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Rinne N, Wikman P, Sahari E, Salmi J, Einarsdóttir E, Kere J, Alho K. Developmental dyslexia susceptibility genes DNAAF4, DCDC2, and NRSN1 are associated with brain function in fluently reading adolescents and young adults. Cereb Cortex 2024; 34:bhae144. [PMID: 38610086 PMCID: PMC11014888 DOI: 10.1093/cercor/bhae144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 04/14/2024] Open
Abstract
Reading skills and developmental dyslexia, characterized by difficulties in developing reading skills, have been associated with brain anomalies within the language network. Genetic factors contribute to developmental dyslexia risk, but the mechanisms by which these genes influence reading skills remain unclear. In this preregistered study (https://osf.io/7sehx), we explored if developmental dyslexia susceptibility genes DNAAF4, DCDC2, NRSN1, and KIAA0319 are associated with brain function in fluently reading adolescents and young adults. Functional MRI and task performance data were collected during tasks involving written and spoken sentence processing, and DNA sequence variants of developmental dyslexia susceptibility genes previously associated with brain structure anomalies were genotyped. The results revealed that variation in DNAAF4, DCDC2, and NRSN1 is associated with brain activity in key language regions: the left inferior frontal gyrus, middle temporal gyrus, and intraparietal sulcus. Furthermore, NRSN1 was associated with task performance, but KIAA0319 did not yield any significant associations. Our findings suggest that individuals with a genetic predisposition to developmental dyslexia may partly employ compensatory neural and behavioral mechanisms to maintain typical task performance. Our study highlights the relevance of these developmental dyslexia susceptibility genes in language-related brain function, even in individuals without developmental dyslexia, providing valuable insights into the genetic factors influencing language processing.
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Affiliation(s)
- Nea Rinne
- Department of Psychology and Logopedics, University of Helsinki, Haartmaninkatu 3, 00014 Helsinki, Finland
| | - Patrik Wikman
- Department of Psychology and Logopedics, University of Helsinki, Haartmaninkatu 3, 00014 Helsinki, Finland
| | - Elisa Sahari
- Department of Psychology and Speech-Language Pathology, University of Turku, Assistentinkatu 7, 20500 Turku, Finland
| | - Juha Salmi
- Department of Neuroscience and Biomedical Engineering, Otakaari 3, Aalto University, (AALTO), P.O. BOX 00076, Espoo, Finland
| | - Elisabet Einarsdóttir
- Science for Life Laboratory, Department of Gene Technology, KTH-Royal Institute of Technology, SE-171 21, Solna, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, H7 Medicin, Huddinge, Sweden
- Folkhälsan Research Center, and Stem Cells and Metabolism Research Program (STEMM), University of Helsinki, PL 63, Haartmaninkatu 8, Helsinki, Finland
| | - Kimmo Alho
- Department of Psychology and Logopedics, University of Helsinki, Haartmaninkatu 3, 00014 Helsinki, Finland
- Advanced Magnetic Imaging Centre, Aalto NeuroImaging, Aalto University, Espoo, Finland
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Huang J, Li B, Wei H, Li C, Liu C, Mi H, Chen S. Integrative analysis of gene expression profiles of substantia nigra identifies potential diagnosis biomarkers in Parkinson's disease. Sci Rep 2024; 14:2167. [PMID: 38272954 PMCID: PMC10810830 DOI: 10.1038/s41598-024-52276-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disease whose etiology is attributed to development of Lewy bodies and degeneration of dopaminergic neurons in the substantia nigra (SN). Currently, there are no definitive diagnostic indicators for PD. In this study, we aimed to identify potential diagnostic biomarkers for PD and analyzed the impact of immune cell infiltrations on disease pathogenesis. The PD expression profile data for human SN tissue, GSE7621, GSE20141, GSE20159, GSE20163 and GSE20164 were downloaded from the Gene Expression Omnibus (GEO) database for use in the training model. After normalization and merging, we identified differentially expressed genes (DEGs) using the Robust rank aggregation (RRA) analysis. Simultaneously, DEGs after batch correction were identified. Gene interactions were determined through venn Diagram analysis. Functional analyses and protein-protein interaction (PPI) networks were used to the identify hub genes, which were visualized through Cytoscape. A Lasso Cox regression model was employed to identify the potential diagnostic genes. The GSE20292 dataset was used for validation. The proportion of infiltrating immune cells in the samples were determined via the CIBERSORT method. Sixty-two DEGs were screened in this study. They were found to be enriched in nerve conduction, dopamine (DA) metabolism, and DA biosynthesis Gene Ontology (GO) terms. The PPI network and Lasso Cox regression analysis revealed seven potential diagnostic genes, namely SLC18A2, TAC1, PCDH8, KIAA0319, PDE6H, AXIN1, and AGTR1, were subsequently validated in peripheral blood samples obtained from healthy control (HC) and PD patients, as well as in the GSE20292 dataset. The results revealed the exceptional sensitivity and specificity of these genes in PD diagnosis and monitoring. Moreover, PD patients exhibited a higher number of plasma cells, compared to HC individuals. The SLC18A2, TAC1, PCDH8, KIAA0319, PDE6H, AXIN1, and AGTR1 are potential diagnostic biomarkers for PD. Our findings also reveal the essential roles of immune cell infiltration in both disease onset and trajectory.
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Affiliation(s)
- Junming Huang
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, 530000, Guangxi, China
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, Guangxi, China
| | - Bowen Li
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, Guangxi, China
| | - Huangwei Wei
- Department of Neurology, The People Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Chengxin Li
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, Guangxi, China
| | - Chao Liu
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Hua Mi
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, Guangxi, China.
| | - Shaohua Chen
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, 530000, Guangxi, China.
