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Yahia A, Li D, Lejerkrans S, Rajagopalan S, Kalnak N, Tammimies K. Whole exome sequencing and polygenic assessment of a Swedish cohort with severe developmental language disorder. Hum Genet 2024; 143:169-183. [PMID: 38300321 PMCID: PMC10881898 DOI: 10.1007/s00439-023-02636-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/25/2023] [Indexed: 02/02/2024]
Abstract
Developmental language disorder (DLD) overlaps clinically, genetically, and pathologically with other neurodevelopmental disorders (NDD), corroborating the concept of the NDD continuum. There is a lack of studies to understand the whole genetic spectrum in individuals with DLD. Previously, we recruited 61 probands with severe DLD from 59 families and examined 59 of them and their families using microarray genotyping with a 6.8% diagnostic yield. Herein, we investigated 53 of those probands using whole exome sequencing (WES). Additionally, we used polygenic risk scores (PRS) to understand the within family enrichment of neurodevelopmental difficulties and examine the associations between the results of language-related tests in the probands and language-related PRS. We identified clinically significant variants in four probands, resulting in a 7.5% (4/53) molecular diagnostic yield. Those variants were in PAK2, MED13, PLCB4, and TNRC6B. We also prioritized additional variants for future studies for their role in DLD, including high-impact variants in PARD3 and DIP2C. PRS did not explain the aggregation of neurodevelopmental difficulties in these families. We did not detect significant associations between the language-related tests and language-related PRS. Our results support using WES as the first-tier genetic test for DLD as it can identify monogenic DLD forms. Large-scale sequencing studies for DLD are needed to identify new genes and investigate the polygenic contribution to the condition.
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Affiliation(s)
- Ashraf Yahia
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Danyang Li
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Sanna Lejerkrans
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Shyam Rajagopalan
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
| | - Nelli Kalnak
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Department of Speech-Language Pathology, Helsingborg Hospital, Helsingborg, Sweden
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden.
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden.
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Espinosa-Mojica AA, Varo Varo C. Determining the Linguistic Profile of Children With Rare Genetic Disorders. JOURNAL OF SPEECH, LANGUAGE, AND HEARING RESEARCH : JSLHR 2024; 67:170-186. [PMID: 38085694 DOI: 10.1044/2023_jslhr-23-00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
PURPOSE Language studies on populations with rare genetic disorders are limited. Hence, there is little data on commonly found or expected developmental linguistic traits and cognitive mechanisms that may be impaired. Based on the hypothesis that there is a close connection between language and cognition and the relevance of specific genetic changes in the development of each, our goal was to provide linguistic data on relationships with other executive functioning mechanisms. METHOD This study assessed language skills, communicative behaviors, and executive functions in four children, aged 7-9 years, with rare genetic disorders, using standardized protocols and tests. RESULTS The findings revealed different levels of language impairment and executive functioning problems in each case. The overall executive function index performance for each of the four cases studied was clinically significantly high, indicating executive dysfunction. CONCLUSIONS The cases analyzed illustrate different types of atypical development that affect both language and other cognitive mechanisms and underscore the importance of executive skills and the various ways in which they are involved in diverse levels of language that might be affected to a greater or lesser degree in rare genetic disorders. In conclusion, we found that language dysfunction is a salient feature of the rare genetic disorders included in our study, although this is not necessarily true for all genetic disorders. Along with these conclusive results, we performed a qualitative analysis of the linguistic and cognitive components that enable functional communication in order to allow optimal interpretation of the data we have collected, laying the foundations for a more effective therapeutic approach.
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Nudel R, Christensen RV, Kalnak N, Schwinn M, Banasik K, Dinh KM, Erikstrup C, Pedersen OB, Burgdorf KS, Ullum H, Ostrowski SR, Hansen TF, Werge T. Developmental language disorder - a comprehensive study of more than 46,000 individuals. Psychiatry Res 2023; 323:115171. [PMID: 36963307 DOI: 10.1016/j.psychres.2023.115171] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/16/2023] [Accepted: 03/14/2023] [Indexed: 03/26/2023]
Abstract
Developmental language disorder (DLD) is characterized by enduring low language abilities with a significant functional impact, in the absence of biomedical conditions in which language impairment is part of a complex of impairments. There is a lack of awareness of DLD even among healthcare professionals. Here we estimated the prevalence of DLD and its links to reading and learning difficulties and physical and mental health in the Danish Blood Donor Study (N = 46,547), where DLD-related information is based on questionnaires (self-report). We compared the questionnaire-derived DLD status with the relevant language-related diagnoses from hospital registers. We also investigated the genetic architecture of DLD in a subset of the cohort (N = 18,380). DLD was significantly associated with reading and learning difficulties and poorer mental and physical health. DLD prevalence was 3.36%-3.70% based on questionnaires, compared with 0.04% in hospital registers. Our genetic analyses identified one genome-wide significant locus, but not a significant heritability estimate. Our study shows that DLD has health-related implications that may last into adulthood, and that DLD may be undiagnosed in general healthcare. Furthermore, DLD is likely more genetically heterogeneous than narrower developmental language phenotypes. Our results emphasize the need to raise awareness of DLD and consider criteria for molecular studies of DLD to reduce case heterogeneity.
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Affiliation(s)
- Ron Nudel
- CORE - Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark.
| | - Rikke Vang Christensen
- Department of Nordic Studies and Linguistics, University of Copenhagen, Emil Holms Kanal 2, Copenhagen 2300, Denmark.
| | - Nelli Kalnak
- Department of Women's and Children's Health, Karolinska Institute, Stockholm, Sweden; Department of Speech-Language Pathology, Helsingborg Hospital, Helsingborg, Sweden.
| | - Michael Schwinn
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Karina Banasik
- Novo Nordisk foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Khoa Manh Dinh
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Ole Birger Pedersen
- Department of Immunology, Næstved Hospital, Næstved, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer Sølvsten Burgdorf
- Department of Immunology, Rigshospitalet, Copenhagen, Denmark; Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Folkmann Hansen
- Novo Nordisk foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Danish Headache Center, Rigshospitalet Glostrup, Glostrup, Denmark
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Institute of Biological Psychiatry, Roskilde, Denmark
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4
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Shikhevich S, Chadaeva I, Khandaev B, Kozhemyakina R, Zolotareva K, Kazachek A, Oshchepkov D, Bogomolov A, Klimova NV, Ivanisenko VA, Demenkov P, Mustafin Z, Markel A, Savinkova L, Kolchanov NA, Kozlov V, Ponomarenko M. Differentially Expressed Genes and Molecular Susceptibility to Human Age-Related Diseases. Int J Mol Sci 2023; 24:ijms24043996. [PMID: 36835409 PMCID: PMC9966505 DOI: 10.3390/ijms24043996] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/02/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Mainstream transcriptome profiling of susceptibility versus resistance to age-related diseases (ARDs) is focused on differentially expressed genes (DEGs) specific to gender, age, and pathogeneses. This approach fits in well with predictive, preventive, personalized, participatory medicine and helps understand how, why, when, and what ARDs one can develop depending on their genetic background. Within this mainstream paradigm, we wanted to find out whether the known ARD-linked DEGs available in PubMed can reveal a molecular marker that will serve the purpose in anyone's any tissue at any time. We sequenced the periaqueductal gray (PAG) transcriptome of tame versus aggressive rats, identified rat-behavior-related DEGs, and compared them with their known homologous animal ARD-linked DEGs. This analysis yielded statistically significant correlations between behavior-related and ARD-susceptibility-related fold changes (log2 values) in the expression of these DEG homologs. We found principal components, PC1 and PC2, corresponding to the half-sum and the half-difference of these log2 values, respectively. With the DEGs linked to ARD susceptibility and ARD resistance in humans used as controls, we verified these principal components. This yielded only one statistically significant common molecular marker for ARDs: an excess of Fcγ receptor IIb suppressing immune cell hyperactivation.
