (H.A.)
| | - Rana Abdullah Alsheikh
- Division of Pediatric Neurology, Department of Pediatrics, King Saud Medical City, Riyadh 11461, Saudi Arabia; (R.A.); (R.A.A.)
| | - Amal Kentab
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia; (A.K.); (M.A.)
- Division of Pediatric Neurology, Department of Pediatrics, King Saud University Medical City, Riyadh 11461, Saudi Arabia; (M.H.H.); (H.A.)
| | - Najd AlTheeb
- College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
| | - Malak Alghamdi
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia; (A.K.); (M.A.)
- Division of Medical Genetics, Department of Pediatrics, King Saud University Medical City, Riyadh 11461, Saudi Arabia
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3
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Al Anazi AH, Ammar AS, Al-Hajj M, Cyrus C, Aljaafari D, Khoda I, Abdelfatah AK, Alsulaiman AA, Alanazi F, Alanazi R, Gandla D, Lad H, Barayan S, Keating BJ, Al-Ali AK. Whole-exome sequencing of a Saudi epilepsy cohort reveals association signals in known and potentially novel loci. Hum Genomics 2022; 16:71. [PMID: 36539902 PMCID: PMC9764464 DOI: 10.1186/s40246-022-00444-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Epilepsy, a serious chronic neurological condition effecting up to 100 million people globally, has clear genetic underpinnings including common and rare variants. In Saudi Arabia, the prevalence of epilepsy is high and caused mainly by perinatal and genetic factors. No whole-exome sequencing (WES) studies have been performed to date in Saudi Arabian epilepsy cohorts. This offers a unique opportunity for the discovery of rare genetic variants impacting this disease as there is a high rate of consanguinity among large tribal pedigrees. RESULTS We performed WES on 144 individuals diagnosed with epilepsy, to interrogate known epilepsy-related genes for known and functional novel variants. We also used an American College of Medical Genetics (ACMG) guideline-based variant prioritization approach in an attempt to discover putative causative variants. We identified 32 potentially causative pathogenic variants across 30 different genes in 44/144 (30%) of these Saudi epilepsy individuals. We also identified 232 variants of unknown significance (VUS) across 101 different genes in 133/144 (92%) subjects. Strong enrichment of variants of likely pathogenicity was observed in previously described epilepsy-associated loci, and a number of putative pathogenic variants in novel loci are also observed. CONCLUSION Several putative pathogenic variants in known epilepsy-related loci were identified for the first time in our population, in addition to several potential new loci which may be prioritized for further investigation.
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Affiliation(s)
- Abdulrahman H. Al Anazi
- grid.411975.f0000 0004 0607 035XDepartment of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Ahmed S. Ammar
- grid.411975.f0000 0004 0607 035XDepartment of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Mahmoud Al-Hajj
- grid.415296.d0000 0004 0607 1539Department of Neurosurgery, King Fahd Hospital, Alhafof, Saudi Arabia
| | - Cyril Cyrus
- grid.411975.f0000 0004 0607 035XDepartment of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, P. O. Box 1982, 31441 Dammam, Saudi Arabia
| | - Danah Aljaafari
- grid.411975.f0000 0004 0607 035XDepartment of Neurology, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Iname Khoda
- grid.411975.f0000 0004 0607 035XDepartment of Neurology, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Ahmed K. Abdelfatah
- grid.411975.f0000 0004 0607 035XDepartment of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Abdullah A. Alsulaiman
- grid.411975.f0000 0004 0607 035XDepartment of Neurology, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Firas Alanazi
- grid.411975.f0000 0004 0607 035XDepartment of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Rawan Alanazi
- grid.411975.f0000 0004 0607 035XDepartment of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Divya Gandla
- grid.25879.310000 0004 1936 8972Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA USA
| | - Hetal Lad
- grid.25879.310000 0004 1936 8972Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA USA
| | - Samar Barayan
- grid.411975.f0000 0004 0607 035XDepartment of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Brendan J. Keating
- grid.25879.310000 0004 1936 8972Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA USA
| | - Amein K. Al-Ali
- grid.411975.f0000 0004 0607 035XDepartment of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, P. O. Box 1982, 31441 Dammam, Saudi Arabia
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4
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Zhang N, Shentu Y, Zhu M, Wang H, Yin X, Du C, Xue F, Fan J, Gong Y, Fan X. Role of Ero1α in cognitive impairment induced by chronic hypoxia. Brain Res 2022; 1797:148117. [PMID: 36220374 DOI: 10.1016/j.brainres.2022.148117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/17/2022] [Accepted: 10/05/2022] [Indexed: 11/02/2022]
Abstract
Recent reports suggested the endoplasmic reticulum stress (ERS)-associated pathway is involved with cognitive impairment in hypoxia condition. ERO1-like protein alpha (Ero1α), an endoplasmic reticulum membrane-bound N-glycoprotein, has been reported to promote oxidative protein folding. However, no studies have reported whether the Ero1α is trapped in hypoxia-induced neuronal loss through the ERS-associated pathways. In our study, this effect of Ero1α was investigated using C57BL/6J mice, the HT22 cells and primary rat neurons. C57BL/6J mice were modeled in a hypoxic chamber for 4 weeks. Behavioral tests were then carried out to test cognitive functions, including the Morris water maze and fear conditioning test. Proteomics showed that Ero1α distinctly upregulated compared with normoxia group and verified using western blotting. Flow cytometry and immunofluorescence were used to analyze the neuroprotective effect of inhibitor EN460 of Ero1α in the HT22 cells. In C57BL/6J mice, hypoxia significantly caused cognitive decline. Brain slice staining results were also used to confirm this effect. Western blot analysis demonstrated that Ero1α, ERS-associated proteins and apoptosis-associated proteins significantly increased in the hypoxia treated groups, further proliferation-related marker protein decreased. EN460, a selective endoplasmic reticulum oxidation 1 (ERO1) inhibitor, counteracted neuronal apoptosis and ameliorated neuronal cell proliferation in the HT22 cells. Taken together, our data indicate that hypoxia induces cognitive impairment, at least in part, by upregulating Ero1α which contributes to neuronal apoptosis through ERS signaling pathway, providing preliminary experimental evidence that the Ero1α is a promising therapeutic target in hypoxia-induced cognitive deficits.