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Price KM, Wigg KG, Eising E, Feng Y, Blokland K, Wilkinson M, Kerr EN, Guger SL, Fisher SE, Lovett MW, Strug LJ, Barr CL. Hypothesis-driven genome-wide association studies provide novel insights into genetics of reading disabilities. Transl Psychiatry 2022; 12:495. [PMID: 36446759 PMCID: PMC9709072 DOI: 10.1038/s41398-022-02250-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/24/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022] Open
Abstract
Reading Disability (RD) is often characterized by difficulties in the phonology of the language. While the molecular mechanisms underlying it are largely undetermined, loci are being revealed by genome-wide association studies (GWAS). In a previous GWAS for word reading (Price, 2020), we observed that top single-nucleotide polymorphisms (SNPs) were located near to or in genes involved in neuronal migration/axon guidance (NM/AG) or loci implicated in autism spectrum disorder (ASD). A prominent theory of RD etiology posits that it involves disturbed neuronal migration, while potential links between RD-ASD have not been extensively investigated. To improve power to identify associated loci, we up-weighted variants involved in NM/AG or ASD, separately, and performed a new Hypothesis-Driven (HD)-GWAS. The approach was applied to a Toronto RD sample and a meta-analysis of the GenLang Consortium. For the Toronto sample (n = 624), no SNPs reached significance; however, by gene-set analysis, the joint contribution of ASD-related genes passed the threshold (p~1.45 × 10-2, threshold = 2.5 × 10-2). For the GenLang Cohort (n = 26,558), SNPs in DOCK7 and CDH4 showed significant association for the NM/AG hypothesis (sFDR q = 1.02 × 10-2). To make the GenLang dataset more similar to Toronto, we repeated the analysis restricting to samples selected for reading/language deficits (n = 4152). In this GenLang selected subset, we found significant association for a locus intergenic between BTG3-C21orf91 for both hypotheses (sFDR q < 9.00 × 10-4). This study contributes candidate loci to the genetics of word reading. Data also suggest that, although different variants may be involved, alleles implicated in ASD risk may be found in the same genes as those implicated in word reading. This finding is limited to the Toronto sample suggesting that ascertainment influences genetic associations.
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Affiliation(s)
- Kaitlyn M Price
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Karen G Wigg
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Else Eising
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Yu Feng
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Kirsten Blokland
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Margaret Wilkinson
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elizabeth N Kerr
- Department of Psychology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Sharon L Guger
- Department of Psychology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Maureen W Lovett
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Lisa J Strug
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Departments of Statistical Sciences and Computer Science, Faculty of Arts and Science and Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Cathy L Barr
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada.
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Galaburda AM. Animal models of developmental dyslexia. Front Neurosci 2022; 16:981801. [PMID: 36452335 PMCID: PMC9702821 DOI: 10.3389/fnins.2022.981801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/28/2022] [Indexed: 09/10/2024] Open
Abstract
As some critics have stated, the term "developmental dyslexia" refers to a strictly human disorder, relating to a strictly human capacity - reading - so it cannot be modeled in experimental animals, much less so in lowly rodents. However, two endophenotypes associated with developmental dyslexia are eminently suitable for animal modeling: Cerebral Lateralization, as illustrated by the association between dyslexia and non-righthandedness, and Cerebrocortical Dysfunction, as illustrated by the described abnormal structural anatomy and/or physiology and functional imaging of the dyslexic cerebral cortex. This paper will provide a brief review of these two endophenotypes in human beings with developmental dyslexia and will describe the animal work done in my laboratory and that of others to try to shed light on the etiology of and neural mechanisms underlying developmental dyslexia. Some thought will also be given to future directions of the research.
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Affiliation(s)
- Albert M. Galaburda
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
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Yu X, Ferradal S, Dunstan J, Carruthers C, Sanfilippo J, Zuk J, Zöllei L, Gagoski B, Ou Y, Grant PE, Gaab N. Patterns of Neural Functional Connectivity in Infants at Familial Risk of Developmental Dyslexia. JAMA Netw Open 2022; 5:e2236102. [PMID: 36301547 PMCID: PMC9614583 DOI: 10.1001/jamanetworkopen.2022.36102] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 08/23/2022] [Indexed: 11/14/2022] Open
Abstract
Importance Developmental dyslexia is a heritable learning disability affecting 7% to 10% of the general population and can have detrimental impacts on mental health and vocational potential. Individuals with dyslexia show altered functional organization of the language and reading neural networks; however, it remains unknown how early in life these neural network alterations might emerge. Objective To determine whether the early emergence of large-scale neural functional connectivity (FC) underlying long-term language and reading development is altered in infants with a familial history of dyslexia (FHD). Design, Setting, and Participants This cohort study included infants recruited at Boston Children's Hospital between May 2011 and February 2019. Participants underwent structural and resting-state functional magnetic resonance imaging in the Department of Radiology at Boston Children's Hospital. Infants with FHD were matched with infants without FHD based on age and sex. Data were analyzed from April 2019 to June 2021. Exposures FHD was defined as having at least 1 first-degree relative with a dyslexia diagnosis or documented reading difficulties. Main Outcomes and Measures Whole-brain FC patterns associated with 20 predefined cerebral regions important for long-term language and reading development were computed for each infant. Multivariate pattern analyses were applied to identify specific FC patterns that differentiated between infants with vs without FHD. For classification performance estimates, 99% CIs were calculated as the classification accuracy minus chance level. Results A total of 98 infants (mean [SD] age, 8.5 [2.3] months; 51 [52.0%] girls) were analyzed, including 35 infants with FHD and 63 infants without FHD. Multivariate pattern analyses identified distinct FC patterns between infants with vs without FHD in the left fusiform gyrus (classification accuracy, 0.55 [99% CI, 0.046-0.062]; corrected P < .001; Cohen d = 0.76). Connections linking left fusiform gyrus to regions in the frontal and parietal language and attention networks were among the paths with the highest contributions to the classification performance. Conclusions and Relevance These findings suggest that on the group level, FHD was associated with an early onset of atypical FC of regions important for subsequent word form recognition during reading acquisition. Longitudinal studies linking the atypical functional network and school-age reading abilities will be essential to further elucidate the ontogenetic mechanisms underlying the development of dyslexia.
