1
|
Cokyaman T, Silan F. Diagnostic Utility of Array Comparative Genomic Hybridization in Children with Neurological Diseases. Fetal Pediatr Pathol 2022; 41:68-76. [PMID: 32401632 DOI: 10.1080/15513815.2020.1764683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION We evaluated the contribution of array comparative genomic hybridization (aCGH) to the final diagnosis in children with neurocognitive disturbances or dysmorphic findings, but lacked a specific diagnosis. MATERIALS AND METHODS Medical files of pediatric patients with neurocognitive disturbances who underwent aCGH analysis were reviewed retrospectively. RESULTS Of 155 patients, 77 copy number variations were detected and 50% (39/77) were considered causative. The aCGH's final diagnostic rate was 25.1% (39/155). CONCLUSION With aCGH analysis, the diagnosis rate for patients with undiagnosed neurocognitive disturbances or dysmorphic syndrome may increase by 25-30%. If the phenotypic findings of the widely known neurocognitive disturbances cannot be identified during the initial clinical assessment, aCGH analysis may be beneficial.
Collapse
Affiliation(s)
- Turgay Cokyaman
- Pediatric Neurology, Faculty of Medicine, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Fatma Silan
- Medical Genetics, Faculty of Medicine, Çanakkale Onsekiz Mart University, Canakkale, Turkey
| |
Collapse
|
2
|
Rounds JC, Corgiat EB, Ye C, Behnke JA, Kelly SM, Corbett AH, Moberg KH. The disease-associated proteins Drosophila Nab2 and Ataxin-2 interact with shared RNAs and coregulate neuronal morphology. Genetics 2022; 220:iyab175. [PMID: 34791182 PMCID: PMC8733473 DOI: 10.1093/genetics/iyab175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 09/27/2021] [Indexed: 01/05/2023] Open
Abstract
Nab2 encodes the Drosophila melanogaster member of a conserved family of zinc finger polyadenosine RNA-binding proteins (RBPs) linked to multiple steps in post-transcriptional regulation. Mutation of the Nab2 human ortholog ZC3H14 gives rise to an autosomal recessive intellectual disability but understanding of Nab2/ZC3H14 function in metazoan nervous systems is limited, in part because no comprehensive identification of metazoan Nab2/ZC3H14-associated RNA transcripts has yet been conducted. Moreover, many Nab2/ZC3H14 functional protein partnerships remain unidentified. Here, we present evidence that Nab2 genetically interacts with Ataxin-2 (Atx2), which encodes a neuronal translational regulator, and that these factors coordinately regulate neuronal morphology, circadian behavior, and adult viability. We then present the first high-throughput identifications of Nab2- and Atx2-associated RNAs in Drosophila brain neurons using RNA immunoprecipitation-sequencing (RIP-Seq). Critically, the RNA interactomes of each RBP overlap, and Nab2 exhibits high specificity in its RNA associations in neurons in vivo, associating with a small fraction of all polyadenylated RNAs. The identities of shared associated transcripts (e.g., drk, me31B, stai) and of transcripts specific to Nab2 or Atx2 (e.g., Arpc2 and tea) promise insight into neuronal functions of, and genetic interactions between, each RBP. Consistent with prior biochemical studies, Nab2-associated neuronal RNAs are overrepresented for internal A-rich motifs, suggesting these sequences may partially mediate Nab2 target selection. These data support a model where Nab2 functionally opposes Atx2 in neurons, demonstrate Nab2 shares associated neuronal RNAs with Atx2, and reveal Drosophila Nab2 associates with a more specific subset of polyadenylated mRNAs than its polyadenosine affinity alone may suggest.
Collapse
Affiliation(s)
- J Christopher Rounds
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Edwin B Corgiat
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Changtian Ye
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Joseph A Behnke
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Seth M Kelly
- Department of Biology, The College of Wooster, Wooster, OH 44691, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
3
|
Khanal P, Hotulainen P. Dendritic Spine Initiation in Brain Development, Learning and Diseases and Impact of BAR-Domain Proteins. Cells 2021; 10:cells10092392. [PMID: 34572042 PMCID: PMC8468246 DOI: 10.3390/cells10092392] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 02/08/2023] Open
Abstract
Dendritic spines are small, bulbous protrusions along neuronal dendrites where most of the excitatory synapses are located. Dendritic spine density in normal human brain increases rapidly before and after birth achieving the highest density around 2-8 years. Density decreases during adolescence, reaching a stable level in adulthood. The changes in dendritic spines are considered structural correlates for synaptic plasticity as well as the basis of experience-dependent remodeling of neuronal circuits. Alterations in spine density correspond to aberrant brain function observed in various neurodevelopmental and neuropsychiatric disorders. Dendritic spine initiation affects spine density. In this review, we discuss the importance of spine initiation in brain development, learning, and potential complications resulting from altered spine initiation in neurological diseases. Current literature shows that two Bin Amphiphysin Rvs (BAR) domain-containing proteins, MIM/Mtss1 and SrGAP3, are involved in spine initiation. We review existing literature and open databases to discuss whether other BAR-domain proteins could also take part in spine initiation. Finally, we discuss the potential molecular mechanisms on how BAR-domain proteins could regulate spine initiation.
Collapse
Affiliation(s)
- Pushpa Khanal
- Minerva Foundation Institute for Medical Research, Tukholmankatu 8, 00290 Helsinki, Finland;
- HiLIFE-Neuroscience Center, University of Helsinki, 00014 Helsinki, Finland
| | - Pirta Hotulainen
- Minerva Foundation Institute for Medical Research, Tukholmankatu 8, 00290 Helsinki, Finland;
- Correspondence:
| |
Collapse
|
4
|
Rasool IG, Zahoor MY, Iqbal M, Anjum AA, Ashraf F, Abbas HQ, Baig HMA, Mahmood T, Shehzad W. Whole exome sequencing revealed novel variants in consanguineous Pakistani families with intellectual disability. Genes Genomics 2021; 43:503-512. [PMID: 33710595 DOI: 10.1007/s13258-021-01070-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 02/19/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND Intellectual disability (ID) is a heterogeneous disorder affecting 1-3% of the population. Elucidation of monogenic variants for ID is a current challenge. These variants can be better demonstrated in consanguineous affected families. OBJECTIVE The study was designed to find the genetic variants of ID in consanguineous families. METHODS We analyzed five unrelated consanguineous Pakistani families affected with ID using whole exome sequencing (WES). Data was analyzed using different bioinformatics tools and software. RESULTS We mapped four variants including three novels in four different ID known genes. Each variant is found in a different family, co-segregating with a recessive pattern of inheritance. The novel variants found are; c. 2_4del (p.?) mapped in ROS1 and c. 718G>A (p.Gly240Arg) in GRM1. Another novel causative variant, c.2673del (p.Gly892Aspfs*17) identified in COL18A1 in a recessive form, a gene reported for Knobloch syndrome that manifests ID along with typical retinal abnormalities, and this phenotype was confirmed on reverse phenotyping. A mutation c.2134C>T (p.Arg712*) in TRAPPC9 has been found first time in the homozygous recessive form in our enrolled three affected siblings while it was previously reported in compound heterozygous form in a Caucasian descent. While fifth family remained unsolved. CONCLUSION These mutations in four different genes with a recessive inheritance would be a contribution to the disease variant database of this devastating disorder.
Collapse
Affiliation(s)
- Iqra Ghulam Rasool
- Molecular Biology and Forensic Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Muhammad Yasir Zahoor
- Molecular Biology and Forensic Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan.
| | - Muhammad Iqbal
- Department of Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Aftab Ahmad Anjum
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Fatima Ashraf
- Molecular Biology and Forensic Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Hafiz Qamar Abbas
- Molecular Biology and Forensic Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | | | - Tariq Mahmood
- Department of Statistics and Computer Science, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Wasim Shehzad
- Molecular Biology and Forensic Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| |
Collapse
|
5
|
Abstract
The past 2 decades have seen fruit flies being widely adopted for research on social behavior and aggression. This fruitful research, however, has not been well tied to fruit flies' natural history. To address this knowledge gap, I conducted a field study. My goal was to inform future research conducted in artificial surroundings, and to inspire new investigations that can rely more heavily on fruit flies' actual natural behavior. My two main novel findings were first, that flies in the field showed significant sociability, as they formed social groups rather than dispersed randomly among fruits of similar quality. Second, males showed fair levels of aggression towards each other as indicated by a lunging rate of 17 per hour, and lower rates of wing threat and boxing. Courtship was the most prominent activity on fruits, with females rejecting almost all males' advances. This resulted in an estimated mating rate of 0.6 per female per day. Flies showed a striking peak of activity early in the mornings, even at cold temperatures, followed by inactivity for much of the day and night. Flies, however, handled well high temperatures approaching 40 °C by hiding away from fruit and concentrating activity in the cooler, early mornings. My field work highlights a few promising lines of future research informed by fruit flies' natural history. Most importantly, we do not understand the intriguing dynamics that generate significant sociability despite frequent aggressive interactions on fruits. Males' responses to female rejection signals varied widely, perhaps because the signals differed in information content perceived by flies but not humans. Finally, flies tolerated cold early mornings perhaps owing to fitness benefits associated with increased mating and feeding opportunities at this time. Flies were adept at handling very high temperatures under the natural daily temperature fluctuations and availability of shelters, and this can inform more realistic research on the effects of global warming on animals in their natural settings.
Collapse
Affiliation(s)
- Reuven Dukas
- Animal Behaviour Group, Department of Psychology, Neuroscience and Behaviour, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada.
| |
Collapse
|
6
|
Andrew DR, Moe ME, Chen D, Tello JA, Doser RL, Conner WE, Ghuman JK, Restifo LL. Spontaneous motor-behavior abnormalities in two Drosophila models of neurodevelopmental disorders. J Neurogenet 2020; 35:1-22. [PMID: 33164597 DOI: 10.1080/01677063.2020.1833005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Mutations in hundreds of genes cause neurodevelopmental disorders with abnormal motor behavior alongside cognitive deficits. Boys with fragile X syndrome (FXS), a leading monogenic cause of intellectual disability, often display repetitive behaviors, a core feature of autism. By direct observation and manual analysis, we characterized spontaneous-motor-behavior phenotypes of Drosophila dfmr1 mutants, an established model for FXS. We recorded individual 1-day-old adult flies, with mature nervous systems and prior to the onset of aging, in small arenas. We scored behavior using open-source video-annotation software to generate continuous activity timelines, which were represented graphically and quantitatively. Young dfmr1 mutants spent excessive time grooming, with increased bout number and duration; both were rescued by transgenic wild-type dfmr1+. By two grooming-pattern measures, dfmr1-mutant flies showed elevated repetitions consistent with perseveration, which is common in FXS. In addition, the mutant flies display a preference for grooming posterior body structures, and an increased rate of grooming transitions from one site to another. We raise the possibility that courtship and circadian rhythm defects, previously reported for dfmr1 mutants, are complicated by excessive grooming. We also observed significantly increased grooming in CASK mutants, despite their dramatically decreased walking phenotype. The mutant flies, a model for human CASK-related neurodevelopmental disorders, displayed consistently elevated grooming indices throughout the assay, but transient locomotory activation immediately after placement in the arena. Based on published data identifying FMRP-target transcripts and functional analyses of mutations causing human genetic neurodevelopmental disorders, we propose the following proteins as candidate mediators of excessive repetitive behaviors in FXS: CaMKIIα, NMDA receptor subunits 2A and 2B, NLGN3, and SHANK3. Together, these fly-mutant phenotypes and mechanistic insights provide starting points for drug discovery to identify compounds that reduce dysfunctional repetitive behaviors.