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Affiliation(s)
- Svetlana Shikhevich
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Bato Khandaev
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Rimma Kozhemyakina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Karina Zolotareva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anna Kazachek
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitry Oshchepkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anton Bogomolov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Natalya V. Klimova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Vladimir A. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Pavel Demenkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Zakhar Mustafin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Arcady Markel
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ludmila Savinkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Vladimir Kozlov
- Research Institute of Fundamental and Clinical Immunology (RIFCI) SB RAS, Novosibirsk 630099, Russia
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- Correspondence: ; Tel.: +7-(383)-363-4963 (ext. 1311)
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Mountford HS, Braden R, Newbury DF, Morgan AT. The Genetic and Molecular Basis of Developmental Language Disorder: A Review. CHILDREN (BASEL, SWITZERLAND) 2022; 9:children9050586. [PMID: 35626763 PMCID: PMC9139417 DOI: 10.3390/children9050586] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/28/2022] [Accepted: 04/12/2022] [Indexed: 01/05/2023]
Abstract
Language disorders are highly heritable and are influenced by complex interactions between genetic and environmental factors. Despite more than twenty years of research, we still lack critical understanding of the biological underpinnings of language. This review provides an overview of the genetic landscape of developmental language disorders (DLD), with an emphasis on the importance of defining the specific features (the phenotype) of DLD to inform gene discovery. We review the specific phenotype of DLD in the genetic literature, and the influence of historic variation in diagnostic inclusion criteria on researchers' ability to compare and replicate genotype-phenotype studies. This review provides an overview of the recently identified gene pathways in populations with DLD and explores current state-of-the-art approaches to genetic analysis based on the hypothesised architecture of DLD. We will show how recent global efforts to unify diagnostic criteria have vastly increased sample size and allow for large multi-cohort metanalyses, leading the identification of a growing number of contributory loci. We emphasise the important role of estimating the genetic architecture of DLD to decipher underlying genetic associations. Finally, we explore the potential for epigenetics and environmental interactions to further unravel the biological basis of language disorders.
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Affiliation(s)
- Hayley S. Mountford
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; (H.S.M.); (D.F.N.)
| | - Ruth Braden
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne 3052, Australia;
| | - Dianne F. Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; (H.S.M.); (D.F.N.)
| | - Angela T. Morgan
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne 3052, Australia;
- Correspondence:
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Family-Based Whole-Exome Analysis of Specific Language Impairment (SLI) Identifies Rare Variants in BUD13, a Component of the Retention and Splicing (RES) Complex. Brain Sci 2021; 12:brainsci12010047. [PMID: 35053791 PMCID: PMC8773923 DOI: 10.3390/brainsci12010047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/18/2021] [Accepted: 12/27/2021] [Indexed: 12/12/2022] Open
Abstract
Specific language impairment (SLI) is a common neurodevelopmental disorder (NDD) that displays high heritability estimates. Genetic studies have identified several loci, but the molecular basis of SLI remains unclear. With the aim to better understand the genetic architecture of SLI, we performed whole-exome sequencing (WES) in a single family (ID: 489; n = 11). We identified co-segregating rare variants in three new genes: BUD13, APLP2, and NDRG2. To determine the significance of these genes in SLI, we Sanger sequenced all coding regions of each gene in unrelated individuals with SLI (n = 175). We observed 13 additional rare variants in 18 unrelated individuals. Variants in BUD13 reached genome-wide significance (p-value < 0.01) upon comparison with similar variants in the 1000 Genomes Project, providing gene level evidence that BUD13 is involved in SLI. Additionally, five BUD13 variants showed cohesive variant level evidence of likely pathogenicity. Bud13 is a component of the retention and splicing (RES) complex. Additional supportive evidence from studies of an animal model (loss-of-function mutations in BUD13 caused a profound neural phenotype) and individuals with an NDD phenotype (carrying a CNV spanning BUD13), indicates BUD13 could be a target for investigation of the neural basis of language.
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Nudel R, Appadurai V, Buil A, Nordentoft M, Werge T. Pleiotropy between language impairment and broader behavioral disorders-an investigation of both common and rare genetic variants. J Neurodev Disord 2021; 13:54. [PMID: 34773992 PMCID: PMC8590378 DOI: 10.1186/s11689-021-09403-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 10/22/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Language plays a major role in human behavior. For this reason, neurodevelopmental and psychiatric disorders in which linguistic ability is impaired could have a big impact on the individual's social interaction and general wellbeing. Such disorders tend to have a strong genetic component, but most past studies examined mostly the linguistic overlaps across these disorders; investigations into their genetic overlaps are limited. The aim of this study was to assess the potential genetic overlap between language impairment and broader behavioral disorders employing methods capturing both common and rare genetic variants. METHODS We employ polygenic risk scores (PRS) trained on specific language impairment (SLI) to evaluate genetic overlap across several disorders in a large case-cohort sample comprising ~13,000 autism spectrum disorder (ASD) cases, including cases of childhood autism and Asperger's syndrome, ~15,000 attention deficit/hyperactivity disorder (ADHD) cases, ~3000 schizophrenia cases, and ~21,000 population controls. We also examine rare variants in SLI/language-related genes in a subset of the sample that was exome-sequenced using the SKAT-O method. RESULTS We find that there is little evidence for genetic overlap between SLI and ADHD, schizophrenia, and ASD, the latter being in line with results of linguistic analyses in past studies. However, we observe a small, significant genetic overlap between SLI and childhood autism specifically, which we do not observe for SLI and Asperger's syndrome. Moreover, we observe that childhood autism cases have significantly higher SLI-trained PRS compared to Asperger's syndrome cases; these results correspond well to the linguistic profiles of both disorders. Our rare variant analyses provide suggestive evidence of association for specific genes with ASD, childhood autism, and schizophrenia. CONCLUSIONS Our study provides, for the first time, to our knowledge, genetic evidence for ASD subtypes based on risk variants for language impairment.
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Affiliation(s)
- Ron Nudel
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- CORE - Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Vivek Appadurai
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Alfonso Buil
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- CORE - Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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8
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Andres EM, Neely HL, Hafeez H, Yasmin T, Kausar F, Basra MAR, Raza MH. Study of rare genetic variants in TM4SF20, NFXL1, CNTNAP2, and ATP2C2 in Pakistani probands and families with language impairment. Meta Gene 2021; 30. [PMID: 34540591 DOI: 10.1016/j.mgene.2021.100966] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Language impairment (LI) is highly heritable and aggregates in families. Genetic investigation of LI has revealed many chromosomal regions and genes of interest, though very few studies have focused on rare variant analysis in non-English speaking or non-European samples. We selected four candidate genes (TM4SF20, NFXL1, CNTNAP2 and ATP2C2) strongly suggested for specific language impairment (SLI), a subtype of LI, and investigated rare protein coding variants through Sanger sequencing of probands with LI ascertained from Pakistan. The probands and their family members completed a speech and language family history questionnaire and a vocabulary measure, the Peabody Picture Vocabulary Test-fourth edition (PPVT-4), translated to Urdu, the national language of Pakistan. Our study aimed to determine the significance of rare variants in these SLI candidate genes through segregation analysis in a novel population with a high rate of consanguinity. In total, we identified 16 rare variants (according to the rare MAF in the global population in gnomAD v2.1.1 database exomes), including eight variants with a MAF <0.5 % in the South Asian population. Most of the identified rare variants aggregated in proband's families, one rare variant (c.*9T>C in CNTNAP2) co-segregated in a small family (PKSLI-64) and another (c.2465C>T in ATP2C2) co-segregated in the proband branch (PKSLI-27). The lack of complete co-segregation of most of the identified rare variants indicates that while these genes could be involved in overall risk for LI, other genes are likely involved in LI in this population. Future investigation of these consanguineous families has the potential to expand our understanding of gene function related to language acquisition and impairment.