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Affiliation(s)
- Xi Yu
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- Fetal Neonatal Neuroimaging and Developmental Science Center, Boston Children’s Hospital, Boston, Massachusetts
| | - Silvina Ferradal
- Department of Intelligent Systems Engineering, Indiana University, Bloomington
| | - Jade Dunstan
- Laboratories of Cognitive Neuroscience, Division of Developmental Medicine, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts
| | - Clarisa Carruthers
- Laboratories of Cognitive Neuroscience, Division of Developmental Medicine, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts
| | - Joseph Sanfilippo
- Laboratories of Cognitive Neuroscience, Division of Developmental Medicine, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts
| | - Jennifer Zuk
- Department of Speech, Language & Hearing Sciences, Boston University, Boston, Massachusetts
| | - Lilla Zöllei
- A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston
| | - Borjan Gagoski
- Fetal Neonatal Neuroimaging and Developmental Science Center, Boston Children’s Hospital, Boston, Massachusetts
- Department of Radiology, Boston Children’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Yangming Ou
- Fetal Neonatal Neuroimaging and Developmental Science Center, Boston Children’s Hospital, Boston, Massachusetts
- Department of Radiology, Boston Children’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - P. Ellen Grant
- Fetal Neonatal Neuroimaging and Developmental Science Center, Boston Children’s Hospital, Boston, Massachusetts
- Department of Radiology, Boston Children’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Nadine Gaab
- Laboratories of Cognitive Neuroscience, Division of Developmental Medicine, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Harvard Graduate School of Education, Cambridge, Massachusetts
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Paniagua S, Cakir B, Hu Y, Kiral FR, Tanaka Y, Xiang Y, Patterson B, Gruen JR, Park IH. Dyslexia associated gene KIAA0319 regulates cell cycle during human neuroepithelial cell development. Front Cell Dev Biol 2022; 10:967147. [PMID: 36016658 PMCID: PMC9395643 DOI: 10.3389/fcell.2022.967147] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 07/07/2022] [Indexed: 11/24/2022] Open
Abstract
Dyslexia, also known as reading disability, is defined as difficulty processing written language in individuals with normal intellectual capacity and educational opportunity. The prevalence of dyslexia is between 5 and 17%, and the heritability ranges from 44 to 75%. Genetic linkage analysis and association studies have identified several genes and regulatory elements linked to dyslexia and reading ability. However, their functions and molecular mechanisms are not well understood. Prominent among these is KIAA0319, encoded in the DYX2 locus of human chromosome 6p22. The association of KIAA0319 with reading performance has been replicated in independent studies and different languages. Rodent models suggest that kiaa0319 is involved in neuronal migration, but its role throughout the cortical development is largely unknown. In order to define the function of KIAA0319 in human cortical development, we applied the neural developmental model of a human embryonic stem cell. We knocked down KIAA0319 expression in hESCs and performed the cortical neuroectodermal differentiation. We found that neuroepithelial cell differentiation is one of the first stages of hESC differentiation that are affected by KIAA0319 knocked down could affect radial migration and thus differentiation into diverse neural populations at the cortical layers.
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Affiliation(s)
- Steven Paniagua
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, United States
| | - Bilal Cakir
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, United States
| | - Yue Hu
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Ferdi Ridvan Kiral
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, United States
| | - Yoshiaki Tanaka
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, United States
- Department of Medicine, Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, QC, Canada
| | - Yangfei Xiang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Benjamin Patterson
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, United States
| | - Jeffrey R. Gruen
- Departments of Pediatrics and of Genetics, Yale School of Medicine, New Haven, CT, United States
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, United States
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KIAA0319 influences cilia length, cell migration and mechanical cell-substrate interaction. Sci Rep 2022; 12:722. [PMID: 35031635 PMCID: PMC8760330 DOI: 10.1038/s41598-021-04539-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 12/17/2021] [Indexed: 01/11/2023] Open
Abstract
Following its association with dyslexia in multiple genetic studies, the KIAA0319 gene has been extensively investigated in different animal models but its function in neurodevelopment remains poorly understood. We developed the first human cellular knockout model for KIAA0319 in RPE1 retinal pigment epithelia cells via CRISPR-Cas9n to investigate its role in processes suggested but not confirmed in previous studies, including cilia formation and cell migration. We observed in the KIAA0319 knockout increased cilia length and accelerated cell migration. Using Elastic Resonator Interference Stress Microscopy (ERISM), we detected an increase in cellular force for the knockout cells that was restored by a rescue experiment. Combining ERISM and immunostaining we show that RPE1 cells exert highly dynamic, piconewton vertical pushing forces through actin-rich protrusions that are surrounded by vinculin-rich pulling sites. This protein arrangement and force pattern has previously been associated to podosomes in other cells. KIAA0319 depletion reduces the fraction of cells forming these actin-rich protrusions. Our results suggest an involvement of KIAA0319 in cilia biology and cell-substrate force regulation.
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Gray Matter Variation in the Posterior Superior Temporal Gyrus Is Associated with Polymorphisms in the KIAA0319 Gene in Chimpanzees ( Pan troglodytes). eNeuro 2021; 8:ENEURO.0169-21.2021. [PMID: 34815295 PMCID: PMC8672446 DOI: 10.1523/eneuro.0169-21.2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 11/23/2022] Open
Abstract
Determining the impact that the KIAA0319 gene has on primate brain morphology can provide insight into the evolution of human cognition and language systems. Here, we tested whether polymorphisms in KIAA0319 in chimpanzees account for gray matter volumetric variation in brain regions implicated in language and communication (particularly within the posterior superior temporal gyrus and inferior frontal gyrus). First, we identified the nature and frequencies of single nucleotide variants (SNVs) in KIAA0319 in a sample of unrelated chimpanzees (Pan troglodytes spp.). Next, we genotyped a subset of SNVs (those important for gene regulation or likely to alter protein structure/function) in a sample of chimpanzees for which in vivo T1-structural magnetic resonance imaging scans had been obtained. We then used source-based morphometry (SBM) to test for whole-brain gray matter covariation differences between chimpanzees with different KIAA0319 alleles. Finally, using histologic sections of 15 postmortem chimpanzee brains, we analyzed microstructural variation related to KIAA0319 polymorphisms in the posterior superior temporal cortex. We found that the SNVs were associated with variation in gray matter within several brain regions, including the posterior superior temporal gyrus (a region associated with language comprehension and production in humans). The microstructure analysis further revealed hemispheric differences in neuropil fraction, indicating that KIAA0319 expression may be involved in regulation of processes related to the formation and maintenance of synapses, dendrites, or axons within regions associated with communication.
