1
|
Mitrakos AK, Kosma K, Makrythanasis P, Tzetis M. The Phenotypic Spectrum of 16p11.2 Recurrent Chromosomal Rearrangements. Genes (Basel) 2024; 15:1053. [PMID: 39202413 PMCID: PMC11354020 DOI: 10.3390/genes15081053] [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: 07/08/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 09/03/2024] Open
Abstract
The human 16p11.2 chromosomal region is rich in segmental duplications which mediate the formation of recurrent CNVs. CNVs affecting the 16p11.2 region are associated with an increased risk for developing neuropsychiatric disorders, including autism spectrum disorder (ASD), schizophrenia, and intellectual disability (ID), as well as abnormal body weight and head circumference and dysmorphic features, with marked phenotypic variability and reduced penetrance. CNVs affecting the 16p11.2 region mainly affect a distal interval of ~220 Kb, between Breakpoints 2 and 3 (BP2-BP3), and a proximal interval of ~593 Kb (BP4-BP5). Here, we report on 15 patients with recurrent 16p11.2 rearrangements that were identified among a cohort of 1600 patients (0.9%) with neurodevelopmental disorders. A total of 13 deletions and two duplications were identified, of which eight deletions included the proximal 16p11.2 region (BP4-BP5) and five included the distal 16p11.2 region (BP2-BP3). Of the two duplications that were identified, one affected the proximal and one the distal 16p11.2 region; however, both patients had additional CNVs contributing to phenotypic severity. The features observed and their severity varied greatly, even between patients within the same family. This article aims to further delineate the clinical spectrum of patients with 16p11.2 recurrent rearrangements in order to aid the counselling of patients and their families.
Collapse
Affiliation(s)
- Anastasios K. Mitrakos
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia Children’s Hospital, 11527 Athens, Greece
- University Research Institute for the Study and Treatment of Genetic and Malignant Disorders of Childhood, 11527 Athens, Greece
| | - Konstantina Kosma
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia Children’s Hospital, 11527 Athens, Greece
| | - Periklis Makrythanasis
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia Children’s Hospital, 11527 Athens, Greece
| | - Maria Tzetis
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia Children’s Hospital, 11527 Athens, Greece
| |
Collapse
|
2
|
Rexrode LE, Hartley J, Showmaker KC, Challagundla L, Vandewege MW, Martin BE, Blair E, Bollavarapu R, Antonyraj RB, Hilton K, Gardiner A, Valeri J, Gisabella B, Garrett MR, Theoharides TC, Pantazopoulos H. Molecular profiling of the hippocampus of children with autism spectrum disorder. Mol Psychiatry 2024; 29:1968-1979. [PMID: 38355786 PMCID: PMC11408253 DOI: 10.1038/s41380-024-02441-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/16/2024]
Abstract
Several lines of evidence point to a key role of the hippocampus in Autism Spectrum Disorders (ASD). Altered hippocampal volume and deficits in memory for person and emotion related stimuli have been reported, along with enhanced ability for declarative memories. Mouse models have demonstrated a critical role of the hippocampus in social memory dysfunction, associated with ASD, together with decreased synaptic plasticity. Chondroitin sulfate proteoglycans (CSPGs), a family of extracellular matrix molecules, represent a potential key link between neurodevelopment, synaptic plasticity, and immune system signaling. There is a lack of information regarding the molecular pathology of the hippocampus in ASD. We conducted RNAseq profiling on postmortem human brain samples containing the hippocampus from male children with ASD (n = 7) and normal male children (3-14 yrs old), (n = 6) from the NIH NeuroBioBank. Gene expression profiling analysis implicated molecular pathways involved in extracellular matrix organization, neurodevelopment, synaptic regulation, and immune system signaling. qRT-PCR and Western blotting were used to confirm several of the top markers identified. The CSPG protein BCAN was examined with multiplex immunofluorescence to analyze cell-type specific expression of BCAN and astrocyte morphology. We observed decreased expression of synaptic proteins PSD95 (p < 0.02) and SYN1 (p < 0.02), increased expression of the extracellular matrix (ECM) protease MMP9 (p < 0.03), and decreased expression of MEF2C (p < 0.03). We also observed increased BCAN expression with astrocytes in children with ASD, together with altered astrocyte morphology. Our results point to alterations in immune system signaling, glia cell differentiation, and synaptic signaling in the hippocampus of children with ASD, together with alterations in extracellular matrix molecules. Furthermore, our results demonstrate altered expression of genes implicated in genetic studies of ASD including SYN1 and MEF2C.
Collapse
Affiliation(s)
- Lindsay E Rexrode
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | - Joshua Hartley
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | | | - Lavanya Challagundla
- Department of Cell and Molecular Biology, University of Mississippi Medical School, Jackson, MS, USA
| | | | - Brigitte E Martin
- Department of Cell and Molecular Biology, University of Mississippi Medical School, Jackson, MS, USA
| | - Estelle Blair
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | - Ratna Bollavarapu
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | - Rhenius B Antonyraj
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | - Keauna Hilton
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | - Alex Gardiner
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | - Jake Valeri
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
- Program in Neuroscience, University of Mississippi Medical School, Jackson, MS, USA
| | - Barbara Gisabella
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
- Program in Neuroscience, University of Mississippi Medical School, Jackson, MS, USA
| | - Michael R Garrett
- Department of Cell and Molecular Biology, University of Mississippi Medical School, Jackson, MS, USA
| | - Theoharis C Theoharides
- Institute of Neuro-Immune Medicine, Nova Southeastern University, Clearwater, FL, USA
- Department of Immunology, Tufts University School of Medicine, Boston, MA, USA
| | - Harry Pantazopoulos
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA.
- Program in Neuroscience, University of Mississippi Medical School, Jackson, MS, USA.
| |
Collapse
|
3
|
Wu D, Wu Y, Lan Y, Lan S, Zhong Z, Li D, Zheng Z, Wang H, Ma L. Chromosomal Aberrations in Pediatric Patients With Moderate/Severe Developmental Delay/Intellectual Disability With Abundant Phenotypic Heterogeneities: A Single-Center Study. Pediatr Neurol 2023; 147:72-81. [PMID: 37566956 DOI: 10.1016/j.pediatrneurol.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/26/2023] [Accepted: 06/06/2023] [Indexed: 08/13/2023]
Abstract
BACKGROUND This study aimed to examine the clinical usefulness of chromosome microarray (CMA) for selective implementation in patients with unexplained moderate or severe developmental delay/intellectual disability (DD/ID) and/or combined with different dysphonic features in the Han Chinese population. METHODS We retrospectively analyzed data on 122 pediatric patients with unexplained isolated moderate/severe DD/ID with or without autism spectrum disorders, epilepsy, dystonia, and congenital abnormalities from a single-center neurorehabilitation clinic in southern China. RESULTS A total of 46 probands (37.7%) had abnormal CMA results among the 122 study patients. With the exclusion of aneuploidies, uniparental disomies, and multiple homozygotes, 37 patients harbored 39 pathogenic copy number variations (pCNVs) (median [interquartile range] size: 3.57 [1.6 to 7.1] Mb; 33 deletions and 6 duplications), enriched in chromosomes 5, 7, 15, 17, and 22, with a markedly high prevalence of Angelman/Prader-Willi syndrome (24.3% [nine of 37]). Three rare deletions in the regions 5q33.2q34, 17p13.2, and 13q33.2 were reported, with specific delineation of clinical phenotypes. The frequencies of pCNVs were 18%, 33.3%, 38.89%, 41.67%, and 100% for patients with 1, 2, 3, 4, and 5 study phenotypes, respectively; patients with more concomitant abnormalities in the heart, brain, craniofacial region, and/or other organs had a higher CMA diagnostic yield and pCNV prevalence (P < 0.05). CONCLUSIONS Clinical application of CMA as a first-tier test among patients with moderate/severe DD/ID combined with congenital structural anomalies improved diagnostic yields and the quality of clinical management in this series of patients.