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Affiliation(s)
- Erin M Andres
- University of Kansas, Child Language Doctoral Program
| | | | - Huma Hafeez
- School of Chemistry, University of the Punjab
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Martinelli A, Rice ML, Talcott JB, Diaz R, Smith S, Raza MH, Snowling MJ, Hulme C, Stein J, Hayiou-Thomas ME, Hawi Z, Kent L, Pitt SJ, Newbury DF, Paracchini S. A rare missense variant in the ATP2C2 gene is associated with language impairment and related measures. Hum Mol Genet 2021; 30:1160-1171. [PMID: 33864365 PMCID: PMC8188402 DOI: 10.1093/hmg/ddab111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 01/02/2023] Open
Abstract
At least 5% of children present unexpected difficulties in expressing and understanding spoken language. This condition is highly heritable and often co-occurs with other neurodevelopmental disorders such as dyslexia and ADHD. Through an exome sequencing analysis, we identified a rare missense variant (chr16:84405221, GRCh38.p12) in the ATP2C2 gene. ATP2C2 was implicated in language disorders by linkage and association studies, and exactly the same variant was reported previously in a different exome sequencing study for language impairment (LI). We followed up this finding by genotyping the mutation in cohorts selected for LI and comorbid disorders. We found that the variant had a higher frequency in LI cases (1.8%, N = 360) compared with cohorts selected for dyslexia (0.8%, N = 520) and ADHD (0.7%, N = 150), which presented frequencies comparable to reference databases (0.9%, N = 24 046 gnomAD controls). Additionally, we observed that carriers of the rare variant identified from a general population cohort (N = 42, ALSPAC cohort) presented, as a group, lower scores on a range of reading and language-related measures compared to controls (N = 1825; minimum P = 0.002 for non-word reading). ATP2C2 encodes for an ATPase (SPCA2) that transports calcium and manganese ions into the Golgi lumen. Our functional characterization suggested that the rare variant influences the ATPase activity of SPCA2. Thus, our results further support the role of ATP2C2 locus in language-related phenotypes and pinpoint the possible effects of a specific rare variant at molecular level.
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Affiliation(s)
| | - Mabel L Rice
- Child Language Doctoral Program, University of Kansas, Lawrence, KS, USA
| | - Joel B Talcott
- Aston Brain Centre, School of Life and Health Sciences, Aston University, Birmingham, UK
| | - Rebeca Diaz
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Shelley Smith
- Department of Neurological Sciences, University of Nebraska Medical Center, Lincoln, NE, USA
| | | | - Margaret J Snowling
- Department of Experimental Psychology and St John's College, University of Oxford, Oxford, UK
| | - Charles Hulme
- Department of Education, University of Oxford, Oxford, UK
| | - John Stein
- Department of Physiology, University of Oxford, Oxford, UK
| | | | - Ziarih Hawi
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, VIC, Australia
| | - Lindsey Kent
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Samantha J Pitt
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Dianne F Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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10
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NFX1, Its Isoforms and Roles in Biology, Disease and Cancer. BIOLOGY 2021; 10:biology10040279. [PMID: 33808060 PMCID: PMC8067315 DOI: 10.3390/biology10040279] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/17/2021] [Accepted: 03/25/2021] [Indexed: 12/20/2022]
Abstract
Simple Summary The NFX1 gene, and its gene products, were identified over 30 years ago. Since then, the literature on NFX1 homologs and NFX1 itself has grown. In this review, we summarize the studies to-date on the NFX1 gene and its proteins across species and in humans, describing their role in gene regulation, embryonic development, cellular growth and differentiation, exogenous stress tolerance and metabolism, and an organism’s immune response. We also highlight the roles NFX1 has in human disease and in cancer, with a strong focus on its collaborative role with high-risk human papillomavirus infections that cause cervical and head and neck cancers. We believe this is the first comprehensive review of NFX1 and its functional significance in organisms ranging from yeast to human. Abstract In 1989, two NFX1 protein products were identified as nuclear proteins with the ability to bind to X-box cis-elements. Since that publication, the NFX1 gene and its homologs have been identified, from yeast to humans. This review article summarizes what is known about the NFX1 gene across species. We describe the gene and protein motifs of NFX1 homologs and their functions in cellular biology, then turn to NFX1 in human biology and disease development. In that, we focus on more recent literature about NFX1 and its two splice variants protein products (NFX1-91 and NFX1-123) that are expressed in epithelial cells. We describe new evidence of conserved protein motifs, direct and indirect gene expression regulation, and critical protein-protein interactions. Finally, we stress the emerging roles of these NFX1 splice variants in high-risk human papillomavirus-associated cancers, and the increased expression of the longer splice variant, NFX1-123, found in these cancers.
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Andres EM, Earnest KK, Smith SD, Rice ML, Raza MH. Pedigree-Based Gene Mapping Supports Previous Loci and Reveals Novel Suggestive Loci in Specific Language Impairment. JOURNAL OF SPEECH, LANGUAGE, AND HEARING RESEARCH : JSLHR 2020; 63:4046-4061. [PMID: 33186502 PMCID: PMC8608229 DOI: 10.1044/2020_jslhr-20-00102] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Purpose Specific language impairment (SLI) is characterized by a delay in language acquisition despite a lack of other developmental delays or hearing loss. Genetics of SLI is poorly understood. The purpose of this study is to identify SLI genetic loci through family-based linkage mapping. Method We performed genome-wide parametric linkage analysis in six families segregating with SLI. An age-appropriate standardized omnibus language measure was used to categorically define the SLI phenotype. Results A suggestive linkage region replicated a previous region of interest with the highest logarithm of odds (LOD) score of 2.40 at 14q11.2-q13.3 in Family 489. A paternal parent-of-origin effect associated with SLI and language phenotypes on a nonsynonymous single nucleotide polymorphism (SNP) in NOP9 (14q12) was reported previously. Linkage analysis identified a new SLI locus at 15q24.3-25.3 with the highest parametric LOD score of 3.06 in Family 315 under a recessive mode of inheritance. Suggestive evidence of linkage was also revealed at 4q31.23-q35.2 in Family 300, with the highest LOD score of 2.41. Genetic linkage was not identified in the other three families included in parametric linkage analysis. Conclusions These results are the first to report genome-wide suggestive linkage with a total language standard score on an age-appropriate omnibus language measure across a wide age range. Our findings confirm previous reports of a language-associated locus on chromosome 14q, report new SLI loci, and validate the pedigree-based parametric linkage analysis approach to mapping genes for SLI. Supplemental Material https://doi.org/10.23641/asha.13203218.