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Animal models of developmental dyslexia: Where we are and what we are missing. Neurosci Biobehav Rev 2021; 131:1180-1197. [PMID: 34699847 DOI: 10.1016/j.neubiorev.2021.10.022] [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: 08/04/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 12/21/2022]
Abstract
Developmental dyslexia (DD) is a complex neurodevelopmental disorder and the most common learning disability among both school-aged children and across languages. Recently, sensory and cognitive mechanisms have been reported to be potential endophenotypes (EPs) for DD, and nine DD-candidate genes have been identified. Animal models have been used to investigate the etiopathological pathways that underlie the development of complex traits, as they enable the effects of genetic and/or environmental manipulations to be evaluated. Animal research designs have also been linked to cutting-edge clinical research questions by capitalizing on the use of EPs. For the present scoping review, we reviewed previous studies of murine models investigating the effects of DD-candidate genes. Moreover, we highlighted the use of animal models as an innovative way to unravel new insights behind the pathophysiology of reading (dis)ability and to assess cutting-edge preclinical models.
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Thomas T, Khalaf S, Grigorenko EL. A systematic review and meta-analysis of imaging genetics studies of specific reading disorder. Cogn Neuropsychol 2021; 38:179-204. [PMID: 34529546 DOI: 10.1080/02643294.2021.1969900] [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: 10/20/2022]
Abstract
The imaging genetics of specific reading disabilities (SRD) is an emerging field that aims to characterize the disabilities' neurobiological causes, including atypical brain structure and function and distinct genetic architecture. The present review aimed to summarize current imaging genetics studies of SRD, characterize the effect sizes of reported results by calculating Cohen's d, complete a Fisher's Combined Probability Test for genes featured in multiple studies, and determine areas for future research. Results demonstrate associations between SRD risk genes and reading network brain phenotypes. The Fisher's test revealed promising results for the genes DCDC2, KIAA0319, FOXP2, SLC2A3, and ROBO1. Future research should focus on exploratory approaches to identify previously undiscovered genes. Using comprehensive neuroimaging (e.g., functional and effective connectivity) and genetic (e.g., sequencing and epigenetic) techniques, and using larger samples, diverse stages of development, and longitudinal investigations, would help researchers understand the neurobiological correlates of SRD to improve early identification.
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Affiliation(s)
- Tina Thomas
- Department of Psychology, University of Houston, Houston, TX, USA.,Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, TX, USA
| | - Shiva Khalaf
- Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, TX, USA
| | - Elena L Grigorenko
- Department of Psychology, University of Houston, Houston, TX, USA.,Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, TX, USA.,Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Kim DH, Sun D, Storck WK, Welker Leng K, Jenkins C, Coleman DJ, Sampson D, Guan X, Kumaraswamy A, Rodansky ES, Urrutia JA, Schwartzman JA, Zhang C, Beltran H, Labrecque MP, Morrissey C, Lucas JM, Coleman IM, Nelson PS, Corey E, Handelman SK, Sexton JZ, Aggarwal R, Abida W, Feng FY, Small EJ, Spratt DE, Bankhead A, Rao A, Gesner EM, Attwell S, Lakhotia S, Campeau E, Yates JA, Xia Z, Alumkal JJ. BET Bromodomain Inhibition Blocks an AR-Repressed, E2F1-Activated Treatment-Emergent Neuroendocrine Prostate Cancer Lineage Plasticity Program. Clin Cancer Res 2021; 27:4923-4936. [PMID: 34145028 PMCID: PMC8416959 DOI: 10.1158/1078-0432.ccr-20-4968] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/15/2021] [Accepted: 06/15/2021] [Indexed: 01/26/2023]
Abstract
PURPOSE Lineage plasticity in prostate cancer-most commonly exemplified by loss of androgen receptor (AR) signaling and a switch from a luminal to alternate differentiation program-is now recognized as a treatment resistance mechanism. Lineage plasticity is a spectrum, but neuroendocrine prostate cancer (NEPC) is the most virulent example. Currently, there are limited treatments for NEPC. Moreover, the incidence of treatment-emergent NEPC (t-NEPC) is increasing in the era of novel AR inhibitors. In contradistinction to de novo NEPC, t-NEPC tumors often express the AR, but AR's functional role in t-NEPC is unknown. Furthermore, targetable factors that promote t-NEPC lineage plasticity are also unclear. EXPERIMENTAL DESIGN Using an integrative systems biology approach, we investigated enzalutamide-resistant t-NEPC cell lines and their parental, enzalutamide-sensitive adenocarcinoma cell lines. The AR is still expressed in these t-NEPC cells, enabling us to determine the role of the AR and other key factors in regulating t-NEPC lineage plasticity. RESULTS AR inhibition accentuates lineage plasticity in t-NEPC cells-an effect not observed in parental, enzalutamide-sensitive adenocarcinoma cells. Induction of an AR-repressed, lineage plasticity program is dependent on activation of the transcription factor E2F1 in concert with the BET bromodomain chromatin reader BRD4. BET inhibition (BETi) blocks this E2F1/BRD4-regulated program and decreases growth of t-NEPC tumor models and a subset of t-NEPC patient tumors with high activity of this program in a BETi clinical trial. CONCLUSIONS E2F1 and BRD4 are critical for activating an AR-repressed, t-NEPC lineage plasticity program. BETi is a promising approach to block this program.