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Affiliation(s)
- Nan Zhang
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yangping Shentu
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Min Zhu
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Hui Wang
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xianghong Yin
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Congkuo Du
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Feng Xue
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Junming Fan
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yongsheng Gong
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Xiaofang Fan
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.
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Zheng J, Luo S, Long Y. Bioinformatic analysis and clinical diagnostic value of hsa_circ_0004099 in acute ischemic stroke. PLoS One 2022; 17:e0277832. [PMID: 36399471 PMCID: PMC9674149 DOI: 10.1371/journal.pone.0277832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022] Open
Abstract
This study investigates the expression and effect of hsa_circ_0004099 in acute ischemic stroke (AIS). We conducted a case-controlled study that included 40 patients with AIS within 24 hours and 40 healthy subjects during the same period as a control group. Differentially expressed circular RNAs (circRNAs) were obtained using GEO2R, and the expression of hsa_circ_0004099 was verified using RT-PCR. Correlation analysis of the National Institutes of Health Stroke Scale (NIHSS) disease severity score and ischemic time with hsa_circ_0004099 expression levels was also performed. The receiver operating characteristic (ROC) curve of hsa_circ_0004099 was constructed, and bioinformatic analysis of hsa_circ_0004099 was performed. NIHSS scores negatively correlated with hsa_circ_0004099 levels (P<0.001, r = -0.7053), whereas infarct time was negatively correlated with hsa_circ_0004099 levels (P<0.001, r = -0.5130); hsa_circ_0004099 could benefit clinical diagnosis (area under the curve [AUC]: 0.923 [95% confidence interval [CI]: 0.8680-0.9904]). Kyoto encyclopedia of genes and genomes (KEGG) analysis showed that hsa_circ_0004099 was enriched in several cancer pathways, which were collectively enriched in four genes namely TCF7L2, NRAS, CTNNB1, and KRAS. Eight core proteins were screened using a protein-protein interaction (PPI) network namely SMAD4, HIF1A, CTNNB1, CDKN1B, CDK6, FOXO3, KRAS, and NRAS. hsa_circ_0004099 is a potential clinical diagnostic marker. In addition, the possible role of hsa_circ_0004099 in the pathogenesis of AIS was analyzed using bioinformatics, which provided a new potential molecular target for AIS treatment.
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Affiliation(s)
- Jiqing Zheng
- Deparment of Rehabilitation, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Shuiming Luo
- Deparment of Rehabilitation, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yaobin Long
- Deparment of Rehabilitation, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
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6
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Lasorsa VA, Montella A, Cantalupo S, Tirelli M, de Torres C, Aveic S, Tonini GP, Iolascon A, Capasso M. Somatic mutations enriched in cis-regulatory elements affect genes involved in embryonic development and immune system response in neuroblastoma. Cancer Res 2022; 82:1193-1207. [PMID: 35101866 DOI: 10.1158/0008-5472.can-20-3788] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/04/2021] [Accepted: 01/27/2022] [Indexed: 11/16/2022]
Abstract
Noncoding cis-regulatory variants have gained interest as cancer drivers, yet progress in understanding their significance is hindered by the numerous challenges and limitations of variant prioritization. To overcome these limitations, we focused on active cis-regulatory elements (aCRE) in order to design a customized panel for the deep sequencing of 56 neuroblastoma tumor and normal DNA sample pairs. In order to search for driver mutations, aCREs were defined by reanalysis of H3K27ac ChiP-seq peaks in 25 neuroblastoma cell lines. These regulatory genomic regions were tested for an excess of somatic mutations and assessed for statistical significance using a global approach that accounted for chromatin accessibility and replication timing. Additional validation was provided by whole genome sequence analysis of 151 neuroblastomas. Analysis of Hi-C data determined the presence of candidate target genes interacting with mutated regions. An excess of somatic mutations in aCREs of diverse genes were identified, including IPO7, HAND2, and ARID3A. CRISPR-Cas9 editing was utilized to assess the functional consequences of mutations in the IPO7 aCRE. Patients with noncoding mutations in aCREs showed inferior overall and event-free survival independent of age at diagnosis, stage, risk stratification, and MYCN status. Expression of aCRE-interacting genes correlated strongly with negative prognostic markers and low survival rates. Moreover, a convergence between the biological functions of aCRE target genes and transcription factors with mutated binding motifs was associated with embryonic development and immune system response. Overall, this strategy enabled the identification of somatic mutations in regulatory elements that collectively promote neuroblastoma tumorigenesis.