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Affiliation(s)
- Erin M. Andres
- Child Language Doctoral Program, University of Kansas, Lawrence
| | | | - Shelley D. Smith
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha
| | - Mabel L. Rice
- Child Language Doctoral Program, University of Kansas, Lawrence
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12
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Mountford HS, Villanueva P, Fernández MA, Jara L, De Barbieri Z, Carvajal-Carmona LG, Cazier JB, Newbury DF. The Genetic Population Structure of Robinson Crusoe Island, Chile. Front Genet 2020; 11:669. [PMID: 32676101 PMCID: PMC7333314 DOI: 10.3389/fgene.2020.00669] [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: 03/17/2020] [Accepted: 06/02/2020] [Indexed: 11/30/2022] Open
Abstract
Studies examining genetic conditions common in Latin America are highly underrepresented in the scientific literature. Understanding of the population structure is limited, particularly Chile, in part due to the lack of available population specific data. An important first-step in elucidating disease mechanisms in Latin America countries is to understand the genetic structure of isolated populations. Robinson Crusoe Island (RCI) is a small land mass off the coast of Chile. The current population of over 900 inhabitants are primarily descended from a small number of founders who colonized the island in the late 1800s. Extensive genealogical records can trace the ancestry of almost the entire population. We perform a comprehensive genetic analysis to investigate the ancestry of the island population, examining ancestral mitochondrial and Y chromosome haplogroups, as well as autosomal admixture. Mitochondrial and Y chromosome haplogroups indicated a substantial European genetic contribution to the current RCI population. Analysis of the mitochondrial haplogroups found in the present-day population revealed that 79.1% of islanders carried European haplogroups, compared to 60.0% of the mainland Chilean controls from Santiago. Both groups showed a substantially lower contribution of indigenous haplogroups than expected. Analysis of the Y chromosome haplogroups also showed predominantly European haplogroups detected in 92.3% of male islanders and 86.7% of mainland Chilean controls. Using the near-complete genealogical data collected from the RCI population, we successfully inferred the ancestral haplogroups of 16/23 founder individuals, revealing genetic ancestry from Northern and Southern Europe. As mitochondrial and Y investigations only provide information for direct maternal and paternal lineages, we expanded this to investigate genetic admixture using the autosomes. Admixture analysis identified substantial indigenous genetic admixture in the RCI population (46.9%), higher than that found in the Santiago mainland Chilean controls (43.4%), but lower than a more representative Chilean population (Chile_GRU) (49.1%). Our study revealed the Robinson Crusoe Island population show a substantial genetic contribution for indigenous Chileans, similar to the level reported in mainland Chileans. However, direct maternal and paternal haplogroup analysis revealed strong European genetic contributions consistent with the history of the Island.
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Affiliation(s)
- Hayley S Mountford
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Pía Villanueva
- Department of Speech Language and Hearing Sciences, Faculty of Medicine, University of Chile, Santiago, Chile.,Human Genetics Division, Faculty of Medicine, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - María Angélica Fernández
- Department of Speech Language and Hearing Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Lilian Jara
- Human Genetics Division, Faculty of Medicine, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Zulema De Barbieri
- Directorate of Academic Development, Academic Vice-Rectory, Research and Postgraduate, Saint Thomas University, Santiago, Chile
| | - Luis G Carvajal-Carmona
- Department of Biochemistry and Molecular Medicine, School of Medicine Genome Center, University of California, Davis, Davis, CA, United States
| | - Jean-Baptiste Cazier
- Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom.,Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Dianne F Newbury
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
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Nudel R, Christiani CAJ, Ohland J, Uddin MJ, Hemager N, Ellersgaard D, Spang KS, Burton BK, Greve AN, Gantriis DL, Bybjerg-Grauholm J, Jepsen JRM, Thorup AAE, Mors O, Werge T, Nordentoft M. Quantitative genome-wide association analyses of receptive language in the Danish High Risk and Resilience Study. BMC Neurosci 2020; 21:30. [PMID: 32635940 PMCID: PMC7341668 DOI: 10.1186/s12868-020-00581-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/28/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND One of the most basic human traits is language. Linguistic ability, and disability, have been shown to have a strong genetic component in family and twin studies, but molecular genetic studies of language phenotypes are scarce, relative to studies of other cognitive traits and neurodevelopmental phenotypes. Moreover, most genetic studies examining such phenotypes do not incorporate parent-of-origin effects, which could account for some of the heritability of the investigated trait. We performed a genome-wide association study of receptive language, examining both child genetic effects and parent-of-origin effects. RESULTS Using a family-based cohort with 400 children with receptive language scores, we found a genome-wide significant paternal parent-of-origin effect with a SNP, rs11787922, on chromosome 9q21.31, whereby the T allele reduced the mean receptive language score by ~ 23, constituting a reduction of more than 1.5 times the population SD (P = 1.04 × 10-8). We further confirmed that this association was not driven by broader neurodevelopmental diagnoses in the child or a family history of psychiatric diagnoses by incorporating covariates for the above and repeating the analysis. CONCLUSIONS Our study reports a genome-wide significant association for receptive language skills; to our knowledge, this is the first documented genome-wide significant association for this phenotype. Furthermore, our study illustrates the importance of considering parent-of-origin effects in association studies, particularly in the case of cognitive or neurodevelopmental traits, in which parental genetic data are not always incorporated.
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Affiliation(s)
- Ron Nudel
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
| | - Camilla A J Christiani
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Jessica Ohland
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Md Jamal Uddin
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
- Section for Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Nicoline Hemager
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Ditte Ellersgaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Katrine S Spang
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre for Child and Adolescent Psychiatry-Research unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Birgitte K Burton
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre for Child and Adolescent Psychiatry-Research unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Aja N Greve
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - Ditte L Gantriis
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Jens Richardt M Jepsen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
- Mental Health Centre for Child and Adolescent Psychiatry-Research unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
- Center for Neuropsychiatric Schizophrenia Research and Center for Clinical Intervention and Neuropsychiatric Schizophrenia Research, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Anne A E Thorup
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre for Child and Adolescent Psychiatry-Research unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark.
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Chintala S, Levan J, Robinson K, Quist K, Katzenellenbogen RA. Genes Regulated by HPV 16 E6 and High Expression of NFX1-123 in Cervical Cancers. Onco Targets Ther 2020; 13:6143-6156. [PMID: 32617009 PMCID: PMC7326398 DOI: 10.2147/ott.s251926] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 05/18/2020] [Indexed: 11/23/2022] Open
Abstract
Purpose High-risk human papillomaviruses (HR HPV) cause cervical cancer, and in these cancers, HPV type 16 is the most common HR type. The HR viral oncogenes E6 and E7 partner with cellular proteins to drive cancer and modulate immune pathways; previously, we demonstrated in keratinocytes that HPV 16 E6 and high expression of the endogenous host protein partner NFX1-123 led to the increased expression of multiple genes, including Notch1, secretory leukocyte peptidase inhibitor (SLPI), and retinoic acid early transcript 1G (RAET1G). The present study was conducted to determine if NFX1-123 was highly expressed in cervical cancer and if genes increased by NFX1-123 and 16E6 in keratinocytes were also increased in cervical cancers. Materials and Methods The Cancer Genome Atlas (TCGA) database and The Human Protein Atlas database were used to compare relative mRNA and protein gene expression, respectively, in the normal cervix and cervical cancers. Formalin-fixed paraffin-embedded (FFPE) normal cervix and HPV 16 positive cervical cancer samples were analyzed for relative protein expression by immunohistochemical staining. Protein expression of a subset of regulated genes was quantified by Western blot of HPV positive and negative cell lines. Results Immunohistochemical staining of HPV 16 positive cervical dysplasias and cancers revealed high NFX1-123, Ki67, and Notch1 expression. NFX1 and NFX1L1 mRNA levels were increased in cervical cancers compared to normal cervix in the TCGA database. Fourteen genes previously identified as upregulated in keratinocytes with 16E6 and overexpressed NFX1-123 also had high mRNA expression and selected genes had high protein expression in cervical cancers and cell lines. Conclusion In cervical cancer, NFX1-123 is highly expressed, and 16E6 and NFX1-123 together alter the expression of a wide set of genes. The involvement of these genes in cell proliferation, differentiation, invasion, and metastasis provides further insight into potential ways that HR HPVs promote cancer initiation and maintenance.