Collapse
Affiliation(s)
- David R Andrew
- Department of Neurology, University of Arizona Health Sciences, Tucson, AZ, USA.,Center for Insect Science, University of Arizona, Tucson, AZ, USA.,Department of Biological Sciences, Lycoming College, Williamsport, PA, USA
| | - Mariah E Moe
- Department of Neurology, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Dailu Chen
- Department of Neurology, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Judith A Tello
- Department of Neurology, University of Arizona Health Sciences, Tucson, AZ, USA.,Graduate Interdisciplinary Program in Neuroscience, University of Arizona, Tucson, AZ, USA
| | - Rachel L Doser
- Department of Neurology, University of Arizona Health Sciences, Tucson, AZ, USA
| | - William E Conner
- Department of Biology, Wake Forest University, Winston-Salem, NC, USA
| | - Jaswinder K Ghuman
- Department of Psychiatry, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Linda L Restifo
- Department of Neurology, University of Arizona Health Sciences, Tucson, AZ, USA.,Center for Insect Science, University of Arizona, Tucson, AZ, USA.,Graduate Interdisciplinary Program in Neuroscience, University of Arizona, Tucson, AZ, USA.,BIO5 Interdisciplinary Research Institute, University of Arizona, Tucson, AZ, USA
| |
Collapse
|
7
|
Chauhan V, Chauhan A. Traumatic injury in female Drosophila melanogaster affects the development and induces behavioral abnormalities in the offspring. Behav Brain Funct 2019; 15:11. [PMID: 31653253 PMCID: PMC6815055 DOI: 10.1186/s12993-019-0163-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/09/2019] [Indexed: 12/26/2022] Open
Abstract
Traumatic injury (TI) during pregnancy increases the risk for developing neurological disorders in the infants. These disorders are a major concern for the well-being of children born after TI during pregnancy. TI during pregnancy may result in preterm labor and delivery, abruptio placentae, and/or fetomaternal hemorrhage. Drosophila melanogaster (fruit fly) is a widely used model to study brain and behavioral disorders in humans. In this study, we analyzed the effects of TI to female fruit flies on the development timing of larvae, social interaction and the behavior of offspring flies. TI to the female flies was found to affect the development of larvae and the behavior of offspring flies. There was a significant increase in the length of larvae delivered by traumatically injured maternal flies as compared to larvae from control maternal flies (without TI). The pupae formation from larvae, and the metamorphosis of pupae to the first generation of flies were faster in the TI group than the control group. Negative geotaxis and distance of the fly to its nearest neighbor are parameters of behavioral assessment in fruit flies. Negative geotaxis significantly decreased in the first generation of both male (p = 0.0021) and female (p = 0.0426) flies. The distance between the first generation of flies to its nearest neighbor was shorter in both male and female offspring flies in the TI group as compared to control group flies. These results indicate that TI to the female flies affected the development of larvae and resulted in early delivery, impaired social interaction and behavioral alterations in the offspring.
Collapse
Affiliation(s)
- Ved Chauhan
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY, 10314, USA.
| | - Abha Chauhan
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY, 10314, USA
| |
Collapse
|
8
|
Identification and In Silico Characterization of a Novel Point Mutation within the Phosphatidylinositol Glycan Anchor Biosynthesis Class G Gene in an Iranian Family with Intellectual Disability. J Mol Neurosci 2019; 69:538-545. [PMID: 31414351 DOI: 10.1007/s12031-019-01376-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/08/2019] [Indexed: 10/26/2022]
Abstract
Intellectual disability (ID) is characterized by limited mental ability and adaptive behavior that imposes a heavy burden on the patients' families and the health care system. This study was aimed at determining the molecular aspect of nonsyndromic ID, in a family from South Khorasan Province in Iran. Exome sequencing was performed, as well as complete clinical examinations of the family. Afterward, in silico studies have been done to examine the changes that occurred in the protein structure, in association with the ID phenotype. The PIGG (NC_000004.12) mutation was found on Chr 4:517639G>A, and this chromosomal location was proposed as the disorder-causing variant. This Arg658Gln alteration was confirmed by Sanger sequencing, using specific primers for PIGG. In conclusion, our study indicated a novel mutation in the PIGG in the affected family. This mutation is a novel variant (p. R658Q) with an autosomal recessive inheritance pattern. These findings could improve genetic counseling in the future.
Collapse
|
9
|
Altıner Ş, Yürür Kutlay N. Importance of patient selection criteria in determining diagnostic copy number variations in patients with multiple congenital anomaly/mental retardation. Mol Cytogenet 2019; 12:23. [PMID: 31149029 PMCID: PMC6537423 DOI: 10.1186/s13039-019-0436-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/17/2019] [Indexed: 11/10/2022] Open
Abstract
Background Etiology of developmental delay/intellectual disability is very heterogeneous. In recent years, genetic causes have been defined through the use of chromosomal microarray analysis as a first step genetic test. Results Samples from 30 patients with multiple congenital anomaly and/or mental retardation were analyzed with array comparative genomic hybridization in the context of this study. Before this analysis, karyotyping, subtelomeric fluorescence in situ hybridization and additionally fragment analysis for fragile X in males, had been routinely made all of which were reported to be normal. The purpose of our study was to determine the copy number variations as well as to investigate methods to increase diagnostic yield of array comparative genomic hybridization and forming a suitable flow chart decision pipeline for test indication especially for developing countries. Genomic changes were identified at a rate of about 27% in our series. Although this ratio is higher than the literature data, it could be due to the patient selection criteria. Conclusion Chromosomal microarray analysis is not easily utilized for all patients because of its high-cost. Thus, for increasing cost-effectiveness, it may be used step by step for defined targets. Along with discussing the patients with copy number variations relevant with the phenotype, we suggest a flow chart for selection of diagnostic test with the highest diagnostic rate and the lowest expenditure which is quite important for developing countries.
Collapse
Affiliation(s)
- Şule Altıner
- Department of Medical Genetics, Trabzon Kanuni Training and Research Hospital, University of Health Sciences, Topal Osman Street 7, 61290 Trabzon, Turkey.,2Department of Medical Genetics, School of Medicine, Ankara University, Ankara, Turkey
| | - Nüket Yürür Kutlay
- 2Department of Medical Genetics, School of Medicine, Ankara University, Ankara, Turkey
| |
Collapse
|
10
|
Hacker B, Schultheiß C, Kurzik-Dumke U. Sequential cleavage of the proteins encoded by HNOT/ALG3, the human counterpart of the Drosophila NOT and yeast ALG3 gene, results in products acting in distinct cellular compartments. Hum Mol Genet 2018; 27:4231-4248. [PMID: 30192950 DOI: 10.1093/hmg/ddy315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/04/2018] [Indexed: 11/12/2022] Open
Abstract
This study provides first insights into the biosynthesis, structure, biochemistry and complex processing of the proteins encoded by hNOT/ALG3, the human counterpart of the Drosophila Neighbour of TID (NOT) and the yeast asparagine linked glycosylation 3 gene (ALG3), which encodes a mannosyltransferase. Unambiguous evidence that both the fly and human proteins act as mannosyltransferases has not been provided yet. Previously, we showed that hNOT/ALG3 encodes two alternatively spliced main transcripts, hNOT-1/ALG3-1 and hNOT-4/ALG3-4, and their 15 truncated derivatives that lack diverse sets of exons and/or carry point mutations that result in premature termination codons. Here we show that the truncated transcripts are not translated. The two main forms hNOT-1/ALG3-1 and -4, distinguishable by alternative exon 1, encode full-length precursors that undergo a complex posttranslational processing. To specifically detect the two full-length hNOT/ALG3 proteins and their distinct derivatives and to examine their expression profiles and cellular location we generated polyclonal antibodies against diverse parts of the putative full-length proteins. We provide experimental evidence for the N-glycosylation of the two precursors. This modification seems to be a prerequisite for their sequential cleavage resulting in derivatives destined to distinct cellular compartments and links them with the N-glycosylation machinery not as its functional component but as molecules functionally dependent on its action. We present the expression profiles and subcellular location of the two full-length proteins, their N-glycosylated forms and distinct cleavage products. Furthermore, using diverse bioinformatics tools, we characterize the properties and predict the 2D and 3D structure of the two proteins and, for comparative purposes, of their Drosophila counterpart.
Collapse
Affiliation(s)
- Benedikt Hacker
- Institute of Medical Microbiology and Hygiene, Laboratory for Comparative Tumour Biology, University Medical Centre, Johannes Gutenberg University, Obere Zahlbacher, Mainz, Germany
| | - Christoph Schultheiß
- Institute of Medical Microbiology and Hygiene, Laboratory for Comparative Tumour Biology, University Medical Centre, Johannes Gutenberg University, Obere Zahlbacher, Mainz, Germany
| | - Ursula Kurzik-Dumke
- Institute of Medical Microbiology and Hygiene, Laboratory for Comparative Tumour Biology, University Medical Centre, Johannes Gutenberg University, Obere Zahlbacher, Mainz, Germany
| |
Collapse
|
11
|
Kazeminasab S, Taskiran II, Fattahi Z, Bazazzadegan N, Hosseini M, Rahimi M, Oladnabi M, Haddadi M, Celik A, Ropers HH, Najmabadi H, Kahrizi K. CNKSR1 gene defect can cause syndromic autosomal recessive intellectual disability. Am J Med Genet B Neuropsychiatr Genet 2018; 177:691-699. [PMID: 30450701 DOI: 10.1002/ajmg.b.32648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The advent of high-throughput sequencing technologies has led to an exponential increase in the identification of novel disease-causing genes in highly heterogeneous diseases. A novel frameshift mutation in CNKSR1 gene was detected by Next-Generation Sequencing (NGS) in an Iranian family with syndromic autosomal recessive intellectual disability (ARID). CNKSR1 encodes a connector enhancer of kinase suppressor of Ras 1, which acts as a scaffold component for receptor tyrosine kinase in mitogen-activated protein kinase (MAPK) cascades. CNKSR1 interacts with proteins which have already been shown to be associated with intellectual disability (ID) in the MAPK signaling pathway and promotes cell migration through RhoA-mediated c-Jun N-terminal kinase (JNK) activation. Lack of CNKSR1 transcripts and protein was observed in lymphoblastoid cells derived from affected patients using qRT-PCR and western blot analysis, respectively. Furthermore, RNAi-mediated knockdown of cnk, the CNKSR1 orthologue in Drosophila melanogaster brain, led to defects in eye and mushroom body (MB) structures. In conclusion, our findings support the possible role of CNKSR1 in brain development which can lead to cognitive impairment.
Collapse
Affiliation(s)
- Somayeh Kazeminasab
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Niloofar Bazazzadegan
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Masoumeh Hosseini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Rahimi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Morteza Oladnabi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mohammad Haddadi
- Department of Biology, Faculty of Science, University of Zabol, Zabol, Iran
| | - Arzu Celik
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
| | - Hans-Hilger Ropers
- Department of Human Molecular Genetics, Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| |
Collapse
|
12
|
Berto S, Nowick K. Species-Specific Changes in a Primate Transcription Factor Network Provide Insights into the Molecular Evolution of the Primate Prefrontal Cortex. Genome Biol Evol 2018; 10:2023-2036. [PMID: 30059966 PMCID: PMC6105097 DOI: 10.1093/gbe/evy149] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2018] [Indexed: 02/07/2023] Open
Abstract
The human prefrontal cortex (PFC) differs from that of other primates with respect to size, histology, and functional abilities. Here, we analyzed genome-wide expression data of humans, chimpanzees, and rhesus macaques to discover evolutionary changes in transcription factor (TF) networks that may underlie these phenotypic differences. We determined the co-expression networks of all TFs with species-specific expression including their potential target genes and interaction partners in the PFC of all three species. Integrating these networks allowed us inferring an ancestral network for all three species. This ancestral network as well as the networks for each species is enriched for genes involved in forebrain development, axonogenesis, and synaptic transmission. Our analysis allows us to directly compare the networks of each species to determine which links have been gained or lost during evolution. Interestingly, we detected that most links were gained on the human lineage, indicating increase TF cooperativity in humans. By comparing network changes between different tissues, we discovered that in brain tissues, but not in the other tissues, the human networks always had the highest connectivity. To pinpoint molecular changes underlying species-specific phenotypes, we analyzed the sub-networks of TFs derived only from genes with species-specific expression changes in the PFC. These sub-networks differed significantly in structure and function between the human and chimpanzee. For example, the human-specific sub-network is enriched for TFs implicated in cognitive disorders and for genes involved in synaptic plasticity and cognitive functions. Our results suggest evolutionary changes in TF networks that might have shaped morphological and functional differences between primate brains, in particular in the human PFC.