Collapse
Affiliation(s)
- Dan Wu
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China; Centre for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia
| | - Yi Wu
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yulong Lan
- Centre for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia; Department of Cardiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Shaocong Lan
- Guangdong Medical College, Zhanjiang, Guangdong, China
| | - Zhiwei Zhong
- Department of Neurosurgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Duo Li
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Zexin Zheng
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Hongwu Wang
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China.
| | - Lian Ma
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China; Department of Hematology and Oncology, Shenzhen Children's Hospital of China Medical University, Shenzhen, Guangdong, China; Shenzhen Public Service Platform of Molecular Medicine in Pediatric Hematology and Oncology, Shenzhen, Guangdong, China; Department of Pediatrics, The Third Affiliated Hospital of Guangzhou Medical University (The Women and Children's Hospital of Guangzhou Medical University), Guangzhou, Guangdong, China.
| |
Collapse
|
4
|
Mitrakos A, Kosma K, Makrythanasis P, Tzetis M. Prenatal Chromosomal Microarray Analysis: Does Increased Resolution Equal Increased Yield? Genes (Basel) 2023; 14:1519. [PMID: 37628571 PMCID: PMC10454647 DOI: 10.3390/genes14081519] [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: 06/26/2023] [Revised: 07/16/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Chromosomal microarray analysis (CMA) is considered a first-tier test for patients with developmental disabilities and congenital anomalies and is also routinely applied in prenatal diagnosis. The current consensus size cut-off for reporting copy number variants (CNVs) in the prenatal setting ranges from 200 Kb to 400 Kb, with the intention of minimizing the impact of variants of uncertain significance (VUS). Very limited data are currently available on the application of higher resolution platforms prenatally. The aim of this study is to investigate the feasibility and impact of applying high-resolution CMA in the prenatal setting. To that end, we report on the outcomes of applying CMA with a size cut-off of 20 Kb in 250 prenatal samples and discuss the findings and diagnostic yield and also provide follow-up for cases with variants of uncertain significance. Overall, 19.6% (49) showed one or more chromosomal abnormalities, with the findings classified as Pathogenic (P) or Likely Pathogenic (LP) in 15.6% and as VUS in 4%. When excluding the cases with known familial aberrations, the diagnostic yield was 12%. The smallest aberration detected was a 32 Kb duplication of the 16p11.2 region. In conclusion, this study demonstrates that prenatal diagnosis with a high-resolution aCGH platform can reliably detect smaller CNVs that are often associated with neurodevelopmental phenotypes while providing an increased diagnostic yield, regardless of the indication for testing, with only a marginal increase in the VUS incidence. Thus, it can be an important tool in the prenatal setting.
Collapse
Affiliation(s)
- Anastasios Mitrakos
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, 11527 Athens, Greece; (K.K.); (P.M.)
| | | | | | - Maria Tzetis
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, 11527 Athens, Greece; (K.K.); (P.M.)
| |
Collapse
|
5
|
Venegas JP, Navarrete M, Orellana-Garcia L, Rojas M, Avello-Duarte F, Nunez-Parra A. Basal Forebrain Modulation of Olfactory Coding In Vivo. Int J Psychol Res (Medellin) 2023; 16:62-86. [PMID: 38106956 PMCID: PMC10723750 DOI: 10.21500/20112084.6486] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/23/2022] [Accepted: 12/07/2022] [Indexed: 12/19/2023] Open
Abstract
Sensory perception is one of the most fundamental brain functions, allowing individuals to properly interact and adapt to a constantly changing environment. This process requires the integration of bottom-up and topdown neuronal activity, which is centrally mediated by the basal forebrain, a brain region that has been linked to a series of cognitive processes such as attention and alertness. Here, we review the latest research using optogenetic approaches in rodents and in vivo electrophysiological recordings that are shedding light on the role of this region, in regulating olfactory processing and decisionmaking. Moreover, we summarize evidence highlighting the anatomical and physiological differences in the basal forebrain of individuals with autism spectrum disorder, which could underpin the sensory perception abnormalities they exhibit, and propose this research line as a potential opportunity to understand the neurobiological basis of this disorder.
Collapse
Affiliation(s)
- Juan Pablo Venegas
- Physiology Laboratory, Biology Department, Faculty of Science, University of Chile, Chile.Universidad de ChileUniversity of ChileChile
| | - Marcela Navarrete
- Physiology Laboratory, Biology Department, Faculty of Science, University of Chile, Chile.Universidad de ChileUniversity of ChileChile
| | - Laura Orellana-Garcia
- Physiology Laboratory, Biology Department, Faculty of Science, University of Chile, Chile.Universidad de ChileUniversity of ChileChile
| | - Marcelo Rojas
- Physiology Laboratory, Biology Department, Faculty of Science, University of Chile, Chile.Universidad de ChileUniversity of ChileChile
| | - Felipe Avello-Duarte
- Physiology Laboratory, Biology Department, Faculty of Science, University of Chile, Chile.Universidad de ChileUniversity of ChileChile
| | - Alexia Nunez-Parra
- Physiology Laboratory, Biology Department, Faculty of Science, University of Chile, Chile.Universidad de ChileUniversity of ChileChile
| |
Collapse
|
6
|
Koevoet D, Deschamps PKH, Kenemans JL. Catecholaminergic and cholinergic neuromodulation in autism spectrum disorder: A comparison to attention-deficit hyperactivity disorder. Front Neurosci 2023; 16:1078586. [PMID: 36685234 PMCID: PMC9853424 DOI: 10.3389/fnins.2022.1078586] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 12/15/2022] [Indexed: 01/09/2023] Open
Abstract
Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder characterized by social impairments and restricted, repetitive behaviors. Treatment of ASD is notoriously difficult and might benefit from identification of underlying mechanisms that overlap with those disturbed in other developmental disorders, for which treatment options are more obvious. One example of the latter is attention-deficit hyperactivity disorder (ADHD), given the efficacy of especially stimulants in treatment of ADHD. Deficiencies in catecholaminergic systems [dopamine (DA), norepinephrine (NE)] in ADHD are obvious targets for stimulant treatment. Recent findings suggest that dysfunction in catecholaminergic systems may also be a factor in at least a subgroup of ASD. In this review we scrutinize the evidence for catecholaminergic mechanisms underlying ASD symptoms, and also include in this analysis a third classic ascending arousing system, the acetylcholinergic (ACh) network. We complement this with a comprehensive review of DA-, NE-, and ACh-targeted interventions in ASD, and an exploratory search for potential treatment-response predictors (biomarkers) in ASD, genetically or otherwise. Based on this review and analysis we propose that (1) stimulant treatment may be a viable option for an ASD subcategory, possibly defined by genetic subtyping; (2) cerebellar dysfunction is pronounced for a relatively small ADHD subgroup but much more common in ASD and in both cases may point toward NE- or ACh-directed intervention; (3) deficiency of the cortical salience network is sizable in subgroups of both disorders, and biomarkers such as eye blink rate and pupillometric data may predict the efficacy of targeting this underlying deficiency via DA, NE, or ACh in both ASD and ADHD.