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Affiliation(s)
- Sreenivasulu Chintala
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Justine Levan
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kristin Robinson
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kevin Quist
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
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Abstract
PURPOSE OF REVIEW To better understand the shared basis of language and mental health, this review examines the behavioral and neurobiological features of aberrant language in five major neuropsychiatric conditions. Special attention is paid to genes implicated in both language and neuropsychiatric disorders, as they reveal biological domains likely to underpin the processes controlling both. RECENT FINDINGS Abnormal language and communication are common manifestations of neuropsychiatric conditions, and children with impaired language are more likely to develop psychiatric disorders than their peers. Major themes in the genetics of both language and psychiatry include master transcriptional regulators, like FOXP2; key developmental regulators, like AUTS2; and mediators of neurotransmission, like GRIN2A and CACNA1C.
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Nudel R, Christiani CAJ, Ohland J, Uddin MJ, Hemager N, Ellersgaard DV, Spang KS, Burton BK, Greve AN, Gantriis DL, Bybjerg-Grauholm J, Jepsen JRM, Thorup AAE, Mors O, Nordentoft M, Werge T. Language deficits in specific language impairment, attention deficit/hyperactivity disorder, and autism spectrum disorder: An analysis of polygenic risk. Autism Res 2019; 13:369-381. [PMID: 31577390 PMCID: PMC7078922 DOI: 10.1002/aur.2211] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/04/2019] [Indexed: 12/27/2022]
Abstract
Language is one of the cognitive domains often impaired across many neurodevelopmental disorders. While for some disorders the linguistic deficit is the primary impairment (e.g., specific language impairment, SLI), for others it may accompany broader behavioral problems (e.g., autism). The precise nature of this phenotypic overlap has been the subject of debate. Moreover, several studies have found genetic overlaps across neurodevelopmental disorders. This raises the question of whether these genetic overlaps may correlate with phenotypic overlaps and, if so, in what manner. Here, we apply a genome‐wide approach to the study of the linguistic deficit in SLI, autism spectrum disorder (ASD), and attention deficit/hyperactivity disorder (ADHD). Using a discovery genome‐wide association study of SLI, we generate polygenic risk scores (PRS) in an independent sample which includes children with language impairment, SLI, ASD or ADHD and age‐matched controls and perform regression analyses across groups. The SLI‐trained PRS significantly predicted risk in the SLI case–control group (adjusted R2 = 6.24%; P = 0.024) but not in the ASD or ADHD case‐control groups (adjusted R2 = 0.0004%, 0.01%; P = 0.984, 0.889, respectively) nor for height, used as a negative control (R2 = 0.2%; P = 0.452). Additionally, there was a significant difference in the normalized PRS between children with SLI and children with ASD (common language effect size = 0.66; P = 0.044). Our study suggests no additive common‐variant genetic overlap between SLI and ASD and ADHD. This is discussed in the context of phenotypic studies of SLI and related disorders. Autism Res 2020, 13: 369–381. © 2019 The Authors. Autism Research published by International Society for Autism Research published by Wiley Periodicals, Inc. Lay Summary Language deficits are characteristic of specific language impairment (SLI), but may also be found in other neurodevelopmental disorders, such as autism spectrum disorder (ASD) and attention deficit/hyperactivity disorder (ADHD). Many studies examined the overlaps and differences across the language deficits in these disorders, but few studies have examined the genetic aspect thereof. In this study, we use a genome‐wide approach to evaluate whether common genetic variants increasing risk of SLI may also be associated with ASD and ADHD in the same manner. Our results suggest that this is not the case, and we discuss this finding in the context of theories concerning the etiologies of these disorders.
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Affiliation(s)
- Ron Nudel
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Camilla A J Christiani
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Jessica Ohland
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Md Jamal Uddin
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark.,Section for Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Nicoline Hemager
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Ditte V Ellersgaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Katrine S Spang
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre for Child and Adolescent Psychiatry - Research Unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Birgitte K Burton
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre for Child and Adolescent Psychiatry - Research Unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Aja N Greve
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Ditte L Gantriis
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Jens Richardt M Jepsen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark.,Mental Health Centre for Child and Adolescent Psychiatry - Research Unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark.,Center for Neuropsychiatric Schizophrenia Research and Center for Clinical Intervention and Neuropsychiatric Schizophrenia Research, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Anne A E Thorup
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre for Child and Adolescent Psychiatry - Research Unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Mountford HS, Villanueva P, Fernández MA, Barbieri ZD, Cazier JB, Newbury DF. Candidate gene variant effects on language disorders in Robinson Crusoe Island. Ann Hum Biol 2019; 46:109-119. [DOI: 10.1080/03014460.2019.1622776] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Hayley S. Mountford
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Pía Villanueva
- Department of Speech Language and Hearing Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
- Institute of Biomedical Sciences, Human Genetics Division, Faculty of Medicine, University of Chile, Santiago, Chile
| | - María Angélica Fernández
- Department of Speech Language and Hearing Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Zulema De Barbieri
- Department of Speech Language and Hearing Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | | | - Dianne F. Newbury
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
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Benítez-Burraco A, Kimura R. Robust Candidates for Language Development and Evolution Are Significantly Dysregulated in the Blood of People With Williams Syndrome. Front Neurosci 2019; 13:258. [PMID: 30971880 PMCID: PMC6444191 DOI: 10.3389/fnins.2019.00258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/05/2019] [Indexed: 01/06/2023] Open
Abstract
Williams syndrome (WS) is a clinical condition, involving cognitive deficits and an uneven language profile, which has been the object of intense inquiry over the last decades. Although WS results from the hemideletion of around two dozen genes in chromosome 7, no gene has yet been probed to account for, or contribute significantly to, the language problems exhibited by the affected people. In this paper we have relied on gene expression profiles in the peripheral blood of WS patients obtained by microarray analysis and show that several robust candidates for language disorders and/or for language evolution in the species, all of them located outside the hemideleted region, are up- or downregulated in the blood of subjects with WS. Most of these genes play a role in the development and function of brain areas involved in language processing, which exhibit structural and functional anomalies in people with this condition. Overall, these genes emerge as robust candidates for language dysfunction in WS.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, Seville, Spain
| | - Ryo Kimura
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Sriganesh R, Joseph Ponniah R. Genetics of language and its implications on language interventions. J Genet 2018; 97:1485-1491. [PMID: 30555099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Genetic variation of language genes affect neurophysiology of brain and can thus influence the way people respond to environmental language input, leading to differences in terms of their response to environmental language learning. Conversely, language learning environment too can affect gene expressions through neuroepigenetic mechanisms, leading to increasedinterindividual differences. Further, language-related cognitive processes such as learning, working memory and perception; and language-related affective factors such as stress and positive emotion involve neuroplasticity, which is also epigenetically regulated. Language intervention methods must understand the extent and the type of difficulties, and must offer personalized learning andmedical solutions. Medical intervention in terms of epigenetics and neurotransmitter regulation is proposed in addition to effectiveteaching methods to aid in effective language acquisition.
