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Agarwal S, Gupta S, Raj R. Identification of potential targetable genes in papillary, follicular, and anaplastic thyroid carcinoma using bioinformatics analysis. Endocrine 2024:10.1007/s12020-024-03836-x. [PMID: 38676768 DOI: 10.1007/s12020-024-03836-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 04/14/2024] [Indexed: 04/29/2024]
Abstract
PURPOSE To perform an extensive exploratory analysis to build a deeper insight into clinically relevant molecular biomarkers in Papillary, Follicular, and Anaplastic thyroid carcinomas (PTC, FTC, ATC). METHODS Thirteen Thyroid Cancer (THCA) datasets incorporating PTC, FTC, and ATC were derived from the Gene Expression Omnibus. Genes differentially expressed (DEGs) between THCA and normal were identified and subjected to GO and KEGG analyses. Multiple topological properties were harnessed and protein-protein interaction (PPI) networks were constructed to identify the hub genes followed by survival analysis and validation. RESULTS There were 70, 87, and 377 DEGs, and 23, 27, and 53 hub genes for PTC, FTC, and ATC samples, respectively. Survival analysis detected 39 overall and 49 relapse-free survival-relevant hub genes. Six hub genes, BCL2, FN1, ITPR1, LYVE1, NTRK2, TBC1D4, were found common to more than one THCA type. The most significant hub genes found in the study were: BCL2, CD44, DCN, FN1, IRS1, ITPR1, MFAP4, MKI67, NTRK2, PCLO, TGFA. The most enriched and significant GO terms were Melanocyte differentiation for PTC, Extracellular region for FTC, and Extracellular exosome for ATC. Prostate cancer for PTC was the most significantly enriched KEGG pathway. The results were validated using TCGA data. CONCLUSIONS The findings unravel potential biomarkers and therapeutic targets of thyroid carcinomas.
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Affiliation(s)
- Shipra Agarwal
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Shikha Gupta
- Department of Computer Science, S.S. College of Business Studies, University of Delhi, New Delhi, India.
| | - Rishav Raj
- Department of Computer Science, S.S. College of Business Studies, University of Delhi, New Delhi, India
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Cavusoglu D, Ozturk G, Turkdogan D, Kurul SH, Yis U, Komur M, Incecik F, Kara B, Sahin T, Unver O, Dilber C, Mert GG, Gunay C, Uzan GS, Ersoy O, Oktay Y, Mermer S, Tuncer GO, Gungor O, Ozcora GDK, Gumus U, Sezer O, Cetin GO, Demir F, Yilmaz A, Gurbuz G, Topcu M, Topaloglu H, Ceylan AC, Ceylaner S, Gleeson JG, Icagasioglu DF, Sonmez FM. Evaluation of the Patients with the Diagnosis of Pontocerebellar Hypoplasia: A Multicenter National Study. CEREBELLUM (LONDON, ENGLAND) 2024:10.1007/s12311-024-01690-1. [PMID: 38622473 DOI: 10.1007/s12311-024-01690-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/27/2024] [Indexed: 04/17/2024]
Abstract
Pontocerebellar hypoplasia (PCH) is a heterogeneous group of neurodegenerative disorders characterized by hypoplasia and degeneration of the cerebellum and pons. We aimed to identify the clinical, laboratory, and imaging findings of the patients with diagnosed PCH with confirmed genetic analysis. We collected available clinical data, laboratory, and imaging findings in our retrospective multicenter national study of 64 patients with PCH in Turkey. The genetic analysis included the whole-exome sequencing (WES), targeted next-generation sequencing (NGS), or single gene analysis. Sixty-four patients with PCH were 28 female (43.8%) and 36 (56.3%) male. The patients revealed homozygous mutation in 89.1%, consanguinity in 79.7%, pregnancy at term in 85.2%, microcephaly in 91.3%, psychomotor retardation in 98.4%, abnormal neurological findings in 100%, seizure in 63.8%, normal biochemistry and metabolic investigations in 92.2%, and dysmorphic findings in 51.2%. The missense mutation was found to be the most common variant type in all patients with PCH. It was detected as CLP1 (n = 17) was the most common PCH related gene. The homozygous missense variant c.419G > A (p.Arg140His) was identified in all patients with CLP1. Moreover, all patients showed the same homozygous missense variant c.919G > T (p.A307S) in TSEN54 group (n = 6). In Turkey, CLP1 was identified as the most common causative gene with the identical variant c.419G > A; p.Arg140His. The current study supports that genotype data on PCH leads to phenotypic variability over a wide phenotypic spectrum.
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Affiliation(s)
- Dilek Cavusoglu
- Departments of Pediatric Neurology, Afyonkarahisar Health Sciences University, Afyon, Turkey
| | - Gulten Ozturk
- Departments of Pediatric Neurology, Marmara University, Istanbul, Turkey
| | - Dilsad Turkdogan
- Departments of Pediatric Neurology, Marmara University, Istanbul, Turkey
| | - Semra Hiz Kurul
- Departments of Pediatric Neurology, Dokuz Eylul University, Izmir, Turkey
| | - Uluc Yis
- Departments of Pediatric Neurology, Dokuz Eylul University, Izmir, Turkey
| | - Mustafa Komur
- Departments of Pediatric Neurology, Mersin University, Mersin, Turkey
| | - Faruk Incecik
- Departments of Pediatric Neurology, Cukurova University, Adana, Turkey
| | - Bulent Kara
- Departments of Pediatric Neurology, Kocaeli University, Kocaeli, Turkey
| | - Turkan Sahin
- Departments of Pediatric Neurology, Bezmialem Vakif University, Istanbul, Turkey
| | - Olcay Unver
- Departments of Pediatric Neurology, Marmara University, Istanbul, Turkey
| | - Cengiz Dilber
- Departments of Pediatric Neurology, Kahramanmaras Sutcu Imam University, Kahramanmaras, Turkey
| | - Gulen Gul Mert
- Departments of Pediatric Neurology, Cukurova University, Adana, Turkey
| | - Cagatay Gunay
- Departments of Pediatric Neurology, Dokuz Eylul University, Izmir, Turkey
| | | | - Ozlem Ersoy
- Departments of Pediatric Neurology, Mersin University, Mersin, Turkey
| | - Yavuz Oktay
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Serdar Mermer
- Departments of Medical Genetics, Mersin University, Mersin, Turkey
| | - Gokcen Oz Tuncer
- Departments of Pediatric Neurology, Ondokuz Mayıs University, Samsun, Turkey
| | - Olcay Gungor
- Departments of Pediatric Neurology, Pamukkale University, Denizli, Turkey
| | | | - Ugur Gumus
- Departments of Medical Genetics, Dr Ersin Arslan Training and Research Hospital, Gaziantep, Turkey
| | - Ozlem Sezer
- Departments of Medical Genetics, Samsun Training and Research Hospital, Samsun, Turkey
| | - Gokhan Ozan Cetin
- Departments of Medical Genetics, Pamukkale University, Denizli, Turkey
| | - Fatma Demir
- Departments of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Arzu Yilmaz
- Departments of Pediatric Neurology, Ankara Training and Research Hospital, Ankara, Turkey
| | - Gurkan Gurbuz
- Departments of Pediatric Neurology, Tekirdag Namik Kemal University, Tekirdag, Turkey
| | - Meral Topcu
- Departments of Pediatric Neurology, Hacettepe University,Retired Lecturer, Ankara, Turkey
| | - Haluk Topaloglu
- Departments of Pediatric Neurology, Yeditepe University, Istanbul, Turkey
| | - Ahmet Cevdet Ceylan
- Departments of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
| | | | - Joseph G Gleeson
- Department of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California, La Jolla, San Diego, CA, USA
| | | | - F Mujgan Sonmez
- Departments of Pediatric Neurology, Department of Child Neurology, Karadeniz Technical University Medical Faculty, Retired Lecturer, Trabzon, Turkey.
- Yuksek Ihtisas University, Faculty of Medicine, Ankara, Turkey.
- , Aziziye Mah. Cinnah Cad. 102/3, Cankaya, Ankara, Türkiye.
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Ghasemi MR, Tehrani Fateh S, Moeinafshar A, Sadeghi H, Karimzadeh P, Mirfakhraie R, Rezaei M, Hashemi-Gorji F, Rezvani Kashani M, Fazeli Bavandpour F, Bagheri S, Moghimi P, Rostami M, Madannejad R, Roudgari H, Miryounesi M. Broadening the phenotype and genotype spectrum of novel mutations in pontocerebellar hypoplasia with a comprehensive molecular literature review. BMC Med Genomics 2024; 17:51. [PMID: 38347586 PMCID: PMC10863249 DOI: 10.1186/s12920-024-01810-0] [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: 04/26/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Pontocerebellar hypoplasia is an umbrella term describing a heterogeneous group of prenatal neurodegenerative disorders mostly affecting the pons and cerebellum, with 17 types associated with 25 genes. However, some types of PCH lack sufficient information, which highlights the importance of investigating and introducing more cases to further elucidate the clinical, radiological, and biochemical features of these disorders. The aim of this study is to provide an in-depth review of PCH and to identify disease genes and their inheritance patterns in 12 distinct Iranian families with clinically confirmed PCH. METHODS Cases included in this study were selected based on their phenotypic and genetic information available at the Center for Comprehensive Genetic Services. Whole-exome sequencing (WES) was used to discover the underlying genetic etiology of participants' problems, and Sanger sequencing was utilized to confirm any suspected alterations. We also conducted a comprehensive molecular literature review to outline the genetic features of the various subtypes of PCH. RESULTS This study classified and described the underlying etiology of PCH into three categories based on the genes involved. Twelve patients also were included, eleven of whom were from consanguineous parents. Ten different variations in 8 genes were found, all of which related to different types of PCH. Six novel variations were reported, including SEPSECS, TSEN2, TSEN54, AMPD2, TOE1, and CLP1. Almost all patients presented with developmental delay, hypotonia, seizure, and microcephaly being common features. Strabismus and elevation in lactate levels in MR spectroscopy were novel phenotypes for the first time in PCH types 7 and 9. CONCLUSIONS This study merges previously documented phenotypes and genotypes with unique novel ones. Due to the diversity in PCH, we provided guidance for detecting and diagnosing these heterogeneous groups of disorders. Moreover, since certain critical conditions, such as spinal muscular atrophy, can be a differential diagnosis, providing cases with novel variations and clinical findings could further expand the genetic and clinical spectrum of these diseases and help in better diagnosis. Therefore, six novel genetic variants and novel clinical and paraclinical findings have been reported for the first time. Further studies are needed to elucidate the underlying mechanisms and potential therapeutic targets for PCH.
