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Pedicone C, Weitzman SA, Renton AE, Goate AM. Unraveling the complex role of MAPT-containing H1 and H2 haplotypes in neurodegenerative diseases. Mol Neurodegener 2024; 19:43. [PMID: 38812061 PMCID: PMC11138017 DOI: 10.1186/s13024-024-00731-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 05/11/2024] [Indexed: 05/31/2024] Open
Abstract
A ~ 1 Mb inversion polymorphism exists within the 17q21.31 locus of the human genome as direct (H1) and inverted (H2) haplotype clades. This inversion region demonstrates high linkage disequilibrium, but the frequency of each haplotype differs across ancestries. While the H1 haplotype exists in all populations and shows a normal pattern of genetic variability and recombination, the H2 haplotype is enriched in European ancestry populations, is less frequent in African ancestry populations, and nearly absent in East Asian ancestry populations. H1 is a known risk factor for several neurodegenerative diseases, and has been associated with many other traits, suggesting its importance in cellular phenotypes of the brain and entire body. Conversely, H2 is protective for these diseases, but is associated with predisposition to recurrent microdeletion syndromes and neurodevelopmental disorders such as autism. Many single nucleotide variants and copy number variants define H1/H2 haplotypes and sub-haplotypes, but identifying the causal variant(s) for specific diseases and phenotypes is complex due to the extended linkage equilibrium. In this review, we assess the current knowledge of this inversion region regarding genomic structure, gene expression, cellular phenotypes, and disease association. We discuss recent discoveries and challenges, evaluate gaps in knowledge, and highlight the importance of understanding the effect of the 17q21.31 haplotypes to promote advances in precision medicine and drug discovery for several diseases.
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Affiliation(s)
- Chiara Pedicone
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah A Weitzman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alan E Renton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alison M Goate
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Rawat P, Sehar U, Bisht J, Selman A, Culberson J, Reddy PH. Phosphorylated Tau in Alzheimer's Disease and Other Tauopathies. Int J Mol Sci 2022; 23:12841. [PMID: 36361631 PMCID: PMC9654278 DOI: 10.3390/ijms232112841] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 07/29/2023] Open
Abstract
Alzheimer's disease (AD) is the leading cause of dementia in elderly people. Amyloid beta (Aβ) deposits and neurofibrillary tangles are the major pathological features in an Alzheimer's brain. These proteins are highly expressed in nerve cells and found in most tissues. Tau primarily provides stabilization to microtubules in the part of axons and dendrites. However, tau in a pathological state becomes hyperphosphorylated, causing tau dysfunction and leading to synaptic impairment and degeneration of neurons. This article presents a summary of the role of tau, phosphorylated tau (p-tau) in AD, and other tauopathies. Tauopathies, including Pick's disease, frontotemporal dementia, corticobasal degeneration, Alzheimer's disease, argyrophilic grain disease, progressive supranuclear palsy, and Huntington's disease, are the result of misprocessing and accumulation of tau within the neuronal and glial cells. This article also focuses on current research on the post-translational modifications and genetics of tau, tau pathology, the role of tau in tauopathies and the development of new drugs targeting p-tau, and the therapeutics for treating and possibly preventing tauopathies.
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Affiliation(s)
- Priyanka Rawat
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Ujala Sehar
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Jasbir Bisht
- Department of Pediatrics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Ashley Selman
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - John Culberson
- Department of Family Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - P. Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Nutritional Sciences Department, College Human Sciences, Texas Tech University, Lubbock, TX 79409, USA
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Neurology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Public Health, Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Speech, Language, and Hearing Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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3
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Harerimana NV, Goate AM, Bowles KR. The influence of 17q21.31 and APOE genetic ancestry on neurodegenerative disease risk. Front Aging Neurosci 2022; 14:1021918. [DOI: 10.3389/fnagi.2022.1021918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Advances in genomic research over the last two decades have greatly enhanced our knowledge concerning the genetic landscape and pathophysiological processes involved in multiple neurodegenerative diseases. However, current insights arise almost exclusively from studies on individuals of European ancestry. Despite this, studies have revealed that genetic variation differentially impacts risk for, and clinical presentation of neurodegenerative disease in non-European populations, conveying the importance of ancestry in predicting disease risk and understanding the biological mechanisms contributing to neurodegeneration. We review the genetic influence of two important disease-associated loci, 17q21.31 (the “MAPT locus”) and APOE, to neurodegenerative disease risk in non-European populations, touching on global population differences and evolutionary genetics by ancestry that may underlie some of these differences. We conclude there is a need to increase representation of non-European ancestry individuals in genome-wide association studies (GWAS) and biomarker analyses in order to help resolve existing disparities in understanding risk for, diagnosis of, and treatment for neurodegenerative diseases in diverse populations.
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Mosley TJ, Johnston HR, Cutler DJ, Zwick ME, Mulle JG. Sex-specific recombination patterns predict parent of origin for recurrent genomic disorders. BMC Med Genomics 2021; 14:154. [PMID: 34107974 PMCID: PMC8190997 DOI: 10.1186/s12920-021-00999-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 06/02/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Structural rearrangements of the genome, which generally occur during meiosis and result in large-scale (> 1 kb) copy number variants (CNV; deletions or duplications ≥ 1 kb), underlie genomic disorders. Recurrent pathogenic CNVs harbor similar breakpoints in multiple unrelated individuals and are primarily formed via non-allelic homologous recombination (NAHR). Several pathogenic NAHR-mediated recurrent CNV loci demonstrate biases for parental origin of de novo CNVs. However, the mechanism underlying these biases is not well understood. METHODS We performed a systematic, comprehensive literature search to curate parent of origin data for multiple pathogenic CNV loci. Using a regression framework, we assessed the relationship between parental CNV origin and the male to female recombination rate ratio. RESULTS We demonstrate significant association between sex-specific differences in meiotic recombination and parental origin biases at these loci (p = 1.07 × 10-14). CONCLUSIONS Our results suggest that parental origin of CNVs is largely influenced by sex-specific recombination rates and highlight the need to consider these differences when investigating mechanisms that cause structural variation.