Collapse
Affiliation(s)
- Damian Koevoet
- Experimental Psychology, Helmholtz Institute, Utrecht University, Utrecht, Netherlands,*Correspondence: Damian Koevoet,
| | - P. K. H. Deschamps
- Department of Psychiatry, University Medical Center Utrecht, Utrecht, Netherlands
| | - J. L. Kenemans
- Experimental Psychology, Helmholtz Institute, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
7
|
Iwahashi-Odano M, Kitamura M, Narumi S. A case of syndromic congenital hypothyroidism with a 15.2 Mb interstitial deletion on 2q12.3q14.2 involving PAX8. Clin Pediatr Endocrinol 2023; 32:65-71. [PMID: 36761496 PMCID: PMC9887295 DOI: 10.1297/cpe.2022-0061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022] Open
Abstract
Paired box 8 (PAX8) mutations are an established genetic cause of congenital hypothyroidism (CH). The majority of these mutations are found in the protein-coding exons of the gene. The proband, a 3-yr-old girl, had tetralogy of Fallot and polydactyly soon after birth. She was diagnosed with CH in the newborn screening for CH. She had a high serum TSH level (239 mU/L) and low free T4 level (0.7 ng/dL). Ultrasonography revealed thyroid hypoplasia. We performed array comparative genomic hybridization because the patient exhibited a variety of symptoms across multiple organ systems. The analysis revealed a novel heterozygous deletion that spanned a 15.2 Mb region in 2q12.3q14.3 (GRCh37; chr2:109,568,260-124,779,449). There were 71 protein-coding genes in this region, including two genes (PAX8 and GLI2) associated with congenital endocrine disorders. The common clinical features of the two previously reported patients with a total PAX8 deletion and our case were CH, short stature and intellectual disability, but the severity of hypothyroidism and other clinical features were variable. In conclusion, we describe a syndromic CH patient with a novel 2q12.3q14.3 deletion involving PAX8. Patients with CH, whose unifying diagnosis is not obvious, could have a genomic deletion involving PAX8.
Collapse
Affiliation(s)
- Megumi Iwahashi-Odano
- Department of Molecular Endocrinology, National Research
Institute for Child Health and Development, Tokyo, Japan,Department of Pediatrics, The Jikei University School of
Medicine, Tokyo, Japan
| | - Miyuki Kitamura
- Department of Pediatrics and Child Health, Kurume University
School of Medicine, Fukuoka, Japan
| | - Satoshi Narumi
- Department of Molecular Endocrinology, National Research
Institute for Child Health and Development, Tokyo, Japan
| |
Collapse
|
8
|
Implications of Genetic Factors and Modifiers in Autism Spectrum Disorders: a Systematic Review. REVIEW JOURNAL OF AUTISM AND DEVELOPMENTAL DISORDERS 2022. [DOI: 10.1007/s40489-022-00333-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
9
|
Alhazmi S, Alzahrani M, Farsi R, Alharbi M, Algothmi K, Alburae N, Ganash M, Azhari S, Basingab F, Almuhammadi A, Alqosaibi A, Alkhatabi H, Elaimi A, Jan M, Aldhalaan HM, Alrafiah A, Alrofaidi A. Multiple Recurrent Copy Number Variations (CNVs) in Chromosome 22 Including 22q11.2 Associated with Autism Spectrum Disorder. Pharmgenomics Pers Med 2022; 15:705-720. [PMID: 35898556 PMCID: PMC9309317 DOI: 10.2147/pgpm.s366826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/14/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction Autism spectrum disorder (ASD) is a developmental disorder that can cause substantial social, communication, and behavioral challenges. Genetic factors play a significant role in ASD, where the risk of ASD has been increased for unclear reasons. Twin studies have shown important evidence of both genetic and environmental contributions in ASD, where the level of contribution of these factors has not been proven yet. It has been suggested that copy number variation (CNV) duplication and the deletion of many genes in chromosome 22 (Ch22) may have a strong association with ASD. This study screened the CNVs in Ch22 in autistic Saudi children and assessed the candidate gene in the CNVs region of Ch22 that is most associated with ASD. Methods This study included 15 autistic Saudi children as well as 4 healthy children as controls; DNA was extracted from samples and analyzed using array comparative genomic hybridization (aCGH) and DNA sequencing. Results The aCGH detected (in only 6 autistic samples) deletion and duplication in many regions of Ch22, including some critical genes. Moreover, DNA sequencing determined a genetic mutation in the TBX1 gene sequence in autistic samples. This study, carried out using aCGH, found that six autistic patients had CNVs in Ch22, and DNA sequencing revealed mutations in the TBX1 gene in autistic samples but none in the control. Conclusion CNV deletion and the duplication of the TBX1 gene could be related to ASD; therefore, this gene needs more analysis in terms of expression levels.
Collapse
Affiliation(s)
- Safiah Alhazmi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maryam Alzahrani
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reem Farsi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mona Alharbi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khloud Algothmi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Najla Alburae
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Magdah Ganash
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sheren Azhari
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fatemah Basingab
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asma Almuhammadi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amany Alqosaibi
- Department of Biology, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Heba Alkhatabi
- Centre of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Aisha Elaimi
- Centre of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed Jan
- College of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hesham M Aldhalaan
- Center for Autism Research at King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Aziza Alrafiah
- Department of Medical Laboratory Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Correspondence: Aziza Alrafiah, Department of Medical Laboratory Science, King Abdulaziz University, P.O Box 80200, Jeddah, 21589, Saudi Arabia, Tel +966 126401000 Ext. 23495, Fax +966 126401000 Ext. 21686, Email
| | - Aisha Alrofaidi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
10
|
Kamath V, Yoganathan S, Thomas MM, Gowri M, Chacko MP. Utility of Chromosomal Microarray in Children with Unexplained Developmental Delay/Intellectual Disability. Fetal Pediatr Pathol 2022; 41:208-218. [PMID: 32701375 DOI: 10.1080/15513815.2020.1791292] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
ObjectiveTo evaluate the chromosomal microarray (CMA) yield among children who presented with global developmental delay/intellectual disability (GDD/ID) with/without co-occurring conditions. Methods: The pathogenic copy number variation (pCNVs) findings on CMA of all children who presented with unexplained GDD/ID were categorized based on the clinical features. The karyotype results were compared with CMA. Results: The overall pCNV yield in children presenting with GDD/ID with or without comorbid conditions constituted 20.9%. Among the 17 pCNVs, 13 were losses and four were gains. Cardiac defect was the only co-morbidity in our study that demonstrated statistically significant prediction for pCNV (odds ratio 6.13, p value- 0.031). Six children who were karyotyped prior to CMA testing showed a structural abnormality. Conclusions: In our study, 20.9% of children with GDD/ID showed pCNVs on CMA. Cardiac defect alongside GDD/ID, emerged as the single strongest phenotype associated with pCNVs. CMA also provided vital information in previously karyotyped patients.
Collapse
Affiliation(s)
- Vandana Kamath
- Department of Cytogenetics, Christian Medical College and Hospital, Vellore, India
| | - Sangeetha Yoganathan
- Department of Neurological Sciences, Christian Medical College and Hospital, Vellore, India
| | - Maya Mary Thomas
- Department of Neurological Sciences, Christian Medical College and Hospital, Vellore, India
| | - Mahasampath Gowri
- Department of Biostatistics, Christian Medical College and Hospital, Vellore, India
| | - Mary Purna Chacko
- Department of Cytogenetics, Christian Medical College and Hospital, Vellore, India
| |
Collapse
|
11
|
Identification of Novel Gene Variants for Autism Spectrum Disorders in the Lebanese Population Using Whole-Exome Sequencing. Genes (Basel) 2022; 13:genes13020186. [PMID: 35205231 PMCID: PMC8871811 DOI: 10.3390/genes13020186] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/10/2022] [Accepted: 01/19/2022] [Indexed: 12/04/2022] Open
Abstract
In our previous study, in which array CGH was used on 19 Lebanese ASD subjects and their parents, we identified rare copy number variants (CNVs) in 14 subjects. The five remaining subjects did not show any CNVs related to autism spectrum disorders (ASD). In the present complementary study, we applied whole-exome sequencing (WES), which allows the identification of rare genetic variations such as single nucleotide variations and small insertions/deletions, to the five negative CNV subjects. After stringent filtering of initial data on the five families, three novel genes potentially related to neurodevelopment were identified, including a de novo mutation in the MIS18BP1 gene. In addition, genes already known to be related to ASD contained sequence variations. Our findings outline the potential involvement of the novel de novo mutation in the MIS18BP1 gene in the genetic etiology and pathophysiology of ASD and highlights the genetic complexity of these disorders. Further studies with larger cohorts of subjects are needed to confirm these observations, and functional analyses need to be performed to understand the precise pathophysiology in these cases.