Collapse
Affiliation(s)
- Stefano Berto
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX.,Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics (IZBI), University of Leipzig, Germany
| | - Katja Nowick
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics (IZBI), University of Leipzig, Germany.,Faculty for Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Germany
| |
Collapse
|
13
|
Hacker B, Schultheiß C, Döring M, Kurzik-Dumke U. Molecular partners of hNOT/ALG3, the human counterpart of the Drosophila NOT and yeast ALG3 gene, suggest its involvement in distinct cellular processes relevant to congenital disorders of glycosylation, cancer, neurodegeneration and a variety of further pathologies. Hum Mol Genet 2018; 27:1858-1878. [DOI: 10.1093/hmg/ddy087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 03/06/2018] [Indexed: 01/04/2023] Open
Affiliation(s)
- Benedikt Hacker
- Laboratory for Comparative Tumour Biology, Institute of Medical Microbiology and Hygiene, University Medical Centre, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Christoph Schultheiß
- Laboratory for Comparative Tumour Biology, Institute of Medical Microbiology and Hygiene, University Medical Centre, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Michael Döring
- Laboratory for Comparative Tumour Biology, Institute of Medical Microbiology and Hygiene, University Medical Centre, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Ursula Kurzik-Dumke
- Laboratory for Comparative Tumour Biology, Institute of Medical Microbiology and Hygiene, University Medical Centre, Johannes Gutenberg University, 55131 Mainz, Germany
| |
Collapse
|
14
|
Abstract
As a laboratory animal, Drosophila melanogaster has made extensive contributions to understanding many areas of fundamental biology as well as being an effective model for human disease. Until recently, there was relatively little known about fly peroxisomes. There were early studies that examined the role of peroxisome enzymes during development of organs like the eye. However, with the advent of a well-annotated, sequenced genome, several groups have collectively determined, first by sequence homology and increasingly by functional studies, Drosophila Peroxins and related peroxisome proteins. Notably, it was shown that Drosophila peroxisome biogenesis is mediated via a well-conserved PTS1 import system. Although the fly genome encodes a Pex7 homologue, a canonical PTS2 import system does not seem to be conserved in Drosophila. Given the homology between Drosophila and Saccharomyces cerevisiae or Homo sapiens peroxisome biogenesis and function, Drosophila has emerged as an effective multicellular system to model human Peroxisome Biogenesis Disorders. Finally, Drosophila peroxisome research has recently come into its own, facilitating new discoveries into the role of peroxisomes within specific tissues, such as testes or immune cells.
Collapse
Affiliation(s)
- Matthew Anderson-Baron
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, 5-14 Medical Sciences, Edmonton, AB, T6G 2H7, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, 5-14 Medical Sciences, Edmonton, AB, T6G 2H7, Canada.
| |
Collapse
|
15
|
Duan Y, Lin S, Xie L, Zheng K, Chen S, Song H, Zeng X, Gu X, Wang H, Zhang L, Shao H, Hong W, Zhang L, Duan S. Exome sequencing identifies a novel mutation of the GDI1 gene in a Chinese non-syndromic X-linked intellectual disability family. Genet Mol Biol 2017; 40:591-596. [PMID: 28863211 PMCID: PMC5596370 DOI: 10.1590/1678-4685-gmb-2016-0249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 03/18/2017] [Indexed: 12/29/2022] Open
Abstract
X-linked intellectual disability (XLID) has been associated with various genes.
Diagnosis of XLID, especially for non-syndromic ones (NS-XLID), is often hampered by
the heterogeneity of this disease. Here we report the case of a Chinese family in
which three males suffer from intellectual disability (ID). The three patients shared
the same phenotype: no typical clinical manifestation other than IQ score ≤ 70. For a
genetic diagnosis for this family we carried out whole exome sequencing on the
proband, and validated 16 variants of interest in the genomic DNA of all the family
members. A missense mutation (c.710G > T), which mapped to exon 6 of the Rab
GDP-Dissociation Inhibitor 1 (GDI1) gene, was found segregating with
the ID phenotype, and this mutation changes the 237th position in the guanosine
diphosphate dissociation inhibitor (GDI) protein from glycine to valine (p.
Gly237Val). Through molecular dynamics simulations we found that this substitution
results in a conformational change of GDI, possibly affecting the Rab-binding
capacity of this protein. In conclusion, our study identified a novel
GDI1 mutation that is possibly NS-XLID causative, and showed that
whole exome sequencing provides advantages for detecting novel ID-associated variants
and can greatly facilitate the genetic diagnosis of the disease.
Collapse
Affiliation(s)
- Yongheng Duan
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Sheng Lin
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Lichun Xie
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Kaifeng Zheng
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Shiguo Chen
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Hui Song
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Xuchun Zeng
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Xueying Gu
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Heyun Wang
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Linghua Zhang
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Hao Shao
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Wenxu Hong
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Lijie Zhang
- College of Pharmacy, Nankai University, Tianjin City, People's Republic of China
| | - Shan Duan
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| |
Collapse
|
16
|
Genetic Defects Underlie the Non-syndromic Autosomal Recessive Intellectual Disability (NS-ARID). Open Life Sci 2017. [DOI: 10.1515/biol-2017-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractIntellectual disability (ID) is a neurodevelopmental disorder which appears frequently as the result of genetic mutations and may be syndromic (S-ID) or non-syndromic (NS-ID). ID causes an important economic burden, for patient's family, health systems, and society. Identifying genes that cause S-ID can easily be evaluated due to the clinical symptoms or physical anomalies. However, in the case of NS-ID due to the absence of co-morbid features, the latest molecular genetic techniques can be used to understand the genetic defects that underlie it. Recent studies have shown that non-syndromic autosomal recessive (NS-ARID) is extremely heterogeneous and contributes much more than X-linked ID. However, very little is known about the genes and loci involved in NS-ARID relative to X-linked ID, and whose complete genetic etiology remains obscure. In this review article, the known genetic etiology of NS-ARID and possible relationships between genes and the associated molecular pathways of their encoded proteins has been reviewed which will enhance our understanding about the underlying genes and mechanisms in NS-ARID.
Collapse
|
17
|
Cairó O. Assessing Relevance of External Cognitive Measures. Front Integr Neurosci 2017; 11:3. [PMID: 28270753 PMCID: PMC5319308 DOI: 10.3389/fnint.2017.00003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/07/2017] [Indexed: 12/03/2022] Open
Abstract
The arrival of modern brain imaging technologies has provided new opportunities for examining the biological essence of human intelligence as well as the relationship between brain size and cognition. Thanks to these advances, we can now state that the relationship between brain size and intelligence has never been well understood. This view is supported by findings showing that cognition is correlated more with brain tissues than sheer brain size. The complexity of cellular and molecular organization of neural connections actually determines the computational capacity of the brain. In this review article, we determine that while genotypes are responsible for defining the theoretical limits of intelligence, what is primarily responsible for determining whether those limits are reached or exceeded is experience (environmental influence). Therefore, we contend that the gene-environment interplay defines the intelligent quotient of an individual.
Collapse
Affiliation(s)
- Osvaldo Cairó
- Department of Computer Science, Instituto Tecnológico Autónomo de México (ITAM) Mexico City, Mexico
| |
Collapse
|
18
|
Huang GH, Sun ZL, Li HJ, Feng DF. Rho GTPase-activating proteins: Regulators of Rho GTPase activity in neuronal development and CNS diseases. Mol Cell Neurosci 2017; 80:18-31. [PMID: 28163190 DOI: 10.1016/j.mcn.2017.01.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 01/06/2017] [Accepted: 01/29/2017] [Indexed: 12/22/2022] Open
Abstract
The Rho family of small GTPases was considered as molecular switches in regulating multiple cellular events, including cytoskeleton reorganization. The Rho GTPase-activating proteins (RhoGAPs) are one of the major families of Rho GTPase regulators. RhoGAPs were initially considered negative mediators of Rho signaling pathways via their GAP domain. Recent studies have demonstrated that RhoGAPs also regulate numerous aspects of neuronal development and are related to various neurodegenerative diseases in GAP-dependent and GAP-independent manners. Moreover, RhoGAPs are regulated through various mechanisms, such as phosphorylation. To date, approximately 70 RhoGAPs have been identified; however, only a small portion has been thoroughly investigated. Thus, the characterization of important RhoGAPs in the central nervous system is crucial to understand their spatiotemporal role during different stages of neuronal development. In this review, we summarize the current knowledge of RhoGAPs in the brain with an emphasis on their molecular function, regulation mechanism and disease implications in the central nervous system.
Collapse
Affiliation(s)
- Guo-Hui Huang
- Department of Neurosurgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201900, China
| | - Zhao-Liang Sun
- Department of Neurosurgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201900, China
| | - Hong-Jiang Li
- Department of Neurosurgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201900, China
| | - Dong-Fu Feng
- Department of Neurosurgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201900, China; Institute of Traumatic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 201900, China.
| |
Collapse
|
19
|
Júnior FEB, Macedo GE, Zemolin AP, Silva GFD, Cruz LCD, Boligon AA, de Menezes IRA, Franco JL, Posser T. Oxidant effects and toxicity of Croton campestris in Drosophila melanogaster. PHARMACEUTICAL BIOLOGY 2016; 54:3068-3077. [PMID: 27417881 DOI: 10.1080/13880209.2016.1207089] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/13/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
CONTEXT Croton campestris A.St.-Hil. (Euphorbiaceae) is a species native to Northeast Brazil used by traditional communities for the treatment of a variety of health problems. However, potential toxicological effects of this plant are unknown. OBJECTIVE The potential toxicity of the hydroalcoholic extract of C. campestris leaves on Drosophila melanogaster insect model, additionally with phytochemical constitution and cellular mechanisms mediating the action of extract were analysed in this study. MATERIALS AND METHODS Constituents of the extract were evaluated by HPLC. In vitro antioxidant potential of extract was analysed by DPPH, ABTS and FRAP. Flies injected culture medium mixed with extract (0.1-50 mg/mL) for 72 h. After, ROS production was evaluated by DCF-DA oxidation. Phosphorylation of MAPK signalling pathway was investigated by Western blotting method. Activity of antioxidant enzymes was analysed in homogenates. RESULTS Major components of the extract include quercetin (38.11 ± 0.06 mg/g), caffeic acid (20.06 ± 0.17 mg/g) and kaempferol (15.45 ± 0.05 mg/g). Consumption of the extract impaired locomotor performance and induced fly death of flies (LC50 of 26.51 mg/mL). Augmented ROS formation and SOD, CAT and GST activity were observed from 0.1 mg/mL. JNK and p38 kinases phosphorylation was modulated and Paraquat-induced toxicity was augmented by extract. DISCUSSION AND CONCLUSION Our data show important toxicological effects of C. campestris leading to increased mortality and impaired locomotor performance accompanied by induction of cell stress markers in flies. The study draws attention to the indiscriminate use of plant extracts.