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Affiliation(s)
- Trenell J Mosley
- Graduate Program in Genetics and Molecular Biology, Laney Graduate School, Emory University, 201 Dowman Drive, Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
| | - H Richard Johnston
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
- Emory Integrated Computational Core, Emory University, 101 Woodruff Circle, Atlanta, GA, 30322, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University School of Medicine, 2015 Uppergate Drive, Atlanta, GA, 30322, USA
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA.
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA.
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5
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H1/H2 MAPT haplotype and Parkinson's disease in Mexican mestizo population. Neurosci Lett 2018; 690:210-213. [PMID: 30339920 DOI: 10.1016/j.neulet.2018.10.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/22/2018] [Accepted: 10/15/2018] [Indexed: 11/23/2022]
Abstract
Parkinson's disease (PD) is characterized by bradykinesia, resting tremor, rigidity and postural instability as well as early symptoms. Previous studies that evaluated the association between H1/H2 MAPT haplotype and PD were mostly conducted in European populations in which the H1 haplotype was a reported risk factor for PD. Despite those findings, some studies have suggested that the association may be ethnically dependent. Since studies conducted in Latin American population have been scarce, we genotyped the H1/H2 MAPT haplotype in Mexican mestizo population as part of a PD case-control study. DNA was extracted from peripheral blood leucocytes in 108 cases and 108 controls and detection of the H1/H2 haplotypes was achieved by determining the MAPT_238 bp deletion/insertion variant at intron 9 through end-point PCR followed by visual 3% agarose gel electrophoresis interpretation. We observed no-association between genotypes and PD risk [OR/CI (Odds ratio/95% Confidence Interval) of 1.60 (0.78-3.29) for H1/H2 genotype and 2.26 (0.20-25.78) for H2/H2]. No-association was maintained when stratifying our groups by central (p = 0.27) and northern regions (p = 0.70). Our data suggest that H1/H2 MAPT haplotype is not a risk factor to PD in our population.
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Alfonso-Sánchez MA, Espinosa I, Gómez-Pérez L, Poveda A, Rebato E, Peña JA. Tau haplotypes support the Asian ancestry of the Roma population settled in the Basque Country. Heredity (Edinb) 2017; 120:91-99. [PMID: 29225349 DOI: 10.1038/s41437-017-0001-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/12/2017] [Accepted: 08/14/2017] [Indexed: 01/29/2023] Open
Abstract
We examined tau haplotype frequencies in two different ethnical groups from the Basque Country (BC): Roma people and residents of European ancestry (general population). In addition, we analyzed the spatial distribution of tau haplotypes in Eurasian populations to explore the genetic affinities of the Romani groups living in Europe in a broader scope. The 17q21.31 genomic region was characterized through the genotyping of two diagnostic single nucleotide polymorphisms, SNPs (rs10514879 and rs199451), which allow the identification of H1 and H2 haplotypes. A significant heterozygous deficit was detected in the Romani for rs10514879. The H2 haplotype frequency proved to be more than twice in the BC general population (0.283) than in the Roma people (0.127). In contrast, H2 frequency proved to be very similar between Basque and Hungarian Romani, and similar to the H2 frequencies found in northwestern India and Pakistan as well. Several statistical analyses unveiled genetic structuring for the MAPT diversity, mirrored in a significant association between geography and genetic distances, with an upward trend of H2 haplotype frequencies from Asia to Europe. Yet, Roma samples did not fit into this general spatial patterning because of their discrepancy between geographical position and H2 frequency. Despite the long spatial coexistence in the Basque region between the residents of European ancestry and the Roma, the latter have preserved their Asian genetic ancestry. Bearing in mind the lack of geographical barriers between both ethnical groups, these findings support the notion that sociocultural mores might promote assortative matings in human populations.
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Affiliation(s)
- Miguel A Alfonso-Sánchez
- Departamento de Genética, Antropología Física y Fisiología Animal, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Bilbao, 48080, Spain
| | - Ibone Espinosa
- Departamento de Genética, Antropología Física y Fisiología Animal, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Bilbao, 48080, Spain
| | - Luis Gómez-Pérez
- Departamento de Genética, Antropología Física y Fisiología Animal, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Bilbao, 48080, Spain
| | - Alaitz Poveda
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Lund University, Malmö, SE-205 02, Sweden
| | - Esther Rebato
- Departamento de Genética, Antropología Física y Fisiología Animal, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Bilbao, 48080, Spain
| | - Jose A Peña
- Departamento de Genética, Antropología Física y Fisiología Animal, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Bilbao, 48080, Spain.