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Affiliation(s)
- Mohammad-Reza Ghasemi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, , Tehran, Iran
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Aysan Moeinafshar
- School of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Hossein Sadeghi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, , Tehran, Iran
| | - Parvaneh Karimzadeh
- Pediatric Neurology Department, Mofid Children's Hospital, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Mirfakhraie
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, , Tehran, Iran
| | - Mitra Rezaei
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzad Hashemi-Gorji
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Morteza Rezvani Kashani
- Pediatric Neurology Department, Mofid Children's Hospital, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Saman Bagheri
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- School of Medicine, Islamic Azad University Tehran Medical Sciences, Tehran, Iran
| | - Parinaz Moghimi
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- School of Medicine, Islamic Azad University Tehran Medical Sciences, Tehran, Iran
| | - Masoumeh Rostami
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rasoul Madannejad
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hassan Roudgari
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Miryounesi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, , Tehran, Iran.
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Bernhardt M, Behrens HM, Krüger S, Röcken C. Exploration of the Tumour Biological Significance of PCLO in Gastric Cancer: Results from a Large Central European Cohort. Pathobiology 2023; 91:187-195. [PMID: 37935138 PMCID: PMC11126201 DOI: 10.1159/000534889] [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: 01/18/2023] [Accepted: 10/16/2023] [Indexed: 11/09/2023] Open
Abstract
INTRODUCTION A recent multiregional whole-exome sequencing of 48 tumour samples from 9 gastric adenocarcinomas discovered PCLO mutations in 23 (47.9%) tumour samples. Based on that unexpected high prevalence of PCLO mutations, we hypothesized a tumour biological significance of PCLO in gastric cancer (GC). METHODS Tumour samples (whole tissue sections) obtained from 466 patients resected for therapy-naive GC were stained with an anti-PCLO antibody. The histoscore for tumour cells and the presence of immunostaining of stromal cells and tumour vessels was documented for each case. An algorithm for PCLO immunopositivity was formed and correlated with clinicopathological patient characteristics. RESULTS 175 GCs were classified as PCLO positive within tumour cells, and 291 as negative. Stromal cells were positive for PCLO in 106 cases and tumour vessels in 84. PCLO-positive GCs more often showed an intestinal phenotype, a lower T category and were more commonly associated with Helicobacter pylori infection. A separate analysis of PCLO expression in intestinal and diffuse type GCs, respectively, showed no significant correlations. Patients with PCLO negative/low tumour cells showed a shortened overall (14.0 ± 1.4 vs. 16.0 ± 1.8 months) and tumour-specific survival (15.0 ± 1.6 months vs. 17.9 ± 3.6). Comparison of PCLOs genotype with its phenotype in 48 tumour samples obtained from nine cases showed no direct correlations with missense mutations. CONCLUSION Our data provide evidence that PCLO is differentially expressed in GC and might delay tumour progression.
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Affiliation(s)
- Maximilian Bernhardt
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig Holstein, Kiel, Germany
| | - Hans-Michael Behrens
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig Holstein, Kiel, Germany
| | - Sandra Krüger
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig Holstein, Kiel, Germany
| | - Christoph Röcken
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig Holstein, Kiel, Germany
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5
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Yang G, Liu R, Rezaei S, Liu X, Wan YJY. Uncovering the Gut-Liver Axis Biomarkers for Predicting Metabolic Burden in Mice. Nutrients 2023; 15:3406. [PMID: 37571345 PMCID: PMC10421148 DOI: 10.3390/nu15153406] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Western diet (WD) intake, aging, and inactivation of farnesoid X receptor (FXR) are risk factors for metabolic and chronic inflammation-related health issues ranging from metabolic dysfunction-associated steatotic liver disease (MASLD) to dementia. The progression of MASLD can be escalated when those risks are combined. Inactivation of FXR, the receptor for bile acid (BA), is cancer prone in both humans and mice. The current study used multi-omics including hepatic transcripts, liver, serum, and urine metabolites, hepatic BAs, as well as gut microbiota from mouse models to classify those risks using machine learning. A linear support vector machine with K-fold cross-validation was used for classification and feature selection. We have identified that increased urine sucrose alone achieved 91% accuracy in predicting WD intake. Hepatic lithocholic acid and serum pyruvate had 100% and 95% accuracy, respectively, to classify age. Urine metabolites (decreased creatinine and taurine as well as increased succinate) or increased gut bacteria (Dorea, Dehalobacterium, and Oscillospira) could predict FXR deactivation with greater than 90% accuracy. Human disease relevance is partly revealed using the metabolite-disease interaction network. Transcriptomics data were also compared with the human liver disease datasets. WD-reduced hepatic Cyp39a1 (cytochrome P450 family 39 subfamily a member 1) and increased Gramd1b (GRAM domain containing 1B) were also changed in human liver cancer and metabolic liver disease, respectively. Together, our data contribute to the identification of noninvasive biomarkers within the gut-liver axis to predict metabolic status.
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Affiliation(s)
- Guiyan Yang
- Department of Medical Pathology, Laboratory Medicine in Sacramento, University of California, Davis, CA 95817, USA;
| | - Rex Liu
- Department of Computer Science, University of California, Davis, CA 95616, USA; (R.L.); (S.R.); (X.L.)
| | - Shahbaz Rezaei
- Department of Computer Science, University of California, Davis, CA 95616, USA; (R.L.); (S.R.); (X.L.)
| | - Xin Liu
- Department of Computer Science, University of California, Davis, CA 95616, USA; (R.L.); (S.R.); (X.L.)
| | - Yu-Jui Yvonne Wan
- Department of Medical Pathology, Laboratory Medicine in Sacramento, University of California, Davis, CA 95817, USA;
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Garner CC, Ackermann F. Synaptic logistics: The presynaptic scaffold protein Piccolo a nodal point tuning synaptic vesicle recycling, maintenance and integrity. Mol Cell Neurosci 2023; 124:103795. [PMID: 36436725 DOI: 10.1016/j.mcn.2022.103795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
Properly working synapses are one important guarantor for a functional and healthy brain. They are small, densely packed structures, where information is transmitted through the release of neurotransmitters from synaptic vesicles (SVs). The latter cycle within the presynaptic terminal as they first fuse with the plasma membrane to deliver their neurotransmitter, and afterwards become recycled and prepared for a new release event. The synapse is an autonomous structure functioning mostly independent of the neuronal soma. Dysfunction in synaptic processes associated with local insults or genetic abnormalities can directly compromise synapse function and integrity and subsequently lead to the onset of neurodegenerative diseases. Therefore, measures need to be in place counteracting these threats for instance through the continuous replacement of old and damaged SV proteins. Interestingly recent studies show that the presynaptic scaffolding protein Piccolo contributes to health, function and integrity of synapses, as it mediates the delivery of synaptic proteins from the trans-Golgi network (TGN) towards synapses, as well as the local recycling and turnover of SV proteins within synaptic terminals. It can fulfill these various tasks through its multi-domain structure and ability to interact with numerous binding partners. In addition, Piccolo has recently been linked with the early onset neurodegenerative disease Pontocerebellar Hypoplasia Type 3 (PCH3) further underlying its importance for neuronal health. In this review, we will focus on Piccolo's contributions to synapse function, health and integrity and make a connection how those may contribute to the disease pattern of PCH3.
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Affiliation(s)
- Craig C Garner
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany; NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, Germany
| | - Frauke Ackermann
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany.
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Sekulovski S, Trowitzsch S. What connects splicing of transfer RNA precursor molecules with pontocerebellar hypoplasia? Bioessays 2023; 45:e2200130. [PMID: 36517085 DOI: 10.1002/bies.202200130] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 01/19/2023]
Abstract
Transfer RNAs (tRNAs) represent the most abundant class of RNA molecules in the cell and are key players during protein synthesis and cellular homeostasis. Aberrations in the extensive tRNA biogenesis pathways lead to severe neurological disorders in humans. Mutations in the tRNA splicing endonuclease (TSEN) and its associated RNA kinase cleavage factor polyribonucleotide kinase subunit 1 (CLP1) cause pontocerebellar hypoplasia (PCH), a heterogeneous group of neurodegenerative disorders, that manifest as underdevelopment of specific brain regions typically accompanied by microcephaly, profound motor impairments, and child mortality. Recently, we demonstrated that mutations leading to specific PCH subtypes destabilize TSEN in vitro and cause imbalances of immature to mature tRNA ratios in patient-derived cells. However, how tRNA processing defects translate to disease on a systems level has not been understood. Recent findings suggested that other cellular processes may be affected by mutations in TSEN/CLP1 and obscure the molecular mechanisms of PCH emergence. Here, we review PCH disease models linked to the TSEN/CLP1 machinery and discuss future directions to study neuropathogenesis.
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Affiliation(s)
- Samoil Sekulovski
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
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Kocaaga A, Yimenicioglu S. Identification of Novel Gene Variants in Children With Drug-Resistant Epilepsy: Expanding the Genetic Spectrum. Pediatr Neurol 2023; 139:7-12. [PMID: 36493596 DOI: 10.1016/j.pediatrneurol.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/09/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Resistance to antiseizure drugs is an important problem in the treatment of individuals with epilepsy. Identifying the molecular etiology of drug-resistant epilepsy (DRE) is crucial for better management of epilepsy. Here, we explore the utility of whole exome sequencing (WES) in identifying causative gene variants in children with DRE. METHODS Forty-five children with DRE who underwent WES tests were included. Genetic examination of all patients included chromosomal analysis and clinical chromosomal microarray followed by WES. The identified variants by WES analysis were classified for pathogenicity based on the American College of Medical Genetics and Genomics guidelines and in silico protein prediction tools. RESULTS The overall diagnostic yield was 55.5% (25 of 45). A total of 26 variants spanning 22 genes were identified in 25 patients. Of note, only 19 of these genes were examined as novel. Ten patients (22.2%) had a pathogenic or likely pathogenic variant. There was a trend associated with a diagnostic genetic test result in girls compared with boys in DRE (P = 0.028). CONCLUSION Our findings expand the mutational spectrum of genes related to DRE. To form disease-specific treatment in children with DRE, the WES analysis should be included in the diagnostic algorithm because of its high diagnostic efficiency.