Collapse
Affiliation(s)
- Francisco E B Júnior
- a Departamento de Química Biológica , Universidade Regional do Cariri , Crato , CE , Brazil
- b Departamento de Química, Programa de Pós Graduação em Bioquímica Toxicológica , Universidade Federal de Santa Maria , Santa Maria , RS , Brazil
| | - Giulianna Echeverria Macedo
- c Oxidative Stress and Cell Signaling Research Group, Centro Interdisciplinar de Pesquisa em Biotecnologia , Universidade Federal do Pampa , Campus São Gabriel , São Gabriel , RS , Brazil
| | - Ana Paula Zemolin
- b Departamento de Química, Programa de Pós Graduação em Bioquímica Toxicológica , Universidade Federal de Santa Maria , Santa Maria , RS , Brazil
| | - Gustavo Felipe da Silva
- c Oxidative Stress and Cell Signaling Research Group, Centro Interdisciplinar de Pesquisa em Biotecnologia , Universidade Federal do Pampa , Campus São Gabriel , São Gabriel , RS , Brazil
| | - Litiele Cezar da Cruz
- b Departamento de Química, Programa de Pós Graduação em Bioquímica Toxicológica , Universidade Federal de Santa Maria , Santa Maria , RS , Brazil
| | - Aline Augusti Boligon
- d Departamento de Farmácia Industrial, Laboratório de Pesquisa em Fitoquímica , Universidade Federal de Santa Maria , Santa Maria , RS , Brazil
| | - Irwin R A de Menezes
- a Departamento de Química Biológica , Universidade Regional do Cariri , Crato , CE , Brazil
| | - Jeferson Luis Franco
- c Oxidative Stress and Cell Signaling Research Group, Centro Interdisciplinar de Pesquisa em Biotecnologia , Universidade Federal do Pampa , Campus São Gabriel , São Gabriel , RS , Brazil
| | - Thaís Posser
- c Oxidative Stress and Cell Signaling Research Group, Centro Interdisciplinar de Pesquisa em Biotecnologia , Universidade Federal do Pampa , Campus São Gabriel , São Gabriel , RS , Brazil
| |
Collapse
|
20
|
Harrington AJ, Raissi A, Rajkovich K, Berto S, Kumar J, Molinaro G, Raduazzo J, Guo Y, Loerwald K, Konopka G, Huber KM, Cowan CW. MEF2C regulates cortical inhibitory and excitatory synapses and behaviors relevant to neurodevelopmental disorders. eLife 2016; 5. [PMID: 27779093 PMCID: PMC5094851 DOI: 10.7554/elife.20059] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/11/2016] [Indexed: 12/23/2022] Open
Abstract
Numerous genetic variants associated with MEF2C are linked to autism, intellectual disability (ID) and schizophrenia (SCZ) – a heterogeneous collection of neurodevelopmental disorders with unclear pathophysiology. MEF2C is highly expressed in developing cortical excitatory neurons, but its role in their development remains unclear. We show here that conditional embryonic deletion of Mef2c in cortical and hippocampal excitatory neurons (Emx1-lineage) produces a dramatic reduction in cortical network activity in vivo, due in part to a dramatic increase in inhibitory and a decrease in excitatory synaptic transmission. In addition, we find that MEF2C regulates E/I synapse density predominantly as a cell-autonomous, transcriptional repressor. Analysis of differential gene expression in Mef2c mutant cortex identified a significant overlap with numerous synapse- and autism-linked genes, and the Mef2c mutant mice displayed numerous behaviors reminiscent of autism, ID and SCZ, suggesting that perturbing MEF2C function in neocortex can produce autistic- and ID-like behaviors in mice. DOI:http://dx.doi.org/10.7554/eLife.20059.001 Abnormal development of the brain contributes to intellectual disability, as well as to a number of psychiatric disorders, including schizophrenia and autism. As the brain develops, neurons establish connections with one another called synapses, which are either excitatory or inhibitory. At excitatory synapses, an electrical signal in the first cell increases the likelihood that the second cell will also produce an electrical signal. At inhibitory synapses, electrical activity in the first cell reduces the chances of the second cell producing an electrical signal. An imbalance between excitatory and inhibitory activity is one of the factors thought to give rise to neurodevelopmental disorders. Many individuals with schizophrenia, autism or intellectual disability possess mutations in, or near, a gene called MEF2C. This gene, which is active in both excitatory and inhibitory neurons, encodes a protein that regulates the activity of many other genes during brain development. Harrington, Raissi et al. therefore hypothesized that alterations in MEF2C might predispose individuals to neurodevelopmental disorders by disrupting the balance of excitatory and inhibitory synapses in the developing brain. To test this idea, Harrington, Raissi et al. generated mice that lack the Mef2c gene in a large proportion of their neurons throughout development. As predicted, the animals showed an imbalance of excitatory and inhibitory synapses in the brain’s outer layer, the cortex. They also displayed changes in behavior like those seen in autism. These included a loss of interest in social interaction and a reduction in vocalizations, suggesting impaired communication. Other behavioral changes included hyperactivity, repetitive movements and severe learning impairments: all features commonly observed in human neurodevelopmental disorders. The next challenge is to understand when, where and how MEF2C acts in the cortex to shape the balance of excitatory and inhibitory connections. Once this is known, further studies can test whether disrupting these processes leads directly to behaviors characteristic of autism, schizophrenia and intellectual disability. This may lead to the development of new drugs that can reverse or improve the symptoms of these conditions in affected individuals. DOI:http://dx.doi.org/10.7554/eLife.20059.002
Collapse
Affiliation(s)
- Adam J Harrington
- Department of Neurosciences, Medical University of South Carolina, Charleston, United States.,Department of Psychiatry, Harvard Medical School, Belmont, United States
| | - Aram Raissi
- Department of Psychiatry, Harvard Medical School, Belmont, United States
| | - Kacey Rajkovich
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Stefano Berto
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Jaswinder Kumar
- Department of Psychiatry, Harvard Medical School, Belmont, United States.,Medical Scientist Training Program, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Gemma Molinaro
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Jonathan Raduazzo
- Department of Psychiatry, Harvard Medical School, Belmont, United States
| | - Yuhong Guo
- Department of Psychiatry, Harvard Medical School, Belmont, United States
| | - Kris Loerwald
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Genevieve Konopka
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Kimberly M Huber
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Christopher W Cowan
- Department of Neurosciences, Medical University of South Carolina, Charleston, United States.,Department of Psychiatry, Harvard Medical School, Belmont, United States
| |
Collapse
|
21
|
Ilie A, Gao AYL, Reid J, Boucher A, McEwan C, Barrière H, Lukacs GL, McKinney RA, Orlowski J. A Christianson syndrome-linked deletion mutation (∆(287)ES(288)) in SLC9A6 disrupts recycling endosomal function and elicits neurodegeneration and cell death. Mol Neurodegener 2016; 11:63. [PMID: 27590723 PMCID: PMC5010692 DOI: 10.1186/s13024-016-0129-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 08/27/2016] [Indexed: 01/19/2023] Open
Abstract
Background Christianson Syndrome, a recently identified X-linked neurodevelopmental disorder, is caused by mutations in the human gene SLC9A6 encoding the recycling endosomal alkali cation/proton exchanger NHE6. The patients have pronounced limitations in cognitive ability, motor skills and adaptive behaviour. However, the mechanistic basis for this disorder is poorly understood as few of the more than 20 mutations identified thus far have been studied in detail. Methods Here, we examined the molecular and cellular consequences of a 6 base-pair deletion of amino acids Glu287 and Ser288 (∆ES) in the predicted seventh transmembrane helix of human NHE6 expressed in established cell lines (CHO/AP-1, HeLa and neuroblastoma SH-SY5Y) and primary cultures of mouse hippocampal neurons by measuring levels of protein expression, stability, membrane trafficking, endosomal function and cell viability. Results In the cell lines, immunoblot analyses showed that the nascent mutant protein was properly synthesized and assembled as a homodimer, but its oligosaccharide maturation and half-life were markedly reduced compared to wild-type (WT) and correlated with enhanced ubiquitination leading to both proteasomal and lysosomal degradation. Despite this instability, a measurable fraction of the transporter was correctly sorted to the plasma membrane. However, the rates of clathrin-mediated endocytosis of the ∆ES mutant as well as uptake of companion vesicular cargo, such as the ligand-bound transferrin receptor, were significantly reduced and correlated with excessive endosomal acidification. Notably, ectopic expression of ∆ES but not WT induced apoptosis when examined in AP-1 cells. Similarly, in transfected primary cultures of mouse hippocampal neurons, membrane trafficking of the ∆ES mutant was impaired and elicited marked reductions in total dendritic length, area and arborization, and triggered apoptotic cell death. Conclusions These results suggest that loss-of-function mutations in NHE6 disrupt recycling endosomal function and trafficking of cargo which ultimately leads to neuronal degeneration and cell death in Christianson Syndrome. Electronic supplementary material The online version of this article (doi:10.1186/s13024-016-0129-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Alina Ilie
- Department of Physiology, McGill University, Bellini Life Sciences Bldg., Rm, 166, 3649 Promenade Sir-William-Osler, Montreal, QC, H3G 0B1, Canada
| | - Andy Y L Gao
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Jonathan Reid
- Department of Physiology, McGill University, Bellini Life Sciences Bldg., Rm, 166, 3649 Promenade Sir-William-Osler, Montreal, QC, H3G 0B1, Canada
| | - Annie Boucher
- Department of Physiology, McGill University, Bellini Life Sciences Bldg., Rm, 166, 3649 Promenade Sir-William-Osler, Montreal, QC, H3G 0B1, Canada
| | - Cassandra McEwan
- Department of Physiology, McGill University, Bellini Life Sciences Bldg., Rm, 166, 3649 Promenade Sir-William-Osler, Montreal, QC, H3G 0B1, Canada
| | - Hervé Barrière
- Department of Physiology, McGill University, Bellini Life Sciences Bldg., Rm, 166, 3649 Promenade Sir-William-Osler, Montreal, QC, H3G 0B1, Canada
| | - Gergely L Lukacs
- Department of Physiology, McGill University, Bellini Life Sciences Bldg., Rm, 166, 3649 Promenade Sir-William-Osler, Montreal, QC, H3G 0B1, Canada
| | - R Anne McKinney
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - John Orlowski
- Department of Physiology, McGill University, Bellini Life Sciences Bldg., Rm, 166, 3649 Promenade Sir-William-Osler, Montreal, QC, H3G 0B1, Canada.
| |
Collapse
|
22
|
A genome-wide analysis of putative functional and exonic variation associated with extremely high intelligence. Mol Psychiatry 2016; 21:1145-51. [PMID: 26239293 PMCID: PMC4650257 DOI: 10.1038/mp.2015.108] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/21/2015] [Accepted: 06/16/2015] [Indexed: 02/07/2023]
Abstract
Although individual differences in intelligence (general cognitive ability) are highly heritable, molecular genetic analyses to date have had limited success in identifying specific loci responsible for its heritability. This study is the first to investigate exome variation in individuals of extremely high intelligence. Under the quantitative genetic model, sampling from the high extreme of the distribution should provide increased power to detect associations. We therefore performed a case-control association analysis with 1409 individuals drawn from the top 0.0003 (IQ >170) of the population distribution of intelligence and 3253 unselected population-based controls. Our analysis focused on putative functional exonic variants assayed on the Illumina HumanExome BeadChip. We did not observe any individual protein-altering variants that are reproducibly associated with extremely high intelligence and within the entire distribution of intelligence. Moreover, no significant associations were found for multiple rare alleles within individual genes. However, analyses using genome-wide similarity between unrelated individuals (genome-wide complex trait analysis) indicate that the genotyped functional protein-altering variation yields a heritability estimate of 17.4% (s.e. 1.7%) based on a liability model. In addition, investigation of nominally significant associations revealed fewer rare alleles associated with extremely high intelligence than would be expected under the null hypothesis. This observation is consistent with the hypothesis that rare functional alleles are more frequently detrimental than beneficial to intelligence.
Collapse
|
23
|
Posthuma D, de Geus EJ. Progress in the Molecular-Genetic Study of Intelligence. CURRENT DIRECTIONS IN PSYCHOLOGICAL SCIENCE 2016. [DOI: 10.1111/j.1467-8721.2006.00426.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The past decade has seen a major shift in the genetic study of human intelligence; where classic studies aimed to quantify the heritability of intelligence, current studies aim to dissect this heritability into its molecular-genetic components. Five whole-genome linkage scans have been published in the past year, converging on several chromosomal (or genomic) regions important to intelligence. A handful of candidate genes, some of which lie in these genomic regions, have shown significant association to intelligence and the associations have been replicated in independent samples. Finding genes brings us closer to an understanding of the neurophysiological basis of human cognition. Furthermore, when genes are no longer latent factors in our models but can actually be measured, it becomes feasible to identify those environmental factors that interact and correlate with genetic makeup. This will supplant the long nature–nurture debate with actual understanding.