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Affiliation(s)
- Vito Alessandro Lasorsa
- Department of Molecular Medicine and Medical Biotechnology, Università degli Studi di Napoli Federico II
| | - Annalaura Montella
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II di Napoli, CEINGE Biotecnologie Avanzate
| | | | | | - Carmen de Torres
- Developmental Tumor Biology Laboratory and Department of Oncology, Hospital Sant Joan de Déu Barcelona
| | - Sanja Aveic
- Neuroblastoma Laboratory, Fondazione Istituto di Ricerca Pediatrica Citta della Speranza
| | | | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II
| | - Mario Capasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II
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7
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Yang M, Johnsson P, Bräutigam L, Yang XR, Thrane K, Gao J, Tobin NP, Zhou Y, Yu R, Nagy N, Engström PG, Tuominen R, Eriksson H, Lundeberg J, Tucker MA, Goldstein AM, Egyhazi-Brage S, Zhao J, Cao Y, Höiom V. Novel loss-of-function variant in DENND5A impedes melanosomal cargo transport and predisposes to familial cutaneous melanoma. Genet Med 2022; 24:157-169. [PMID: 34906508 PMCID: PMC10617683 DOI: 10.1016/j.gim.2021.09.003] [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: 05/05/2021] [Revised: 08/05/2021] [Accepted: 09/10/2021] [Indexed: 11/18/2022] Open
Abstract
PURPOSE More than half of the familial cutaneous melanomas have unknown genetic predisposition. This study aims at characterizing a novel melanoma susceptibility gene. METHODS We performed exome and targeted sequencing in melanoma-prone families without any known melanoma susceptibility genes. We analyzed the expression of candidate gene DENND5A in melanoma samples in relation to pigmentation and UV signature. Functional studies were carried out using microscopic approaches and zebrafish model. RESULTS We identified a novel DENND5A truncating variant that segregated with melanoma in a Swedish family and 2 additional rare DENND5A variants, 1 of which segregated with the disease in an American family. We found that DENND5A is significantly enriched in pigmented melanoma tissue. Our functional studies show that loss of DENND5A function leads to decrease in melanin content in vitro and pigmentation defects in vivo. Mechanistically, harboring the truncating variant or being suppressed leads to DENND5A losing its interaction with SNX1 and its ability to transport the SNX1-associated vesicles from melanosomes. Consequently, untethered SNX1-premelanosome protein and redundant tyrosinase are redirected to lysosomal degradation by default, causing decrease in melanin content. CONCLUSION Our findings provide evidence of a physiological role of DENND5A in the skin context and link its variants to melanoma susceptibility.
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Affiliation(s)
- Muyi Yang
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Per Johnsson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Ludwig Institute for Cancer Research, Stockholm, Sweden
| | - Lars Bräutigam
- Comparative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD
| | - Kim Thrane
- Department of Gene Technology, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jiwei Gao
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Nicholas P Tobin
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Yitian Zhou
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Rong Yu
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Noemi Nagy
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Pär G Engström
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, SciLifeLab, Stockholm University, Stockholm, Sweden
| | - Rainer Tuominen
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Hanna Eriksson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden
| | - Joakim Lundeberg
- Department of Gene Technology, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD
| | | | - Jian Zhao
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
| | - Yihai Cao
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Veronica Höiom
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden.
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8
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Altered expression of DENND5B in patients with epilepsy and its regulation of seizures in mice. Epilepsy Res 2021; 178:106817. [PMID: 34837825 DOI: 10.1016/j.eplepsyres.2021.106817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 10/20/2021] [Accepted: 11/11/2021] [Indexed: 11/20/2022]
Abstract
Epilepsy is a high incidence neurological disease, and its repeated attacks cause serious physical and psychological damage to the patient. Differentially expressed in normal and neoplastic cells (DENN) domain containing 5B (DENND5B) is a lipoprotein binding protein that mediates synaptic vesicle transport and regulates neuroplasticity and lipid metabolism. Nevertheless, the effect of DENND5B on seizures remains unclear. We aimed to investigate the association of DENND5B with epilepsy, detect its expression and distribution in the nervous system, and explore its role in epileptogenesis through western blot, immunofluorescence staining, and behavioral studies. In this experiment, two C57BL/6 mice models, which induced seizures by pentylenetetrazole and kainic acid, were established. We observed that the expression of DENND5B was reduced in the brains of patients with temporal lobe epilepsy, and its expression was also similarly decreased in both chronic epileptic mice. The findings strongly suggest that DENND5B may be associated with epileptic seizures. Results of immunofluorescence showed that DENND5B was mainly expressed in the hippocampal region and co-located with neurons but not with astrocytes. Next, we used lentivirus to induce both lentiviral vector-mediated overexpression and knockdown of DENND5B in mice to test the change of susceptibility and severity of seizures in the two chronic seizure models. Knockdown of DENND5B was found to promote epileptic seizures, increase chronic spontaneous recurrent epileptic seizures and epileptic discharge, and reduce the incubation period. However, overexpression of DENND5B showed the opposite effect. These results suggest that DENND5B overexpression decreased the behavioral phenotype of epileptic seizures, but DENND5B downregulation had the opposite effect. In summary, our findings suggest that DENND5B can regulate epileptic seizures and may provide a new target for antiepileptic therapy.