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Affiliation(s)
- Dae-Hwan Kim
- Knight Cancer Institute, Oregon Health & Science University (OHSU), Portland, Oregon
| | - Duanchen Sun
- Knight Cancer Institute, Oregon Health & Science University (OHSU), Portland, Oregon
| | - William K. Storck
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Katherine Welker Leng
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Chelsea Jenkins
- Knight Cancer Institute, Oregon Health & Science University (OHSU), Portland, Oregon
| | - Daniel J. Coleman
- Knight Cancer Institute, Oregon Health & Science University (OHSU), Portland, Oregon
| | - David Sampson
- Knight Cancer Institute, Oregon Health & Science University (OHSU), Portland, Oregon
| | - Xiangnan Guan
- Knight Cancer Institute, Oregon Health & Science University (OHSU), Portland, Oregon
| | - Anbarasu Kumaraswamy
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Eva S. Rodansky
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Joshua A. Urrutia
- Knight Cancer Institute, Oregon Health & Science University (OHSU), Portland, Oregon
| | - Jacob A. Schwartzman
- Knight Cancer Institute, Oregon Health & Science University (OHSU), Portland, Oregon
| | - Chao Zhang
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Himisha Beltran
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Mark P. Labrecque
- Department of Urology, University of Washington, Seattle, Washington
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, Washington
| | - Jared M. Lucas
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ilsa M. Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Peter S. Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, Washington
| | - Samuel K. Handelman
- Center for Drug Repurposing, Department of Internal Medicine, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Jonathan Z. Sexton
- Center for Drug Repurposing, Department of Internal Medicine, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Wassim Abida
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Felix Y. Feng
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Eric J. Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Daniel E. Spratt
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan.,Department of Radiation Oncology, University Hospitals, Case Western Reserve University, Cleveland, Ohio
| | - Armand Bankhead
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan.,Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan.,Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
| | - Arvind Rao
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan.,Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | | | | | | | - Eric Campeau
- Zenith Epigenetics Ltd, Calgary, Alberta, Canada
| | - Joel A. Yates
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Zheng Xia
- Knight Cancer Institute, Oregon Health & Science University (OHSU), Portland, Oregon.,Corresponding Authors: Joshi J. Alumkal, Phone: 734-936-9868; Fax: 734-647-9480; E-mail: and Zheng Xia, Phone: 503-494-9726; E-mail:
| | - Joshi J. Alumkal
- Knight Cancer Institute, Oregon Health & Science University (OHSU), Portland, Oregon.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan.,Corresponding Authors: Joshi J. Alumkal, Phone: 734-936-9868; Fax: 734-647-9480; E-mail: and Zheng Xia, Phone: 503-494-9726; E-mail:
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12
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Tangeman JA, Luz-Madrigal A, Sreeskandarajan S, Grajales-Esquivel E, Liu L, Liang C, Tsonis PA, Del Rio-Tsonis K. Transcriptome Profiling of Embryonic Retinal Pigment Epithelium Reprogramming. Genes (Basel) 2021; 12:genes12060840. [PMID: 34072522 PMCID: PMC8226911 DOI: 10.3390/genes12060840] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/05/2021] [Accepted: 05/22/2021] [Indexed: 12/27/2022] Open
Abstract
The plasticity of human retinal pigment epithelium (RPE) has been observed during proliferative vitreoretinopathy, a defective repair process during which injured RPE gives rise to fibrosis. In contrast, following injury, the RPE of the embryonic chicken can be reprogrammed to regenerate neural retina in a fibroblast growth factor 2 (FGF2)-dependent manner. To better explore the mechanisms underlying embryonic RPE reprogramming, we used laser capture microdissection to isolate RNA from (1) intact RPE, (2) transiently reprogrammed RPE (t-rRPE) 6 h post-retinectomy, and (3) reprogrammed RPE (rRPE) 6 h post-retinectomy with FGF2 treatment. Using RNA-seq, we observed the acute repression of genes related to cell cycle progression in the injured t-rRPE, as well as up-regulation of genes associated with injury. In contrast, the rRPE was strongly enriched for mitogen-activated protein kinase (MAPK)-responsive genes and retina development factors, confirming that FGF2 and the downstream MAPK cascade are the main drivers of embryonic RPE reprogramming. Clustering and pathway enrichment analysis was used to create an integrated network of the core processes associated with RPE reprogramming, including key terms pertaining to injury response, migration, actin dynamics, and cell cycle progression. Finally, we employed gene set enrichment analysis to suggest a previously uncovered role for epithelial-mesenchymal transition (EMT) machinery in the initiation of embryonic chick RPE reprogramming. The EMT program is accompanied by extensive, coordinated regulation of extracellular matrix (ECM) associated factors, and these observations together suggest an early role for ECM and EMT-like dynamics during reprogramming. Our study provides for the first time an in-depth transcriptomic analysis of embryonic RPE reprogramming and will prove useful in guiding future efforts to understand proliferative disorders of the RPE and to promote retinal regeneration.
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Affiliation(s)
- Jared A. Tangeman
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH 45056, USA; (J.A.T.); (A.L.-M.); (S.S.); (E.G.-E.); (L.L.); (C.L.)
| | - Agustín Luz-Madrigal
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH 45056, USA; (J.A.T.); (A.L.-M.); (S.S.); (E.G.-E.); (L.L.); (C.L.)
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI 53705, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sutharzan Sreeskandarajan
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH 45056, USA; (J.A.T.); (A.L.-M.); (S.S.); (E.G.-E.); (L.L.); (C.L.)
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Erika Grajales-Esquivel
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH 45056, USA; (J.A.T.); (A.L.-M.); (S.S.); (E.G.-E.); (L.L.); (C.L.)
| | - Lin Liu
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH 45056, USA; (J.A.T.); (A.L.-M.); (S.S.); (E.G.-E.); (L.L.); (C.L.)
| | - Chun Liang
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH 45056, USA; (J.A.T.); (A.L.-M.); (S.S.); (E.G.-E.); (L.L.); (C.L.)
- Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA
| | - Panagiotis A. Tsonis
- Department of Biology, University of Dayton and Center for Tissue Regeneration and Engineering at the University of Dayton (TREND), Dayton, OH 45469, USA;
| | - Katia Del Rio-Tsonis
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH 45056, USA; (J.A.T.); (A.L.-M.); (S.S.); (E.G.-E.); (L.L.); (C.L.)