Collapse
Affiliation(s)
- Danielle Posthuma
- Department of Biological Psychology and Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, The Netherlands
| | - Eco J.C. de Geus
- Department of Biological Psychology and Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, The Netherlands
| |
Collapse
|
24
|
Jeong JW, Sundaram S, Behen ME, Chugani HT. Relationship between genotype and arcuate fasciculus morphology in six young children with global developmental delay: Preliminary DTI stuy. J Magn Reson Imaging 2016; 44:1504-1512. [PMID: 27251476 DOI: 10.1002/jmri.25306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/26/2016] [Indexed: 11/06/2022] Open
Abstract
PURPOSE To investigate whether different genetic mutations observed in children with global developmental delay (GD) are associated with unique patterns of the arcuate fasciculus dysmorphology. MATERIALS AND METHODS Six children with GD (age: 36.8 ± 14.1 months, 5 boys) having mutations in MID1, CDK4, SFRP1, EN2, RXRG-GLRB, or MECP2, and five children with typical development (TD, age: 38.5 ± 20.5 months, 4 boys) underwent a 3 Tesla MRI including diffusion weighted imaging (DWI). Five language pathway segments in the left hemisphere, "C1 : Broca's to Wernicke's area," "C2 : Broca's to premotor area," "C3 : premotor to Wernicke's area," "C4 : Wernicke's to inferior parietal area," and "C5 : premotor to inferior parietal area" were objectively identified using the DWI "maximum a posteriori probability" classifier. RESULTS Affinity propagation clustering analysis found that three arcuate pathway segments, C1,2,4 , of MID1, CDK4, EN2, and MECP2 had a similar pattern of volume ratio while those of SFRP1 and RXRG-GLRB had a heterogeneous pattern of volume ratio (net similarity = -0.01). Using receiver operating characteristic curve analysis, the fiber ratios of C1,2,4 showed a high probability to discriminate between GD and TD, yielding an accuracy of 0.91, 0.91, 1.00, respectively. The fiber volumes of C1 and C4 showed a strong correlation with expressive language (R2 = 0.6019; P-value = 0.033) and receptive language (R2 = 0.6379; P-value = 0.028), respectively. CONCLUSION The findings of the present study provide preliminary evidence to suggest that different segments of the arcuate fasciculus are formed under the regulation of different genes which, when mutated, may result in developmental delay. J. Magn. Reson. Imaging 2016;44:1504-1512.
Collapse
Affiliation(s)
- Jeong-Won Jeong
- Carman and Ann Adams Department of Pediatrics Wayne State University School of Medicine, Detroit, Michigan, USA.,Department of Neurology, Wayne State University School of Medicine, Detroit, Michigan, USA.,Translational Imaging Laboratory, PET center, Children's Hospital of Michigan, Detroit, Michigan, USA
| | - Senthil Sundaram
- Carman and Ann Adams Department of Pediatrics Wayne State University School of Medicine, Detroit, Michigan, USA.,Department of Neurology, Wayne State University School of Medicine, Detroit, Michigan, USA.,Translational Imaging Laboratory, PET center, Children's Hospital of Michigan, Detroit, Michigan, USA
| | - Michael E Behen
- Carman and Ann Adams Department of Pediatrics Wayne State University School of Medicine, Detroit, Michigan, USA.,Department of Neurology, Wayne State University School of Medicine, Detroit, Michigan, USA.,Translational Imaging Laboratory, PET center, Children's Hospital of Michigan, Detroit, Michigan, USA
| | - Harry T Chugani
- Department of Neurology, Nemours DuPont Hospital for Children, Wilmington, Delaware, USA.,Thomas Jefferson University School of Medicine, Philadelphia, Pennsylvania, USA
| |
Collapse
|
25
|
Abstract
Intellectual disability is the most common developmental disorder characterized by a congenital limitation in intellectual functioning and adaptive behavior. It often co-occurs with other mental conditions like attention deficit/hyperactivity disorder and autism spectrum disorder, and can be part of a malformation syndrome that affects other organs. Considering the heterogeneity of its causes (environmental and genetic), its frequency worldwide varies greatly. This review focuses on known genes underlying (syndromic and non-syndromic) intellectual disability, it provides a succinct analysis of their Gene Ontology, and it suggests the use of transcriptional profiling for the prioritization of candidate genes.
Collapse
Affiliation(s)
- Pietro Chiurazzi
- Institute of Genomic Medicine, Catholic University School of Medicine, Rome, Italy
| | - Filomena Pirozzi
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| |
Collapse
|
26
|
Berto S, Perdomo-Sabogal A, Gerighausen D, Qin J, Nowick K. A Consensus Network of Gene Regulatory Factors in the Human Frontal Lobe. Front Genet 2016; 7:31. [PMID: 27014338 PMCID: PMC4782181 DOI: 10.3389/fgene.2016.00031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/18/2016] [Indexed: 01/29/2023] Open
Abstract
Cognitive abilities, such as memory, learning, language, problem solving, and planning, involve the frontal lobe and other brain areas. Not much is known yet about the molecular basis of cognitive abilities, but it seems clear that cognitive abilities are determined by the interplay of many genes. One approach for analyzing the genetic networks involved in cognitive functions is to study the coexpression networks of genes with known importance for proper cognitive functions, such as genes that have been associated with cognitive disorders like intellectual disability (ID) or autism spectrum disorders (ASD). Because many of these genes are gene regulatory factors (GRFs) we aimed to provide insights into the gene regulatory networks active in the human frontal lobe. Using genome wide human frontal lobe expression data from 10 independent data sets, we first derived 10 individual coexpression networks for all GRFs including their potential target genes. We observed a high level of variability among these 10 independently derived networks, pointing out that relying on results from a single study can only provide limited biological insights. To instead focus on the most confident information from these 10 networks we developed a method for integrating such independently derived networks into a consensus network. This consensus network revealed robust GRF interactions that are conserved across the frontal lobes of different healthy human individuals. Within this network, we detected a strong central module that is enriched for 166 GRFs known to be involved in brain development and/or cognitive disorders. Interestingly, several hubs of the consensus network encode for GRFs that have not yet been associated with brain functions. Their central role in the network suggests them as excellent new candidates for playing an essential role in the regulatory network of the human frontal lobe, which should be investigated in future studies.
Collapse
Affiliation(s)
- Stefano Berto
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University LeipzigLeipzig, Germany; Paul-Flechsig Institute for Brain Research, University of LeipzigLeipzig, Germany; Department of Neuroscience, University of Texas Southwestern Medical CenterDallas, TX, USA
| | - Alvaro Perdomo-Sabogal
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig Leipzig, Germany
| | - Daniel Gerighausen
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig Leipzig, Germany
| | - Jing Qin
- Department of Mathematics and Computer Sciences, University of Southern DenmarkOdense, Denmark; Institute for Theoretical Chemistry, University of ViennaVienna, Austria
| | - Katja Nowick
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University LeipzigLeipzig, Germany; Paul-Flechsig Institute for Brain Research, University of LeipzigLeipzig, Germany
| |
Collapse
|
27
|
Kochinke K, Zweier C, Nijhof B, Fenckova M, Cizek P, Honti F, Keerthikumar S, Oortveld M, Kleefstra T, Kramer J, Webber C, Huynen M, Schenck A. Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules. Am J Hum Genet 2016; 98:149-64. [PMID: 26748517 DOI: 10.1016/j.ajhg.2015.11.024] [Citation(s) in RCA: 200] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/25/2015] [Indexed: 10/22/2022] Open
Abstract
Intellectual disability (ID) disorders are genetically and phenotypically extremely heterogeneous. Can this complexity be depicted in a comprehensive way as a means of facilitating the understanding of ID disorders and their underlying biology? We provide a curated database of 746 currently known genes, mutations in which cause ID (ID-associated genes [ID-AGs]), classified according to ID manifestation and associated clinical features. Using this integrated resource, we show that ID-AGs are substantially enriched with co-expression, protein-protein interactions, and specific biological functions. Systematic identification of highly enriched functional themes and phenotypes revealed typical phenotype combinations characterizing process-defined groups of ID disorders, such as chromatin-related disorders and deficiencies in DNA repair. Strikingly, phenotype classification efficiently breaks down ID-AGs into subsets with significantly elevated biological coherence and predictive power. Custom-made functional Drosophila datasets revealed further characteristic phenotypes among ID-AGs and specific clinical classes. Our study and resource provide systematic insights into the molecular and clinical landscape of ID disorders, represent a significant step toward overcoming current limitations in ID research, and prove the utility of systematic human and cross-species phenomics analyses in highly heterogeneous genetic disorders.
Collapse
|
28
|
Erickson RP. The importance of de novo mutations for pediatric neurological disease--It is not all in utero or birth trauma. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2016; 767:42-58. [PMID: 27036065 DOI: 10.1016/j.mrrev.2015.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/23/2015] [Accepted: 12/23/2015] [Indexed: 01/30/2023]
Abstract
The advent of next generation sequencing (NGS, which consists of massively parallel sequencing to perform TGS (total genome sequencing) or WES (whole exome sequencing)) has abundantly discovered many causative mutations in patients with pediatric neurological disease. A surprisingly high number of these are de novo mutations which have not been inherited from either parent. For epilepsy, autism spectrum disorders, and neuromotor disorders, including cerebral palsy, initial estimates put the frequency of causative de novo mutations at about 15% and about 10% of these are somatic. There are some shared mutated genes between these three classes of disease. Studies of copy number variation by comparative genomic hybridization (CGH) proceded the NGS approaches but they also detect de novo variation which is especially important for ASDs. There are interesting differences between the mutated genes detected by CGS and NGS. In summary, de novo mutations cause a very significant proportion of pediatric neurological disease.
Collapse
Affiliation(s)
- Robert P Erickson
- Dept. of Pediatrics, University of Arizona College of Medicine, Tucson, AZ 85724, United States.
| |
Collapse
|
29
|
Iliadi KG, Gluscencova OB, Boulianne GL. Psychomotor Behavior: A Practical Approach in Drosophila. Front Psychiatry 2016; 7:153. [PMID: 27630583 PMCID: PMC5005351 DOI: 10.3389/fpsyt.2016.00153] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/19/2016] [Indexed: 11/13/2022] Open
Abstract
Psychomotor behaviors are governed by fine relationships between physical activity and cognitive functions. Disturbances in psychomotor development and performance are a hallmark of many mental illnesses and often appear as observable and measurable behaviors. Here, we describe a new method called an "equilibrist test," which can be used to quantify psychomotor learning and performance in Drosophila. We also show how this test can be used to quantify motor disturbances at relatively early stages in the development of neurodegenerative diseases.