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9
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Ithal D, Sukumaran SK, Bhattacharjee D, Vemula A, Nadella R, Mahadevan J, Sud R, Viswanath B, Purushottam M, Jain S. Exome hits demystified: The next frontier. Asian J Psychiatr 2021; 59:102640. [PMID: 33892377 DOI: 10.1016/j.ajp.2021.102640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/26/2021] [Indexed: 12/13/2022]
Abstract
Severe mental illnesses such as schizophrenia and bipolar disorder have complex inheritance patterns, involving both common and rare variants. Whole exome sequencing is a promising approach to find out the rare genetic variants. We had previously reported several rare variants in multiplex families with severe mental illnesses. The current article tries to summarise the biological processes and pattern of expression of genes harbouring the aforementioned variants, linking them to known clinical manifestations through a methodical narrative review. Of the 28 genes considered for this review from 7 families with multiple affected individuals, 6 genes are implicated in various neuropsychiatric manifestations including some variations in the brain morphology assessed by magnetic resonance imaging. Another 15 genes, though associated with neuropsychiatric manifestations, did not have established brain morphological changes whereas the remaining 7 genes did not have any previously recorded neuropsychiatric manifestations at all. Wnt/b-catenin signaling pathway was associated with 6 of these genes and PI3K/AKT, calcium signaling, ERK, RhoA and notch signaling pathways had at least 2 gene associations. We present a comprehensive review of biological and clinical knowledge about the genes previously reported in multiplex families with severe mental illness. A 'disease in dish approach' can be helpful to further explore the fundamental mechanisms.
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Affiliation(s)
- Dhruva Ithal
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Salil K Sukumaran
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Debanjan Bhattacharjee
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Alekhya Vemula
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Ravi Nadella
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Jayant Mahadevan
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Reeteka Sud
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Biju Viswanath
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Meera Purushottam
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India.
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
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10
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Liu J, Huang Y, Li T, Jiang Z, Zeng L, Hu Z. The role of the Golgi apparatus in disease (Review). Int J Mol Med 2021; 47:38. [PMID: 33537825 PMCID: PMC7891830 DOI: 10.3892/ijmm.2021.4871] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 01/15/2021] [Indexed: 02/07/2023] Open
Abstract
The Golgi apparatus is known to underpin many important cellular homeostatic functions, including trafficking, sorting and modifications of proteins or lipids. These functions are dysregulated in neurodegenerative diseases, cancer, infectious diseases and cardiovascular diseases, and the number of disease-related genes associated with Golgi apparatus is on the increase. Recently, many studies have suggested that the mutations in the genes encoding Golgi resident proteins can trigger the occurrence of diseases. By summarizing the pathogenesis of these genetic diseases, it was found that most of these diseases have defects in membrane trafficking. Such defects typically result in mislocalization of proteins, impaired glycosylation of proteins, and the accumulation of undegraded proteins. In the present review, we aim to understand the patterns of mutations in the genes encoding Golgi resident proteins and decipher the interplay between Golgi resident proteins and membrane trafficking pathway in cells. Furthermore, the detection of Golgi resident protein in human serum samples has the potential to be used as a diagnostic tool for diseases, and its central role in membrane trafficking pathways provides possible targets for disease therapy. Thus, we also introduced the clinical value of Golgi apparatus in the present review.
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Affiliation(s)
- Jianyang Liu
- Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Yan Huang
- Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Ting Li
- Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Zheng Jiang
- Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Liuwang Zeng
- Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Zhiping Hu
- Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
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11
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Fu Y, Sun C, Li Q, Qian F, Li C, Xi X, Shang D, Wang C, Peng X, Piao M, Qu W, Tian J, Yu B, Gu X, Tian J. Differential RNA expression profiles and competing endogenous RNA-associated regulatory networks during the progression of atherosclerosis. Epigenomics 2021; 13:99-112. [PMID: 33406894 DOI: 10.2217/epi-2020-0252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aim: To identify differential mRNA and ncRNA expression profiles and competing endogenous RNA-associated regulatory networks during the progression of atherosclerosis (AS). Materials & methods: We systematically analyzed whole-transcriptome sequencing of samples from different stages of AS to evaluate their long noncoding RNA (lncRNA), circular RNA (circRNA), miRNA and mRNA profiles. Results: We constructed three AS-related competing endogenous RNA regulatory networks of differentially expressed circRNAs, lncRNAs, miRNAs and mRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that the circRNAs in the network were enriched in lipid metabolic processes and participated in the PPAR signaling pathway. Furthermore, lncRNAs were related to receptor activity, myofibrils and cardiovascular system development. Conclusion: The current findings further clarified the regulatory mechanisms at different stages of AS and may provide new ideas and targets for AS.
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Affiliation(s)
- Yahong Fu
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China.,Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, 541004, Guangxi, China
| | - Changbin Sun
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China
| | - Qi Li
- Department of Pathology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Fengcui Qian
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, Heilongjiang, China
| | - Chunquan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, Heilongjiang, China
| | - Xiangwen Xi
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China
| | - Desi Shang
- College of Bioinformatics Science & Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Chuhan Wang
- Department of Pathology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xiang Peng
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China
| | - Minghui Piao
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China
| | - Wenbo Qu
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China
| | - Jinwei Tian
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China.,Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, 541004, Guangxi, China
| | - Bo Yu
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China
| | - Xia Gu
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China.,Heilongjiang Provincial Hospital, Harbin, 150030, Heilongjiang, China
| | - Jiangtian Tian
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China
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12
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Whole exome sequencing highlights variants in association with Keratoconus in Jordanian families. BMC MEDICAL GENETICS 2020; 21:177. [PMID: 32887565 PMCID: PMC7650294 DOI: 10.1186/s12881-020-01112-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/31/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND Keratoconus (KC) is usually bilateral, noninflammatory progressive corneal ectasia in which the cornea becomes progressively thin and conical, resulting in myopia, irregular astigmatism, and corneal scarring. METHODS Eight families characterized by consanguineous marriages and/or multiple keratoconic individuals were examined genetically. Whole exome sequencing was done as trio or quadro per family. The output of the filtration procedure, based on minor allele frequency (MAF) less than 0.01 for homozygous variants and MAF equals 0 for heterozygous variants, is 22 missense variants. RESULTS Based on the gene/protein function five candidate variants were highlighted in four families. Two variants were highlighted in one family within the genes MYOF and STX2, and one variant is highlighted in each of the other three families within the genes: COL6A5, ZNF676 and ZNF765. CONCLUSION This study is one of the very rare that highlights genetic variants in association with KC.