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7
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Trampush JW, Yang MLZ, Yu J, Knowles E, Davies G, Liewald DC, Starr JM, Djurovic S, Melle I, Sundet K, Christoforou A, Reinvang I, DeRosse P, Lundervold AJ, Steen VM, Espeseth T, Räikkönen K, Widen E, Palotie A, Eriksson JG, Giegling I, Konte B, Roussos P, Giakoumaki S, Burdick KE, Payton A, Ollier W, Horan M, Chiba-Falek O, Attix DK, Need AC, Cirulli ET, Voineskos AN, Stefanis NC, Avramopoulos D, Hatzimanolis A, Arking DE, Smyrnis N, Bilder RM, Freimer NA, Cannon TD, London E, Poldrack RA, Sabb FW, Congdon E, Conley ED, Scult MA, Dickinson D, Straub RE, Donohoe G, Morris D, Corvin A, Gill M, Hariri AR, Weinberger DR, Pendleton N, Bitsios P, Rujescu D, Lahti J, Le Hellard S, Keller MC, Andreassen OA, Deary IJ, Glahn DC, Malhotra AK, Lencz T. GWAS meta-analysis reveals novel loci and genetic correlates for general cognitive function: a report from the COGENT consortium. Mol Psychiatry 2017; 22:336-345. [PMID: 28093568 PMCID: PMC5322272 DOI: 10.1038/mp.2016.244] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/30/2016] [Accepted: 11/03/2016] [Indexed: 01/12/2023]
Abstract
The complex nature of human cognition has resulted in cognitive genomics lagging behind many other fields in terms of gene discovery using genome-wide association study (GWAS) methods. In an attempt to overcome these barriers, the current study utilized GWAS meta-analysis to examine the association of common genetic variation (~8M single-nucleotide polymorphisms (SNP) with minor allele frequency ⩾1%) to general cognitive function in a sample of 35 298 healthy individuals of European ancestry across 24 cohorts in the Cognitive Genomics Consortium (COGENT). In addition, we utilized individual SNP lookups and polygenic score analyses to identify genetic overlap with other relevant neurobehavioral phenotypes. Our primary GWAS meta-analysis identified two novel SNP loci (top SNPs: rs76114856 in the CENPO gene on chromosome 2 and rs6669072 near LOC105378853 on chromosome 1) associated with cognitive performance at the genome-wide significance level (P<5 × 10-8). Gene-based analysis identified an additional three Bonferroni-corrected significant loci at chromosomes 17q21.31, 17p13.1 and 1p13.3. Altogether, common variation across the genome resulted in a conservatively estimated SNP heritability of 21.5% (s.e.=0.01%) for general cognitive function. Integration with prior GWAS of cognitive performance and educational attainment yielded several additional significant loci. Finally, we found robust polygenic correlations between cognitive performance and educational attainment, several psychiatric disorders, birth length/weight and smoking behavior, as well as a novel genetic association to the personality trait of openness. These data provide new insight into the genetics of neurocognitive function with relevance to understanding the pathophysiology of neuropsychiatric illness.
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Affiliation(s)
- J W Trampush
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY, USA
| | - M L Z Yang
- Institute of Mental Health, Singapore, Singapore
| | - J Yu
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY, USA,Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA
| | - E Knowles
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - G Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - D C Liewald
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - J M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - S Djurovic
- Department of Medical Genetics, Oslo University Hospital, University of Bergen, Oslo, Norway,NORMENT, K.G. Jebsen Centre for Psychosis Research, University of Bergen, Bergen, Norway
| | - I Melle
- NORMENT, K.G. Jebsen Centre for Psychosis Research, University of Bergen, Bergen, Norway,Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - K Sundet
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway,Department of Psychology, University of Oslo, Oslo, Norway
| | - A Christoforou
- NORMENT, K.G. Jebsen Centre for Psychosis Research, University of Bergen, Bergen, Norway,Dr Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - I Reinvang
- Department of Psychology, University of Oslo, Oslo, Norway
| | - P DeRosse
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY, USA,Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA
| | - A J Lundervold
- Department of Biological and Medical Psychology, University of Bergen, Bergen, Norway
| | - V M Steen
- NORMENT, K.G. Jebsen Centre for Psychosis Research, University of Bergen, Bergen, Norway,Dr Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - T Espeseth
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway,Department of Psychology, University of Oslo, Oslo, Norway
| | - K Räikkönen
- Institute of Behavioural Sciences, University of Helsinki, Helsinki, Finland
| | - E Widen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - A Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK,Department of Medical Genetics, University of Helsinki and University Central Hospital, Helsinki, Finland
| | - J G Eriksson
- National Institute for Health and Welfare, Helsinki, Finland,Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Finland,Helsinki University Central Hospital, Unit of General Practice, Helsinki, Finland,Folkhälsan Research Centre, Helsinki, Finland
| | - I Giegling
- Department of Psychiatry, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - B Konte
- Department of Psychiatry, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - P Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Mental Illness Research, Education, and Clinical Center (VISN 3), James J. Peters VA Medical Center, Bronx, NY, USA
| | - S Giakoumaki
- Department of Psychology, University of Crete, Rethymno, Greece
| | - K E Burdick
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Mental Illness Research, Education, and Clinical Center (VISN 3), James J. Peters VA Medical Center, Bronx, NY, USA
| | - A Payton
- Manchester Centre for Audiology and Deafness, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK,Division of Evolution and Genomic Sciences, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - W Ollier
- Centre for Integrated Genomic Medical Research, Institute of Population Health, University of Manchester, Manchester, UK
| | - M Horan
- Manchester Medical School, Institute of Brain, Behaviour, and Mental Health, University of Manchester, Manchester, UK
| | - O Chiba-Falek
- Department of Neurology, Bryan Alzheimer's Disease Research Center, and Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