Collapse
Affiliation(s)
- Konstantin G Iliadi
- Program in Developmental and Stem Cell Biology, The Hospital For Sick Children , Toronto, ON , Canada
| | - Oxana B Gluscencova
- Program in Developmental and Stem Cell Biology, The Hospital For Sick Children , Toronto, ON , Canada
| | - Gabrielle L Boulianne
- Program in Developmental and Stem Cell Biology, The Hospital For Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
30
|
Anderson BB, Scott A, Dukas R. Social behavior and activity are decoupled in larval and adult fruit flies. Behav Ecol 2015. [DOI: 10.1093/beheco/arv225] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
31
|
Block A, Ahmed MM, Dhanasekaran AR, Tong S, Gardiner KJ. Sex differences in protein expression in the mouse brain and their perturbations in a model of Down syndrome. Biol Sex Differ 2015; 6:24. [PMID: 26557979 PMCID: PMC4640233 DOI: 10.1186/s13293-015-0043-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/01/2015] [Indexed: 01/08/2023] Open
Abstract
Background While many sex differences in structure and function of the mammalian brain have been described, the molecular correlates of these differences are not broadly known. Also unknown is how sex differences at the protein level are perturbed by mutations that lead to intellectual disability (ID). Down syndrome (DS) is the most common genetic cause of ID and is due to trisomy of human chromosome 21 (Hsa21) and the resulting increased expression of Hsa21-encoded genes. The Dp(10)1Yey mouse model (Dp10) of DS is trisomic for orthologs of 39 Hsa21 protein-coding genes that map to mouse chromosome 10 (Mmu10), including four genes with known sex differences in functional properties. How these genes contribute to the DS cognitive phenotype is not known. Methods Using reverse phase protein arrays, levels of ~100 proteins/protein modifications were measured in the hippocampus, cerebellum, and cortex of female and male controls and their trisomic Dp10 littermates. Proteins were chosen for their known roles in learning/memory and synaptic plasticity and include components of the MAPK, MTOR, and apoptosis pathways, immediate early genes, and subunits of ionotropic glutamate receptors. Protein levels were compared between genotypes, sexes, and brain regions using a three-level mixed effects model and the Benjamini-Hochberg correction for multiple testing. Results In control mice, levels of approximately one half of the proteins differ significantly between females and males in at least one brain region; in the hippocampus alone, levels of 40 % of the proteins are significantly higher in females. Trisomy of the Mmu10 segment differentially affects female and male profiles, perturbing protein levels most in the cerebellum of female Dp10 and most in the hippocampus of male Dp10. Cortex is minimally affected by sex and genotype. Diverse pathways and processes are implicated in both sex and genotype differences. Conclusions The extensive sex differences in control mice in levels of proteins involved in learning/memory illustrate the molecular complexity underlying sex differences in normal neurological processes. The sex-specific abnormalities in the Dp10 suggest the possibility of sex-specific phenotypic features in DS and reinforce the need to use female as well as male mice, in particular in preclinical evaluations of drug responses. Electronic supplementary material The online version of this article (doi:10.1186/s13293-015-0043-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Aaron Block
- Department of Pediatrics, Linda Crnic Institute for Down Syndrome, Aurora, USA
| | - Md Mahiuddin Ahmed
- Department of Pediatrics, Linda Crnic Institute for Down Syndrome, Aurora, USA
| | | | - Suhong Tong
- Colorado School of Public Health, Aurora, USA
| | - Katheleen J Gardiner
- Department of Pediatrics, Linda Crnic Institute for Down Syndrome, Aurora, USA ; Human Medical Genetics and Genomics, and Neuroscience Programs, University of Colorado Denver School of Medicine, 12700 E 19th Avenue, Mail Stop 8608, Aurora, CO 80045 USA
| |
Collapse
|
32
|
A de novo microdeletion in NRXN1 in a Dutch patient with mild intellectual disability, microcephaly and gonadal dysgenesis. Genet Res (Camb) 2015; 97:e19. [PMID: 26438105 DOI: 10.1017/s001667231500021x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
This report is regarding a Dutch female with microcephaly, mild intellectual disability (ID), gonadal dysgenesis and dysmorphic facial features with synophrys. Upon genotyping, an ~455 kb de novo deletion encompassing the first exon of NRXN1 was found. Bidirectional sequencing of the coding exons of the NRXN1 alpha isoform was subsequently performed to investigate the possibility of a pathogenic mutation on the other allele, but we could not find any other mutation. Previously, many heterozygous mutations as well as microdeletions in NRXN1 were shown to be associated with ID, autism, schizophrenia, and other psychiatric and psychotic disorders. Our results are in agreement with other reports that show that NRXN1 deletions can lead to ID, microcephaly and mild dysmorphic features. However, this is the first report of gonadal dysgenesis being associated with such deletions. It is not clear whether there is a causal relationship between the NRXN1 deletion and gonadal dysgenesis, but it is of interest that the FSHR gene, which encodes the follicle-stimulating hormone receptor causative correlation that is mutated in ovarian dysgenesis, is located proximal to the NRXN1 gene. Given that most of the females carrying NRXN1 deletions have been diagnosed at a prepubertal age, gynecologic screening of female carriers of a NRXN1 deletion is warranted.
Collapse
|
33
|
Johnson W, Carothers A, Deary IJ. A Role for the X Chromosome in Sex Differences in Variability in General Intelligence? PERSPECTIVES ON PSYCHOLOGICAL SCIENCE 2015; 4:598-611. [PMID: 26161735 DOI: 10.1111/j.1745-6924.2009.01168.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
There is substantial evidence that males are more variable than females in general intelligence. In recent years, researchers have presented this as a reason that, although there is little, if any, mean sex difference in general intelligence, males tend to be overrepresented at both ends of its overall distribution. Part of the explanation could be the presence of genes on the X chromosome related both to syndromal disorders involving mental retardation and to population variation in general intelligence occurring normally. Genes on the X chromosome appear overrepresented among genes with known involvement in mental retardation, which is consistent with a model we developed of the population distribution of general intelligence as a mixture of two normal distributions. Using this model, we explored the expected ratios of males to females at various points in the distribution and estimated the proportion of variance in general intelligence potentially due to genes on the X chromosome. These estimates provide clues to the extent to which biologically based sex differences could be manifested in the environment as sex differences in displayed intellectual abilities. We discuss these observations in the context of sex differences in specific cognitive abilities and evolutionary theories of sexual selection.
Collapse
Affiliation(s)
- Wendy Johnson
- University of Edinburgh, United Kingdom University of Minnesota-Twin Cities, and
| | - Andrew Carothers
- Public Health Sciences, University of Edinburgh Medical School, United Kingdom
| | | |
Collapse
|
34
|
Madabattula ST, Strautman JC, Bysice AM, O'Sullivan JA, Androschuk A, Rosenfelt C, Doucet K, Rouleau G, Bolduc F. Quantitative Analysis of Climbing Defects in a Drosophila Model of Neurodegenerative Disorders. J Vis Exp 2015:e52741. [PMID: 26132637 DOI: 10.3791/52741] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Locomotive defects resulting from neurodegenerative disorders can be a late onset symptom of disease, following years of subclinical degeneration, and thus current therapeutic treatment strategies are not curative. Through the use of whole exome sequencing, an increasing number of genes have been identified to play a role in human locomotion. Despite identifying these genes, it is not known how these genes are crucial to normal locomotive functioning. Therefore, a reliable assay, which utilizes model organisms to elucidate the role of these genes in order to identify novel targets of therapeutic interest, is needed more than ever. We have designed a sensitized version of the negative geotaxis assay that allows for the detection of milder defects earlier and has the ability to evaluate these defects over time. The assay is performed in a glass graduated cylinder, which is sealed with a wax barrier film. By increasing the threshold distance to be climbed to 17.5 cm and increasing the experiment duration to 2 min we have observed a greater sensitivity in detecting mild mobility dysfunctions. The assay is cost effective and does not require extensive training to obtain highly reproducible results. This makes it an excellent technique for screening candidate drugs in Drosophila mutants with locomotion defects.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Kacy Doucet
- Department of Pediatrics, University of Alberta
| | - Guy Rouleau
- Montreal Neurological Institute and Hospital, McGill University
| | | |
Collapse
|
35
|
Farrell MS, Werge T, Sklar P, Owen MJ, Ophoff RA, O'Donovan MC, Corvin A, Cichon S, Sullivan PF. Evaluating historical candidate genes for schizophrenia. Mol Psychiatry 2015; 20:555-62. [PMID: 25754081 PMCID: PMC4414705 DOI: 10.1038/mp.2015.16] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 11/14/2014] [Accepted: 01/05/2015] [Indexed: 12/19/2022]
Abstract
Prior to the genome-wide association era, candidate gene studies were a major approach in schizophrenia genetics. In this invited review, we consider the current status of 25 historical candidate genes for schizophrenia (for example, COMT, DISC1, DTNBP1 and NRG1). The initial study for 24 of these genes explicitly evaluated common variant hypotheses about schizophrenia. Our evaluation included a meta-analysis of the candidate gene literature, incorporation of the results of the largest genomic study yet published for schizophrenia, ratings from informed researchers who have published on these genes, and ratings from 24 schizophrenia geneticists. On the basis of current empirical evidence and mostly consensual assessments of informed opinion, it appears that the historical candidate gene literature did not yield clear insights into the genetic basis of schizophrenia. A likely reason why historical candidate gene studies did not achieve their primary aims is inadequate statistical power. However, the considerable efforts embodied in these early studies unquestionably set the stage for current successes in genomic approaches to schizophrenia.
Collapse
Affiliation(s)
- M S Farrell
- Center for Psychiatric Genomics, Department of Genetics, Genomic Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - T Werge
- 1] Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Denmark [2] Department of Clinical Medicine, University of Copenhagen, Copenhagen, Aarhus, Denmark [3] The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - P Sklar
- 1] Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA [2] Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA [3] Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M J Owen
- 1] MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK [2] National Centre for Mental Health, Cardiff University, Cardiff, UK
| | - R A Ophoff
- 1] Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA [2] Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA [3] Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, The Netherlands
| | - M C O'Donovan
- 1] MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK [2] National Centre for Mental Health, Cardiff University, Cardiff, UK
| | - A Corvin
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College Dublin, Ireland
| | - S Cichon
- 1] Division of Medical Genetics, Department of Biomedicine, University Basel, Basel, Switzerland [2] Institute of Human Genetics, University of Bonn, Bonn, Germany [3] Department of Genomics, Life and Brain Center, Bonn, Germany
| | - P F Sullivan
- 1] Center for Psychiatric Genomics, Department of Genetics, Genomic Medicine, University of North Carolina, Chapel Hill, NC, USA [2] Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden [3] Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| |
Collapse
|
36
|
Kaur K, Simon AF, Chauhan V, Chauhan A. Effect of bisphenol A on Drosophila melanogaster behavior – A new model for the studies on neurodevelopmental disorders. Behav Brain Res 2015; 284:77-84. [DOI: 10.1016/j.bbr.2015.02.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 01/30/2015] [Accepted: 02/01/2015] [Indexed: 02/07/2023]
|
37
|
Contribution of copy number variants (CNVs) to congenital, unexplained intellectual and developmental disabilities in Lebanese patients. Mol Cytogenet 2015; 8:26. [PMID: 25922617 PMCID: PMC4411788 DOI: 10.1186/s13039-015-0130-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/23/2015] [Indexed: 11/10/2022] Open
Abstract
Background Chromosomal microarray analysis (CMA) is currently the most widely adopted clinical test for patients with unexplained intellectual disability (ID), developmental delay (DD), and congenital anomalies. Its use has revealed the capacity to detect copy number variants (CNVs), as well as regions of homozygosity, that, based on their distribution on chromosomes, indicate uniparental disomy or parental consanguinity that is suggestive of an increased probability of recessive disease. Results We screened 149 Lebanese probands with ID/DD and 99 healthy controls using the Affymetrix Cyto 2.7 M and SNP6.0 arrays. We report all identified CNVs, which we divided into groups. Pathogenic CNVs were identified in 12.1% of the patients. We review the genotype/phenotype correlation in a patient with a 1q44 microdeletion and refine the minimal critical regions responsible for the 10q26 and 16q monosomy syndromes. Several likely causative CNVs were also detected, including new homozygous microdeletions (9p23p24.1, 10q25.2, and 8p23.1) in 3 patients born to consanguineous parents, involving potential candidate genes. However, the clinical interpretation of several other CNVs remains uncertain, including a microdeletion affecting ATRNL1. This CNV of unknown significance was inherited from the patient’s unaffected-mother; therefore, additional ethnically matched controls must be screened to obtain enough evidence for classification of this CNV. Conclusion This study has provided supporting evidence that whole-genome analysis is a powerful method for uncovering chromosomal imbalances, regardless of consanguinity in the parents of patients and despite the challenge presented by analyzing some CNVs. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0130-y) contains supplementary material, which is available to authorized users.
Collapse
|
38
|
Xie B, Agam G, Balasubramanian S, Xu J, Gilliam TC, Maltsev N, Börnigen D. Disease gene prioritization using network and feature. J Comput Biol 2015; 22:313-23. [PMID: 25844670 PMCID: PMC4808289 DOI: 10.1089/cmb.2015.0001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Identifying high-confidence candidate genes that are causative for disease phenotypes, from the large lists of variations produced by high-throughput genomics, can be both time-consuming and costly. The development of novel computational approaches, utilizing existing biological knowledge for the prioritization of such candidate genes, can improve the efficiency and accuracy of the biomedical data analysis. It can also reduce the cost of such studies by avoiding experimental validations of irrelevant candidates. In this study, we address this challenge by proposing a novel gene prioritization approach that ranks promising candidate genes that are likely to be involved in a disease or phenotype under study. This algorithm is based on the modified conditional random field (CRF) model that simultaneously makes use of both gene annotations and gene interactions, while preserving their original representation. We validated our approach on two independent disease benchmark studies by ranking candidate genes using network and feature information. Our results showed both high area under the curve (AUC) value (0.86), and more importantly high partial AUC (pAUC) value (0.1296), and revealed higher accuracy and precision at the top predictions as compared with other well-performed gene prioritization tools, such as Endeavour (AUC-0.82, pAUC-0.083) and PINTA (AUC-0.76, pAUC-0.066). We were able to detect more target genes (9/18/19/27) on top positions (1/5/10/20) compared to Endeavour (3/11/14/23) and PINTA (6/10/13/18). To demonstrate its usability, we applied our method to a case study for the prediction of molecular mechanisms contributing to intellectual disability and autism. Our approach was able to correctly recover genes related to both disorders and provide suggestions for possible additional candidates based on their rankings and functional annotations.