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Kalnak N, Stamouli S, Peyrard-Janvid M, Rabkina I, Becker M, Klingberg T, Kere J, Forssberg H, Tammimies K. Enrichment of rare copy number variation in children with developmental language disorder. Clin Genet 2018; 94:313-320. [PMID: 29851021 DOI: 10.1111/cge.13389] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/23/2018] [Accepted: 05/27/2018] [Indexed: 02/04/2023]
Abstract
Developmental language disorder (DLD) is a common neurodevelopmental disorder with largely unknown etiology. Rare copy number variants (CNVs) have been implicated in the genetic architecture of other neurodevelopmental disorders (NDDs), which have led to clinical genetic testing recommendations for these disorders; however, the evidence is still lacking for DLD. We analyzed rare and de novo CNVs in 58 probands with severe DLD, their 159 family members and 76 Swedish typically developing children using high-resolution microarray. DLD probands had larger rare CNVs as measured by total length (P = .05), and average length (P = .04). In addition, the rate of rare CNVs overlapping coding genes was increased (P = .03 and P = .01) and in average more genes were affected (P = .006 and P = .03) in the probands and their siblings, respectively. De novo CNVs were found in 4.8% DLD probands (2/42) and 2.4% (1/42) siblings. Clinically significant CNVs or chromosomal anomalies were found in 6.9% (4/58) of the probands of which 2 carried 16p11.2 deletions. We provide further evidence that rare CNVs contribute to the etiology of DLD in loci that overlap with other NDDs. Based on our results and earlier literature, families with DLD should be offered molecular genetic testing as a routine in their clinical follow-up.
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Affiliation(s)
- N Kalnak
- Department of Women and Children's Health, Neuropediatric Unit, Karolinska Institutet, Astrid Lindgren Children's Hospital, Solna, Sweden.,Department of Clinical Sciences Lund, Child, and Adolescent Psychiatry Unit, Faculty of Medicine, Lund University, Lund, Sweden
| | - S Stamouli
- Department of Women and Children's Health, Center of Neurodevelopmental Disorders, Karolinska Institutet, Sweden and Centre for Psychiatry Research, Stockholm County Council, Stockholm, Sweden
| | - M Peyrard-Janvid
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - I Rabkina
- Department of Women and Children's Health, Center of Neurodevelopmental Disorders, Karolinska Institutet, Sweden and Centre for Psychiatry Research, Stockholm County Council, Stockholm, Sweden
| | - M Becker
- Department of Women and Children's Health, Center of Neurodevelopmental Disorders, Karolinska Institutet, Sweden and Centre for Psychiatry Research, Stockholm County Council, Stockholm, Sweden
| | - T Klingberg
- Department of Clinical Neuroscience, Karolinska Institutet, Solna, Sweden
| | - J Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,School of Basic and Medical Biosciences, King's College London, London, UK.,Molecular Neurology Research Program, University of Helsinki, and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - H Forssberg
- Department of Women and Children's Health, Neuropediatric Unit, Karolinska Institutet, Astrid Lindgren Children's Hospital, Solna, Sweden
| | - K Tammimies
- Department of Women and Children's Health, Center of Neurodevelopmental Disorders, Karolinska Institutet, Sweden and Centre for Psychiatry Research, Stockholm County Council, Stockholm, Sweden
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22
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De Barbieri Z, Fernández MA, Newbury DF, Villanueva P. Family aggregation of language impairment in an isolated Chilean population from Robinson Crusoe Island. INTERNATIONAL JOURNAL OF LANGUAGE & COMMUNICATION DISORDERS 2018; 53:643-655. [PMID: 29575355 DOI: 10.1111/1460-6984.12377] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 01/18/2018] [Accepted: 01/20/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND It has been reported that the inhabitants of the Chilean Robinson Crusoe Island have an increased frequency of specific language impairment (SLI) or developmental language disorder (DLD). AIMS To explore the familial aggregation of DLD in this community. METHODS & PROCEDURES We assessed the frequency of DLD amongst colonial children between the ages of 3 and 8;11 years (50 individuals from 45 nuclear families). Familial aggregation rates of language disorder were calculated by assessing all available first-degree relatives (n = 107, 77 parents, 25 siblings, five half-siblings) of the probands. OUTCOMES & RESULTS We found that 71% of the child population performed significantly below expected in measures of phonological production or expressive and receptive morphology. The majority of these children presented with severe expressive and/or receptive language difficulties. One-quarter of language-disordered probands primarily had phonological difficulties. Family members of affected probands experienced a higher risk of language disorder than those of typically developing probands. This increased risk was apparent regardless of non-verbal IQ. CONCLUSIONS & IMPLICATIONS The study substantiates the existence of a familial form of speech and language disorder on Robinson Crusoe Island. Furthermore, we find that the familiarity is stable regardless of non-verbal IQ, supporting the recent movement to reduce the importance of non-verbal IQ criterion in DLD diagnoses.
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Affiliation(s)
- Zulema De Barbieri
- Department of Speech language and Hearing Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - María Angélica Fernández
- Department of Speech language and Hearing Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Dianne F Newbury
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Pía Villanueva
- Department of Speech language and Hearing Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Institute of Biomedical Sciences, Human Genetics Division, Faculty of Medicine, Universidad de Chile, Santiago, Chile
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23
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Abstract
The post-genomic era is an exciting time for researchers interested in the biology of speech and language. Substantive advances in molecular methodologies have opened up entire vistas of investigation that were not previously possible, or in some cases even imagined. Speculations concerning the origins of human cognitive traits are being transformed into empirically addressable questions, generating specific hypotheses that can be explicitly tested using data collected from both the natural world and experimental settings. In this article, I discuss a number of promising lines of research in this area. For example, the field has begun to identify genes implicated in speech and language skills, including not just disorders but also the normal range of abilities. Such genes provide powerful entry points for gaining insights into neural bases and evolutionary origins, using sophisticated experimental tools from molecular neuroscience and developmental neurobiology. At the same time, sequencing of ancient hominin genomes is giving us an unprecedented view of the molecular genetic changes that have occurred during the evolution of our species. Synthesis of data from these complementary sources offers an opportunity to robustly evaluate alternative accounts of language evolution. Of course, this endeavour remains challenging on many fronts, as I also highlight in the article. Nonetheless, such an integrated approach holds great potential for untangling the complexities of the capacities that make us human.
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24
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Becker N, Vasconcelos M, Oliveira V, Santos FCD, Bizarro L, Almeida RMMD, Salles JFD, Carvalho MRS. Genetic and environmental risk factors for developmental dyslexia in children: systematic review of the last decade. Dev Neuropsychol 2017; 42:423-445. [PMID: 29068706 DOI: 10.1080/87565641.2017.1374960] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Despite advances in the characterization of developmental dyslexia (DD), several questions regarding the interplay between DD-susceptibility genes and environmental risk factors remain open. This systematic review aimed at answering the following questions: What has been the impact of new resources on the knowledge about DD? Which questions remain open? What is the investigative agenda for the short term? Forty-six studies were analyzed. Despite the growing literature on DD candidate genes, most studies have not been replicated. We found large effects on causative genes and smaller environmental contributions, involving maternal smoking during pregnancy, SES and the DYX1C1-1259C/G marker. Implications are discussed.