- Correspondence: ; Tel.: +513-529-3128; Fax: +513-529-6900
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13
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The Polygenic Nature and Complex Genetic Architecture of Specific Learning Disorder. Brain Sci 2021; 11:brainsci11050631. [PMID: 34068951 PMCID: PMC8156942 DOI: 10.3390/brainsci11050631] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/16/2022] Open
Abstract
Specific Learning Disorder (SLD) is a multifactorial, neurodevelopmental disorder which may involve persistent difficulties in reading (dyslexia), written expression and/or mathematics. Dyslexia is characterized by difficulties with speed and accuracy of word reading, deficient decoding abilities, and poor spelling. Several studies from different, but complementary, scientific disciplines have investigated possible causal/risk factors for SLD. Biological, neurological, hereditary, cognitive, linguistic-phonological, developmental and environmental factors have been incriminated. Despite worldwide agreement that SLD is highly heritable, its exact biological basis remains elusive. We herein present: (a) an update of studies that have shaped our current knowledge on the disorder’s genetic architecture; (b) a discussion on whether this genetic architecture is ‘unique’ to SLD or, alternatively, whether there is an underlying common genetic background with other neurodevelopmental disorders; and, (c) a brief discussion on whether we are at a position of generating meaningful correlations between genetic findings and anatomical data from neuroimaging studies or specific molecular/cellular pathways. We conclude with open research questions that could drive future research directions.
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14
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Thomas T, Perdue MV, Khalaf S, Landi N, Hoeft F, Pugh K, Grigorenko EL. Neuroimaging genetic associations between SEMA6D, brain structure, and reading skills. J Clin Exp Neuropsychol 2021; 43:276-289. [PMID: 33960276 PMCID: PMC8225580 DOI: 10.1080/13803395.2021.1912300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/30/2021] [Indexed: 01/15/2023]
Abstract
Specific reading disability (SRD) is defined by genetic and neural risk factors that are not fully understood. The current study used imaging genetics methodology to investigate relationships between SEMA6D, brain structure, and reading. SEMA6D, located on SRD risk locus DYX1, is involved in axon guidance, synapse formation, and dendrite development. SEMA6D's associations with brain structure in reading-related regions of interest (ROIs) were investigated in a sample of children with a range of reading performance, from sites in Connecticut, CT (n = 67, 6-13 years, mean age = 9.07) and San Francisco, SF (n = 28, 5-8 years, mean age = 6.5). Multiple regression analyses revealed significant associations between SEMA6D's rs16959669 and cortical thickness in the fusiform gyrus and rs4270119 and gyrification in the supramarginal gyrus in the CT sample, but this was not replicated in the SF sample. Significant clusters were not associated with reading. For white matter volume, combined analyses across both samples revealed associations between reading and the left transverse temporal gyrus, left pars triangularis, left cerebellum, and right cerebellum. White matter volume in the left transverse temporal gyrus was nominally related to rs1817178, rs12050859, and rs1898110 in SEMA6D, and rs1817178 was significantly related to reading. Haplotype analyses revealed significant associations between the whole gene and brain phenotypes. Results suggest SEMA6D likely has an impact on multiple reading-related neural structures, but only white matter volume in the transverse temporal gyrus was significantly related to reading in the current sample. As the sample was young, the transverse temporal gyrus, involved in auditory perception, may be more strongly involved in reading because phonological processing is still being learned. The relationship between SEMA6D and reading may change as different brain regions are involved during reading development. Future research should examine mediating effects, use additional brain measures, and use an older sample to better understand effects.
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Affiliation(s)
- Tina Thomas
- Department of Psychology, University of Houston, Houston, TX, USA
| | - Meaghan V. Perdue
- University of Connecticut Dept. of Psychological Sciences, Storrs, CT, USA
- Haskins Laboratories, University of Connecticut, New Haven, CT, USA
| | - Shiva Khalaf
- Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, TX, USA
| | - Nicole Landi
- University of Connecticut Dept. of Psychological Sciences, Storrs, CT, USA
- Haskins Laboratories, University of Connecticut, New Haven, CT, USA
| | - Fumiko Hoeft
- University of Connecticut Dept. of Psychological Sciences, Storrs, CT, USA
- Department of Psychiatry, University of California, San Francisco, CA, USA
| | - Kenneth Pugh
- University of Connecticut Dept. of Psychological Sciences, Storrs, CT, USA
- Haskins Laboratories, University of Connecticut, New Haven, CT, USA
| | - Elena L. Grigorenko
- Department of Psychology, University of Houston, Houston, TX, USA
- Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, TX, USA
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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15
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Dumas G, Malesys S, Bourgeron T. Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition. Genome Res 2021; 31:484-496. [PMID: 33441416 PMCID: PMC7919455 DOI: 10.1101/gr.262113.120] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 01/06/2021] [Indexed: 12/11/2022]
Abstract
The human brain differs from that of other primates, but the genetic basis of these differences remains unclear. We investigated the evolutionary pressures acting on almost all human protein-coding genes (N = 11,667; 1:1 orthologs in primates) based on their divergence from those of early hominins, such as Neanderthals, and non-human primates. We confirm that genes encoding brain-related proteins are among the most strongly conserved protein-coding genes in the human genome. Combining our evolutionary pressure metrics for the protein-coding genome with recent data sets, we found that this conservation applied to genes functionally associated with the synapse and expressed in brain structures such as the prefrontal cortex and the cerebellum. Conversely, several genes presenting signatures commonly associated with positive selection appear as causing brain diseases or conditions, such as micro/macrocephaly, Joubert syndrome, dyslexia, and autism. Among those, a number of DNA damage response genes associated with microcephaly in humans such as BRCA1, NHEJ1, TOP3A, and RNF168 show strong signs of positive selection and might have played a role in human brain size expansion during primate evolution. We also showed that cerebellum granule neurons express a set of genes also presenting signatures of positive selection and that may have contributed to the emergence of fine motor skills and social cognition in humans. This resource is available online and can be used to estimate evolutionary constraints acting on a set of genes and to explore their relative contributions to human traits.