Collapse
Affiliation(s)
- Bingqing Xie
- Department of Computer Science, Illinois Institute of Technology, Chicago, Illinois
| | - Gady Agam
- Department of Computer Science, Illinois Institute of Technology, Chicago, Illinois
| | | | - Jinbo Xu
- Toyota Technological Institute of Chicago, Chicago, Illinois
| | - T. Conrad Gilliam
- Department of Human Genetics, University of Chicago, Chicago, Illinois
| | - Natalia Maltsev
- Department of Human Genetics, University of Chicago, Chicago, Illinois
| | - Daniela Börnigen
- Department of Human Genetics, University of Chicago, Chicago, Illinois
- Toyota Technological Institute of Chicago, Chicago, Illinois
| |
Collapse
|
39
|
Petrosyan A, Hsieh IH, Phillips JP, Saberi K. Enhanced tethered-flight duration and locomotor activity by overexpression of the human gene SOD1 in Drosophila motorneurons. Genet Mol Biol 2015; 38:107-14. [PMID: 25983632 PMCID: PMC4415569 DOI: 10.1590/s1415-475738138120140132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 11/06/2014] [Indexed: 03/12/2023] Open
Abstract
Mutation of the human gene superoxide dismutase (hSOD1) is associated with the fatal neurodegenerative disease familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Selective overexpression of hSOD1 in Drosophila motorneurons increases lifespan to 140% of normal. The current study was designed to determine resistance to lifespan decline and failure of sensorimotor functions by overexpressing hSOD1 in Drosophila's motorneurons. First, we measured the ability to maintain continuous flight and wingbeat frequency (WBF) as a function of age (5 to 50 days). Flies overexpressing hSOD1 under the D42-GAL4 activator were able to sustain flight significantly longer than controls, with the largest effect observed in the middle stages of life. The hSOD1-expressed line also had, on average, slower wingbeat frequencies in late, but not early life relative to age-matched controls. Second, we examined locomotor (exploratory walking) behavior in late life when flies had lost the ability to fly (age ≥ 60 d). hSOD1-expressed flies showed significantly more robust walking activity relative to controls. Findings show patterns of functional decline dissimilar to those reported for other life-extended lines, and suggest that the hSOD1 gene not only delays death but enhances sensorimotor abilities critical to survival even in late life.
Collapse
Affiliation(s)
- Agavni Petrosyan
- Department of Cognitive Sciences, University of California, Irvine, CA,
USA
| | - I-Hui Hsieh
- Institute of Cognitive Neuroscience, National Central University,
Jhongli City, Taiwan
| | - John P. Phillips
- Department of Molecular Biology and Genetics, University of Guelph,
Guelph, Ontario, Canada
| | - Kourosh Saberi
- Department of Cognitive Sciences, University of California, Irvine, CA,
USA
| |
Collapse
|
40
|
Franić S, Groen-Blokhuis MM, Dolan CV, Kattenberg MV, Pool R, Xiao X, Scheet PA, Ehli EA, Davies GE, van der Sluis S, Abdellaoui A, Hansell NK, Martin NG, Hudziak JJ, van Beijsterveldt CEM, Swagerman SC, Hulshoff Pol HE, de Geus EJC, Bartels M, Ropers HH, Hottenga JJ, Boomsma DI. Intelligence: shared genetic basis between Mendelian disorders and a polygenic trait. Eur J Hum Genet 2015; 23:1378-83. [PMID: 25712083 DOI: 10.1038/ejhg.2015.3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 12/16/2014] [Accepted: 12/25/2014] [Indexed: 11/09/2022] Open
Abstract
Multiple inquiries into the genetic etiology of human traits indicated an overlap between genes underlying monogenic disorders (eg, skeletal growth defects) and those affecting continuous variability of related quantitative traits (eg, height). Extending the idea of a shared genetic basis between a Mendelian disorder and a classic polygenic trait, we performed an association study to examine the effect of 43 genes implicated in autosomal recessive cognitive disorders on intelligence in an unselected Dutch population (N=1316). Using both single-nucleotide polymorphism (SNP)- and gene-based association testing, we detected an association between intelligence and the genes of interest, with genes ELP2, TMEM135, PRMT10, and RGS7 showing the strongest associations. This is a demonstration of the relevance of genes implicated in monogenic disorders of intelligence to normal-range intelligence, and a corroboration of the utility of employing knowledge on monogenic disorders in identifying the genetic variability underlying complex traits.
Collapse
Affiliation(s)
- Sanja Franić
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Maria M Groen-Blokhuis
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Conor V Dolan
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands.,Department of Psychological Methods, University of Amsterdam, Amsterdam, The Netherlands
| | - Mathijs V Kattenberg
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - René Pool
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Xiangjun Xiao
- Division of OVP, Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul A Scheet
- Division of OVP, Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Erik A Ehli
- Avera Institute for Human Genetics, Avera McKennan Hospital, University Health Center, Sioux Falls, SD, USA
| | - Gareth E Davies
- Avera Institute for Human Genetics, Avera McKennan Hospital, University Health Center, Sioux Falls, SD, USA
| | - Sophie van der Sluis
- Section Functional Genomics, Department of Clinical Genetics, VU Medical Center Amsterdam, Amsterdam, The Netherlands
| | - Abdel Abdellaoui
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Narelle K Hansell
- Genetic Epidemiology, Molecular Epidemiology and Neurogenetics Laboratories, Queensland Institute of Medical Research, Brisbane, Australia
| | - Nicholas G Martin
- Genetic Epidemiology, Molecular Epidemiology and Neurogenetics Laboratories, Queensland Institute of Medical Research, Brisbane, Australia
| | - James J Hudziak
- Department of Psychiatry and Medicine, University of Vermont, Burlington, VT, USA
| | | | - Suzanne C Swagerman
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Hilleke E Hulshoff Pol
- Neuroimaging Research Group, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Eco J C de Geus
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Meike Bartels
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - H Hilger Ropers
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
41
|
Androschuk A, Bolduc FV. Modeling Intellectual Disability in Drosophila. ANIMAL MODELS OF NEURODEVELOPMENTAL DISORDERS 2015. [DOI: 10.1007/978-1-4939-2709-8_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
42
|
Tian Y, Voineagu I, Paşca SP, Won H, Chandran V, Horvath S, Dolmetsch RE, Geschwind DH. Alteration in basal and depolarization induced transcriptional network in iPSC derived neurons from Timothy syndrome. Genome Med 2014; 6:75. [PMID: 25360157 PMCID: PMC4213483 DOI: 10.1186/s13073-014-0075-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/15/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Common genetic variation and rare mutations in genes encoding calcium channel subunits have pleiotropic effects on risk for multiple neuropsychiatric disorders, including autism spectrum disorder (ASD) and schizophrenia. To gain further mechanistic insights by extending previous gene expression data, we constructed co-expression networks in Timothy syndrome (TS), a monogenic condition with high penetrance for ASD, caused by mutations in the L-type calcium channel, Cav1.2. METHODS To identify patient-specific alterations in transcriptome organization, we conducted a genome-wide weighted co-expression network analysis (WGCNA) on neural progenitors and neurons from multiple lines of induced pluripotent stem cells (iPSC) derived from normal and TS (G406R in CACNA1C) individuals. We employed transcription factor binding site enrichment analysis to assess whether TS associated co-expression changes reflect calcium-dependent co-regulation. RESULTS We identified reproducible developmental and activity-dependent gene co-expression modules conserved in patient and control cell lines. By comparing cell lines from case and control subjects, we also identified co-expression modules reflecting distinct aspects of TS, including intellectual disability and ASD-related phenotypes. Moreover, by integrating co-expression with transcription factor binding analysis, we showed the TS-associated transcriptional changes were predicted to be co-regulated by calcium-dependent transcriptional regulators, including NFAT, MEF2, CREB, and FOXO, thus providing a mechanism by which altered Ca(2+) signaling in TS patients leads to the observed molecular dysregulation. CONCLUSIONS We applied WGCNA to construct co-expression networks related to neural development and depolarization in iPSC-derived neural cells from TS and control individuals for the first time. These analyses illustrate how a systems biology approach based on gene networks can yield insights into the molecular mechanisms of neural development and function, and provide clues as to the functional impact of the downstream effects of Ca(2+) signaling dysregulation on transcription.
Collapse
Affiliation(s)
- Yuan Tian
- />Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
- />Interdepartmental Ph.D. Program in Bioinformatics, University of California, Los Angeles, CA 90095 USA
| | - Irina Voineagu
- />School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Sergiu P Paşca
- />Department of Psychiatry & Behavioral Sciences, Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Hyejung Won
- />Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
| | - Vijayendran Chandran
- />Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
| | - Steve Horvath
- />Department of Human Genetics, David Geffen Sch. of Medicine, UCLA, Los Angeles, CA USA
| | - Ricardo E Dolmetsch
- />Department of Neurobiology, Stanford University, Stanford, CA 94305-5345 USA
- />Novartis Institutes for Biomedical Research, Cambridge, MA 02139 USA
| | - Daniel H Geschwind
- />Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
- />Interdepartmental Ph.D. Program in Bioinformatics, University of California, Los Angeles, CA 90095 USA
- />Department of Human Genetics, David Geffen Sch. of Medicine, UCLA, Los Angeles, CA USA
| |
Collapse
|
43
|
Stein JL, de la Torre-Ubieta L, Tian Y, Parikshak NN, Hernández IA, Marchetto MC, Baker DK, Lu D, Hinman CR, Lowe JK, Wexler EM, Muotri AR, Gage FH, Kosik KS, Geschwind DH. A quantitative framework to evaluate modeling of cortical development by neural stem cells. Neuron 2014; 83:69-86. [PMID: 24991955 PMCID: PMC4277209 DOI: 10.1016/j.neuron.2014.05.035] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2014] [Indexed: 01/19/2023]
Abstract
Neural stem cells have been adopted to model a wide range of neuropsychiatric conditions in vitro. However, how well such models correspond to in vivo brain has not been evaluated in an unbiased, comprehensive manner. We used transcriptomic analyses to compare in vitro systems to developing human fetal brain and observed strong conservation of in vivo gene expression and network architecture in differentiating primary human neural progenitor cells (phNPCs). Conserved modules are enriched in genes associated with ASD, supporting the utility of phNPCs for studying neuropsychiatric disease. We also developed and validated a machine learning approach called CoNTExT that identifies the developmental maturity and regional identity of in vitro models. We observed strong differences between in vitro models, including hiPSC-derived neural progenitors from multiple laboratories. This work provides a systems biology framework for evaluating in vitro systems and supports their value in studying the molecular mechanisms of human neurodevelopmental disease.
Collapse
Affiliation(s)
- Jason L Stein
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Luis de la Torre-Ubieta
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yuan Tian
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Neelroop N Parikshak
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Israel A Hernández
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Maria C Marchetto
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Dylan K Baker
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daning Lu
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Cassidy R Hinman
- Center for Stem Cell Biology and Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Jennifer K Lowe
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eric M Wexler
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alysson R Muotri
- School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fred H Gage
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Kenneth S Kosik
- Molecular, Cellular and Developmental Biology and Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Daniel H Geschwind
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
44
|
Garcia-Reyero N, Tingaud-Sequeira A, Cao M, Zhu Z, Perkins EJ, Hu W. Endocrinology: advances through omics and related technologies. Gen Comp Endocrinol 2014; 203:262-73. [PMID: 24726988 DOI: 10.1016/j.ygcen.2014.03.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/20/2014] [Accepted: 03/22/2014] [Indexed: 12/27/2022]
Abstract
The rapid development of new omics technologies to measure changes at genetic, transcriptomic, proteomic, and metabolomics levels together with the evolution of methods to analyze and integrate the data at a systems level are revolutionizing the study of biological processes. Here we discuss how new approaches using omics technologies have expanded our knowledge especially in nontraditional models. Our increasing knowledge of these interactions and evolutionary pathway conservation facilitates the use of nontraditional species, both invertebrate and vertebrate, as new model species for biological and endocrinology research. The increasing availability of technology to create organisms overexpressing key genes in endocrine function allows manipulation of complex regulatory networks such as growth hormone (GH) in transgenic fish where disregulation of GH production to produce larger fish has also permitted exploration of the role that GH plays in testis development, suggesting that it does so through interactions with insulin-like growth factors. The availability of omics tools to monitor changes at nearly any level in any organism, manipulate gene expression and behavior, and integrate data across biological levels, provides novel opportunities to explore endocrine function across many species and understand the complex roles that key genes play in different aspects of the endocrine function.