Collapse
|
12
|
Liu Y, Lv Y, Zarrei M, Dong R, Yang X, Higginbotham EJ, Li Y, Zhao D, Song F, Yang Y, Zhang H, Wang Y, Scherer SW, Gai Z. Chromosomal microarray analysis of 410 Han Chinese patients with autism spectrum disorder or unexplained intellectual disability and developmental delay. NPJ Genom Med 2022; 7:1. [PMID: 35022430 PMCID: PMC8755789 DOI: 10.1038/s41525-021-00271-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 11/09/2021] [Indexed: 12/20/2022] Open
Abstract
Copy number variants (CNVs) are recognized as a crucial genetic cause of neurodevelopmental disorders (NDDs). Chromosomal microarray analysis (CMA), the first-tier diagnostic test for individuals with NDDs, has been utilized to detect CNVs in clinical practice, but most reports are still from populations of European ancestry. To contribute more worldwide clinical genomics data, we investigated the genetic etiology of 410 Han Chinese patients with NDDs (151 with autism and 259 with unexplained intellectual disability (ID) and developmental delay (DD)) using CMA (Affymetrix) after G-banding karyotyping. Among all the NDD patients, 109 (26.6%) carried clinically relevant CNVs or uniparental disomies (UPDs), and 8 (2.0%) had aneuploidies (6 with trisomy 21 syndrome, 1 with 47,XXY, 1 with 47,XYY). In total, we found 129 clinically relevant CNVs and UPDs, including 32 CNVs in 30 ASD patients, and 92 CNVs and 5 UPDs in 79 ID/DD cases. When excluding the eight patients with aneuploidies, the diagnostic yield of pathogenic and likely pathogenic CNVs and UPDs was 20.9% for all NDDs (84/402), 3.3% in ASD (5/151), and 31.5% in ID/DD (79/251). When aneuploidies were included, the diagnostic yield increased to 22.4% for all NDDs (92/410), and 33.6% for ID/DD (87/259). We identified a de novo CNV in 14.9% (60/402) of subjects with NDDs. Interestingly, a higher diagnostic yield was observed in females (31.3%, 40/128) compared to males (16.1%, 44/274) for all NDDs (P = 4.8 × 10-4), suggesting that a female protective mechanism exists for deleterious CNVs and UPDs.
Collapse
Affiliation(s)
- Yi Liu
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Yuqiang Lv
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Mehdi Zarrei
- The Centre for Applied Genomics and Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Rui Dong
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Xiaomeng Yang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Edward J Higginbotham
- The Centre for Applied Genomics and Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Yue Li
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Dongmei Zhao
- Pediatric Health Care Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Fengling Song
- Pediatric Health Care Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Yali Yang
- Rehabilitation Center, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Haiyan Zhang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Ying Wang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Stephen W Scherer
- The Centre for Applied Genomics and Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada. .,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada.
| | - Zhongtao Gai
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China.
| |
Collapse
|
13
|
Kosma K, Varvagiannis K, Mitrakos A, Tsipi M, Traeger-Synodinos J, Tzetis M. 239-kb Microdeletion Spanning KMT2E in a Child with Developmental Delay: Further Delineation of the Phenotype. Mol Syndromol 2021; 12:321-326. [PMID: 34602960 PMCID: PMC8436641 DOI: 10.1159/000516635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/20/2021] [Indexed: 11/19/2022] Open
Abstract
Pathogenic KMT2E variants underly O'Donnell-Luria-Rodan syndrome, a recently described neurodevelopmental disorder characterized by global developmental delay, variable degrees of intellectual disability, and subtle facial dysmorphism. Less common findings include autism, seizures, gastrointestinal (GI) problems, and abnormal head circumference. Occurrence of mostly truncating variants as well as the similar phenotype observed in individuals with deletions spanning KMT2E suggest haploinsufficiency of this gene as a common mechanism for the disorder, while a gain-of-function or dominant-negative effect cannot be ruled out for some missense variants. Deletions reported in the literature encompass several additional known or presumed haploinsufficient genes, thus leading to more complex phenotypes. Here, we describe a male with antenatal onset hydronephrosis, hypotonia, global developmental delay, prominent GI symptoms as well as facial dysmorphism. Chromosomal microarray revealed a 239-kb de novo microdeletion spanning KMT2E and LHFPL3. Clinical presentation of our proband, harboring one of the smallest deletions of the region confirms the core features of this disorder, suggests GI symptoms as a prominent finding in affected individuals while expanding the phenotypic spectrum to abnormalities of the urinary tract.
Collapse
Affiliation(s)
- Konstantina Kosma
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos Varvagiannis
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Anastasios Mitrakos
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- University Research Institute of Maternal and Child Health & Precision Medicine, Athens, Greece
| | - Maria Tsipi
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Joanne Traeger-Synodinos
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- University Research Institute of Maternal and Child Health & Precision Medicine, Athens, Greece
| | - Maria Tzetis
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| |
Collapse
|
14
|
Capkova Z, Capkova P, Srovnal J, Adamova K, Prochazka M, Hajduch M. Duplication of 9p24.3 in three unrelated patients and their phenotypes, considering affected genes, and similar recurrent variants. Mol Genet Genomic Med 2021; 9:e1592. [PMID: 33455084 PMCID: PMC8104183 DOI: 10.1002/mgg3.1592] [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: 05/22/2020] [Revised: 11/22/2020] [Accepted: 12/15/2020] [Indexed: 11/18/2022] Open
Abstract
Background Recent studies suggest that duplication of the 9p24.3 chromosomal locus, which includes the DOCK8 and KANK1 genes, is associated with autism spectrum disorders (ASD), intellectual disability/developmental delay (ID/DD), learning problems, language disorders, hyperactivity, and epilepsy. Correlation between this duplication and the carrier phenotype needs further discussion. Methods In this study, three unrelated patients with ID/DD and ASD underwent SNP aCGH and MLPA testing. Similarities in the phenotypes of patients with 9p24.3, 15q11.2, and 16p11.2 duplications were also observed. Results All patients with ID/DD and ASD carried the 9p24.3 duplication and showed intragenic duplication of DOCK8. Additionally, two patients had ADHD, one was hearing impaired and obese, and one had macrocephaly. Inheritance of the 9p24.3 duplication was confirmed in one patient and his sibling. In one patient KANK1 was duplicated along with DOCK8. Carriers of 9p24.3, 15q11.2, and 16p11.2 duplications showed several phenotypic similarities, with ID/DD more strongly associated with duplication of 9p24.3 than of 15q11.2 and 16p11.2. Conclusion We concluded that 9p24.3 is a likely cause of ASD and ID/DD, especially in cases of DOCK8 intragenic duplication. DOCK8 is a likely causative gene, and KANK1 aberrations a modulator, of the clinical phenotype observed. Other modulators were not excluded.