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13
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Intracranial calcifications in childhood: Part 2. Pediatr Radiol 2020; 50:1448-1475. [PMID: 32642802 DOI: 10.1007/s00247-020-04716-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/03/2020] [Accepted: 05/12/2020] [Indexed: 02/08/2023]
Abstract
This article is the second of a two-part series on intracranial calcification in childhood. In Part 1, the authors discussed the main differences between physiological and pathological intracranial calcification. They also outlined histological intracranial calcification characteristics and how these can be detected across different neuroimaging modalities. Part 1 emphasized the importance of age at presentation and intracranial calcification location and proposed a comprehensive neuroimaging approach toward the differential diagnosis of the causes of intracranial calcification. Pathological intracranial calcification can be divided into infectious, congenital, endocrine/metabolic, vascular, and neoplastic. In Part 2, the chief focus is on discussing endocrine/metabolic, vascular, and neoplastic intracranial calcification etiologies of intracranial calcification. Endocrine/metabolic diseases causing intracranial calcification are mainly from parathyroid and thyroid dysfunction and inborn errors of metabolism, such as mitochondrial disorders (MELAS, or mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes; Kearns-Sayre; and Cockayne syndromes), interferonopathies (Aicardi-Goutières syndrome), and lysosomal disorders (Krabbe disease). Specific noninfectious causes of intracranial calcification that mimic TORCH (toxoplasmosis, other [syphilis, varicella-zoster, parvovirus B19], rubella, cytomegalovirus, and herpes) infections are known as pseudo-TORCH. Cavernous malformations, arteriovenous malformations, arteriovenous fistulas, and chronic venous hypertension are also known causes of intracranial calcification. Other vascular-related causes of intracranial calcification include early atherosclerosis presentation (children with risk factors such as hyperhomocysteinemia, familial hypercholesterolemia, and others), healed hematoma, radiotherapy treatment, old infarct, and disorders of the microvasculature such as COL4A1- and COL4A2-related diseases. Intracranial calcification is also seen in several pediatric brain tumors. Clinical and familial information such as age at presentation, maternal exposure to teratogens including viruses, and association with chromosomal abnormalities, pathogenic genes, and postnatal infections facilitates narrowing the differential diagnosis of the multiple causes of intracranial calcification.
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14
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Isik E, Yilmaz S, Atik T, Aktan G, Onay H, Gokben S, Ozkinay F. The utility of whole exome sequencing for identification of the molecular etiology in autosomal recessive developmental and epileptic encephalopathies. Neurol Sci 2020; 41:3729-3739. [DOI: 10.1007/s10072-020-04619-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 07/19/2020] [Indexed: 12/15/2022]
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15
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Yarwood R, Hellicar J, Woodman PG, Lowe M. Membrane trafficking in health and disease. Dis Model Mech 2020; 13:13/4/dmm043448. [PMID: 32433026 PMCID: PMC7197876 DOI: 10.1242/dmm.043448] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Membrane trafficking pathways are essential for the viability and growth of cells, and play a major role in the interaction of cells with their environment. In this At a Glance article and accompanying poster, we outline the major cellular trafficking pathways and discuss how defects in the function of the molecular machinery that mediates this transport lead to various diseases in humans. We also briefly discuss possible therapeutic approaches that may be used in the future treatment of trafficking-based disorders. Summary: This At a Glance article and poster summarise the major intracellular membrane trafficking pathways and associated molecular machineries, and describe how defects in these give rise to disease in humans.
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Affiliation(s)
- Rebecca Yarwood
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - John Hellicar
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Philip G Woodman
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Martin Lowe
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
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16
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Murgoci AN, Cardon T, Aboulouard S, Duhamel M, Fournier I, Cizkova D, Salzet M. Reference and Ghost Proteins Identification in Rat C6 Glioma Extracellular Vesicles. iScience 2020; 23:101045. [PMID: 32334413 PMCID: PMC7182720 DOI: 10.1016/j.isci.2020.101045] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/23/2020] [Accepted: 04/03/2020] [Indexed: 01/08/2023] Open
Abstract
Extracellular vesicles (EVs) mediate intercellular communication and regulate a broad range of biological processes. Novel therapeutic strategies have emerged based on the use of EVs as biological nanoparticles. To separate isolated EVs from protein aggregates and the external part of EVs membrane proteins, we performed a Trypsin/Lys C digestion treatment of EVs pellets, followed by Amicon filtration. After these steps, all the fractions have been subjected to proteomic analyses. Comparison between 6 h Trypsin/Lys C treatment or non-treated EVs revealed a quantitative variation of the surface proteins. Some surface proteins have been demasked after 6 h enzymatic digestion like CD81, CD82, Ust, Vcan, Lamp 1, Rab43, Annexin A2, Synthenin, and VSP37b. Moreover, six ghost proteins have also been identified and one corresponds to a long noncoding RNA. We thus demonstrate the presence of ghost proteins in EVs produced by glioma cells that can contribute to tumorigenesis. Glioma C6 extracellular vesicle protein mapping Quick steps protocols to map outer/inner membrane EV membrane proteins C6 glioma cell line EVs contain ghost proteins
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Affiliation(s)
- Adriana-Natalia Murgoci
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava 84510, Slovakia
| | - Tristan Cardon
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Soulaimane Aboulouard
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Marie Duhamel
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Isabelle Fournier
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Dasa Cizkova
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava 84510, Slovakia; Department of Anatomy, Histology and Physiology, University of Veterinary Medicine and Pharmacy in Košice, Košice 04181, Slovakia.
| | - Michel Salzet
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France.