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Affiliation(s)
- Ayca Kocaaga
- Department of Medical Genetics, Eskisehir City Hospital, Eskişehir, Turkey.
| | - Sevgi Yimenicioglu
- Department of Pediatric Neurology, Eskisehir City Hospital, Eskişehir, Turkey
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Xu R, Yang L, Zhang Z, Liao Y, Yu Y, Zhou D, Li J, Guan H, Xiao W. Cancer-associated fibroblast related gene signature in Helicobacter pylori-based subtypes of gastric carcinoma for prognosis and tumor microenvironment estimation in silico analysis. Front Med (Lausanne) 2023; 10:1079470. [PMID: 36744128 PMCID: PMC9889637 DOI: 10.3389/fmed.2023.1079470] [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: 10/25/2022] [Accepted: 01/03/2023] [Indexed: 01/20/2023] Open
Abstract
Introduction Gastric cancer (GC) remains the major constituent of cancer-related deaths and a global public health challenge with a high incidence rate. Helicobacter pylori (HP) plays an essential role in promoting the occurrence and progression of GC. Cancer-associated fibroblasts (CAFs) are regarded as a significant component in the tumor microenvironment (TME), which is related to the metastasis of GC. However, the regulation mechanisms of CAFs in HP-related GC are not elucidated thoroughly. Methods HP-related genes (HRGs) were downloaded from the GSE84437 and TCGA-GC databases. The two databases were combined into one cohort for training. Furthermore, the consensus unsupervised clustering analysis was obtained to sort the training cohort into different groups for the identification of differential expression genes (DEGs). Weighted correlation network analysis (WGCNA) was performed to verify the correlation between the DEGs and cancer-associated fibroblasts which were key components in the tumor microenvironment. The least absolute shrinkage and selection operator (LASSO) was executed to find cancer-associated fibroblast-related differential expression genes (CDEGs) for the further establishment of a prognostic model. Results and discussion In this study, 52 HP-related genes (HRGs) were screened out based on the GSE84437 and TCGA-GC databases. A total of 804 GC samples were analyzed, respectively, and clustered into two HP-related subtypes. The DEGs identified from the two subtypes were proved to have a relationship with TME. After WGCNA and LASSO, the CAFs-related module was identified, from which 21 gene signatures were confirmed. Then, a CDEGs-Score was constructed and its prediction efficiency in GC patients was conducted for validation. Overall, a highly precise nomogram was established for enhancing the adaptability of the CDEGs-Score. Furthermore, our findings revealed the applicability of CDEGs-Score in the sensitivity of chemotherapeutic drugs. In general, our research provided brand-new possibilities for comprehending HP-related GC, evaluating survival, and more efficient therapeutic strategies.
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Affiliation(s)
- Ruofan Xu
- Department of Infectious Disease, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Le Yang
- Department of Infectious Disease, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Zhewen Zhang
- Department of Infectious Disease, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Yuxuan Liao
- National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yao Yu
- Department of Infectious Disease, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Dawei Zhou
- Department of Infectious Disease, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Jiahao Li
- Department of Infectious Disease, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Haoyu Guan
- Department of Infectious Disease, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Wei Xiao
- Department of Infectious Disease, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Wei Xiao,
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Jin Y, Zhai RG. Presynaptic Cytomatrix Proteins. ADVANCES IN NEUROBIOLOGY 2023; 33:23-42. [PMID: 37615862 DOI: 10.1007/978-3-031-34229-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
The Cytomatrix Assembled at the active Zone (CAZ) of a presynaptic terminal displays electron-dense appearance and defines the center of the synaptic vesicle release. The protein constituents of CAZ are multiple-domain scaffolds that interact extensively with each other and also with an ensemble of synaptic vesicle proteins to ensure docking, fusion, and recycling. Reflecting the central roles of the active zone in synaptic transmission, CAZ proteins are highly conserved throughout evolution. As the nervous system increases complexity and diversity in types of neurons and synapses, CAZ proteins expand in the number of gene and protein isoforms and interacting partners. This chapter summarizes the discovery of the core CAZ proteins and current knowledge of their functions.
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Affiliation(s)
- Yishi Jin
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
| | - R Grace Zhai
- Department of Molecular and Cellular Pharmacology, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA.
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11
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Cohen-Paes ADN, de Carvalho DC, Pastana LF, Dobbin EAF, Moreira FC, de Souza TP, Fernandes MR, Leal DFDVB, de Sá RBA, de Alcântara AL, Guerreiro JF, Ribeiro-dos-Santos Â, dos Santos SEB, de Assumpção PP, dos Santos NPC. Characterization of PCLO Gene in Amazonian Native American Populations. Genes (Basel) 2022; 13:genes13030499. [PMID: 35328053 PMCID: PMC8950494 DOI: 10.3390/genes13030499] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 11/16/2022] Open
Abstract
Genetic variations in PCLO have been associated with different pathologies in global literature, but there are no data regarding this gene in Native American populations. The Amazonian Native American populations have lower genetic diversity and are more different from other continental groups. We investigated 18 genetic variants in the PCLO gene in Amazonian indigenous and compared our results with the ones found in global populations, which were publicly available in the 1000 Genomes Project, gnmAD and ABraOM databases. The results demonstrated that the variants of the PCLO, especially rs17156844, rs550369696, rs61741659 and rs2877, have a significantly higher frequency in Amerindian populations in comparison with other continental populations. These data outline the singular genetic profile of the Native American population from the Brazilian Amazon region.
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Affiliation(s)
- Amanda de Nazaré Cohen-Paes
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Darlen Cardoso de Carvalho
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
| | - Lucas Favacho Pastana
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Elizabeth Ayres Fragoso Dobbin
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Fabiano Cordeiro Moreira
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Tatiane Piedade de Souza
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Marianne Rodrigues Fernandes
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
- Correspondence: ; Tel.: +55-91-99123-4727
| | - Diana Feio da Veiga Borges Leal
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Roberta Borges Andrade de Sá
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Angélica Leite de Alcântara
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - João Farias Guerreiro
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Ândrea Ribeiro-dos-Santos
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Sidney Emanuel Batista dos Santos
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Paulo Pimentel de Assumpção
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
| | - Ney Pereira Carneiro dos Santos
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
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Marine Neurotoxins' Effects on Environmental and Human Health: An OMICS Overview. Mar Drugs 2021; 20:md20010018. [PMID: 35049872 PMCID: PMC8778346 DOI: 10.3390/md20010018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/27/2022] Open
Abstract
Harmful algal blooms (HAB), and the consequent release of toxic metabolites, can be responsible for seafood poisoning outbreaks. Marine wildlife can accumulate these toxins throughout the food chain, which presents a threat to consumers’ health. Some of these toxins, such as saxitoxin (STX), domoic acid (DA), ciguatoxin (CTX), brevetoxin (BTX), tetrodotoxin (TTX), and β-N-methylamino-L-alanine (BMAA), cause severe neurological symptoms in humans. Considerable information is missing, however, notably the consequences of toxin exposures on changes in gene expression, protein profile, and metabolic pathways. This information could lead to understanding the consequence of marine neurotoxin exposure in aquatic organisms and humans. Nevertheless, recent contributions to the knowledge of neurotoxins arise from OMICS-based research, such as genomics, transcriptomics, proteomics, and metabolomics. This review presents a comprehensive overview of the most recent research and of the available solutions to explore OMICS datasets in order to identify new features in terms of ecotoxicology, food safety, and human health. In addition, future perspectives in OMICS studies are discussed.
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Park J, Khan S, Yun DH, Ku T, Villa KL, Lee JE, Zhang Q, Park J, Feng G, Nedivi E, Chung K. Epitope-preserving magnified analysis of proteome (eMAP). SCIENCE ADVANCES 2021; 7:eabf6589. [PMID: 34767453 PMCID: PMC8589305 DOI: 10.1126/sciadv.abf6589] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 09/24/2021] [Indexed: 05/28/2023]
Abstract
Synthetic tissue-hydrogel methods have enabled superresolution investigation of biological systems using diffraction-limited microscopy. However, chemical modification by fixatives can cause loss of antigenicity, limiting molecular interrogation of the tissue gel. Here, we present epitope-preserving magnified analysis of proteome (eMAP) that uses purely physical tissue-gel hybridization to minimize the loss of antigenicity while allowing permanent anchoring of biomolecules. We achieved success rates of 96% and 94% with synaptic antibodies for mouse and marmoset brains, respectively. Maximal preservation of antigenicity allows imaging of nanoscopic architectures in 1000-fold expanded tissues without additional signal amplification. eMAP-processed tissue gel can endure repeated staining and destaining without epitope loss or structural damage, enabling highly multiplexed proteomic analysis. We demonstrated the utility of eMAP as a nanoscopic proteomic interrogation tool by investigating molecular heterogeneity in inhibitory synapses in the mouse brain neocortex and characterizing the spatial distributions of synaptic proteins within synapses in mouse and marmoset brains.