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Affiliation(s)
- Natalia Becker
- a Cognitive Neuropsychology Research Center (Neurocog), Department of Developmental and Personality Psychology , Post-Graduation Program in Psychology, Institute of Psychology, Universidade Federal do Rio Grande do Sul (UFRGS) , Porto Alegre , Rio Grande do Sul , Brazil
| | - Mailton Vasconcelos
- b Experimental Psychology, Neuroscience and Behavior Lab, Department of Developmental and Personality Psychology , Post-Graduation Program in Psychology, Institute of Psychology, Universidade Federal do Rio Grande do Sul (UFRGS) , Porto Alegre , Rio Grande do Sul , Brazil
| | - Vanessa Oliveira
- b Experimental Psychology, Neuroscience and Behavior Lab, Department of Developmental and Personality Psychology , Post-Graduation Program in Psychology, Institute of Psychology, Universidade Federal do Rio Grande do Sul (UFRGS) , Porto Alegre , Rio Grande do Sul , Brazil
| | - Fernanda Caroline Dos Santos
- c Departamento de Biologia Geral , Post-Graduation Program in Genetics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG) , Pampulha, Belo Horizonte , Minas Gerais , Brazil
| | - Lisiane Bizarro
- b Experimental Psychology, Neuroscience and Behavior Lab, Department of Developmental and Personality Psychology , Post-Graduation Program in Psychology, Institute of Psychology, Universidade Federal do Rio Grande do Sul (UFRGS) , Porto Alegre , Rio Grande do Sul , Brazil
| | - Rosa M M De Almeida
- b Experimental Psychology, Neuroscience and Behavior Lab, Department of Developmental and Personality Psychology , Post-Graduation Program in Psychology, Institute of Psychology, Universidade Federal do Rio Grande do Sul (UFRGS) , Porto Alegre , Rio Grande do Sul , Brazil
| | - Jerusa Fumagalli De Salles
- a Cognitive Neuropsychology Research Center (Neurocog), Department of Developmental and Personality Psychology , Post-Graduation Program in Psychology, Institute of Psychology, Universidade Federal do Rio Grande do Sul (UFRGS) , Porto Alegre , Rio Grande do Sul , Brazil
| | - Maria Raquel Santos Carvalho
- c Departamento de Biologia Geral , Post-Graduation Program in Genetics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG) , Pampulha, Belo Horizonte , Minas Gerais , Brazil
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25
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Deriziotis P, Fisher SE. Speech and Language: Translating the Genome. Trends Genet 2017; 33:642-656. [DOI: 10.1016/j.tig.2017.07.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 01/30/2023]
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26
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Abstract
Human genetic studies have been the driving force in bringing to light the underlying biology of psychiatric conditions. As these studies fill in the gaps in our knowledge of the mechanisms at play, we will be better equipped to design therapies in rational and targeted ways, or repurpose existing therapies in previously unanticipated ways. This review is intended for those unfamiliar with psychiatric genetics as a field and provides a primer on different modes of genetic variation, the technologies currently used to probe them, and concepts that provide context for interpreting the gene-phenotype relationship. Like other subfields in human genetics, psychiatric genetics is moving from microarray technology to sequencing-based approaches as barriers of cost and expertise are removed, and the ramifications of this transition are discussed here. A summary is then given of recent genetic discoveries in a number of neuropsychiatric conditions, with particular emphasis on neurodevelopmental conditions. The general impact of genetics on drug development has been to underscore the extensive etiological heterogeneity in seemingly cohesive diagnostic categories. Consequently, the path forward is not in therapies hoping to reach large swaths of patients sharing a clinically defined diagnosis, but rather in targeting patients belonging to specific "biotypes" defined through a combination of objective, quantifiable data, including genotype.
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Affiliation(s)
- Jacob J Michaelson
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA.
- Department of Biomedical Engineering, University of Iowa College of Engineering, Iowa City, IA, USA.
- Department of Communication Sciences and Disorders, University of Iowa College of Liberal Arts and Sciences, Iowa City, IA, USA.
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA.
- Genetics Cluster Initiative, University of Iowa, Iowa City, IA, USA.
- The DeLTA Center, University of Iowa, Iowa City, IA, USA.
- University of Iowa Informatics Initiative, University of Iowa, Iowa City, IA, USA.
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27
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Chen XS, Reader RH, Hoischen A, Veltman JA, Simpson NH, Francks C, Newbury DF, Fisher SE. Next-generation DNA sequencing identifies novel gene variants and pathways involved in specific language impairment. Sci Rep 2017; 7:46105. [PMID: 28440294 PMCID: PMC5404330 DOI: 10.1038/srep46105] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/08/2017] [Indexed: 12/22/2022] Open
Abstract
A significant proportion of children have unexplained problems acquiring proficient linguistic skills despite adequate intelligence and opportunity. Developmental language disorders are highly heritable with substantial societal impact. Molecular studies have begun to identify candidate loci, but much of the underlying genetic architecture remains undetermined. We performed whole-exome sequencing of 43 unrelated probands affected by severe specific language impairment, followed by independent validations with Sanger sequencing, and analyses of segregation patterns in parents and siblings, to shed new light on aetiology. By first focusing on a pre-defined set of known candidates from the literature, we identified potentially pathogenic variants in genes already implicated in diverse language-related syndromes, including ERC1, GRIN2A, and SRPX2. Complementary analyses suggested novel putative candidates carrying validated variants which were predicted to have functional effects, such as OXR1, SCN9A and KMT2D. We also searched for potential “multiple-hit” cases; one proband carried a rare AUTS2 variant in combination with a rare inherited haplotype affecting STARD9, while another carried a novel nonsynonymous variant in SEMA6D together with a rare stop-gain in SYNPR. On broadening scope to all rare and novel variants throughout the exomes, we identified biological themes that were enriched for such variants, including microtubule transport and cytoskeletal regulation.
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Affiliation(s)
- Xiaowei Sylvia Chen
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Rose H Reader
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Clinical Genetics, University of Maastricht, Maastricht, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Nuala H Simpson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Clyde Francks
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Dianne F Newbury
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.,Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
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28
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Bartha-Doering L, Regele S, Deuster D, Seidl R, Bogdanova N, Röpke A, Wieacker P, Am Zehnhoff-Dinnesen A. Intrafamilial phenotypic variability of Specific Language Impairment. BRAIN AND LANGUAGE 2016; 159:102-108. [PMID: 27388785 DOI: 10.1016/j.bandl.2016.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 06/08/2016] [Accepted: 06/15/2016] [Indexed: 06/06/2023]
Abstract
We investigated language functions in 32 members of a four generation family with several members affected by Specific Language Impairment with an extensive language test battery in order to determine the prevalence, overlap, and homogeneity of linguistic deficits within one pedigree. In sum, one fourth of all family members tested fulfilled the criteria of Specific Language Impairment. Despite of some similarities in language abilities, different combinations of language deficits were observed, and individual language profiles varied substantially. Thus, though there is a high prevalence of language deficits in this family which raises the likelihood of a genetic origin of these deficits, and though all affected study participants displayed selective linguistic deficits with normal non-verbal functioning, language testing showed considerable variance in overlap and homogeneity of linguistic deficits. Thus, even in one genetic population, an underlying linguistic disorder manifests itself in different language abilities to a variant degree.
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Affiliation(s)
- Lisa Bartha-Doering
- Department of Pediatrics and Adolescent Medicine, Medical University Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria.
| | - Sabrina Regele
- Department of Phoniatrics and Pedaudiology, University Hospital of Muenster, Kardinal-von-Galen Ring 10, 48149 Muenster, Germany.
| | - Dirk Deuster
- Department of Phoniatrics and Pedaudiology, University Hospital of Muenster, Kardinal-von-Galen Ring 10, 48149 Muenster, Germany.
| | - Rainer Seidl
- Department of Pediatrics and Adolescent Medicine, Medical University Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria.
| | - Nadja Bogdanova
- Institute of Human Genetics, University Hospital Muenster, Vesaliusweg 12-14, 48149 Muenster, Germany.
| | - Albrecht Röpke
- Institute of Human Genetics, University Hospital Muenster, Vesaliusweg 12-14, 48149 Muenster, Germany.
| | - Peter Wieacker
- Institute of Human Genetics, University Hospital Muenster, Vesaliusweg 12-14, 48149 Muenster, Germany.
| | - Antoinette Am Zehnhoff-Dinnesen
- Department of Phoniatrics and Pedaudiology, University Hospital of Muenster, Kardinal-von-Galen Ring 10, 48149 Muenster, Germany.