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17
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Froukh T, Nafie O, Al Hait SAS, Laugwitz L, Sommerfeld J, Sturm M, Baraghiti A, Issa T, Al-Nazer A, Koch PA, Hanselmann J, Kootz B, Bauer P, Al-Ameri W, Abou Jamra R, Alfrook AJ, Hamadallah M, Sofan L, Riess A, Haack TB, Riess O, Buchert R. Genetic basis of neurodevelopmental disorders in 103 Jordanian families. Clin Genet 2020; 97:621-627. [PMID: 32056211 DOI: 10.1111/cge.13720] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/15/2020] [Accepted: 02/05/2020] [Indexed: 10/25/2022]
Abstract
We recruited 103 families from Jordan with neurodevelopmental disorders (NDD) and patterns of inheritance mostly suggestive of autosomal recessive inheritance. In each family, we investigated at least one affected individual using exome sequencing and an in-house diagnostic variant interpretation pipeline including a search for copy number variation. This approach led us to identify the likely molecular defect in established disease genes in 37 families. We could identify 25 pathogenic nonsense and 11 missense variants as well as 3 pathogenic copy number variants and 1 repeat expansion. Notably, 11 of the disease-causal variants occurred de novo. In addition, we prioritized a homozygous frameshift variant in PUS3 in two sisters with intellectual disability. To our knowledge, PUS3 has been postulated only recently as a candidate disease gene for intellectual disability in a single family with three affected siblings. Our findings provide additional evidence to establish loss of PUS3 function as a cause of intellectual disability.
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Affiliation(s)
- Tawfiq Froukh
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman, Jordan
| | - Omar Nafie
- Faculty of Medicine, Mutah University, Alkarak, Jordan
| | | | - Lucia Laugwitz
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Julia Sommerfeld
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Aya Baraghiti
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman, Jordan
| | - Tala Issa
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman, Jordan
| | - Anis Al-Nazer
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman, Jordan
| | - Philipp A Koch
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Johannes Hanselmann
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Beate Kootz
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Peter Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | | | - Rami Abou Jamra
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, Germany
| | | | | | - Linda Sofan
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman, Jordan
| | - Angelika Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
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18
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Yuan S, Li H, Xie J, Sun X. Quantitative Trait Module-Based Genetic Analysis of Alzheimer's Disease. Int J Mol Sci 2019; 20:E5912. [PMID: 31775305 PMCID: PMC6928939 DOI: 10.3390/ijms20235912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 01/02/2023] Open
Abstract
The pathological features of Alzheimer's Disease (AD) first appear in the medial temporal lobe and then in other brain structures with the development of the disease. In this work, we investigated the association between genetic loci and subcortical structure volumes of AD on 393 samples in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. Brain subcortical structures were clustered into modules using Pearson's correlation coefficient of volumes across all samples. Module volumes were used as quantitative traits to identify not only the main effect loci but also the interactive effect loci for each module. Thirty-five subcortical structures were clustered into five modules, each corresponding to a particular brain structure/area, including the limbic system (module I), the corpus callosum (module II), thalamus-cerebellum-brainstem-pallidum (module III), the basal ganglia neostriatum (module IV), and the ventricular system (module V). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results indicate that the gene annotations of the five modules were distinct, with few overlaps between different modules. We identified several main effect loci and interactive effect loci for each module. All these loci are related to the function of module structures and basic biological processes such as material transport and signal transduction.
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Affiliation(s)
| | | | | | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (S.Y.)
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19
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Nashabat M, Al Qahtani XS, Almakdob S, Altwaijri W, Ba-Armah DM, Hundallah K, Al Hashem A, Al Tala S, Maddirevula S, Alkuraya FS, Tabarki B, Alfadhel M. The landscape of early infantile epileptic encephalopathy in a consanguineous population. Seizure 2019; 69:154-172. [PMID: 31054490 DOI: 10.1016/j.seizure.2019.04.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 04/21/2019] [Accepted: 04/24/2019] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Epileptic encephalopathies (EE), are a group of age-related disorders characterized by intractable seizures and electroencephalogram (EEG) abnormalities that may result in cognitive and motor delay. Early infantile epileptic encephalopathies (EIEE) manifest in the first year of life. EIEE are highly heterogeneous genetically but a genetic etiology is only identified in half of the cases, typically in the form of de novo dominant mutations. METHOD This is a descriptive retrospective study of a consecutive series of patients diagnosed with EIEE from the participating hospitals. A chart review was performed for all patients. The diagnosis of epileptic encephalopathy was confirmed by molecular investigations in commercial labs. In silico study was done for all novel mutations. A systematic search was done for all the types of EIEE and their correlated genes in the literature using the Online Mendelian Inheritance In Man and PubMed databases. RESULTS In this case series, we report 72 molecularly characterized EIEE from a highly consanguineous population, and review their clinical course. We identified 50 variants, 26 of which are novel, causing 26 different types of EIEE. Unlike outbred populations, autosomal recessive EIEE accounted for half the cases. The phenotypes ranged from self-limiting and drug-responsive to severe refractory seizures or even death. CONCLUSIONS We reported the largest EIEE case series in the region with confirmed molecular testing and detailed clinical phenotyping. The number autosomal recessive predominance could be explained by the society's high consanguinity. We reviewed all the EIEE registered causative genes in the literature and proposed a functional classification.