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Affiliation(s)
- Joha Park
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
| | - Sarim Khan
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Department of Chemical Engineering, Indian Institute of Technology (IIT), Roorkee, Uttarakhand 247667, India
| | - Dae Hee Yun
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Taeyun Ku
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
| | - Katherine L. Villa
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Jiachen E. Lee
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Qiangge Zhang
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Juhyuk Park
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
- Department of Chemical Engineering, MIT, Cambridge, MA 02142, USA
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
| | - Guoping Feng
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Elly Nedivi
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Kwanghun Chung
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
- Department of Chemical Engineering, MIT, Cambridge, MA 02142, USA
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
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Chen CH, Huang YS, Liao DL, Huang CY, Lin CH, Fang TH. Identification of Rare Mutations of Two Presynaptic Cytomatrix Genes BSN and PCLO in Schizophrenia and Bipolar Disorder. J Pers Med 2021; 11:jpm11111057. [PMID: 34834409 PMCID: PMC8625612 DOI: 10.3390/jpm11111057] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/11/2021] [Accepted: 10/19/2021] [Indexed: 12/14/2022] Open
Abstract
Schizophrenia and bipolar disorder are severe mental disorders with a major component of genetic factors in their etiology. Rare mutations play a significant role in these two disorders, and they are highly heterogeneous and personalized. Identification of personalized mutations is essential for the establishment of molecular diagnosis, providing insight into pathogenesis and guiding the personalized treatment for each affected patient. We conducted whole-genome sequencing analysis of families with schizophrenia and bipolar disorder to search for their genetic underpinnings. This report identified a rare missense mutation Arg1087Gln of BSN (bassoon presynaptic cytomatrix protein) co-segregating with schizophrenia in a family with multiple affected members. Furthermore, we identified the rare missense mutation Ser1535Leu of PCLO (piccolo presynaptic cytomatrix protein) in two sisters with bipolar disorder and another rare missense mutation, His5142Arg in PCLO, in a patient with schizophrenia. These three missense mutations were very rare and were predicted to be pathogenic. The BSN and PCLO genes encode two structurally related proteins of the presynaptic cytomatrix at the active zone that regulates neurotransmission at the presynaptic neuronal terminal. Our findings suggest the involvement of the presynaptic matrix in the pathogenesis of schizophrenia and bipolar disorder, and BSN and PCLO are the risk genes for schizophrenia and bipolar disorder.
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Affiliation(s)
- Chia-Hsiang Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan;
- Department and Institute of Biomedical Sciences, Chang Gung University, Taoyuan 333, Taiwan;
- Correspondence:
| | - Yu-Shu Huang
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan;
| | - Ding-Lieh Liao
- Taoyuan Psychiatric Center, Department of General Psychiatry, Taoyuan 330, Taiwan; (D.-L.L.); (C.-H.L.)
| | - Cheng-Yi Huang
- Bali Psychiatric Center, Department of Community Psychiatry, New Taipei City 249, Taiwan;
| | - Chia-Heng Lin
- Taoyuan Psychiatric Center, Department of General Psychiatry, Taoyuan 330, Taiwan; (D.-L.L.); (C.-H.L.)
| | - Ting-Hsuan Fang
- Department and Institute of Biomedical Sciences, Chang Gung University, Taoyuan 333, Taiwan;
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Piccolo is essential for the maintenance of mouse retina but not cochlear hair cell function. Aging (Albany NY) 2021; 13:11678-11695. [PMID: 33882456 PMCID: PMC8109093 DOI: 10.18632/aging.202861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/16/2021] [Indexed: 12/14/2022]
Abstract
Piccolo is a presynaptic protein with high conservation among different species, and the expression of Piccolo is extensive in vertebrates. Recently, a small fragment of Piccolo (Piccolino), arising due to the incomplete splicing of intron 5/6, was found to be present in the synapses of retinas and cochleae. However, the comprehensive function of Piccolo in the retina and cochlea remains unclear. In this study, we generated Piccolo knockout mice using CRISPR-Cas9 technology to explore the function of Piccolo. Unexpectedly, whereas no abnormalities were found in the cochlear hair cells of the mutant mice, significant differences were found in the retinas, in which two layers (the outer nuclear layer and the outer plexiform layer) were absent. Additionally, the amplitudes of electroretinograms were significantly reduced and pigmentation was observed in the fundoscopy of the mutant mouse retinas. The expression levels of Bassoon, a homolog of Piccolo, as well as synapse-associated proteins CtBP1, CtBP2, Kif3A, and Rim1 were down-regulated. The numbers of ribbon synapses in the retinas of the mutant mice were also reduced. Altogether, the phenotype of Piccolo-/- mice resembled the symptoms of retinitis pigmentosa (RP) in humans, suggesting Piccolo might be a candidate gene of RP and indicates Piccolo knockout mice are a good model for elucidating the molecular mechanisms of RP.
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Biallelic hypomorphic mutations in HEATR5B, encoding HEAT repeat-containing protein 5B, in a neurological syndrome with pontocerebellar hypoplasia. Eur J Hum Genet 2021; 29:957-964. [PMID: 33824466 DOI: 10.1038/s41431-021-00832-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/12/2021] [Accepted: 02/09/2021] [Indexed: 11/09/2022] Open
Abstract
HEAT repeats are 37-47 amino acid flexible tandem repeat structural motifs occurring in a wide variety of eukaryotic proteins with diverse functions. Due to their ability to undergo elastic conformational changes, they often serve as scaffolds at sites of protein interactions. Here, we describe four affected children from two families presenting with pontocerebellar hypoplasia manifest clinically with neonatal seizures, severe intellectual disability, and motor delay. Whole exome sequencing identified biallelic variants at predicted splice sites in intron 31 of HEATR5B, encoding the HEAT repeat-containing protein 5B segregating in a recessive fashion. Aberrant splicing was found in patient fibroblasts, which correlated with reduced levels of HEATR5B protein. HEATR5B is expressed during brain development in human, and we failed to recover live-born homozygous Heatr5b knockout mice. Taken together, our results implicate loss of HEATR5B in pontocerebellar hypoplasia.
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John A, Ng-Cordell E, Hanna N, Brkic D, Baker K. The neurodevelopmental spectrum of synaptic vesicle cycling disorders. J Neurochem 2021; 157:208-228. [PMID: 32738165 DOI: 10.1111/jnc.15135] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 12/11/2022]
Abstract
In this review, we describe and discuss neurodevelopmental phenotypes arising from rare, high penetrance genomic variants which directly influence synaptic vesicle cycling (SVC disorders). Pathogenic variants in each SVC disorder gene lead to disturbance of at least one SVC subprocess, namely vesicle trafficking (e.g. KIF1A and GDI1), clustering (e.g. TRIO, NRXN1 and SYN1), docking and priming (e.g. STXBP1), fusion (e.g. SYT1 and PRRT2) or re-uptake (e.g. DNM1, AP1S2 and TBC1D24). We observe that SVC disorders share a common set of neurological symptoms (movement disorders, epilepsies), cognitive impairments (developmental delay, intellectual disabilities, cerebral visual impairment) and mental health difficulties (autism, ADHD, psychiatric symptoms). On the other hand, there is notable phenotypic variation between and within disorders, which may reflect selective disruption to SVC subprocesses, spatiotemporal and cell-specific gene expression profiles, mutation-specific effects, or modifying factors. Understanding the common cellular and systems mechanisms underlying neurodevelopmental phenotypes in SVC disorders, and the factors responsible for variation in clinical presentations and outcomes, may translate to personalized clinical management and improved quality of life for patients and families.
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Affiliation(s)
- Abinayah John
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
| | - Elise Ng-Cordell
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
| | - Nancy Hanna
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
| | - Diandra Brkic
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
| | - Kate Baker
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
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Abstract
Cerebellar hypoplasia (CH) refers to a cerebellum of reduced volume with preserved shape. CH is associated with a broad heterogeneity in neuroradiologic features, etiologies, clinical characteristics, and neurodevelopmental outcomes, challenging physicians evaluating children with CH. Traditionally, neuroimaging has been a key tool to categorize CH based on the pattern of cerebellar involvement (e.g., hypoplasia of cerebellar vermis only vs. hypoplasia of both the vermis and cerebellar hemispheres) and the presence of associated brainstem and cerebral anomalies. With the advances in genetic technologies of the recent decade, many novel CH genes have been identified, and consequently, a constant updating of the literature and revision of the classification of cerebellar malformations are needed. Here, we review the current literature on CH. We propose a systematic approach to recognize specific neuroimaging patterns associated with CH, based on whether the CH is isolated or associated with posterior cerebrospinal fluid anomalies, specific brainstem or cerebellar malformations, brainstem hypoplasia with or without cortical migration anomalies, or dysplasia. The CH radiologic pattern and clinical assessment will allow the clinician to guide his investigations and genetic testing, give a more precise diagnosis, screen for associated comorbidities, and improve prognostication of associated neurodevelopmental outcomes.
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Appelhof B, Wagner M, Hoefele J, Heinze A, Roser T, Koch-Hogrebe M, Roosendaal SD, Dehghani M, Mehrjardi MYV, Torti E, Houlden H, Maroofian R, Rajabi F, Sticht H, Baas F, Wieczorek D, Jamra RA. Pontocerebellar hypoplasia due to bi-allelic variants in MINPP1. Eur J Hum Genet 2020; 29:411-421. [PMID: 33168985 PMCID: PMC7940488 DOI: 10.1038/s41431-020-00749-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/11/2020] [Accepted: 09/22/2020] [Indexed: 12/24/2022] Open
Abstract
Pontocerebellar hypoplasia (PCH) describes a group of rare heterogeneous neurodegenerative diseases with prenatal onset. Here we describe eight children with PCH from four unrelated families harboring the homozygous MINPP1 (NM_004897.4) variants; c.75_94del, p.(Leu27Argfs*39), c.851 C > A, p.(Ala284Asp), c.1210 C > T, p.(Arg404*), and c.992 T > G, p.(Ile331Ser). The homozygous p.(Leu27Argfs*39) change is predicted to result in a complete absence of MINPP1. The p.(Arg404*) would likely lead to a nonsense mediated decay, or alternatively, a loss of several secondary structure elements impairing protein folding. The missense p.(Ala284Asp) affects a buried, hydrophobic residue within the globular domain. The introduction of aspartic acid is energetically highly unfavorable and therefore predicted to cause a significant reduction in protein stability. The missense p.(Ile331Ser) affects the tight hydrophobic interactions of the isoleucine by the disruption of the polar side chain of serine, destabilizing the structure of MINPP1. The overlap of the above-mentioned genotypes and phenotypes is highly improbable by chance. MINPP1 is the only enzyme that hydrolyses inositol phosphates in the endoplasmic reticulum lumen and several studies support its role in stress induced apoptosis. The pathomechanism explaining the disease mechanism remains unknown, however several others genes of the inositol phosphatase metabolism (e.g., INPP5K, FIG4, INPP5E, ITPR1) are correlated with phenotypes of neurodevelopmental disorders. Taken together, we present MINPP1 as a novel autosomal recessive pontocerebellar hypoplasia gene.