| | - D K Attix
- Department of Neurology, Bryan Alzheimer's Disease Research Center, and Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA,Division of Medical Psychology, Department of Neurology, Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC, USA
| | - A C Need
- Division of Brain Sciences, Department of Medicine, Imperial College, London, UK
| | - E T Cirulli
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - A N Voineskos
- Campbell Family Mental Health Institute, Centre for Addiction and Mental Health, University of Toronto, Toronto, ON, Canada
| | - N C Stefanis
- Department of Psychiatry, University of Athens School of Medicine, Eginition Hospital, Athens, Greece,University Mental Health Research Institute, Athens, Greece,Neurobiology Research Institute, Theodor Theohari Cozzika Foundation, Athens, Greece
| | - D Avramopoulos
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Department of Psychiatry and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - A Hatzimanolis
- Department of Psychiatry, University of Athens School of Medicine, Eginition Hospital, Athens, Greece,University Mental Health Research Institute, Athens, Greece,Neurobiology Research Institute, Theodor Theohari Cozzika Foundation, Athens, Greece
| | - D E Arking
- Department of Psychiatry and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - N Smyrnis
- Department of Psychiatry, University of Athens School of Medicine, Eginition Hospital, Athens, Greece,University Mental Health Research Institute, Athens, Greece
| | - R M Bilder
- UCLA Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA, USA
| | - N A Freimer
- UCLA Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA, USA
| | - T D Cannon
- Department of Psychology, Yale University, New Haven, CT, USA
| | - E London
- UCLA Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA, USA
| | - R A Poldrack
- Department of Psychology, Stanford University, Palo Alto, CA, USA
| | - F W Sabb
- Robert and Beverly Lewis Center for Neuroimaging, University of Oregon, Eugene, OR, USA
| | - E Congdon
- UCLA Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA, USA
| | | | - M A Scult
- Department of Psychology & Neuroscience, Laboratory of NeuroGenetics, Duke University, Durham, NC, USA
| | - D Dickinson
- Clinical and Translational Neuroscience Branch, Intramural Research Program, National Institute of Mental Health, National Institute of Health, Bethesda, MD, USA
| | - R E Straub
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - G Donohoe
- Department of Psychology, National University of Ireland, Galway, Ireland
| | - D Morris
- Department of Psychiatry, Neuropsychiatric Genetics Research Group, Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - A Corvin
- Department of Psychiatry, Neuropsychiatric Genetics Research Group, Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - M Gill
- Department of Psychiatry, Neuropsychiatric Genetics Research Group, Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - A R Hariri
- Department of Psychology & Neuroscience, Laboratory of NeuroGenetics, Duke University, Durham, NC, USA
| | - D R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - N Pendleton
- Centre for Integrated Genomic Medical Research, Institute of Population Health, University of Manchester, Manchester, UK,Manchester Medical School, Institute of Brain, Behaviour, and Mental Health, University of Manchester, Manchester, UK
| | - P Bitsios
- Department of Psychiatry and Behavioral Sciences, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - D Rujescu
- Department of Psychiatry, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - J Lahti
- Institute of Behavioural Sciences, University of Helsinki, Helsinki, Finland,Helsinki Collegium for Advanced Studies, University of Helsinki, Helsinki, Finland
| | - S Le Hellard
- NORMENT, K.G. Jebsen Centre for Psychosis Research, University of Bergen, Bergen, Norway,Dr Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - M C Keller
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA
| | - O A Andreassen
- NORMENT, K.G. Jebsen Centre for Psychosis Research, University of Bergen, Bergen, Norway,Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - I J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - D C Glahn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - A K Malhotra
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY, USA,Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA,Department of Psychiatry, Hofstra Northwell School of Medicine, Hempstead, NY, USA
| | - T Lencz
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY, USA,Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA,Department of Psychiatry, Hofstra Northwell School of Medicine, Hempstead, NY, USA,Division of Psychiatry Research, Zucker Hillside Hospital, 75-59 263rd Street, Glen Oaks, NY 11004, USA. E-mail:
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8
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An exploratory study of predisposing genetic factors for DiGeorge/velocardiofacial syndrome. Sci Rep 2017; 7:40031. [PMID: 28059126 PMCID: PMC5216377 DOI: 10.1038/srep40031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 12/01/2016] [Indexed: 12/13/2022] Open
Abstract
DiGeorge/velocardiofacial syndrome (DGS/VCFS) is a disorder caused by a 22q11.2 deletion mediated by non-allelic homologous recombination (NAHR) between low-copy repeats (LCRs). We have evaluated the role of LCR22 genomic architecture and PRDM9 variants as DGS/VCFS predisposing factors. We applied FISH using fosmid probes on chromatin fibers to analyze the number of tandem repeat blocks in LCR22 in two DGS/VCFS fathers-of-origin with proven 22q11.2 NAHR susceptibility. Results revealed copy number variations (CNVs) of L9 and K3 fosmids in these individuals compared to controls. The total number of L9 and K3 copies was also characterized using droplet digital PCR (ddPCR). Although we were unable to confirm variations, we detected an additional L9 amplicon corresponding to a pseudogene. Moreover, none of the eight DGS/VCFS parents-of-origin was heterozygote for the inv(22)(q11.2) haplotype. PRDM9 sequencing showed equivalent allelic distributions between DGS/VCFS parents-of-origin and controls, although a new PRDM9 allele (L50) was identified in one case. Our results support the hypothesis that LCR22s variations influences 22q11.2 NAHR events, however further studies are needed to confirm this association and clarify the contribution of pseudogenes and rare PDRM9 alleles to NAHR susceptibility.