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Affiliation(s)
- Guillaume Dumas
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, Paris 75015, France
- Department of Psychiatry, Université de Montreal, CHU Sainte-Justine Hospital, Montreal H3T 1C5, Quebec, Canada
| | - Simon Malesys
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, Paris 75015, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, Paris 75015, France
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16
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Bieder A, Yoshihara M, Katayama S, Krjutškov K, Falk A, Kere J, Tapia-Páez I. Dyslexia Candidate Gene and Ciliary Gene Expression Dynamics During Human Neuronal Differentiation. Mol Neurobiol 2020; 57:2944-2958. [PMID: 32445086 PMCID: PMC7320047 DOI: 10.1007/s12035-020-01905-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/19/2020] [Indexed: 11/30/2022]
Abstract
Developmental dyslexia (DD) is a neurodevelopmental condition with complex genetic mechanisms. A number of candidate genes have been identified, some of which are linked to neuronal development and migration and to ciliary functions. However, expression and regulation of these genes in human brain development and neuronal differentiation remain uncharted. Here, we used human long-term self-renewing neuroepithelial stem (lt-NES, here termed NES) cells derived from human induced pluripotent stem cells to study neuronal differentiation in vitro. We characterized gene expression changes during differentiation by using RNA sequencing and validated dynamics for selected genes by qRT-PCR. Interestingly, we found that genes related to cilia were significantly enriched among upregulated genes during differentiation, including genes linked to ciliopathies with neurodevelopmental phenotypes. We confirmed the presence of primary cilia throughout neuronal differentiation. Focusing on dyslexia candidate genes, 33 out of 50 DD candidate genes were detected in NES cells by RNA sequencing, and seven candidate genes were upregulated during differentiation to neurons, including DYX1C1 (DNAAF4), a highly replicated DD candidate gene. Our results suggest a role of ciliary genes in differentiating neuronal cells and show that NES cells provide a relevant human neuronal model to study ciliary and DD candidate genes.
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Affiliation(s)
- Andrea Bieder
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden.
| | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden.,Competence Centre on Health Technologies, Tartu, Estonia.,Research Program of Molecular Neurology, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden. .,Research Program of Molecular Neurology, Research Programs Unit, University of Helsinki, Helsinki, Finland. .,Folkhälsan Institute of Genetics, Helsinki, Finland. .,School of Basic and Medical Biosciences, King's College London, London, UK.
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17
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Genetic Study on Small Insertions and Deletions in Psoriasis Reveals a Role in Complex Human Diseases. J Invest Dermatol 2019; 139:2302-2312.e14. [PMID: 31078570 DOI: 10.1016/j.jid.2019.03.1157] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 11/20/2022]
Abstract
Genetic studies based on single-nucleotide polymorphisms have provided valuable insights into the genetic architecture of complex diseases. However, a large fraction of heritability for most of these diseases remains unexplained, and the impact of small insertions and deletions (InDels) has been neglected. We performed a comprehensive screen on the exome sequence data of 1,326 genes using the SOAP-PopIndel method for InDels in 32,043 Chinese Han individuals and identified 29 unreported InDels within 25 susceptibility genes associated with psoriasis. Specifically, we identified 12 common, 9 low-frequency, and 8 rare InDels that explained approximately 1.29% of the heritability of psoriasis. Further analyses identified KIAA0319, RELN, NCAPG, ABO, AADACL2, LMAN1, FLG, HERC5, CCDC66, LEKR1, AFF3, ABCG2, ANXA7, SYTL2,GIPR, METTL1, and FYCO1 as unreported genes for psoriasis. In addition, identified InDels were associated with the following reported genes: IFIH1, ERAP1, ERAP2, LNPEP, UBLCP1, and STAT3; unreported independent associations for exonic InDels were found within GJB2 and ZNF816A. Our study enriched the genetic basis and pathogenesis of psoriasis and highlighted the non-negligible impact of InDels on complex human diseases.
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18
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Gostic M, Martinelli A, Tucker C, Yang Z, Gasparoli F, Ewart JY, Dholakia K, Sillar KT, Tello JA, Paracchini S. The dyslexia susceptibility KIAA0319 gene shows a specific expression pattern during zebrafish development supporting a role beyond neuronal migration. J Comp Neurol 2019; 527:2634-2643. [PMID: 30950042 PMCID: PMC6767054 DOI: 10.1002/cne.24696] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 03/20/2019] [Accepted: 03/29/2019] [Indexed: 01/17/2023]
Abstract
Dyslexia is a common neurodevelopmental disorder caused by a significant genetic component. The KIAA0319 gene is one of the most robust dyslexia susceptibility factors but its function remains poorly understood. Initial RNA-interference studies in rats suggested a role in neuronal migration whereas subsequent work with double knock-out mouse models for both Kiaa0319 and its paralogue Kiaa0319-like reported effects in the auditory system but not in neuronal migration. To further understand the role of KIAA0319 during neurodevelopment, we carried out an expression study of its zebrafish orthologue at different embryonic stages. We used different approaches including RNAscope in situ hybridization combined with light-sheet microscopy. The results show particularly high expression during the first few hours of development. Later, expression becomes localized in well-defined structures. In addition to high expression in the brain, we report for the first time expression in the eyes and the notochord. Surprisingly, kiaa0319-like, which generally shows a similar expression pattern to kiaa0319, was not expressed in the notochord suggesting a distinct role for kiaa0319 in this structure. This observation was supported by the identification of notochord enhancers enriched upstream of the KIAA0319 transcription start site, in both zebrafish and humans. This study supports a developmental role for KIAA0319 in the brain as well as in other developing structures, particularly in the notochord which, is key for establishing body patterning in vertebrates.
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Affiliation(s)
- Monika Gostic
- School of Medicine, University of St Andrews, St Andrews, UK.,Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK
| | - Angela Martinelli
- School of Medicine, University of St Andrews, St Andrews, UK.,Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK
| | - Carl Tucker
- College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, UK
| | - Zhengyi Yang
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, UK.,School of Psychology and Neuroscience, University of St Andrews, St Andrews, UK
| | | | - Jade-Yi Ewart
- School of Medicine, University of St Andrews, St Andrews, UK.,School of Psychology and Neuroscience, University of St Andrews, St Andrews, UK
| | - Kishan Dholakia
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK.,SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, UK
| | - Keith T Sillar
- School of Psychology and Neuroscience, University of St Andrews, St Andrews, UK
| | - Javier A Tello
- School of Medicine, University of St Andrews, St Andrews, UK.,Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK
| | - Silvia Paracchini
- School of Medicine, University of St Andrews, St Andrews, UK.,Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK
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19
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Guidi LG, Velayos‐Baeza A, Martinez‐Garay I, Monaco AP, Paracchini S, Bishop DVM, Molnár Z. The neuronal migration hypothesis of dyslexia: A critical evaluation 30 years on. Eur J Neurosci 2018; 48:3212-3233. [PMID: 30218584 PMCID: PMC6282621 DOI: 10.1111/ejn.14149] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/06/2018] [Accepted: 08/13/2018] [Indexed: 12/29/2022]
Abstract
The capacity for language is one of the key features underlying the complexity of human cognition and its evolution. However, little is known about the neurobiological mechanisms that mediate normal or impaired linguistic ability. For developmental dyslexia, early postmortem studies conducted in the 1980s linked the disorder to subtle defects in the migration of neurons in the developing neocortex. These early studies were reinforced by human genetic analyses that identified dyslexia susceptibility genes and subsequent evidence of their involvement in neuronal migration. In this review, we examine recent experimental evidence that does not support the link between dyslexia and neuronal migration. We critically evaluate gene function studies conducted in rodent models and draw attention to the lack of robust evidence from histopathological and imaging studies in humans. Our review suggests that the neuronal migration hypothesis of dyslexia should be reconsidered, and the neurobiological basis of dyslexia should be approached with a fresh start.