Collapse
Affiliation(s)
- Natàlia Garcia-Reyero
- Institute for Genomics Biocomputing and Biotechnology, Mississippi State University, Starkville, MS 39759, USA.
| | - Angèle Tingaud-Sequeira
- Laboratoire MRMG, Maladies Rares: Génétique et Métabolisme, Université de Bordeaux, 33405 Talence Cedex, France
| | - Mengxi Cao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zuoyan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Edward J Perkins
- US Army Engineer Research and Development Center, Vicksburg, MS 39180, USA
| | - Wei Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| |
Collapse
|
45
|
Szatkiewicz JP, O'Dushlaine C, Chen G, Chambert K, Moran JL, Neale BM, Fromer M, Ruderfer D, Akterin S, Bergen SE, Kähler A, Magnusson PKE, Kim Y, Crowley JJ, Rees E, Kirov G, O'Donovan MC, Owen MJ, Walters J, Scolnick E, Sklar P, Purcell S, Hultman CM, McCarroll SA, Sullivan PF. Copy number variation in schizophrenia in Sweden. Mol Psychiatry 2014; 19:762-73. [PMID: 24776740 PMCID: PMC4271733 DOI: 10.1038/mp.2014.40] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 02/25/2014] [Accepted: 03/20/2014] [Indexed: 12/13/2022]
Abstract
Schizophrenia (SCZ) is a highly heritable neuropsychiatric disorder of complex genetic etiology. Previous genome-wide surveys have revealed a greater burden of large, rare copy number variations (CNVs) in SCZ cases and identified multiple rare recurrent CNVs that increase risk of SCZ although with incomplete penetrance and pleiotropic effects. Identification of additional recurrent CNVs and biological pathways enriched for SCZ CNVs requires greater sample sizes. We conducted a genome-wide survey for CNVs associated with SCZ using a Swedish national sample (4719 cases and 5917 controls). High-confidence CNV calls were generated using genotyping array intensity data, and their effect on risk of SCZ was measured. Our data confirm increased burden of large, rare CNVs in SCZ cases as well as significant associations for recurrent 16p11.2 duplications, 22q11.2 deletions and 3q29 deletions. We report a novel association for 17q12 duplications (odds ratio=4.16, P=0.018), previously associated with autism and mental retardation but not SCZ. Intriguingly, gene set association analyses implicate biological pathways previously associated with SCZ through common variation and exome sequencing (calcium channel signaling and binding partners of the fragile X mental retardation protein). We found significantly increased burden of the largest CNVs (>500 kb) in genes present in the postsynaptic density, in genomic regions implicated via SCZ genome-wide association studies and in gene products localized to mitochondria and cytoplasm. Our findings suggest that multiple lines of genomic inquiry--genome-wide screens for CNVs, common variation and exonic variation--are converging on similar sets of pathways and/or genes.
Collapse
Affiliation(s)
- J P Szatkiewicz
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - C O'Dushlaine
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - G Chen
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - K Chambert
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - J L Moran
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - B M Neale
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - M Fromer
- Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA
| | - D Ruderfer
- Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA
| | - S Akterin
- Department of Medical Epidemiology, Karolinska Institutet, Stockholm, Sweden
| | - S E Bergen
- 1] Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA [2] Department of Medical Epidemiology, Karolinska Institutet, Stockholm, Sweden
| | - A Kähler
- Department of Medical Epidemiology, Karolinska Institutet, Stockholm, Sweden
| | - P K E Magnusson
- Department of Medical Epidemiology, Karolinska Institutet, Stockholm, Sweden
| | - Y Kim
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - J J Crowley
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - E Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - G Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - M C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - M J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - J Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - E Scolnick
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - P Sklar
- Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA
| | - S Purcell
- 1] Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA [2] Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA
| | - C M Hultman
- Department of Medical Epidemiology, Karolinska Institutet, Stockholm, Sweden
| | - S A McCarroll
- 1] Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA [2] Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - P F Sullivan
- 1] Department of Genetics, University of North Carolina, Chapel Hill, NC, USA [2] Department of Medical Epidemiology, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
46
|
Ilie A, Weinstein E, Boucher A, McKinney RA, Orlowski J. Impaired posttranslational processing and trafficking of an endosomal Na+/H+ exchanger NHE6 mutant (Δ370WST372) associated with X-linked intellectual disability and autism. Neurochem Int 2014; 73:192-203. [DOI: 10.1016/j.neuint.2013.09.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/23/2013] [Accepted: 09/24/2013] [Indexed: 01/23/2023]
|
47
|
San Martín A, Pagani MR. Understanding intellectual disability through RASopathies. ACTA ACUST UNITED AC 2014; 108:232-9. [PMID: 24859216 DOI: 10.1016/j.jphysparis.2014.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 04/20/2014] [Accepted: 05/13/2014] [Indexed: 12/18/2022]
Abstract
Intellectual disability, commonly known as mental retardation in the International Classification of Disease from World Health Organization, is the term that describes an intellectual and adaptive cognitive disability that begins in early life during the developmental period. Currently the term intellectual disability is the preferred one. Although our understanding of the physiological basis of learning and learning disability is poor, a general idea is that such condition is quite permanent. However, investigations in animal models suggest that learning disability can be functional in nature and as such reversible through pharmacology or appropriate learning paradigms. A fraction of the cases of intellectual disability is caused by point mutations or deletions in genes that encode for proteins of the RAS/MAP kinase signaling pathway known as RASopathies. Here we examined the current understanding of the molecular mechanisms involved in this group of genetic disorders focusing in studies which provide evidence that intellectual disability is potentially treatable and curable. The evidence presented supports the idea that with the appropriate understanding of the molecular mechanisms involved, intellectual disability could be treated pharmacologically and perhaps through specific mechanistic-based teaching strategies.
Collapse
Affiliation(s)
- Alvaro San Martín
- Genetics of Learning Laboratory, Systems Neuroscience Section, Department of Physiology and Biophysics, School of Medicine, University of Buenos Aires, IFIBIO-Houssay-CONICET, C1121ABG Buenos Aires, Argentina
| | - Mario Rafael Pagani
- Genetics of Learning Laboratory, Systems Neuroscience Section, Department of Physiology and Biophysics, School of Medicine, University of Buenos Aires, IFIBIO-Houssay-CONICET, C1121ABG Buenos Aires, Argentina.
| |
Collapse
|
48
|
Wright FA, Sullivan PF, Brooks AI, Zou F, Sun W, Xia K, Madar V, Jansen R, Chung W, Zhou YH, Abdellaoui A, Batista S, Butler C, Chen G, Chen TH, D'Ambrosio D, Gallins P, Ha MJ, Hottenga JJ, Huang S, Kattenberg M, Kochar J, Middeldorp CM, Qu A, Shabalin A, Tischfield J, Todd L, Tzeng JY, van Grootheest G, Vink JM, Wang Q, Wang W, Wang W, Willemsen G, Smit JH, de Geus EJ, Yin Z, Penninx BWJH, Boomsma DI. Heritability and genomics of gene expression in peripheral blood. Nat Genet 2014; 46:430-7. [PMID: 24728292 PMCID: PMC4012342 DOI: 10.1038/ng.2951] [Citation(s) in RCA: 248] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Accepted: 03/14/2014] [Indexed: 12/14/2022]
Abstract
We assessed gene expression profiles in 2,752 twins, using a classic twin design to quantify expression heritability and quantitative trait loci (eQTLs) in peripheral blood. The most highly heritable genes (∼777) were grouped into distinct expression clusters, enriched in gene-poor regions, associated with specific gene function or ontology classes, and strongly associated with disease designation. The design enabled a comparison of twin-based heritability to estimates based on dizygotic identity-by-descent sharing and distant genetic relatedness. Consideration of sampling variation suggests that previous heritability estimates have been upwardly biased. Genotyping of 2,494 twins enabled powerful identification of eQTLs, which we further examined in a replication set of 1,895 unrelated subjects. A large number of non-redundant local eQTLs (6,756) met replication criteria, whereas a relatively small number of distant eQTLs (165) met quality control and replication standards. Our results provide a new resource toward understanding the genetic control of transcription.
Collapse
Affiliation(s)
- Fred A Wright
- 1] Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA. [2] Department of Statistics, North Carolina State University, Raleigh, North Carolina, USA. [3] Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA. [4]
| | - Patrick F Sullivan
- 1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2]
| | - Andrew I Brooks
- Department of Genetics, Rutgers University, New Brunswick, New Jersey, USA
| | - Fei Zou
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Wei Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kai Xia
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Vered Madar
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Rick Jansen
- Department of Psychiatry, VU Medical Center, Amsterdam, The Netherlands
| | - Wonil Chung
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yi-Hui Zhou
- 1] Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA. [2] Department of Statistics, North Carolina State University, Raleigh, North Carolina, USA
| | - Abdel Abdellaoui
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Sandra Batista
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Casey Butler
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Guanhua Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ting-Huei Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David D'Ambrosio
- Environmental and Occupational Health Sciences Institute, Rutgers University, New Brunswick, New Jersey, USA
| | - Paul Gallins
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Min Jin Ha
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jouke Jan Hottenga
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Shunping Huang
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mathijs Kattenberg
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Jaspreet Kochar
- Environmental and Occupational Health Sciences Institute, Rutgers University, New Brunswick, New Jersey, USA
| | | | - Ani Qu
- Environmental and Occupational Health Sciences Institute, Rutgers University, New Brunswick, New Jersey, USA
| | - Andrey Shabalin
- Department of Pharmacotherapy and Outcomes Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Jay Tischfield
- Department of Genetics, Rutgers University, New Brunswick, New Jersey, USA
| | - Laura Todd
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jung-Ying Tzeng
- 1] Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA. [2] Department of Statistics, North Carolina State University, Raleigh, North Carolina, USA
| | | | - Jacqueline M Vink
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Qi Wang
- Environmental and Occupational Health Sciences Institute, Rutgers University, New Brunswick, New Jersey, USA
| | - Wei Wang
- Department of Computer Science, University of California, Los Angeles, Los Angeles, California, USA
| | - Weibo Wang
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Johannes H Smit
- Department of Psychiatry, VU Medical Center, Amsterdam, The Netherlands
| | - Eco J de Geus
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Zhaoyu Yin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Dorret I Boomsma
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| |
Collapse
|
49
|
Parikshak NN, Luo R, Zhang A, Won H, Lowe JK, Chandran V, Horvath S, Geschwind DH. Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. Cell 2014; 155:1008-21. [PMID: 24267887 DOI: 10.1016/j.cell.2013.10.031] [Citation(s) in RCA: 708] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 07/31/2013] [Accepted: 10/03/2013] [Indexed: 01/09/2023]
Abstract
Genetic studies have identified dozens of autism spectrum disorder (ASD) susceptibility genes, raising two critical questions: (1) do these genetic loci converge on specific biological processes, and (2) where does the phenotypic specificity of ASD arise, given its genetic overlap with intellectual disability (ID)? To address this, we mapped ASD and ID risk genes onto coexpression networks representing developmental trajectories and transcriptional profiles representing fetal and adult cortical laminae. ASD genes tightly coalesce in modules that implicate distinct biological functions during human cortical development, including early transcriptional regulation and synaptic development. Bioinformatic analyses suggest that translational regulation by FMRP and transcriptional coregulation by common transcription factors connect these processes. At a circuit level, ASD genes are enriched in superficial cortical layers and glutamatergic projection neurons. Furthermore, we show that the patterns of ASD and ID risk genes are distinct, providing a biological framework for further investigating the pathophysiology of ASD.
Collapse
Affiliation(s)
- Neelroop N Parikshak
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Interdepartmental Program in Neuroscience, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Rao A, O'Donnell S, Bain N, Meldrum C, Shorter D, Goel H. An intragenic deletion of the NFIA gene in a patient with a hypoplastic corpus callosum, craniofacial abnormalities and urinary tract defects. Eur J Med Genet 2014; 57:65-70. [DOI: 10.1016/j.ejmg.2013.12.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 12/31/2013] [Indexed: 10/25/2022]
|