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Alves JM, Lima AC, Pais IA, Amir N, Celestino R, Piras G, Monne M, Comas D, Heutink P, Chikhi L, Amorim A, Lopes AM. Reassessing the Evolutionary History of the 17q21 Inversion Polymorphism. Genome Biol Evol 2015; 7:3239-48. [PMID: 26560338 PMCID: PMC4700947 DOI: 10.1093/gbe/evv214] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A polymorphic inversion that lies on chromosome 17q21 comprises two major haplotype families (H1 and H2) that not only differ in orientation but also in copy-number. Although the processes driving the spread of the inversion-associated lineage (H2) in humans remain unclear, a selective advantage has been proposed for one of its subtypes. Here, we genotyped a large panel of individuals from previously overlooked populations using a custom array with a unique panel of H2-specific single nucleotide polymorphisms and found a patchy distribution of H2 haplotypes in Africa, with North Africans displaying a higher frequency of inverted subtypes, when compared with Sub-Saharan groups. Interestingly, North African H2s were found to be closer to "non-African" chromosomes further supporting that these populations may have diverged more recently from groups outside Africa. Our results uncovered higher diversity within the H2 family than previously described, weakening the hypothesis of a strong selective sweep on all inverted chromosomes and suggesting a rather complex evolutionary history at this locus.
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Affiliation(s)
- Joao M Alves
- Doctoral Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Portugal Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal Instituto de Patologia e Imunologia Molecular da Universidade do Porto-IPATIMUP, Portugal Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal Present address: Department of Biochemistry, Genetics and Immunology and Institute of Biomedical Research of Vigo (IBIV), University of Vigo, Vigo, Spain
| | - Ana C Lima
- Doctoral Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Portugal Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal Instituto de Patologia e Imunologia Molecular da Universidade do Porto-IPATIMUP, Portugal Department of Genetics, Washington University School of Medicine, St. Louis
| | - Isa A Pais
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
| | - Nadir Amir
- Laboratoire de Biochimie Appliquée, Faculté des Sciences de la Nature et de la Vie, Université Abedrrahmane Mira de Bejaia, Algerie
| | - Ricardo Celestino
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal Instituto de Patologia e Imunologia Molecular da Universidade do Porto-IPATIMUP, Portugal School of Allied Health Technologies, Polytechnic of Porto, Porto, Portugal
| | - Giovanna Piras
- Department of Hematology, Centro di Diagnostica Biomoleculare et Citogenetica Emato-Oncologica, San Francesco Hospital-ASL, Nuoro, Italy
| | - Maria Monne
- Department of Hematology, Centro di Diagnostica Biomoleculare et Citogenetica Emato-Oncologica, San Francesco Hospital-ASL, Nuoro, Italy
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Peter Heutink
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal CNRS (Centre National de la Recherche Scientifique), Université Paul Sabatier, École Nationale de Formation Agronomique, Unité Mixte de Recherche 5174 EDB (Laboratoire Évolution & Diversit Biologique), Toulouse, France
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal Instituto de Patologia e Imunologia Molecular da Universidade do Porto-IPATIMUP, Portugal Faculdade de Ciências da Universidade do Porto, Portugal
| | - Alexandra M Lopes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal Instituto de Patologia e Imunologia Molecular da Universidade do Porto-IPATIMUP, Portugal
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Abstract
Polymorphic inversions are a type of structural variants that are difficult to analyze owing to their balanced nature and the location of breakpoints within complex repeated regions. So far, only a handful of inversions have been studied in detail in humans and current knowledge about their possible functional effects is still limited. However, inversions have been related to phenotypic changes and adaptation in multiple species. In this review, we summarize the evidences of the functional impact of inversions in the human genome. First, given that inversions have been shown to inhibit recombination in heterokaryotes, chromosomes displaying different orientation are expected to evolve independently and this may lead to distinct gene-expression patterns. Second, inversions have a role as disease-causing mutations both by directly affecting gene structure or regulation in different ways, and by predisposing to other secondary arrangements in the offspring of inversion carriers. Finally, several inversions show signals of being selected during human evolution. These findings illustrate the potential of inversions to have phenotypic consequences also in humans and emphasize the importance of their inclusion in genome-wide association studies.
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Caillet-Boudin ML, Buée L, Sergeant N, Lefebvre B. Regulation of human MAPT gene expression. Mol Neurodegener 2015; 10:28. [PMID: 26170022 PMCID: PMC4499907 DOI: 10.1186/s13024-015-0025-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/30/2015] [Indexed: 12/12/2022] Open
Abstract
The number of known pathologies involving deregulated Tau expression/metabolism is increasing. Indeed, in addition to tauopathies, which comprise approximately 30 diseases characterized by neuronal aggregation of hyperphosphorylated Tau in brain neurons, this protein has also been associated with various other pathologies such as cancer, inclusion body myositis, and microdeletion/microduplication syndromes, suggesting its possible function in peripheral tissues. In addition to Tau aggregation, Tau deregulation can occur at the expression and/or splicing levels, as has been clearly demonstrated in some of these pathologies. Here, we aim to review current knowledge regarding the regulation of human MAPT gene expression at the DNA and RNA levels to provide a better understanding of its possible deregulation. Several aspects, including repeated motifs, CpG island/methylation, and haplotypes at the DNA level, as well as the key regions involved in mRNA expression and stability and the splicing patterns of different mRNA isoforms at the RNA level, will be discussed.