Collapse
Affiliation(s)
- Zuzana Capkova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic.,Department of Medical Genetics, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Pavlina Capkova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic.,Department of Medical Genetics, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Josef Srovnal
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic.,Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Katerina Adamova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic.,Department of Medical Genetics, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Martin Prochazka
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic.,Department of Medical Genetics, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
| |
Collapse
|
15
|
Genovese A, Butler MG. Clinical Assessment, Genetics, and Treatment Approaches in Autism Spectrum Disorder (ASD). Int J Mol Sci 2020; 21:E4726. [PMID: 32630718 PMCID: PMC7369758 DOI: 10.3390/ijms21134726] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/24/2020] [Accepted: 06/27/2020] [Indexed: 12/16/2022] Open
Abstract
Autism spectrum disorder (ASD) consists of a genetically heterogenous group of neurobehavioral disorders characterized by impairment in three behavioral domains including communication, social interaction, and stereotypic repetitive behaviors. ASD affects more than 1% of children in Western societies, with diagnoses on the rise due to improved recognition, screening, clinical assessment, and diagnostic testing. We reviewed the role of genetic and metabolic factors which contribute to the causation of ASD with the use of new genetic technology. Up to 40 percent of individuals with ASD are now diagnosed with genetic syndromes or have chromosomal abnormalities including small DNA deletions or duplications, single gene conditions, or gene variants and metabolic disturbances with mitochondrial dysfunction. Although the heritability estimate for ASD is between 70 and 90%, there is a lower molecular diagnostic yield than anticipated. A likely explanation may relate to multifactorial causation with etiological heterogeneity and hundreds of genes involved with a complex interplay between inheritance and environmental factors influenced by epigenetics and capabilities to identify causative genes and their variants for ASD. Behavioral and psychiatric correlates, diagnosis and genetic evaluation with testing are discussed along with psychiatric treatment approaches and pharmacogenetics for selection of medication to treat challenging behaviors or comorbidities commonly seen in ASD. We emphasize prioritizing treatment based on targeted symptoms for individuals with ASD, as treatment will vary from patient to patient based on diagnosis, comorbidities, causation, and symptom severity.
Collapse
Affiliation(s)
| | - Merlin G. Butler
- Department of Psychiatry & Behavioral Sciences, University of Kansas Medical Center, Kansas City, KS 66160, USA;
| |
Collapse
|
16
|
Frye RE, Vassall S, Kaur G, Lewis C, Karim M, Rossignol D. Emerging biomarkers in autism spectrum disorder: a systematic review. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:792. [PMID: 32042808 DOI: 10.21037/atm.2019.11.53] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Autism spectrum disorder (ASD) affects approximately 2% of children in the United States (US) yet its etiology is unclear and effective treatments are lacking. Therapeutic interventions are most effective if started early in life, yet diagnosis often remains delayed, partly because the diagnosis of ASD is based on identifying abnormal behaviors that may not emerge until the disorder is well established. Biomarkers that identify children at risk during the pre-symptomatic period, assist with early diagnosis, confirm behavioral observations, stratify patients into subgroups, and predict therapeutic response would be a great advance. Here we underwent a systematic review of the literature on ASD to identify promising biomarkers and rated the biomarkers in regards to a Level of Evidence and Grade of Recommendation using the Oxford Centre for Evidence-Based Medicine scale. Biomarkers identified by our review included physiological biomarkers that identify neuroimmune and metabolic abnormalities, neurological biomarkers including abnormalities in brain structure, function and neurophysiology, subtle behavioral biomarkers including atypical development of visual attention, genetic biomarkers and gastrointestinal biomarkers. Biomarkers of ASD may be found prior to birth and after diagnosis and some may predict response to specific treatments. Many promising biomarkers have been developed for ASD. However, many biomarkers are preliminary and need to be validated and their role in the diagnosis and treatment of ASD needs to be defined. It is likely that biomarkers will need to be combined to be effective to identify ASD early and guide treatment.
Collapse
Affiliation(s)
- Richard E Frye
- Barrow Neurological Institute at Phoenix Children's Hospital, Phoenix, AZ, USA.,Deparment of Child Health, University of Arizona College of Medicine, Phoenix, AZ, USA
| | - Sarah Vassall
- Barrow Neurological Institute at Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Gurjot Kaur
- Barrow Neurological Institute at Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Christina Lewis
- Barrow Neurological Institute at Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Mohammand Karim
- Barrow Neurological Institute at Phoenix Children's Hospital, Phoenix, AZ, USA.,Deparment of Child Health, University of Arizona College of Medicine, Phoenix, AZ, USA
| | | |
Collapse
|
17
|
Chromosomal Aberrations in Pediatric Patients with Developmental Delay/Intellectual Disability: A Single-Center Clinical Investigation. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9352581. [PMID: 31781653 PMCID: PMC6875000 DOI: 10.1155/2019/9352581] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/03/2019] [Accepted: 09/18/2019] [Indexed: 12/12/2022]
Abstract
Introduction Chromosomal microarray analysis (CMA) has currently been considered as the first-tier genetic test for patients with developmental delay/intellectual disability (DD/ID) in many countries. In this study, we performed an extensive assessment of the value of CMA for the diagnosis of children with ID/DD in China. Methods A total of 633 patients diagnosed with DD/ID in West China Second University Hospital, Sichuan University, were recruited from January 2014 to March 2019. The patients were classified into 4 subgroups: isolated DD/ID, DD/ID with multiple congenital anomalies (MCA), isolated autism spectrum disorders (ASDs), and DD/ID with epilepsy. CMA was performed on Affymetrix 750K platform. Results Among the 633 patients, 127 cases were identified as having pathogenic copy number variations (pCNVs) with an overall positive rate of 20.06%. Of the 127 cases with abnormal results, 76 cases had 35 types of microdeletion/microduplication syndromes (59.84%) including 5 cases caused by uniparental disomy (UPD), and 18 cases had unbalanced rearrangements (14.17%) including 10 cases inherited from parental balanced translocations or pericentric inversions. The diagnostic yields of pCNVs for the subgroups of isolated DD/ID, DD/ID with MCA, isolated ASD, and DD/ID with epilepsy were 18.07% (60/332), 34.90% (52/149), 3.70% (3/81), and 16.90% (12/71), respectively. The diagnostic yield of pCNVs in DD/ID patients with MCA was significantly higher than that of the other three subgroups, and the diagnostic yield of pCNVs in isolated ASD patients was significantly lower than that of the other three subgroups (p < 0.05). Conclusion Microdeletion/microduplication syndromes and unbalanced rearrangements are probably the main genetic etiological factors for DD/ID. DD/ID patients with MCA have a higher rate of chromosomal aberrations. Parents of DD/ID children with submicroscopic unbalance rearrangements are more likely to have chromosome balanced translocations or pericentric inversions, which might have been missed by karyotyping. CMA can significantly improve the diagnostic rate for patients with DD/ID, which is of great value for medical management and clinical guidance for genetic counseling.
Collapse
|
18
|
Zouvelou V, Yubero D, Apostolakopoulou L, Kokkinou E, Bilanakis M, Dalivigka Z, Nikas I, Kollia E, Perez-Dueñas B, Macaya A, Marcé-Grau A, Voutetakis A, Anagnostopoulou K, Kekou K, Sofocleus C, Veltra D, Kokkinis X, Fryssira H, Torres RJ, Amstrong J, Santorelli FM, Artuch R, Pons R. The genetic etiology in cerebral palsy mimics: The results from a Greek tertiary care center. Eur J Paediatr Neurol 2019; 23:427-437. [PMID: 30799092 DOI: 10.1016/j.ejpn.2019.02.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/20/2019] [Accepted: 02/07/2019] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Non-progressive genetic disorders may present with motor dysfunction resembling cerebral palsy (CP). Such patients are often characterized as CP mimics. The purpose of this work was to delineate the clinical manifestations and molecular findings of CP mimic patients, with the ultimate goal to offer specific disease-modifying therapy and genetic counseling. METHODS Retrospective study of 47 patients diagnosed with CP and no acquired etiology. Chart review of clinical, neuroradiological, biochemical and molecular data was performed. RESULTS 31,91% of patients manifested with features resembling dyskinetic CP, 19,14% spastic CP, 10,63% ataxic CP and 38,30% mixed CP. In 23 patients molecular diagnosis was reached and included 5 hereditary spastic paraplegia genes (SPG) in spastic CP mimics; HPRT1, TH, QDPR, DDC in dystonic CP mimics; ADCY5 and NIKX2-1 in choreic CP mimics; CANA1A in ataxic CP mimics; and SPG, PDHA1, NIKX2-1, AT, SLC2A1 and SPR in mixed CP mimics. In 14 patients, the etiological diagnosis led to specific treatment. CONCLUSIONS CP mimics show a number of features that differ from classic CP and can be used as diagnostic clues, including presence of mixed motor features, minor dysmorphic features, oculogyric movements, multiple features of autonomic dysfunction, and acquired microcephaly. A more stringent use of the concept of CP focused on acquired lesions during the perinatal and infancy periods, and excluding disorders that could be of genetic origin, could contribute to a purer use of the term. Identification of a specific genetic cause for CP mimics may in certain cases lead to etiologic treatment.