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Affiliation(s)
- Marwan Nashabat
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Xena S Al Qahtani
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Salwa Almakdob
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Waleed Altwaijri
- Division of Pediatric Neurology, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Duaa M Ba-Armah
- Division of Pediatric Neurology, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Khalid Hundallah
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Amal Al Hashem
- Division of Genetics, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Saeed Al Tala
- Division of Genetics, Department of Pediatrics, Armed Forces Hospital, Khamis Mushayt, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia; Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Brahim Tabarki
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia.
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20
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Rasika S, Passemard S, Verloes A, Gressens P, El Ghouzzi V. Golgipathies in Neurodevelopment: A New View of Old Defects. Dev Neurosci 2019; 40:396-416. [PMID: 30878996 DOI: 10.1159/000497035] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 01/16/2019] [Indexed: 11/19/2022] Open
Abstract
The Golgi apparatus (GA) is involved in a whole spectrum of activities, from lipid biosynthesis and membrane secretion to the posttranslational processing and trafficking of most proteins, the control of mitosis, cell polarity, migration and morphogenesis, and diverse processes such as apoptosis, autophagy, and the stress response. In keeping with its versatility, mutations in GA proteins lead to a number of different disorders, including syndromes with multisystem involvement. Intriguingly, however, > 40% of the GA-related genes known to be associated with disease affect the central or peripheral nervous system, highlighting the critical importance of the GA for neural function. We have previously proposed the term "Golgipathies" in relation to a group of disorders in which mutations in GA proteins or their molecular partners lead to consequences for brain development, in particular postnatal-onset microcephaly (POM), white-matter defects, and intellectual disability (ID). Here, taking into account the broader role of the GA in the nervous system, we refine and enlarge this emerging concept to include other disorders whose symptoms may be indicative of altered neurodevelopmental processes, from neurogenesis to neuronal migration and the secretory function critical for the maturation of postmitotic neurons and myelination.
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Affiliation(s)
- Sowmyalakshmi Rasika
- NeuroDiderot, INSERM UMR1141, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,AP HP, Hôpital Robert Debré, UF de Génétique Clinique, Paris, France
| | - Sandrine Passemard
- NeuroDiderot, INSERM UMR1141, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,AP HP, Hôpital Robert Debré, UF de Génétique Clinique, Paris, France
| | - Alain Verloes
- NeuroDiderot, INSERM UMR1141, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,AP HP, Hôpital Robert Debré, UF de Génétique Clinique, Paris, France
| | - Pierre Gressens
- NeuroDiderot, INSERM UMR1141, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Centre for the Developing Brain, Division of Imaging Sciences and Biomedical Engineering, King's College London, King's Health Partners, St. Thomas' Hospital, London, United Kingdom
| | - Vincent El Ghouzzi
- NeuroDiderot, INSERM UMR1141, Université Paris Diderot, Sorbonne Paris Cité, Paris, France,
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21
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First Record Mutations in the Genes ASPA and ARSA Causing Leukodystrophy in Jordan. BIOMED RESEARCH INTERNATIONAL 2019; 2019:7235914. [PMID: 30834272 PMCID: PMC6374869 DOI: 10.1155/2019/7235914] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 10/19/2018] [Accepted: 11/08/2018] [Indexed: 11/17/2022]
Abstract
Leukodystrophies (LDs) are heterogeneous genetic disorders characterized by abnormal white matter in the central nervous system. Some of the LDs are progressive and often fatal. In general, LD is primarily diagnosed based on the neuroimaging; however, definitive diagnosis of the LD type is done using genetic testing such as next-generation sequencing. The aim of this study is to identify the genetic causes of LD in two independent Jordanian cases that exhibit MRI findings confirming LD with no definitive diagnosis using whole exome sequencing (WES). The most likely causative variants were identified. In one case, the homozygous pathogenic variant NM_000049.2:c.914C>A;p.Ala305Glu, which is previously reported in ClinVar, in the gene ASPA was identified causing Canavan disease. In the second case, the homozygous novel variant NM_000487.5:c.256C>G;p.Arg86Gly in the gene ARSA was identified causing metachromatic leukodystrophy. The two variants segregate in their families. The phenotypes of the two studied cases overlap with assigned diseases. The present study raises the importance of using WES to identify the precise neurodevelopmental diseases in Jordan.
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22
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Calhoun JD, Carvill GL. Unravelling the genetic architecture of autosomal recessive epilepsy in the genomic era. J Neurogenet 2018; 32:295-312. [PMID: 30247086 DOI: 10.1080/01677063.2018.1513509] [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] [Indexed: 12/27/2022]
Abstract
The technological advancement of next-generation sequencing has greatly accelerated the pace of variant discovery in epilepsy. Despite an initial focus on autosomal dominant epilepsy due to the tractable nature of variant discovery with trios under a de novo model, more and more variants are being reported in families with epilepsies consistent with autosomal recessive (AR) inheritance. In this review, we touch on the classical AR epilepsy variants such as the inborn errors of metabolism and malformations of cortical development. However, we also highlight recently reported genes that are being identified by next-generation sequencing approaches and online 'matchmaking' platforms. Syndromes mainly characterized by seizures and complex neurodevelopmental disorders comorbid with epilepsy are discussed as an example of the wide phenotypic spectrum associated with the AR epilepsies. We conclude with a foray into the future, from the application of whole-genome sequencing to identify elusive epilepsy variants, to the promise of precision medicine initiatives to provide novel targeted therapeutics specific to the individual based on their clinical genetic testing.