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29
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Nudel R. An investigation of NFXL1, a gene implicated in a study of specific language impairment. J Neurodev Disord 2016; 8:13. [PMID: 27053962 PMCID: PMC4822306 DOI: 10.1186/s11689-016-9146-9] [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: 02/03/2016] [Accepted: 03/30/2016] [Indexed: 11/10/2022] Open
Abstract
Background A recent study identified NFXL1 as a candidate gene for specific language impairment. The protein encoded by this gene is predicted to be a transcription factor based on domain similarities with NFX1, a repressor of HLA class II genes, which have themselves been implicated in specific language impairment. However, there is very little literature on the function of NFXL1. Methods This report describes a study of NFXL1 expression in several human tissues and an investigation of differential expression in several specific brain regions through quantitative PCR as well as a study of the protein’s sub-cellular localization in HEK cells and SH-SY5Y cells through immunofluorescence. Results The NFXL1 transcript was found in all investigated tissues. In the brain, a high level of NFXL1 expression was found in the cerebellum. An analysis of the sub-cellular localization of the protein showed a cytoplasmic pattern in the investigated cells. Conclusions The NFXL1 transcript was present in samples from different tissues; in the brain, a high expression level was found in a region implicated in some language-related pathologies. NFXL1 did not show nuclear localization, suggesting that, if it regulates transcription, certain conditions may be required for it to translocate to the nucleus. Electronic supplementary material The online version of this article (doi:10.1186/s11689-016-9146-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ron Nudel
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
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30
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Kornilov SA, Rakhlin N, Koposov R, Lee M, Yrigollen C, Caglayan AO, Magnuson JS, Mane S, Chang JT, Grigorenko EL. Genome-Wide Association and Exome Sequencing Study of Language Disorder in an Isolated Population. Pediatrics 2016; 137:peds.2015-2469. [PMID: 27016271 PMCID: PMC4811310 DOI: 10.1542/peds.2015-2469] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/26/2016] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND AND OBJECTIVE Developmental language disorder (DLD) is a highly prevalent neurodevelopmental disorder associated with negative outcomes in different domains; the etiology of DLD is unknown. To investigate the genetic underpinnings of DLD, we performed genome-wide association and whole exome sequencing studies in a geographically isolated population with a substantially elevated prevalence of the disorder (ie, the AZ sample). METHODS DNA samples were collected from 359 individuals for the genome-wide association study and from 12 severely affected individuals for whole exome sequencing. Multifaceted phenotypes, representing major domains of expressive language functioning, were derived from collected speech samples. RESULTS Gene-based analyses revealed a significant association between SETBP1 and complexity of linguistic output (P = 5.47 × 10(-7)). The analysis of exome variants revealed coding sequence variants in 14 genes, most of which play a role in neural development. Targeted enrichment analysis implicated myocyte enhancer factor-2 (MEF2)-regulated genes in DLD in the AZ population. The main findings were successfully replicated in an independent cohort of children at risk for related disorders (n = 372). CONCLUSIONS MEF2-regulated pathways were identified as potential candidate pathways in the etiology of DLD. Several genes (including the candidate SETBP1 and other MEF2-related genes) seem to jointly influence certain, but not all, facets of the DLD phenotype. Even when genetic and environmental diversity is reduced, DLD is best conceptualized as etiologically complex. Future research should establish whether the signals detected in the AZ population can be replicated in other samples and languages and provide further characterization of the identified pathway.
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Affiliation(s)
- Sergey A. Kornilov
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut;,Department of Psychology, University of Connecticut, Storrs, Connecticut;,Haskins Laboratories, New Haven, Connecticut;,Department of Psychology, Moscow State University, Moscow, Russia;,Department of Psychology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Natalia Rakhlin
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut;,Department of Communication Sciences and Disorders, Wayne State University, Detroit, Michigan
| | - Roman Koposov
- Regional Centre for Child and Youth Mental Health and Child Welfare, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maria Lee
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut
| | - Carolyn Yrigollen
- The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ahmet Okay Caglayan
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut;,Department of Medical Genetics, Istanbul Bilim University, Istanbul, Turkey; and
| | - James S. Magnuson
- Department of Psychology, University of Connecticut, Storrs, Connecticut;,Haskins Laboratories, New Haven, Connecticut
| | - Shrikant Mane
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut
| | - Joseph T. Chang
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut
| | - Elena L. Grigorenko
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut;,Haskins Laboratories, New Haven, Connecticut;,Department of Psychology, Saint Petersburg State University, Saint Petersburg, Russia;,Moscow State University for Psychology and Education, Moscow, Russia
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31
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Mozzi A, Forni D, Clerici M, Pozzoli U, Mascheretti S, Guerini FR, Riva S, Bresolin N, Cagliani R, Sironi M. The evolutionary history of genes involved in spoken and written language: beyond FOXP2. Sci Rep 2016; 6:22157. [PMID: 26912479 PMCID: PMC4766443 DOI: 10.1038/srep22157] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/08/2016] [Indexed: 12/14/2022] Open
Abstract
Humans possess a communication system based on spoken and written language. Other animals can learn vocalization by imitation, but this is not equivalent to human language. Many genes were described to be implicated in language impairment (LI) and developmental dyslexia (DD), but their evolutionary history has not been thoroughly analyzed. Herein we analyzed the evolution of ten genes involved in DD and LI. Results show that the evolutionary history of LI genes for mammals and aves was comparable in vocal-learner species and non-learners. For the human lineage, several sites showing evidence of positive selection were identified in KIAA0319 and were already present in Neanderthals and Denisovans, suggesting that any phenotypic change they entailed was shared with archaic hominins. Conversely, in FOXP2, ROBO1, ROBO2, and CNTNAP2 non-coding changes rose to high frequency after the separation from archaic hominins. These variants are promising candidates for association studies in LI and DD.
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Affiliation(s)
- Alessandra Mozzi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
| | - Diego Forni
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, 20090 Milan, Italy
- Don C. Gnocchi Foundation ONLUS, IRCCS, 20100 Milan, Italy
| | - Uberto Pozzoli
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
| | - Sara Mascheretti
- Child Psychopathology Unit, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy
| | | | - Stefania Riva
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
| | - Nereo Bresolin
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
- Dino Ferrari Centre, Department of Physiopathology and Transplantation, University of Milan, Fondazione Ca’ Granda IRCCS Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Rachele Cagliani
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
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32
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Abstract
Language is a defining characteristic of the human species, but its foundations remain mysterious. Heritable disorders offer a gateway into biological underpinnings, as illustrated by the discovery that FOXP2 disruptions cause a rare form of speech and language impairment. The genetic architecture underlying language-related disorders is complex, and although some progress has been made, it has proved challenging to pinpoint additional relevant genes with confidence. Next-generation sequencing and genome-wide association studies are revolutionizing understanding of the genetic bases of other neurodevelopmental disorders, like autism and schizophrenia, and providing fundamental insights into the molecular networks crucial for typical brain development. We discuss how a similar genomic perspective, brought to the investigation of language-related phenotypes, promises to yield equally informative discoveries. Moreover, we outline how follow-up studies of genetic findings using cellular systems and animal models can help to elucidate the biological mechanisms involved in the development of brain circuits supporting language.
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Affiliation(s)
- Sarah A Graham
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands;
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands; .,Donders Institute for Brain, Cognition and Behavior, Radboud University, 6525 EN Nijmegen, The Netherlands;
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33
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Correction: Exome Sequencing in an Admixed Isolated Population Indicates NFXL1 Variants Confer a Risk for Specific Language Impairment. PLoS Genet 2015; 11:e1005336. [PMID: 26114769 PMCID: PMC4483266 DOI: 10.1371/journal.pgen.1005336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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