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Affiliation(s)
- Bart Appelhof
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Matias Wagner
- Institute of Neurogenomics, Helmholtz Zentrum Munich, Neuherberg, Germany, Technical University of Munich, Munich, Germany.,Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Anja Heinze
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, Germany
| | - Timo Roser
- Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Department of Pediatrics, Dr. von Haunersches Children's Hospital, Ludwig-Maximilian-University of Munich, Munich, Germany
| | | | - Stefan D Roosendaal
- Department of Radiology, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Mohammadreza Dehghani
- Medical Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | | | - Henry Houlden
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Reza Maroofian
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Farrah Rajabi
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachussetts, USA
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander -Nürnberg, Erlangen, Germany
| | - Frank Baas
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands.
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, Germany.
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Sabaie H, Ahangar NK, Ghafouri-Fard S, Taheri M, Rezazadeh M. Clinical and genetic features of PEHO and PEHO-Like syndromes: A scoping review. Biomed Pharmacother 2020; 131:110793. [PMID: 33152950 DOI: 10.1016/j.biopha.2020.110793] [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: 07/08/2020] [Revised: 09/09/2020] [Accepted: 09/19/2020] [Indexed: 01/15/2023] Open
Abstract
Progressive encephalopathy with edema, hypsarrhythmia, and optic atrophy (PEHO) syndrome is a genetic neurological condition characterized by extreme cerebellar atrophy. PEHO-Like syndrome is comparable to PEHO syndrome, with the exception that there is no typical neuro-radiologic or neuro-ophthalmic findings. PEHO spectrum disorders are highly clinically and genetically heterogeneous, and this has challenged their diagnosis. This scoping review aims to summarize and discuss common clinical and genetic features of these syndromes to help future researches. This study was performed according to a six-stage methodology structure and PRISMA guideline. A systematic search of seven databases was performed to find eligible publications prior to June 2020. Articles screening and data extraction were independently performed by two reviewers and quantitative and qualitative analyses were conducted. Thirty-eight articles were identified that fulfill the inclusion criteria. Cerebellar atrophy was the main clinical difference between the two groups but data on optic atrophy and infantile spasms/hypsarrhythmia were not consistent with the previously essential diagnostic criteria. Genetic analysis was performed in several studies, leading to identification of pathogenic variants in different genes that caused these conditions due to different mechanisms. Genetic studies could revolutionize the diagnosis process and our understanding of the etiology of this challenging group of patients by providing targeted sequencing panels and exome- or genome-scale studies in the future.
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Affiliation(s)
- Hani Sabaie
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Noora Karim Ahangar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Maryam Rezazadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Lazensky R, Hunter ME, Moraga Amador D, Al-Khedery B, Yu F, Walsh C, Gitzendanner MA, Tripp K, Walsh MT, Denslow ND. Investigating the gene expression profiles of rehabilitated Florida manatees (Trichechus manatus latirostris) following red tide exposure. PLoS One 2020; 15:e0234150. [PMID: 32614830 PMCID: PMC7331979 DOI: 10.1371/journal.pone.0234150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/19/2020] [Indexed: 01/14/2023] Open
Abstract
To investigate a Florida manatee (Trichechus manatus latirostris) mortality event following a red tide bloom in Southwest Florida, an RNA sequencing experiment was conducted. Gene expression changes in white blood cells were assessed in manatees rescued from a red tide affected area (n = 4) and a control group (n = 7) using RNA sequencing. The genes with the largest fold changes were compared between the two groups to identify molecular pathways related to cellular and disease processes. In total, 591 genes (false discovery rate <0.05) were differentially expressed in the red tide group. Of these, 158 were upregulated and 433 were downregulated. This suggests major changes in white blood cell composition following an exposure to red tide. The most highly upregulated gene, Osteoclast associated 2C immunoglobulin-like receptor (OSCAR), was upregulated 12-fold. This gene is involved in initiating the immune response and maintaining a role in adaptive and innate immunity. The most highly downregulated gene, Piccolo presynaptic cytomatrix protein (PCLO), was downregulated by a factor of 977-fold. This gene is associated with cognitive functioning and neurotransmitter release. Downregulation of this gene in other studies was associated with neuronal loss and neuron synapse dysfunction. Among the cellular pathways that were most affected, immune response, including inflammation, wounds and injuries, cell proliferation, and apoptosis were the most predominant. The pathway with the most differentially expressed genes was the immune response pathway with 98 genes involved, many of them downregulated. Assessing the changes in gene expression associated with red tide exposure enhances our understanding of manatee immune response to the red tide toxins and will aid in the development of red tide biomarkers.
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Affiliation(s)
- Rebecca Lazensky
- Department of Physiological Sciences and Center for Environmental & Human Toxicology, University of Florida, Gainesville, Florida, United States of America
- Aquatic Animal Health Program, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Margaret E. Hunter
- Wetland and Aquatic Research Center, U. S. Geological Survey, Sirenia Project, Gainesville, Florida, United States of America
| | - David Moraga Amador
- Interdisciplinary Center for Biotechnology Research, Gainesville, Florida, United States of America
| | - Basima Al-Khedery
- Interdisciplinary Center for Biotechnology Research, Gainesville, Florida, United States of America
| | - Fahong Yu
- Interdisciplinary Center for Biotechnology Research, Gainesville, Florida, United States of America
| | - Cathy Walsh
- Mote Marine Laboratory, Sarasota, Florida, United States of America
| | - Matthew A. Gitzendanner
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - Katie Tripp
- Save the Manatee Club, Maitland, Florida, United States of America
| | - Michael T. Walsh
- Aquatic Animal Health Program, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
- Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
- * E-mail: (NDD); (MTW)
| | - Nancy D. Denslow
- Department of Physiological Sciences and Center for Environmental & Human Toxicology, University of Florida, Gainesville, Florida, United States of America
- * E-mail: (NDD); (MTW)
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Pontocerebellar hypoplasia type 11: Does the genetic defect determine timing of cerebellar pathology? Eur J Med Genet 2020; 63:103938. [PMID: 32360255 DOI: 10.1016/j.ejmg.2020.103938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/17/2020] [Accepted: 04/23/2020] [Indexed: 11/24/2022]
Abstract
Pontocerebellar hypoplasia (PCH) comprises a clinically and genetically heterogeneous group of disorders characterized by hypoplasia and degeneration of the cerebellum and ventral pons. To date at least 18 different clinical subtypes of PCH associated with pathogenic variants in 19 different genes have been described. Only recently, bi-allelic variants in TBC1D23 have been reported as the underlying molecular defect in seven index cases with a suspected non-degenerative form of PCH, PCH type 11 (PCH11). We used exome sequencing to investigate an individual with global developmental delay, ataxia, seizures, and progressive PCH. Brain volume was evaluated over a disease course of 14 years using volumetric magnetic resonance imaging (MRI). Volume alterations were compared to age-matched controls as well as data from children with PCH2. We identified a homozygous frameshift variant in exon 9 of 18 of TBC1D23 predicting a loss of protein function. Brain morphometry revealed a pattern of pontine, brain stem, and supratentorial volume loss similar to PCH2 patients although less pronounced. Intriguingly, cerebral MRI findings at the age of 1 and 15 years clearly showed progressive atrophy of the cerebellum, especially the hemispheres. In four of the cases reported in the literature cerebellar hemispheres could be evaluated on the MRIs displayed, they also showed atrophic foliae. While pontine hypoplasia and pronounced microcephaly are in line with previous reports on PCH11, our observations of clearly postnatal atrophy of the cerebellum argues for a different pathomechanism than in the other forms of PCH and supports the hypothesis that TBC1D23 deficiency predominantly interferes with postnatal rather than with prenatal cerebellar development.
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Falck J, Bruns C, Hoffmann-Conaway S, Straub I, Plautz EJ, Orlando M, Munawar H, Rivalan M, Winter Y, Izsvák Z, Schmitz D, Hamra FK, Hallermann S, Garner CC, Ackermann F. Loss of Piccolo Function in Rats Induces Cerebellar Network Dysfunction and Pontocerebellar Hypoplasia Type 3-like Phenotypes. J Neurosci 2020; 40:2943-2959. [PMID: 32122952 PMCID: PMC7117892 DOI: 10.1523/jneurosci.2316-19.2020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 12/16/2022] Open
Abstract
Piccolo, a presynaptic active zone protein, is best known for its role in the regulated assembly and function of vertebrate synapses. Genetic studies suggest a further link to several psychiatric disorders as well as Pontocerebellar Hypoplasia type 3 (PCH3). We have characterized recently generated Piccolo KO (Pclogt/gt ) rats. Analysis of rats of both sexes revealed a dramatic reduction in brain size compared with WT (Pclowt/wt ) animals, attributed to a decrease in the size of the cerebral cortical, cerebellar, and pontine regions. Analysis of the cerebellum and brainstem revealed a reduced granule cell layer and a reduction in size of pontine nuclei. Moreover, the maturation of mossy fiber afferents from pontine neurons and the expression of the α6 GABAA receptor subunit at the mossy fiber-granule cell synapse are perturbed, as well as the innervation of Purkinje cells by cerebellar climbing fibers. Ultrastructural and functional studies revealed a reduced size of mossy fiber boutons, with fewer synaptic vesicles and altered synaptic transmission. These data imply that Piccolo is required for the normal development, maturation, and function of neuronal networks formed between the brainstem and cerebellum. Consistently, behavioral studies demonstrated that adult Pclogt/gt rats display impaired motor coordination, despite adequate performance in tasks that reflect muscle strength and locomotion. Together, these data suggest that loss of Piccolo function in patients with PCH3 could be involved in many of the observed anatomical and behavioral symptoms, and that the further analysis of these animals could provide fundamental mechanistic insights into this devastating disorder.SIGNIFICANCE STATEMENT Pontocerebellar Hypoplasia Type 3 is a devastating developmental disorder associated with severe developmental delay, progressive microcephaly with brachycephaly, optic atrophy, seizures, and hypertonia with hyperreflexia. Recent genetic studies have identified non-sense mutations in the coding region of the PCLO gene, suggesting a functional link between this disorder and the presynaptic active zone. Our analysis of Piccolo KO rats supports this hypothesis, formally demonstrating that anatomical and behavioral phenotypes seen in patients with Pontocerebellar Hypoplasia Type 3 are also exhibited by these Piccolo deficient animals.