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Affiliation(s)
- Jeffrey D Calhoun
- a Department of Neurology , Northwestern University Feinberg School of Medicine , Chicago , IL , USA
| | - Gemma L Carvill
- a Department of Neurology , Northwestern University Feinberg School of Medicine , Chicago , IL , USA
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23
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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.
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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
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24
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Molecular Insights into the Roles of Rab Proteins in Intracellular Dynamics and Neurodegenerative Diseases. Neuromolecular Med 2018; 20:18-36. [PMID: 29423895 DOI: 10.1007/s12017-018-8479-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/27/2018] [Indexed: 02/01/2023]
Abstract
In eukaryotes, the cellular functions are segregated to membrane-bound organelles. This inherently requires sorting of metabolites to membrane-limited locations. Sorting the metabolites from ribosomes to various organelles along the intracellular trafficking pathways involves several integral cellular processes, including an energy-dependent step, in which the sorting of metabolites between organelles is catalyzed by membrane-anchoring protein Rab-GTPases (Rab). They contribute to relaying the switching of the secretory proteins between hydrophobic and hydrophilic environments. The intracellular trafficking routes include exocytic and endocytic pathways. In these pathways, numerous Rab-GTPases are participating in discrete shuttling of cargoes. Long-distance trafficking of cargoes is essential for neuronal functions, and Rabs are critical for these functions, including the transport of membranes and essential proteins for the development of axons and neurites. Rabs are also the key players in exocytosis of neurotransmitters and recycling of neurotransmitter receptors. Thus, Rabs are critical for maintaining neuronal communication, as well as for normal cellular physiology. Therefore, cellular defects of Rab components involved in neural functions, which severely affect normal brain functions, can produce neurological complications, including several neurodegenerative diseases. In this review, we provide a comprehensive overview of the current understanding of the molecular signaling pathways of Rab proteins and the impact of their defects on different neurodegenerative diseases. The insights gathered into the dynamics of Rabs that are described in this review provide new avenues for developing effective treatments for neurodegenerative diseases-associated with Rab defects.
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25
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Fernández-Marmiesse A, Gouveia S, Couce ML. NGS Technologies as a Turning Point in Rare Disease Research , Diagnosis and Treatment. Curr Med Chem 2018; 25:404-432. [PMID: 28721829 PMCID: PMC5815091 DOI: 10.2174/0929867324666170718101946] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/19/2017] [Accepted: 07/14/2017] [Indexed: 01/17/2023]
Abstract
Approximately 25-50 million Americans, 30 million Europeans, and 8% of the Australian population have a rare disease. Rare diseases are thus a common problem for clinicians and account for enormous healthcare costs worldwide due to the difficulty of establishing a specific diagnosis. In this article, we review the milestones achieved in our understanding of rare diseases since the emergence of next-generation sequencing (NGS) technologies and analyze how these advances have influenced research and diagnosis. The first half of this review describes how NGS has changed diagnostic workflows and provided an unprecedented, simple way of discovering novel disease-associated genes. We focus particularly on metabolic and neurodevelopmental disorders. NGS has enabled cheap and rapid genetic diagnosis, highlighted the relevance of mosaic and de novo mutations, brought to light the wide phenotypic spectrum of most genes, detected digenic inheritance or the presence of more than one rare disease in the same patient, and paved the way for promising new therapies. In the second part of the review, we look at the limitations and challenges of NGS, including determination of variant causality, the loss of variants in coding and non-coding regions, and the detection of somatic mosaicism variants and epigenetic mutations, and discuss how these can be overcome in the near future.
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Affiliation(s)
- Ana Fernández-Marmiesse
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sofía Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - María L. Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
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26
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Xu J, McPherson PS. Regulation of DENND3, the exchange factor for the small GTPase Rab12 through an intramolecular interaction. J Biol Chem 2017; 292:7274-7282. [PMID: 28249939 DOI: 10.1074/jbc.m116.772434] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/21/2017] [Indexed: 12/26/2022] Open
Abstract
The Rab family of small GTPases functions in multiple aspects of cellular membrane trafficking. Proteins bearing a differentially expressed in normal and neoplastic cells (DENN) domain have emerged as the largest family of Rab-activating guanine nucleotide exchange factors (GEFs). Rab12 functions in the initiation of starvation-induced autophagy, and our previous work revealed that its activator, DENN domain-containing protein 3 (DENND3), is phosphorylated and activated upon starvation. However, how the GEF activity of DENND3 toward Rab12 is regulated at the molecular level is still not understood. Here, we combine size-exclusion chromatography, Förster resonance energy transfer, pulldown, and in vitro GEF assays to demonstrate that regulation of GEF activity is achieved through an intramolecular interaction that is controlled by a key residue in DENND3, tyrosine 940. Our study sheds light on the regulation of Rab12 activation and lays the groundwork for characterizing the regulation of other DENN domain-containing proteins.
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Affiliation(s)
- Jie Xu
- From the Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Peter S McPherson
- From the Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
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