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Affiliation(s)
| | - Luc Buée
- Univ. Lille, UMR-S 1172, Inserm, CHU, 59000, Lille, France
| | | | - Bruno Lefebvre
- Univ. Lille, UMR-S 1172, Inserm, CHU, 59000, Lille, France
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Vergés L, Molina O, Geán E, Vidal F, Blanco J. Deletions and duplications of the 22q11.2 region in spermatozoa from DiGeorge/velocardiofacial fathers. Mol Cytogenet 2014; 7:86. [PMID: 25435913 PMCID: PMC4247602 DOI: 10.1186/s13039-014-0086-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 11/04/2014] [Indexed: 11/12/2022] Open
Abstract
Background DiGeorge/velocardiofacial syndrome (DGS/VCFS) is the most common deletion syndrome in humans. Low copy repeats flanking the 22q11.2 region confer a substrate for non-allelic homologous recombination (NAHR) events leading to rearrangements. This study sought to identify DGS/VCFS fathers with increased susceptibility to deletions and duplications at the 22q11.2 region in spermatozoa and to assess the particular contribution of intra-chromatid and/or inter-chromatid NAHR. Semen samples from nine DGS/VCFS fathers were analyzed by triple-color FISH using a probe combination that discriminated between normal, deleted and duplicated genotypes. Microsatellite analysis were performed in the parents and the affected children to determine the parental origin of the deleted chromosome 22. Results A significant increase in 22q11.2 deletions was observed in the sperm of two out of nine DGS/VCFS fathers (odds ratio 2.03-fold, P < 0.01), and in both cases the deletion in the offspring was transmitted by the father. Patients with significant increases in sperm anomalies presented a disturbed deletion:duplication 1:1 ratio (P < 0.01). Conclusions Altogether, results support that intra-chromatid NAHR is the mechanism responsible for the higher rate of sperm deletions, which is directly related to the transmission of the deleted chromosome 22 to offspring. Accordingly, the screening of sperm anomalies in the 22q11.2 region should be taken into account in the genetic counseling of DGS/VCFS families.
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Affiliation(s)
- Laia Vergés
- Unitat de Biologia Cellular (Facultat de Biociències). Universitat Autònoma de Barcelona, 08193-Bellaterra, Cerdanyola del Vallès, Spain
| | - Oscar Molina
- Unitat de Biologia Cellular (Facultat de Biociències). Universitat Autònoma de Barcelona, 08193-Bellaterra, Cerdanyola del Vallès, Spain ; Current address: Wellcome Trust Center for Cell Biology, University of Edinburgh, Edinburgh, Scotland United Kingdom
| | - Esther Geán
- Secció de Genètica Clínica. Hospital Universitari Sant Joan de Déu, 08950-Esplugues de Llobregat, Barcelona, Spain
| | - Francesca Vidal
- Unitat de Biologia Cellular (Facultat de Biociències). Universitat Autònoma de Barcelona, 08193-Bellaterra, Cerdanyola del Vallès, Spain
| | - Joan Blanco
- Unitat de Biologia Cellular (Facultat de Biociències). Universitat Autònoma de Barcelona, 08193-Bellaterra, Cerdanyola del Vallès, Spain
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13
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A case of 17q21.31 microduplication and 7q31.33 microdeletion, associated with developmental delay, microcephaly, and mild dysmorphic features. Case Rep Genet 2014; 2014:658570. [PMID: 24649381 PMCID: PMC3932285 DOI: 10.1155/2014/658570] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 12/02/2013] [Indexed: 12/19/2022] Open
Abstract
Concurrent cryptic microdeletion and microduplication syndromes have recently started to reveal themselves with the advent of microarray technology. Analysis has shown that low-copy repeats (LCRs) have allowed chromosome regions throughout the genome to become hotspots for nonallelic homologous recombination to take place. Here, we report a case of a 7.5-year-old girl who manifests microcephaly, developmental delay, and mild dysmorphic features. Microarray analysis identified a microduplication in chromosome 17q21.31, which encompasses the CRHR1, MAPT, and KANSL1 genes, as well as a microdeletion in chromosome 7q31.33 that is localised within the GRM8 gene. To our knowledge this is one of only a few cases of 17q21.31 microduplication. The clinical phenotype of patients with this microduplication is milder than of those carrying the reciprocal microdeletions, and suggests that the lower incidence of the former compared to the latter may be due to underascertainment.
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14
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Alves JM, Lopes AM, Chikhi L, Amorim A. On the structural plasticity of the human genome: chromosomal inversions revisited. Curr Genomics 2013; 13:623-32. [PMID: 23730202 PMCID: PMC3492802 DOI: 10.2174/138920212803759703] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 09/23/2012] [Accepted: 09/24/2012] [Indexed: 01/02/2023] Open
Abstract
With the aid of novel and powerful molecular biology techniques, recent years have witnessed a dramatic increase in the number of studies reporting the involvement of complex structural variants in several genomic disorders. In fact, with the discovery of Copy Number Variants (CNVs) and other forms of unbalanced structural variation, much attention has been directed to the detection and characterization of such rearrangements, as well as the identification of the mechanisms involved in their formation. However, it has long been appreciated that chromosomes can undergo other forms of structural changes - balanced rearrangements - that do not involve quantitative variation of genetic material. Indeed, a particular subtype of balanced rearrangement – inversions – was recently found to be far more common than had been predicted from traditional cytogenetics. Chromosomal inversions alter the orientation of a specific genomic sequence and, unless involving breaks in coding or regulatory regions (and, disregarding complex trans effects, in their close vicinity), appear to be phenotypically silent. Such a surprising finding, which is difficult to reconcile with the classical interpretation of inversions as a mechanism causing subfertility (and ultimately reproductive isolation), motivated a new series of theoretical and empirical studies dedicated to understand their role in human genome evolution and to explore their possible association to complex genetic disorders. With this review, we attempt to describe the latest methodological improvements to inversions detection at a genome wide level, while exploring some of the possible implications of inversion rearrangements on the evolution of the human genome.