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Affiliation(s)
- Joanne Falck
- German Center for Neurodegenerative Diseases, Charité Medical University, 10117 Berlin, Germany
| | - Christine Bruns
- German Center for Neurodegenerative Diseases, Charité Medical University, 10117 Berlin, Germany
| | - Sheila Hoffmann-Conaway
- German Center for Neurodegenerative Diseases, Charité Medical University, 10117 Berlin, Germany
| | - Isabelle Straub
- Carl-Ludwig Institute for Physiology, 04103 Leipzig, Germany
| | - Erik J Plautz
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern, Dallas, Texas 75390
| | - Marta Orlando
- Charité Medical University Berlin and Berlin Institute of Health, NeuroCure Cluster of Excellence, 10117 Berlin, Germany
| | - Humaira Munawar
- Department of Biology, Humboldt University, 10099 Berlin, Germany
| | - Marion Rivalan
- Charité Medical University Berlin and Berlin Institute of Health, NeuroCure Cluster of Excellence, 10117 Berlin, Germany
- Department of Biology, Humboldt University, 10099 Berlin, Germany
| | - York Winter
- Charité Medical University Berlin and Berlin Institute of Health, NeuroCure Cluster of Excellence, 10117 Berlin, Germany
- Department of Biology, Humboldt University, 10099 Berlin, Germany
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, 13125 Berlin, Germany, and
| | - Dietmar Schmitz
- Charité Medical University Berlin and Berlin Institute of Health, NeuroCure Cluster of Excellence, 10117 Berlin, Germany
| | - F Kent Hamra
- Department of Obstetrics and Gynecology, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern, Dallas, Texas 75390
| | | | - Craig Curtis Garner
- German Center for Neurodegenerative Diseases, Charité Medical University, 10117 Berlin, Germany
| | - Frauke Ackermann
- German Center for Neurodegenerative Diseases, Charité Medical University, 10117 Berlin, Germany,
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Krishnamurthy K, Castellano-Sanchez AA, Febres-Aldana CA, Kochiyil J, Brathwaite C, Poppiti RJ. Pontocerebellar Hypoplasia Maps to Chromosome 7q11.23: An Autopsy Case Report of a Novel Genetic Variant. Case Rep Pediatr 2019; 2019:7048537. [PMID: 31885998 PMCID: PMC6925823 DOI: 10.1155/2019/7048537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 11/08/2019] [Accepted: 11/21/2019] [Indexed: 11/29/2022] Open
Abstract
Pontocerebellar hypoplasias are a group of autosomal recessive neurodevelopmetal disorders with varied phenotypic presentations and extensive genetic mutational landscape that are currently classified into ten subtypes. This classification is based predominantly on the genetic iterations as the phenotypic presentations are often broad and overlapping. Pontocerebellar hypoplasia type-3 (PCH3) is an autosomal recessive disorder characterized by a small cerebellar vermis, hyperreflexia, and seizures, described in Middle Eastern families in association with a homozygous truncating mutation of the PCLO gene in locus 7q11-21. This is a case of PCH, with previously unreported novel genetic alterations. The patient is a 1-week-old girl, born at term to a 26-year-old G4P0A3 woman in a nonconsanguinous relation. At birth, the baby was depressed and hypertonic with abnormal tonic-clonic movements of extremities. MRI revealed cerebellar and brainstem hypoplasia. Postmortem examination revealed a palmar simian crease. The cerebellum measured 2.5 cm from side to side and 1 cm from rostral to caudal. The vermis was rudimentary. Sectioning revealed a flattened linear fourth ventricle, scant abortive cerebellar foliae, and a markedly small cerebellum when compared with the cerebrum and with age-matched size. H&E-stained sections of cerebellum revealed scant rudimentary foliae. A rudimentary unilateral embolliform nucleus was identified. The remaining cerebellar nuclei were absent. Chromosomal microarray showed an interstitial duplication of 841 kB on chromosome 7q11.23. Locus 7q11.23 contains FGL2 and GSAP genes and is 5 MB upstream of the 7q11-21 region, suggesting a possible linkage. This novel genomic finding possibly represents a new familial variant of PCH closely associated with PCH-3 and further strengthens its association with the 7q11 locus.
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Affiliation(s)
- Kritika Krishnamurthy
- A. M. Rywlin MD Department of Pathology, Mount Sinai Medical Center, Miami Beach, FL, USA
| | - Amilcar A. Castellano-Sanchez
- A. M. Rywlin MD Department of Pathology, Mount Sinai Medical Center, Miami Beach, FL, USA
- Florida International University, Herbert Wertheim College of Medicine, Miami, FL, USA
| | | | - Jyotsna Kochiyil
- Department of Radiology, Mount Sinai Medical Center, Miami Beach, FL, USA
| | - Carole Brathwaite
- Florida International University, Herbert Wertheim College of Medicine, Miami, FL, USA
- Department of Pathology, Nicklaus Children's Hospital, Miami, FL, USA
| | - Robert J. Poppiti
- A. M. Rywlin MD Department of Pathology, Mount Sinai Medical Center, Miami Beach, FL, USA
- Florida International University, Herbert Wertheim College of Medicine, Miami, FL, USA
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Pontocerebellar hypoplasia with rhombencephalosynapsis and microlissencephaly expands the spectrum of PCH type 1B. Eur J Med Genet 2019; 63:103814. [PMID: 31770597 DOI: 10.1016/j.ejmg.2019.103814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/14/2019] [Accepted: 11/11/2019] [Indexed: 11/20/2022]
Abstract
Rhombencephalosynapsis is a rare cerebellar malformation developing during embryogenesis defined by vermian agenesis or hypogenesis with fusion of the cerebellar hemispheres. It occurs either alone or in association with other cerebral and/or extracerebral anomalies. Its association with microlissencephaly is exceedingly rare and to date, only a heterozygous de novo missense variant in ADGRL2, a gene encoding Adhesion G-Protein-Coupled Receptor L2, has been identified. We report on two siblings of Roma origin presenting with severe growth retardation, fetal akinesia, microlissencephaly and small cerebellum with vermian agenesis. Neuropathological studies revealed extreme paucity in pontine transverse fibres, rudimentary olivary nuclei and rhombencephalosynapsis with vanishing spinal motoneurons in both fetuses. Comparative fetus-parent exome sequencing revealed in both fetuses a homozygous variant in exon 1 of the EXOSC3 gene encoding a core component of the RNA exosome, c.92G > C; p.(Gly31Ala). EXOSC3 accounts for 40%-75% of patients affected by ponto-cerebellar hypoplasia with spinal muscular atrophy (PCH1B). The c.92G > C variant is a founder mutation in the Roma population and has been reported in severe PCH1B. PCH1B is characterized by a broad phenotypic spectrum, ranging from mild phenotypes with spasticity, mild to moderate intellectual disability, pronounced distal muscular and cerebellar atrophy/hypoplasia, to severe phenotypes with profound global developmental delay, progressive microcephaly and atrophy of the cerebellar hemispheres. In PCH1B, the usual cerebellar lesions affect mainly the hemispheres with relative sparing of vermis that radically differs from rhombencephalosynapsis. This unusual foetal presentation expands the spectrum of PCH1B and highlights the diversity of rhombencephalosynapsis etiologies.
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Kim SC, Shin R, Seo HY, Kim M, Park JW, Jeong SY, Ku JL. Identification of a Novel Fusion Gene, FAM174A-WWC1, in Early-Onset Colorectal Cancer: Establishment and Characterization of Four Human Cancer Cell Lines from Early-Onset Colorectal Cancers. Transl Oncol 2019; 12:1185-1195. [PMID: 31228769 PMCID: PMC6600802 DOI: 10.1016/j.tranon.2019.05.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/28/2019] [Accepted: 05/29/2019] [Indexed: 12/20/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer diagnosed worldwide and represents the second most common cause of all cancer-related deaths in Korea. Although epidemiological data indicate a sharp increase in the incidence of CRC among individuals older than 50 years, more than 10% of CRCs occur before reaching 50. These are known as early-onset CRCs (EOCRCs) and are likely to be suggestive of hereditary predisposition. However, known familial CRC syndromes account for only 20% of genetic aberrations of EOCRC, and the remaining 80% are still in question. Therefore, we aimed to establish reproducible biological resources and contribute to expand the mutation database of EOCRC. Four cell lines derived from the original tumor mass of CRC patients diagnosed under age 30 years were established, and next-generation sequencing technique was used to identify the genetic features of EOCRC. We have identified one novel fusion gene, FAM174A-WWC1, and analyzed its functional role. The induction of FAM174A-WWC1 to normal fibroblast caused alternations in cellular morphology as well as intercellular expression of E-cadherin and N-cadherin. Moreover, WWC1 carrying the fused FAM174A domain not only abrogated the membrane expression of YAP1 but also significantly increased the levels of nucleic YAP1. As a result, the FAM174A-WWC1 expression increased the oncogenic capacity and invasiveness of normal fibroblasts, which suggests its role as a potential driver mutation of EOCRC.
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Affiliation(s)
- Soon-Chan Kim
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Rumi Shin
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Surgery, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul 07061
| | - Ha-Young Seo
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Minjung Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Division of Colorectal Surgery, Department of Surgery, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Ji Won Park
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Division of Colorectal Surgery, Department of Surgery, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Seung-Yong Jeong
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Division of Colorectal Surgery, Department of Surgery, Seoul National University Hospital, Seoul 03080, Republic of Korea.
| | - Ja-Lok Ku
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.
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Ackermann F, Schink KO, Bruns C, Izsvák Z, Hamra FK, Rosenmund C, Garner CC. Critical role for Piccolo in synaptic vesicle retrieval. eLife 2019; 8:46629. [PMID: 31074746 PMCID: PMC6541439 DOI: 10.7554/elife.46629] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/09/2019] [Indexed: 12/30/2022] Open
Abstract
Loss of function of the active zone protein Piccolo has recently been linked to a disease, Pontocerebellar Hypoplasia type 3, which causes brain atrophy. Here, we address how Piccolo inactivation in rat neurons adversely affects synaptic function and thus may contribute to neuronal loss. Our analysis shows that Piccolo is critical for the recycling and maintenance of synaptic vesicles. We find that boutons lacking Piccolo have deficits in the Rab5/EEA1 dependent formation of early endosomes and thus the recycling of SVs. Mechanistically, impaired Rab5 function was caused by reduced synaptic recruitment of Pra1, known to interact selectively with the zinc finger domains of Piccolo. Importantly, over-expression of GTPase deficient Rab5 or the Znf1 domain of Piccolo restores the size and recycling of SV pools. These data provide a molecular link between the active zone and endosome sorting at synapses providing hints to how Piccolo contributes to developmental and psychiatric disorders.