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Affiliation(s)
- Luiz G. Guidi
- Department of Physiology, Anatomy, and GeneticsUniversity of OxfordOxfordUK
- Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Antonio Velayos‐Baeza
- Department of Physiology, Anatomy, and GeneticsUniversity of OxfordOxfordUK
- Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Isabel Martinez‐Garay
- Department of Physiology, Anatomy, and GeneticsUniversity of OxfordOxfordUK
- Division of NeuroscienceSchool of BiosciencesCardiff UniversityCardiffUK
| | | | | | | | - Zoltán Molnár
- Department of Physiology, Anatomy, and GeneticsUniversity of OxfordOxfordUK
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20
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Centanni TM, Pantazis D, Truong DT, Gruen JR, Gabrieli JDE, Hogan TP. Increased variability of stimulus-driven cortical responses is associated with genetic variability in children with and without dyslexia. Dev Cogn Neurosci 2018; 34:7-17. [PMID: 29894888 PMCID: PMC6969288 DOI: 10.1016/j.dcn.2018.05.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 05/14/2018] [Accepted: 05/24/2018] [Indexed: 12/17/2022] Open
Abstract
Individuals with dyslexia exhibit increased brainstem variability in response to sound. It is unknown as to whether increased variability extends to neocortical regions associated with audition and reading, extends to visual stimuli, and whether increased variability characterizes all children with dyslexia or, instead, a specific subset of children. We evaluated the consistency of stimulus-evoked neural responses in children with (N = 20) or without dyslexia (N = 12) as measured by magnetoencephalography (MEG). Approximately half of the children with dyslexia had significantly higher levels of variability in cortical responses to both auditory and visual stimuli in multiple nodes of the reading network. There was a significant and positive relationship between the number of risk alleles at rs6935076 in the dyslexia-susceptibility gene KIAA0319 and the degree of neural variability in primary auditory cortex across all participants. This gene has been linked with neural variability in rodents and in typical readers. These findings indicate that unstable representations of auditory and visual stimuli in auditory and other reading-related neocortical regions are present in a subset of children with dyslexia and support the link between the gene KIAA0319 and the auditory neural variability across children with or without dyslexia.
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Affiliation(s)
- T M Centanni
- McGovern Institute for Brain Research and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Psychology, Texas Christian University, Fort Worth, TX, USA.
| | - D Pantazis
- McGovern Institute for Brain Research and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - D T Truong
- Departments of Pediatrics and Genetics, Yale University, New Haven, CT, USA
| | - J R Gruen
- Departments of Pediatrics and Genetics, Yale University, New Haven, CT, USA
| | - J D E Gabrieli
- McGovern Institute for Brain Research and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - T P Hogan
- Communication Sciences and Disorders, MGH Institute of Health Professions, Boston, MA, USA
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Guidi LG, Mattley J, Martinez-Garay I, Monaco AP, Linden JF, Velayos-Baeza A, Molnár Z. Knockout Mice for Dyslexia Susceptibility Gene Homologs KIAA0319 and KIAA0319L have Unaffected Neuronal Migration but Display Abnormal Auditory Processing. Cereb Cortex 2017; 27:5831-5845. [PMID: 29045729 PMCID: PMC5939205 DOI: 10.1093/cercor/bhx269] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Developmental dyslexia is a neurodevelopmental disorder that affects reading ability caused by genetic and non-genetic factors. Amongst the susceptibility genes identified to date, KIAA0319 is a prime candidate. RNA-interference experiments in rats suggested its involvement in cortical migration but we could not confirm these findings in Kiaa0319-mutant mice. Given its homologous gene Kiaa0319L (AU040320) has also been proposed to play a role in neuronal migration, we interrogated whether absence of AU040320 alone or together with KIAA0319 affects migration in the developing brain. Analyses of AU040320 and double Kiaa0319;AU040320 knockouts (dKO) revealed no evidence for impaired cortical lamination, neuronal migration, neurogenesis or other anatomical abnormalities. However, dKO mice displayed an auditory deficit in a behavioral gap-in-noise detection task. In addition, recordings of click-evoked auditory brainstem responses revealed suprathreshold deficits in wave III amplitude in AU040320-KO mice, and more general deficits in dKOs. These findings suggest that absence of AU040320 disrupts firing and/or synchrony of activity in the auditory brainstem, while loss of both proteins might affect both peripheral and central auditory function. Overall, these results stand against the proposed role of KIAA0319 and AU040320 in neuronal migration and outline their relationship with deficits in the auditory system.
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Affiliation(s)
- Luiz G Guidi
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Jane Mattley
- Ear Institute, University College London, London WC1X 8EE, UK
| | - Isabel Martinez-Garay
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | - Anthony P Monaco
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Current address: Office of the President, Ballou Hall, Tufts University, Medford, MA 02155, USA
| | - Jennifer F Linden
- Ear Institute, University College London, London WC1X 8EE, UK
- Department of Neuroscience, Physiology & Pharmacology, University College London, London WC1E 6BT, UK
| | | | - Zoltán Molnár
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, UK
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22
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Psychometric Markers of Genuine and Feigned Neurodevelopmental Disorders in the Context of Applying for Academic Accommodations. PSYCHOLOGICAL INJURY & LAW 2017. [DOI: 10.1007/s12207-017-9287-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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