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Affiliation(s)
- Joao M Alves
- Doctoral Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Portugal ; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal ; Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
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15
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de Jong S, Chepelev I, Janson E, Strengman E, van den Berg LH, Veldink JH, Ophoff RA. Common inversion polymorphism at 17q21.31 affects expression of multiple genes in tissue-specific manner. BMC Genomics 2012; 13:458. [PMID: 22950410 PMCID: PMC3582489 DOI: 10.1186/1471-2164-13-458] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 08/27/2012] [Indexed: 11/12/2022] Open
Abstract
Background Chromosome 17q21.31 contains a common inversion polymorphism of approximately 900 kb in populations with European ancestry. Two divergent MAPT haplotypes, H1 and H2 are described with distinct linkage disequilibrium patterns across the region reflecting the inversion status at this locus. The MAPT H1 haplotype has been associated with progressive supranuclear palsy, corticobasal degeneration, Parkinson’s disease and Alzheimer’s disease, while the H2 is linked to recurrent deletion events associated with the 17q21.31 microdeletion syndrome, a disease characterized by developmental delay and learning disability. Results In this study, we investigate the effect of the inversion on the expression of genes in the 17q21.31 region. We find the expression of several genes in and at the borders of the inversion to be affected; specific either to whole blood or different regions of the human brain. The H1 haplotype was found to be associated with an increased expression of LRRC37A4, PLEKH1M and MAPT. In contrast, a decreased expression of MGC57346, LRRC37A and CRHR1 was associated with H1. Conclusions Studies thus far have focused on the expression of MAPT in the inversion region. However, our results show that the inversion status affects expression of other genes in the 17q21.31 region as well. Given the link between the inversion status and different neurological diseases, these genes may also be involved in disease pathology, possibly in a tissue-specific manner.
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Affiliation(s)
- Simone de Jong
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht3584 CG, The Netherlands
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16
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Steinberg KM, Antonacci F, Sudmant PH, Kidd JM, Campbell CD, Vives L, Malig M, Scheinfeldt L, Beggs W, Ibrahim M, Lema G, Nyambo TB, Omar SA, Bodo JM, Froment A, Donnelly MP, Kidd KK, Tishkoff SA, Eichler EE. Structural diversity and African origin of the 17q21.31 inversion polymorphism. Nat Genet 2012; 44:872-80. [PMID: 22751100 PMCID: PMC3408829 DOI: 10.1038/ng.2335] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 06/01/2012] [Indexed: 12/12/2022]
Abstract
The 17q21.31 inversion polymorphism exists either as direct (H1) or inverted (H2) haplotypes with differential predispositions to disease and selection. We investigated its genetic diversity in 2,700 individuals, with an emphasis on African populations. We characterize eight structural haplotypes due to complex rearrangements that vary in size from 1.08-1.49 Mb and provide evidence for a 30-kb H1-H2 double recombination event. We show that recurrent partial duplications of the KANSL1 gene have occurred on both the H1 and H2 haplotypes and have risen to high frequency in European populations. We identify a likely ancestral H2 haplotype (H2') lacking these duplications that is enriched among African hunter-gatherer groups yet essentially absent from West African populations. Whereas H1 and H2 segmental duplications arose independently and before human migration out of Africa, they have reached high frequencies recently among Europeans, either because of extraordinary genetic drift or selective sweeps.
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Gregor A, Krumbiegel M, Kraus C, Reis A, Zweier C. De novo triplication of the MAPT gene from the recurrent 17q21.31 microdeletion region in a patient with moderate intellectual disability and various minor anomalies. Am J Med Genet A 2012; 158A:1765-70. [PMID: 22678764 DOI: 10.1002/ajmg.a.35427] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Accepted: 03/26/2012] [Indexed: 11/09/2022]
Abstract
We report on a 16-year-old male patient with moderate intellectual disability, behavioral problems, and further anomalies such as facial dysmorphism, heart defect, and urogenital anomalies. By molecular karyotyping we identified the first de novo copy number gain to four copies on chromosome 17q21.31 including the MAPT gene but not the entire recurrent microdeletion/microduplication region. Recurrent microdeletions of this region including the MAPT and the CHRH1 genes have been shown to be a relatively frequent cause of intellectual disability, while only a few reciprocal duplications in patients with variable cognitive disorders have been published so far. A common inversion polymorphism in this region has been linked to a distinct H2 haplotype and seems to be associated with an increased risk for microdeletions and -duplications. Our patient and his father were both heterozygous for the H1/H2 haplotype, whereas the mother was homozygous for the H2 haplotype. In our patient the dosage gain apparently occurred on the paternal H1 allele and did not involve the H2 allele as in the previously published cases. This patient further delineates the genotypic and phenotypic variability associated with copy number variants from the 17q21.31 microdeletion region.
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Affiliation(s)
- Anne Gregor
- Institute of Human Genetics, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
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Terrone G, D'Amico A, Imperati F, Carella M, Palumbo O, Gentile M, Canani RB, Melis D, Romano A, Parente I, Riccitelli M, Del Giudice E. A further contribution to the delineation of the 17q21.31 microdeletion syndrome: central nervous involvement in two Italian patients. Eur J Med Genet 2012; 55:466-71. [PMID: 22659270 DOI: 10.1016/j.ejmg.2012.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 04/11/2012] [Indexed: 10/28/2022]
Abstract
The 17q21.31 microdeletion syndrome is a genetic disorder characterized by intellectual disability, facial dysmorphisms and a typical behavioral phenotype. Patients are usually described as friendly and cooperative but they can also show behavioral problems such as hyperactivity, bad humor, temper tantrums and poor interaction. Central nervous system involvement includes callosal dysgenesis/absence, enlargement of lateral ventricles and abnormalities of cyngulate gyrus. We report on two Italian patients with the 17q21.31 microdeletion syndrome better emphasizing neuroimaging and neuropsychological characteristics. In particular, we carried out an assessment of intellectual efficiency and behavior that turned out to be within the mild-moderate range of mental retardation, as already reported in the literature. To the best of our knowledge this is the first report of a patient with the 17q21.31 microdeletion and a Chiari malformation type 1 coexisting with a mild anomaly of medulla oblongata. This malformation should be considered in patients with the 17q21.31 microdeletion syndrome, presenting suggestive symptoms (headache, neck pain, cerebellar signs or muscle weakness).