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Affiliation(s)
- Frauke Ackermann
- German Center for Neurodegenerative Diseases e.V. (DZNE), Charité Medical University, Berlin, Germany
| | - Kay Oliver Schink
- Center for Cancer Biomedicine, University of Oslo, Norwegian Radium Hospital, Oslo, Norway
| | - Christine Bruns
- German Center for Neurodegenerative Diseases e.V. (DZNE), Charité Medical University, Berlin, Germany
| | - Zsuzsanna Izsvák
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - F Kent Hamra
- Department of Obstetrics and Gynecology, University of Texas Southwestern, Dallas, United States
| | - Christian Rosenmund
- NeuroCure Cluster of Excellence, Neuroscience Research Center, Charité Medical University, Berlin, Germany
| | - Craig Curtis Garner
- German Center for Neurodegenerative Diseases e.V. (DZNE), Charité Medical University, Berlin, Germany
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29
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Chitre M, Nahorski MS, Stouffer K, Dunning-Davies B, Houston H, Wakeling EL, Brady AF, Zuberi SM, Suri M, Parker APJ, Woods CG. PEHO syndrome: the endpoint of different genetic epilepsies. J Med Genet 2018; 55:803-813. [DOI: 10.1136/jmedgenet-2018-105288] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 07/10/2018] [Accepted: 08/17/2018] [Indexed: 01/08/2023]
Abstract
BackgroundProgressive encephalopathy, hypsarrhythmia and optic atrophy (PEHO) has been described as a clinically distinct syndrome. It has been postulated that it is an autosomal recessive condition. However, the aetiology is poorly understood, and the genetic basis of the condition has not been fully elucidated. Our objective was to discover if PEHO syndrome is a single gene disorder.MethodChildren with PEHO and PEHO-like syndrome were recruited. Clinical, neurological and dysmorphic features were recorded; EEG reports and MRI scans were reviewed. Where possible, exome sequencing was carried out first to seek mutations in known early infantile developmental and epileptic encephalopathy (DEE) genes and then to use an agnostic approach to seek novel candidate genes. We sought intra–interfamilial phenotypic correlations and genotype–phenotype correlations when pathological mutations were identified.ResultsTwenty-three children were recruited from a diverse ethnic background, 19 of which were suitable for inclusion. They were similar in many of the core and the supporting features of PEHO, but there was significant variation in MRI and ophthalmological findings, even between siblings with the same mutation. A pathogenic genetic variant was identified in 15 of the 19 children. One further girl’s DNA failed analysis, but her two affected sisters shared confirmed variants. Pathogenic variants were identified in seven different genes.ConclusionsWe found significant clinical and genetic heterogeneity. Given the intrafamily variation demonstrated, we question whether the diagnostic criteria for MRI and ophthalmic findings should be altered. We also question whether PEHO and PEHO-like syndrome represent differing points on a clinical spectrum of the DEE. We conclude that PEHO and PEHO-like syndrome are clinically and genetically diverse entities—and are phenotypic endpoints of many severe genetic encephalopathies.
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30
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Nguyen TL, Duchon A, Manousopoulou A, Loaëc N, Villiers B, Pani G, Karatas M, Mechling AE, Harsan LA, Limanton E, Bazureau JP, Carreaux F, Garbis SD, Meijer L, Herault Y. Correction of cognitive deficits in mouse models of Down syndrome by a pharmacological inhibitor of DYRK1A. Dis Model Mech 2018; 11:dmm035634. [PMID: 30115750 PMCID: PMC6176987 DOI: 10.1242/dmm.035634] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/01/2018] [Indexed: 12/13/2022] Open
Abstract
Growing evidence supports the implication of DYRK1A in the development of cognitive deficits seen in Down syndrome (DS) and Alzheimer's disease (AD). We here demonstrate that pharmacological inhibition of brain DYRK1A is able to correct recognition memory deficits in three DS mouse models with increasing genetic complexity [Tg(Dyrk1a), Ts65Dn, Dp1Yey], all expressing an extra copy of Dyrk1a Overexpressed DYRK1A accumulates in the cytoplasm and at the synapse. Treatment of the three DS models with the pharmacological DYRK1A inhibitor leucettine L41 leads to normalization of DYRK1A activity and corrects the novel object cognitive impairment observed in these models. Brain functional magnetic resonance imaging reveals that this cognitive improvement is paralleled by functional connectivity remodelling of core brain areas involved in learning/memory processes. The impact of Dyrk1a trisomy and L41 treatment on brain phosphoproteins was investigated by a quantitative phosphoproteomics method, revealing the implication of synaptic (synapsin 1) and cytoskeletal components involved in synaptic response and axonal organization. These results encourage the development of DYRK1A inhibitors as drug candidates to treat cognitive deficits associated with DS and AD.
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Affiliation(s)
- Thu Lan Nguyen
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, 67400 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67400 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, 67400 Illkirch, France
- Université de Strasbourg, 67400 Illkirch, France
- ManRos Therapeutics, Perharidy Research Center, 29680 Roscoff, Bretagne, France
| | - Arnaud Duchon
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, 67400 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67400 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, 67400 Illkirch, France
- Université de Strasbourg, 67400 Illkirch, France
| | - Antigoni Manousopoulou
- Faculty of Medicine/Cancer Sciences & Clinical and Experimental Medicine, University of Southampton, Center for Proteomic Research, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Nadège Loaëc
- ManRos Therapeutics, Perharidy Research Center, 29680 Roscoff, Bretagne, France
| | - Benoît Villiers
- ManRos Therapeutics, Perharidy Research Center, 29680 Roscoff, Bretagne, France
| | - Guillaume Pani
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, 67400 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67400 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, 67400 Illkirch, France
- Université de Strasbourg, 67400 Illkirch, France
| | - Meltem Karatas
- Laboratory of Engineering, Informatics and Imaging (ICube), Integrative multimodal imaging in healthcare (IMIS), UMR 7357, and University Hospital Strasbourg, Department of Biophysics and Nuclear Medicine, University of Strasbourg, 67400 Illkirch, France
- Department of Radiology, Medical Physics, Medical Center - University of Freiburg, Breisacher Strasse 60a, 79106 Freiburg, Germany
| | - Anna E Mechling
- Department of Radiology, Medical Physics, Medical Center - University of Freiburg, Breisacher Strasse 60a, 79106 Freiburg, Germany
| | - Laura-Adela Harsan
- Laboratory of Engineering, Informatics and Imaging (ICube), Integrative multimodal imaging in healthcare (IMIS), UMR 7357, and University Hospital Strasbourg, Department of Biophysics and Nuclear Medicine, University of Strasbourg, 67400 Illkirch, France
- Department of Radiology, Medical Physics, Medical Center - University of Freiburg, Breisacher Strasse 60a, 79106 Freiburg, Germany
| | - Emmanuelle Limanton
- Université de Rennes 1, ISCR (Institut des sciences chimiques de Rennes)-UMR, 6226, 35000 Rennes, France
| | - Jean-Pierre Bazureau
- Université de Rennes 1, ISCR (Institut des sciences chimiques de Rennes)-UMR, 6226, 35000 Rennes, France
| | - François Carreaux
- Université de Rennes 1, ISCR (Institut des sciences chimiques de Rennes)-UMR, 6226, 35000 Rennes, France
| | - Spiros D Garbis
- Faculty of Medicine/Cancer Sciences & Clinical and Experimental Medicine, University of Southampton, Center for Proteomic Research, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Laurent Meijer
- ManRos Therapeutics, Perharidy Research Center, 29680 Roscoff, Bretagne, France
| | - Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, 67400 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67400 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, 67400 Illkirch, France
- Université de Strasbourg, 67400 Illkirch, France
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31
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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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32
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van Dijk T, Baas F, Barth PG, Poll-The BT. What's new in pontocerebellar hypoplasia? An update on genes and subtypes. Orphanet J Rare Dis 2018; 13:92. [PMID: 29903031 PMCID: PMC6003036 DOI: 10.1186/s13023-018-0826-2] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 05/16/2018] [Indexed: 12/25/2022] Open
Abstract
Background Pontocerebellar hypoplasia (PCH) describes a rare, heterogeneous group of neurodegenerative disorders mainly with a prenatal onset. Patients have severe hypoplasia or atrophy of cerebellum and pons, with variable involvement of supratentorial structures, motor and cognitive impairments. Based on distinct clinical features and genetic causes, current classification comprises 11 types of PCH. Main text In this review we describe the clinical, neuroradiological and genetic characteristics of the different PCH subtypes, summarize the differential diagnosis and reflect on potential disease mechanisms in PCH. Seventeen PCH-related genes are now listed in the OMIM database, most of them have a function in RNA processing or translation. It is unknown why defects in these apparently ubiquitous processes result in a brain-specific phenotype. Conclusions Many new PCH related genes and phenotypes have been described due to the appliance of next generation sequencing techniques. By including such a broad range of phenotypes, including non-degenerative and postnatal onset disorders, the current classification gives rise to confusion. Despite the discovery of new pathways involved in PCH, treatment is still symptomatic. However, correct diagnosis of PCH is important to provide suitable care and counseling regarding prognosis, and offer appropriate (prenatal) genetic testing to families.
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Affiliation(s)
- Tessa van Dijk
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands.,Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Frank Baas
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter G Barth
- Department of Pediatric Neurology, Academic Medical Center, Amsterdam, The Netherlands
| | - Bwee Tien Poll-The
- Department of Pediatric Neurology, Academic Medical Center, Amsterdam, The Netherlands.