Collapse
Affiliation(s)
- Vasiliki Zouvelou
- First Department of Pediatrics, Agia Sofia Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Delia Yubero
- Department of Clinical Biochemistry, Institut de Recerca Sant Joan de Déu, Sant Joan de Deu Hospital, Center for Biomedical Research on Rare Diseases (CIBERER), Barcelona, Spain
| | - Loukia Apostolakopoulou
- First Department of Pediatrics, Agia Sofia Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Eleftheria Kokkinou
- First Department of Pediatrics, Agia Sofia Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Manolis Bilanakis
- First Department of Pediatrics, Agia Sofia Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Zoi Dalivigka
- Pediatric Rehabilitation Unit, "Pan & Aglaia's Kyriakou" Children's Hospital, Greece
| | - Ioannis Nikas
- Radiology Department, Agia Sofia Children's Hospital Hospital, Athens, Greece
| | - Elissavet Kollia
- First Department of Pediatrics, Agia Sofia Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Belen Perez-Dueñas
- Pediatric Neurology Research Group Vall d'Hebron Research, Institute Autonomous University of Barcelona Barcelona, Spain
| | - Alfons Macaya
- Pediatric Neurology Research Group Vall d'Hebron Research, Institute Autonomous University of Barcelona Barcelona, Spain
| | - Anna Marcé-Grau
- Pediatric Neurology Research Group Vall d'Hebron Research, Institute Autonomous University of Barcelona Barcelona, Spain
| | - Antonis Voutetakis
- First Department of Pediatrics, Agia Sofia Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Kiriaki Kekou
- Medical Genetics, School of Medicine, National and Kapodistrian University of Athens, Greece
| | - Christalena Sofocleus
- Medical Genetics, School of Medicine, National and Kapodistrian University of Athens, Greece
| | - Danae Veltra
- Medical Genetics, School of Medicine, National and Kapodistrian University of Athens, Greece
| | - Xaralabos Kokkinis
- Medical Genetics, School of Medicine, National and Kapodistrian University of Athens, Greece
| | - Helen Fryssira
- Medical Genetics, School of Medicine, National and Kapodistrian University of Athens, Greece
| | - Rosa J Torres
- La Paz University Hospital Health Research Institute (FIBHULP), IdiPaz, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Spain
| | - Judith Amstrong
- Department of Clinical Biochemistry, Institut de Recerca Sant Joan de Déu, Sant Joan de Deu Hospital, Center for Biomedical Research on Rare Diseases (CIBERER), Barcelona, Spain
| | - Filippo M Santorelli
- Molecular Medicine and Neurogenetics, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Rafael Artuch
- Department of Clinical Biochemistry, Institut de Recerca Sant Joan de Déu, Sant Joan de Deu Hospital, Center for Biomedical Research on Rare Diseases (CIBERER), Barcelona, Spain
| | - Roser Pons
- First Department of Pediatrics, Agia Sofia Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece.
| |
Collapse
|
19
|
Forés-Martos J, Catalá-López F, Sánchez-Valle J, Ibáñez K, Tejero H, Palma-Gudiel H, Climent J, Pancaldi V, Fañanás L, Arango C, Parellada M, Baudot A, Vogt D, Rubenstein JL, Valencia A, Tabarés-Seisdedos R. Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer. Mol Autism 2019; 10:17. [PMID: 31007884 PMCID: PMC6454734 DOI: 10.1186/s13229-019-0262-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/19/2019] [Indexed: 12/27/2022] Open
Abstract
Background Epidemiological and clinical evidence points to cancer as a comorbidity in people with autism spectrum disorders (ASD). A significant overlap of genes and biological processes between both diseases has also been reported. Methods Here, for the first time, we compared the gene expression profiles of ASD frontal cortex tissues and 22 cancer types obtained by differential expression meta-analysis and report gene, pathway, and drug set-based overlaps between them. Results Four cancer types (brain, thyroid, kidney, and pancreatic cancers) presented a significant overlap in gene expression deregulations in the same direction as ASD whereas two cancer types (lung and prostate cancers) showed differential expression profiles significantly deregulated in the opposite direction from ASD. Functional enrichment and LINCS L1000 based drug set enrichment analyses revealed the implication of several biological processes and pathways that were affected jointly in both diseases, including impairments of the immune system, and impairments in oxidative phosphorylation and ATP synthesis among others. Our data also suggest that brain and kidney cancer have patterns of transcriptomic dysregulation in the PI3K/AKT/MTOR axis that are similar to those found in ASD. Conclusions Comparisons of ASD and cancer differential gene expression meta-analysis results suggest that brain, kidney, thyroid, and pancreatic cancers are candidates for direct comorbid associations with ASD. On the other hand, lung and prostate cancers are candidates for inverse comorbid associations with ASD. Joint perturbations in a set of specific biological processes underlie these associations which include several pathways previously implicated in both cancer and ASD encompassing immune system alterations, impairments of energy metabolism, cell cycle, and signaling through PI3K and G protein-coupled receptors among others. These findings could help to explain epidemiological observations pointing towards direct and inverse comorbid associations between ASD and specific cancer types and depict a complex scenario regarding the molecular patterns of association between ASD and cancer. Electronic supplementary material The online version of this article (10.1186/s13229-019-0262-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jaume Forés-Martos
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain
| | - Ferrán Catalá-López
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,2Teaching Unit of Psychiatry and Psychological Medicine, Department of Medicine, University of Valencia, Blasco-Ibañez 15, 46010 Valencia, Spain.,3INCLIVA Health Research Institute, Valencia, Spain.,4Department of Health Planning and Economics, National School of Public Health/IMIENS, Institute of Health Carlos III, Madrid, Spain
| | | | | | - Héctor Tejero
- 7Structural Biology Program, Spanish National Cancer Research Program (CNIO), Madrid, Spain
| | - Helena Palma-Gudiel
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,8Anthropology Section, Department of Evolutionary Biology, Ecology and Environmental Sciences, Biomedicine Institute (IBUB), University of Barcelona (UB), Barcelona, Spain
| | - Joan Climent
- 3INCLIVA Health Research Institute, Valencia, Spain.,9Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Calle Ramon y Cajal s/n 46115 Alfara del Patriarca, Valencia, Spain
| | - Vera Pancaldi
- 5Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Lourdes Fañanás
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,8Anthropology Section, Department of Evolutionary Biology, Ecology and Environmental Sciences, Biomedicine Institute (IBUB), University of Barcelona (UB), Barcelona, Spain
| | - Celso Arango
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,Department of Child and Adolescent Psychiatry, Hospital General Universitario Gregorio Marañón, IiSGM, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Mara Parellada
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,Department of Child and Adolescent Psychiatry, Hospital General Universitario Gregorio Marañón, IiSGM, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Anaïs Baudot
- 11Aix-Marseille Univ, Inserm, MMG, Marseille Medical Genetics, Marseille, France
| | - Daniel Vogt
- 12Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI 48824 USA
| | - John L Rubenstein
- 13Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, CA 94158 USA.,14Department of Psychiatry, University of California, San Francisco, CA 94158 USA
| | - Alfonso Valencia
- 5Barcelona Supercomputing Center (BSC), Barcelona, Spain.,15Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Rafael Tabarés-Seisdedos
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,2Teaching Unit of Psychiatry and Psychological Medicine, Department of Medicine, University of Valencia, Blasco-Ibañez 15, 46010 Valencia, Spain.,3INCLIVA Health Research Institute, Valencia, Spain
| |
Collapse
|
20
|
Array-CGH Analysis in a Cohort of Phenotypically Well-Characterized Individuals with "Essential" Autism Spectrum Disorders. J Autism Dev Disord 2019; 48:442-449. [PMID: 29027068 DOI: 10.1007/s10803-017-3329-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Copy-number variants (CNVs) are associated with susceptibility to autism spectrum disorder (ASD). To detect the presence of CNVs, we conducted an array-comparative genomic hybridization (array-CGH) analysis in 133 children with "essential" ASD phenotype. Genetic analyses documented that 12 children had causative CNVs (C-CNVs), 29 children had non-causative CNVs (NC-CNVs) and 92 children without CNVs (W-CNVs). Results on clinical evaluation showed no differences in cognitive abilities among the three groups, and a higher number of ASD symptoms and of non-verbal children in the C-CNVs group compared to the W-CNVs and NC-CNVs groups. Our results highlighted the importance of the array-CGH analyses and showed that the presence of specific CNVs may differentiate clinical outputs in children with ASD.
Collapse
|
21
|
Rose S, Niyazov DM, Rossignol DA, Goldenthal M, Kahler SG, Frye RE. Clinical and Molecular Characteristics of Mitochondrial Dysfunction in Autism Spectrum Disorder. Mol Diagn Ther 2018; 22:571-593. [PMID: 30039193 PMCID: PMC6132446 DOI: 10.1007/s40291-018-0352-x] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Autism spectrum disorder (ASD) affects ~ 2% of children in the United States. The etiology of ASD likely involves environmental factors triggering physiological abnormalities in genetically sensitive individuals. One of these major physiological abnormalities is mitochondrial dysfunction, which may affect a significant subset of children with ASD. Here we systematically review the literature on human studies of mitochondrial dysfunction related to ASD. Clinical aspects of mitochondrial dysfunction in ASD include unusual neurodevelopmental regression, especially if triggered by an inflammatory event, gastrointestinal symptoms, seizures, motor delays, fatigue and lethargy. Traditional biomarkers of mitochondrial disease are widely reported to be abnormal in ASD, but appear non-specific. Newer biomarkers include buccal cell enzymology, biomarkers of fatty acid metabolism, non-mitochondrial enzyme function, apoptosis markers and mitochondrial antibodies. Many genetic abnormalities are associated with mitochondrial dysfunction in ASD, including chromosomal abnormalities, mitochondrial DNA mutations and large-scale deletions, and mutations in both mitochondrial and non-mitochondrial nuclear genes. Mitochondrial dysfunction has been described in immune and buccal cells, fibroblasts, muscle and gastrointestinal tissue and the brains of individuals with ASD. Several environmental factors, including toxicants, microbiome metabolites and an oxidized microenvironment are shown to modulate mitochondrial function in ASD tissues. Investigations of treatments for mitochondrial dysfunction in ASD are promising but preliminary. The etiology of mitochondrial dysfunction and how to define it in ASD is currently unclear. However, preliminary evidence suggests that the mitochondria may be a fruitful target for treatment and prevention of ASD. Further research is needed to better understand the role of mitochondrial dysfunction in the pathophysiology of ASD.
Collapse
Affiliation(s)
- Shannon Rose
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Dmitriy M Niyazov
- Section of Medical Genetics, Ochsner Health System, New Orleans, LA, USA
| | | | - Michael Goldenthal
- Department of Pediatrics, Neurology Section, St. Christopher's Hospital for Children, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Stephen G Kahler
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Richard E Frye
- Division of Neurodevelopmental Disorders, Department of Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, 1919 E Thomas St, Phoenix, AZ, USA.
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA.
| |
Collapse
|
22
|
Rare structural variants in the DOCK8 gene identified in a cohort of 439 patients with neurodevelopmental disorders. Sci Rep 2018; 8:9449. [PMID: 29930340 PMCID: PMC6013431 DOI: 10.1038/s41598-018-27824-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/08/2018] [Indexed: 01/05/2023] Open
Abstract
Detection of copy number variations (CNVs) is a first-tier clinical diagnostic test for children with neurodevelopmental disorders (NDD), which reveals the genetic cause of the disorder in more than 20%. These are mostly known microdeletion/microduplication syndromes, but variants of unknown clinical significance (VOUS) and ambiguous CNVs can also be detected. An example of the last two are abnormalities in the DOCK8 gene. Conflicting interpretations of CNVs affecting DOCK8 can be found in the literature. Deletions were predicted to have a impact in carriers with variable clinical manifestations, where duplications have been proposed as benign variants. In our study, CNV screening was performed in a cohort involving 439 probands with suspected NDD. We identified known microdeletion/microduplication syndromes in 19% and VOUS CNVs in 8% of patients. Among these, three patients had a CNV encompassing the DOCK8 gene. Although diverse clinical presentations are noted in our three patients, comparison of their phenotypes revealed that abnormalities in cognition and communication, aggressive behaviour and mood swings are common to all of them. Therefore, a clinical relevance, in terms of influencing the psychiatric clinical picture of patients, is proposed for the CNVs disrupting the DOCK8 gene, regardless of whether it is a deletion or duplication.
Collapse
|
23
|
Chromosomal microarray analysis in developmental delay and intellectual disability with comorbid conditions. BMC Med Genomics 2018; 11:49. [PMID: 29793483 PMCID: PMC5968608 DOI: 10.1186/s12920-018-0368-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 05/15/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Developmental delay (DD) and intellectual disability (ID) are frequently associated with a broad spectrum of additional phenotypes. Chromosomal microarray analysis (CMA) has been recommended as a first-tier test for DD/ID in general, whereas the diagnostic yield differs significantly among DD/ID patients with different comorbid conditions. METHODS To investigate the genotype-phenotype correlation, we examined the characteristics of identified pathogenic copy number variations (pCNVs) and compared the diagnostic yields among patient subgroups with different co-occurring conditions. RESULTS This study is a retrospective review of CMA results generated from a mixed cohort of 710 Chinese patients with DD/ID. A total of 247 pCNVs were identified in 201 patients (28%). A large portion of these pCNVs were copy number losses, and the size of copy number losses was generally smaller than gains. The diagnostic yields were significantly higher in subgroups with co-occurring congenital heart defects (55%), facial dysmorphism (39%), microcephaly (34%) or hypotonia (35%), whereas co-occurring conditions of skeletal malformation (26%), brain malformation (24%) or epilepsy (24%) did not alter the yield. In addition, the diagnostic yield nominally correlated with ID severity. CONCLUSION Varied yields exist in DD/ID patients with different phenotypic presentation. The presence of comorbid conditions can be among factors to consider when planning CMA.
Collapse
|
24
|
Sekine M, Makino T. Inference of Causative Genes for Alzheimer's Disease Due to Dosage Imbalance. Mol Biol Evol 2017; 34:2396-2407. [PMID: 28666362 DOI: 10.1093/molbev/msx183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Copy number variations (CNVs) have recently drawn attention as an important genetic factor for diseases, especially common neuropsychiatric disorders including Alzheimer's disease (AD). Because most of the pathogenic CNV regions overlap with multiple genes, it has been challenging to identify the true disease-causing genes amongst them. Notably, a recent study reported that CNV regions containing ohnologs, which are dosage-sensitive genes, are likely to be deleterious. Utilizing the unique feature of ohnologs could be useful for identifying causative genes with pathogenic CNVs, however its effectiveness is still unclear. Although it has been reported that AD is strongly affected by CNVs, most of AD-causing genes with pathogenic CNVs have not been identified yet. Here, we show that dosage-sensitive ohnologs within CNV regions reported in patients with AD are related to the nervous system and are highly expressed in the brain, similar to other known susceptible genes for AD. We found that CNV regions in patients with AD contained dosage-sensitive genes, which are ohnologs not overlapping with control CNV regions, frequently. Furthermore, these dosage-sensitive genes in pathogenic CNV regions had a strong enrichment in the nervous system for mouse knockout phenotype and high expression in the brain similar to the known susceptible genes for AD. Our results demonstrated that selecting dosage-sensitive ohnologs out of multiple genes with pathogenic CNVs is effective in identifying the causative genes for AD. This methodology can be applied to other diseases caused by dosage imbalance and might help to establish the medical diagnosis by analysis of CNVs.