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33
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Wan J, Steffen J, Yourshaw M, Mamsa H, Andersen E, Rudnik-Schöneborn S, Pope K, Howell KB, McLean CA, Kornberg AJ, Joseph J, Lockhart PJ, Zerres K, Ryan MM, Nelson SF, Koehler CM, Jen JC. Loss of function of SLC25A46 causes lethal congenital pontocerebellar hypoplasia. Brain 2017; 139:2877-2890. [PMID: 27543974 DOI: 10.1093/brain/aww212] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/01/2016] [Indexed: 01/17/2023] Open
Abstract
Disturbed mitochondrial fusion and fission have been linked to various neurodegenerative disorders. In siblings from two unrelated families who died soon after birth with a profound neurodevelopmental disorder characterized by pontocerebellar hypoplasia and apnoea, we discovered a missense mutation and an exonic deletion in the SLC25A46 gene encoding a mitochondrial protein recently implicated in optic atrophy spectrum disorder. We performed functional studies that confirmed the mitochondrial localization and pro-fission properties of SLC25A46. Knockdown of slc24a46 expression in zebrafish embryos caused brain malformation, spinal motor neuron loss, and poor motility. At the cellular level, we observed abnormally elongated mitochondria, which was rescued by co-injection of the wild-type but not the mutant slc25a46 mRNA. Conversely, overexpression of the wild-type protein led to mitochondrial fragmentation and disruption of the mitochondrial network. In contrast to mutations causing non-lethal optic atrophy, missense mutations causing lethal congenital pontocerebellar hypoplasia markedly destabilize the protein. Indeed, the clinical severity appears inversely correlated with the relative stability of the mutant protein. This genotype-phenotype correlation underscores the importance of SLC25A46 and fine tuning of mitochondrial fission and fusion in pontocerebellar hypoplasia and central neurodevelopment in addition to optic and peripheral neuropathy across the life span.
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Affiliation(s)
- Jijun Wan
- Department of Neurology, University of California, Los Angeles, CA, USA
| | - Janos Steffen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Michael Yourshaw
- Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Hafsa Mamsa
- Department of Neurology, University of California, Los Angeles, CA, USA
| | - Erik Andersen
- Royal Children's Hospital, Murdoch Children's Research Institute, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Kate Pope
- Royal Children's Hospital, Murdoch Children's Research Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Katherine B Howell
- Royal Children's Hospital, Murdoch Children's Research Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Catriona A McLean
- Anatomical Pathology, The Alfred Hospital; Howard Florey Neuroscience Institute, Melbourne, Victoria, Australia
| | - Andrew J Kornberg
- Royal Children's Hospital, Murdoch Children's Research Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Jörg Joseph
- Department of Neonatology, Bürgerhospital Frankfurt am Main, Germany
| | - Paul J Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Klaus Zerres
- Institut für Humangenetik der RWTH Aachen, Aachen, Germany
| | - Monique M Ryan
- Royal Children's Hospital, Murdoch Children's Research Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Stanley F Nelson
- Department of Human Genetics, University of California, Los Angeles, CA, USA.,Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, USA
| | - Carla M Koehler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Joanna C Jen
- Department of Neurology, University of California, Los Angeles, CA, USA.,Department of Neurobiology, University of California, Los Angeles, CA, USA
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Ivanova EL, Mau-Them FT, Riazuddin S, Kahrizi K, Laugel V, Schaefer E, de Saint Martin A, Runge K, Iqbal Z, Spitz MA, Laura M, Drouot N, Gérard B, Deleuze JF, de Brouwer APM, Razzaq A, Dollfus H, Assir MZ, Nitchké P, Hinckelmann MV, Ropers H, Riazuddin S, Najmabadi H, van Bokhoven H, Chelly J. Homozygous Truncating Variants in TBC1D23 Cause Pontocerebellar Hypoplasia and Alter Cortical Development. Am J Hum Genet 2017; 101:428-440. [PMID: 28823707 DOI: 10.1016/j.ajhg.2017.07.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/19/2017] [Indexed: 01/03/2023] Open
Abstract
Pontocerebellar hypoplasia (PCH) is a heterogeneous group of rare recessive disorders with prenatal onset, characterized by hypoplasia of pons and cerebellum. Mutations in a small number of genes have been reported to cause PCH, and the vast majority of PCH cases are explained by mutations in TSEN54, which encodes a subunit of the tRNA splicing endonuclease complex. Here we report three families with homozygous truncating mutations in TBC1D23 who display moderate to severe intellectual disability and microcephaly. MRI data from available affected subjects revealed PCH, small normally proportioned cerebellum, and corpus callosum anomalies. Furthermore, through in utero electroporation, we show that downregulation of TBC1D23 affects cortical neuron positioning. TBC1D23 is a member of the Tre2-Bub2-Cdc16 (TBC) domain-containing RAB-specific GTPase-activating proteins (TBC/RABGAPs). Members of this protein family negatively regulate RAB proteins and modulate the signaling between RABs and other small GTPases, some of which have a crucial role in the trafficking of intracellular vesicles and are involved in neurological disorders. Here, we demonstrate that dense core vesicles and lysosomal trafficking dynamics are affected in fibroblasts harboring TBC1D23 mutation. We propose that mutations in TBC1D23 are responsible for a form of PCH with small, normally proportioned cerebellum and should be screened in individuals with syndromic pontocereballar hypoplasia.
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Affiliation(s)
- Ekaterina L Ivanova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, 67400 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Frédéric Tran Mau-Them
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaire de Strasbourg, 67000 Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, 67400 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Saima Riazuddin
- Department of Otorhinolaryngology-Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; Shaheed Zulfiqar Ali Bhutto Medical University, Pakistan Institute of Medical Sciences, Islamabad 44000, Pakistan
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, 1985713834 Tehran, Iran
| | - Vincent Laugel
- Department of Pediatrics, Strasbourg University Hospital, 67000 Strasbourg, France; Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, 67000 Strasbourg, France
| | - Elise Schaefer
- Service de Génétique Médicale, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Anne de Saint Martin
- Department of Pediatrics, Strasbourg University Hospital, 67000 Strasbourg, France
| | - Karen Runge
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, 67400 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Zafar Iqbal
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Department of Neurology, Oslo University Hospital, 0450 Oslo, Norway
| | - Marie-Aude Spitz
- Department of Pediatrics, Strasbourg University Hospital, 67000 Strasbourg, France; Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, 67000 Strasbourg, France
| | - Mary Laura
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaire de Strasbourg, 67000 Strasbourg, France
| | - Nathalie Drouot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, 67400 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Bénédicte Gérard
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaire de Strasbourg, 67000 Strasbourg, France
| | | | - Arjan P M de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Attia Razzaq
- Shaheed Zulfiqar Ali Bhutto Medical University, Pakistan Institute of Medical Sciences, Islamabad 44000, Pakistan
| | - Hélène Dollfus
- Service de Génétique Médicale, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Muhammad Zaman Assir
- Shaheed Zulfiqar Ali Bhutto Medical University, Pakistan Institute of Medical Sciences, Islamabad 44000, Pakistan; Allama Iqbal Medical College, University of Health Sciences, 54000 Lahore, Pakistan
| | - Patrick Nitchké
- Institut Imagine, Bioinformatics Platform, Université Paris Descartes, 75015 Paris, France
| | - Maria-Victoria Hinckelmann
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, 67400 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Hilger Ropers
- Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Sheikh Riazuddin
- Shaheed Zulfiqar Ali Bhutto Medical University, Pakistan Institute of Medical Sciences, Islamabad 44000, Pakistan; Allama Iqbal Medical College, University of Health Sciences, 54000 Lahore, Pakistan
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, 1985713834 Tehran, Iran
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Jamel Chelly
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaire de Strasbourg, 67000 Strasbourg, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, 67400 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France; Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, 67000 Strasbourg, France.
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35
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Abstract
In 2009, the first genome-wide association study (GWAS) for major depressive disorder (MDD) highlighted an association with PCLO locus on chromosome 7, although not reaching genome-wide significance level. In the present study, we revisited the original GWAS after increasing the overall sample size and the number of interrogated SNPs. In an analysis comparing 1,942 cases with lifetime diagnosis of MDD and 4,565 controls, PCLO showed a genome-wide significant association with MDD at SNP (rs2715157, p = 2.91 × 10-8) and gene-based (p = 1.48 × 10-7) level. Our results confirm the potential role of the PCLO gene in MDD, which is worth further replication and functional studies.
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36
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Siddique A, Willoughby J, McNeill A. A 7q21.11 microdeletion presenting with apparent intellectual disability without epilepsy. Am J Med Genet A 2017; 173:1128-1130. [PMID: 28240412 DOI: 10.1002/ajmg.a.38136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/14/2016] [Accepted: 12/24/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Azeem Siddique
- Sheffield Institute for Translational Neuroscience, Sheffield, South Yorkshire, UK
| | - Josh Willoughby
- Sheffield Diagnostic Genetics Service, Sheffield Children's Hospital NHS Foundation Trust, Western Bank, Sheffield, South Yorkshire, UK
| | | | - Alisdair McNeill
- Sheffield Institute for Translational Neuroscience, Sheffield, South Yorkshire, UK.,Sheffield Diagnostic Genetics Service, Sheffield Children's Hospital NHS Foundation Trust, Western Bank, Sheffield, South Yorkshire, UK.,INSIGNEO Institute for In Silico Medicine, The University of Sheffield, Sheffield, South Yorkshire, UK
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37
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Abstract
The cerebellum has long been recognized for its role in motor co-ordination, but it is also increasingly appreciated for its role in complex cognitive behavior. Historically, the cerebellum has been overwhelmingly understudied compared to the neocortex in both humans and model organisms. However, this tide is changing as advances in neuroimaging, neuropathology, and neurogenetics have led to clinical classification and gene identification for numerous developmental disorders that impact cerebellar structure and function associated with significant overall neurodevelopmental dysfunction. Given the broad range in prognosis and associated medical and neurodevelopmental concerns accompanying cerebellar malformations, a working knowledge of these disorders and their causes is critical for obstetricians, perinatologists, and neonatologists. Here we present an update on the genetic causes for cerebellar malformations that can be recognized by neuroimaging and clinical characteristics during the prenatal and postnatal periods.
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38
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Lucchese G, Kanduc D. Zika virus and autoimmunity: From microcephaly to Guillain-Barré syndrome, and beyond. Autoimmun Rev 2016; 15:801-8. [DOI: 10.1016/j.autrev.2016.03.020] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 03/18/2016] [Indexed: 10/22/2022]
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39
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Piccolo paralogs and orthologs display conserved patterns of alternative splicing within the C2A and C2B domains. Genes Genomics 2016. [DOI: 10.1007/s13258-015-0383-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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