Collapse
Affiliation(s)
- Mizuka Sekine
- Department of Biology, Faculty of Science, Tohoku University, Sendai, Japan
| | - Takashi Makino
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| |
Collapse
|
25
|
Hnoonual A, Thammachote W, Tim-Aroon T, Rojnueangnit K, Hansakunachai T, Sombuntham T, Roongpraiwan R, Worachotekamjorn J, Chuthapisith J, Fucharoen S, Wattanasirichaigoon D, Ruangdaraganon N, Limprasert P, Jinawath N. Chromosomal microarray analysis in a cohort of underrepresented population identifies SERINC2 as a novel candidate gene for autism spectrum disorder. Sci Rep 2017; 7:12096. [PMID: 28935972 PMCID: PMC5608768 DOI: 10.1038/s41598-017-12317-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 09/07/2017] [Indexed: 01/11/2023] Open
Abstract
Chromosomal microarray (CMA) is now recognized as the first-tier genetic test for detection of copy number variations (CNVs) in patients with autism spectrum disorder (ASD). The aims of this study were to identify known and novel ASD associated-CNVs and to evaluate the diagnostic yield of CMA in Thai patients with ASD. The Infinium CytoSNP-850K BeadChip was used to detect CNVs in 114 Thai patients comprised of 68 retrospective ASD patients (group 1) with the use of CMA as a second line test and 46 prospective ASD and developmental delay patients (group 2) with the use of CMA as the first-tier test. We identified 7 (6.1%) pathogenic CNVs and 22 (19.3%) variants of uncertain clinical significance (VOUS). A total of 29 patients with pathogenic CNVs and VOUS were found in 22% (15/68) and 30.4% (14/46) of the patients in groups 1 and 2, respectively. The difference in detected CNV frequencies between the 2 groups was not statistically significant (Chi square = 1.02, df = 1, P = 0.31). In addition, we propose one novel ASD candidate gene, SERINC2, which warrants further investigation. Our findings provide supportive evidence that CMA studies using population-specific reference databases in underrepresented populations are useful for identification of novel candidate genes.
Collapse
Affiliation(s)
- Areerat Hnoonual
- Graduate Program in Biomedical Sciences, Prince of Songkla University, Songkhla, Thailand
| | - Weerin Thammachote
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Thipwimol Tim-Aroon
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Kitiwan Rojnueangnit
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine, Thammasart University, Pathumthani, Thailand
| | - Tippawan Hansakunachai
- Division of Child Development, Department of Pediatrics, Faculty of Medicine, Thammasart University, Pathumthani, Thailand
| | - Tasanawat Sombuntham
- Division of Developmental-Behavioral Pediatrics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Rawiwan Roongpraiwan
- Division of Developmental-Behavioral Pediatrics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Juthamas Worachotekamjorn
- Division of Child Development, Department of Pediatrics, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Jariya Chuthapisith
- Division of Developmental-Behavioral Pediatrics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Suthat Fucharoen
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Duangrurdee Wattanasirichaigoon
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Nichara Ruangdaraganon
- Division of Developmental-Behavioral Pediatrics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pornprot Limprasert
- Division of Human Genetics, Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
| | - Natini Jinawath
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand. .,Integrative Computational Bioscience Center, Mahidol University, Salaya, Nakhon Pathom, Thailand.
| |
Collapse
|
26
|
Zhang J, Gambin T, Yuan B, Szafranski P, Rosenfeld JA, Balwi MA, Alswaid A, Al-Gazali L, Shamsi AMA, Komara M, Ali BR, Roeder E, McAuley L, Roy DS, Manchester DK, Magoulas P, King LE, Hannig V, Bonneau D, Denommé-Pichon AS, Charif M, Besnard T, Bézieau S, Cogné B, Andrieux J, Zhu W, He W, Vetrini F, Ward PA, Cheung SW, Bi W, Eng CM, Lupski JR, Yang Y, Patel A, Lalani SR, Xia F, Stankiewicz P. Haploinsufficiency of the E3 ubiquitin-protein ligase gene TRIP12 causes intellectual disability with or without autism spectrum disorders, speech delay, and dysmorphic features. Hum Genet 2017; 136:377-386. [PMID: 28251352 PMCID: PMC5543723 DOI: 10.1007/s00439-017-1763-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/08/2017] [Indexed: 02/05/2023]
Abstract
Impairment of ubiquitin-proteasome system activity involving ubiquitin ligase genes UBE3A, UBE3B, and HUWE1 and deubiquitinating enzyme genes USP7 and USP9X has been reported in patients with neurodevelopmental delays. To date, only a handful of single-nucleotide variants (SNVs) and copy-number variants (CNVs) involving TRIP12, encoding a member of the HECT domain E3 ubiquitin ligases family on chromosome 2q36.3 have been reported. Using chromosomal microarray analysis and whole-exome sequencing (WES), we have identified, respectively, five deletion CNVs and four inactivating SNVs (two frameshifts, one missense, and one splicing) in TRIP12. Seven of these variants were found to be de novo; parental studies could not be completed in two families. Quantitative PCR analyses of the splicing mutation showed a dramatically decreased level of TRIP12 mRNA in the proband compared to the family controls, indicating a loss-of-function mechanism. The shared clinical features include intellectual disability with or without autistic spectrum disorders, speech delay, and facial dysmorphism. Our findings demonstrate that E3 ubiquitin ligase TRIP12 plays an important role in nervous system development and function. The nine presented pathogenic variants further document that TRIP12 haploinsufficiency causes a childhood-onset neurodevelopmental disorder. Finally, our data enable expansion of the phenotypic spectrum of ubiquitin-proteasome dependent disorders.
Collapse
Affiliation(s)
- Jing Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Institute of Computer Science, Warsaw University of Technology, Warsaw, 02-038, Poland
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, 01-211, Poland
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Mohammed Al Balwi
- Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, 11246, Saudi Arabia
| | | | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Aisha M Al Shamsi
- Department of Pediatrics, Tawam Hospital, Al Ain, United Arab Emirates
| | - Makanko Komara
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Elizabeth Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, San Antonio, TX, 78230, USA
| | - Laura McAuley
- UT Southwestern Medical Center, Children's Health Children's Medical Center, Dallas, TX, 75235, USA
| | - Daniel S Roy
- Tripler Army Medical Center, Honolulu, 96859, USA
| | | | - Pilar Magoulas
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Lauren E King
- Vanderbilt Children's Hospital, Nashville, TN, 37232, USA
| | - Vickie Hannig
- Vanderbilt Children's Hospital, Nashville, TN, 37232, USA
| | - Dominique Bonneau
- Department of Biochemistry and Genetics, University Hospital, 49933, Angers Cedex 9, France
- UMR CNRS 6015-INSERM 1083 and PREMMI, University of Angers, 49933, Angers Cedex 9, France
| | - Anne-Sophie Denommé-Pichon
- Department of Biochemistry and Genetics, University Hospital, 49933, Angers Cedex 9, France
- UMR CNRS 6015-INSERM 1083 and PREMMI, University of Angers, 49933, Angers Cedex 9, France
| | - Majida Charif
- UMR CNRS 6015-INSERM 1083 and PREMMI, University of Angers, 49933, Angers Cedex 9, France
| | - Thomas Besnard
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes Cedex 1, France
| | - Stéphane Bézieau
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes Cedex 1, France
| | - Benjamin Cogné
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes Cedex 1, France
| | - Joris Andrieux
- Institute of Medical Genetics, Jeanne de Flandre Hospital, Lille University Hospital, Lille, 59800, France
| | - Wenmiao Zhu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Weimin He
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Francesco Vetrini
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Patricia A Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Baylor Genetics, Houston, TX, 77021, USA.
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Baylor Genetics, Houston, TX, 77021, USA.
| |
Collapse
|