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Affiliation(s)
- Gaetano Terrone
- Department of Pediatrics, Federico II University, Via Pansini n°5, Naples, Italy.
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Molina O, Anton E, Vidal F, Blanco J. High rates of de novo 15q11q13 inversions in human spermatozoa. Mol Cytogenet 2012; 5:11. [PMID: 22309495 PMCID: PMC3293048 DOI: 10.1186/1755-8166-5-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 02/06/2012] [Indexed: 11/22/2022] Open
Abstract
Low-Copy Repeats predispose the 15q11-q13 region to non-allelic homologous recombination. We have already demonstrated that a significant percentage of Prader-Willi syndrome (PWS) fathers have an increased susceptibility to generate 15q11q13 deletions in spermatozoa, suggesting the participation of intrachromatid exchanges. This work has been focused on assessing the incidence of de novo 15q11q13 inversions in spermatozoa of control donors and PWS fathers in order to determine the basal rates of inversions and to confirm the intrachromatid mechanism as the main cause of 15q11q13 anomalies. Semen samples from 10 control donors and 16 PWS fathers were processed and analyzed by triple-color FISH. Three differentially labeled BAC-clones were used: one proximal and two distal of the 15q11-q13 region. Signal associations allowed the discrimination between normal and inverted haplotypes, which were confirmed by laser-scanning confocal microscopy. Two types of inversions were detected which correspond to the segments involved in Class I and II PWS deletions. No significant differences were observed in the mean frequencies of inversions between controls and PWS fathers (3.59% ± 0.46 and 9.51% ± 0.87 vs 3.06% ± 0.33 and 10.07% ± 0.74). Individual comparisons showed significant increases of inversions in four PWS fathers (P < 0.05) previously reported as patients with increases of 15q11q13 deletions. Results suggest that the incidence of heterozygous inversion carriers in the general population could reach significant values. This situation could have important implications, as they have been described as predisposing haplotypes for genomic disorders. As a whole, results confirm the high instability of the 15q11-q13 region, which is prone to different types of de novo reorganizations by intrachromatid NAHR.
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Affiliation(s)
- Oscar Molina
- Unitat de Biologia Cel·lular (Facultat de Biociències), Universitat Autònoma de Barcelona, 08193-Bellaterra (Cerdanyola del Vallès), SPAIN.
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Maloney B, Lahiri DK. Structural and functional characterization of H2 haplotype MAPT promoter: unique neurospecific domains and a hypoxia-inducible element would enhance rationally targeted tauopathy research for Alzheimer's disease. Gene 2012; 501:63-78. [PMID: 22310385 DOI: 10.1016/j.gene.2012.01.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 01/19/2012] [Accepted: 01/20/2012] [Indexed: 11/29/2022]
Abstract
Alzheimer's disease (AD) is the leading cause of dementia in the elderly. Extraneuronal plaque comprising mostly the amyloid β peptide and intraneuronal tangles of hyperphosphorylated microtubule-associated τ protein (τ, gene MAPT) are typical of AD. Misfolded τ is also implicated in Parkinson's disease and frontotemporal dementia. We aim to understand the regulation of the human MAPT promoter by mapping its functional domains. We subcloned a 4868 base pair (bp) fragment from human BAC RPCI-11 100C5. Sequence analysis revealed an H2 haplotype MAPT promoter, 5'-UTR, and intronal fragment. Database analysis of the fragment showed 50%-75% homology with mouse and >90% with rhesus monkey. Comparison with human H1 sequences revealed differences that crossed predicted transcription factor sites. DNA-protein interaction studies by electrophoretic mobility shift assay suggested hypoxia response and an active specificity protein 1 (SP1) site in the 5'-untranslated region. Transfection of a series of MAPT promoter deletions revealed unique functional domains. The distal-most had different activities in neuronal vs. non-neuronal cells. We have cloned, sequenced, and functionally characterized a 4868bp fragment of the human MAPT 5'-flanking region, including the core promoter region (-302/+4), neurospecific domains (-4364/-1992 and +293/+504, relative to +1 TSS), and a hypoxia-inducible element (+60/+84). Our work extended functional analysis of the MAPT sequence further upstream, and explores cell-type specificity of MAPT promoter activity. Finally, we provided direct comparison of likely transcription factor binding sites, which are useful to understand differences between H1/H2 pathogenic associations.
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Affiliation(s)
- Bryan Maloney
- Laboratory of Molecular Neurogenetics, Department of Psychiatry, Institute of Psychiatric Research Indiana University School of Medicine, Indianapolis, IN 46202, USA
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21
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Deak KL, Horn SR, Rehder CW. The evolving picture of microdeletion/microduplication syndromes in the age of microarray analysis: variable expressivity and genomic complexity. Clin Lab Med 2011; 31:543-64, viii. [PMID: 22118736 DOI: 10.1016/j.cll.2011.08.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several new microdeletion and microduplication syndromes have been discovered in a genotype-first approach. Many of these disorders are caused by nonallelic homologous recombination between blocks of segmental duplication. The authors describe 9 regions for which copy number alteration is proposed to cause an abnormal phenotype. Some of these disorders have been observed in affected individuals and individuals lacking a clearly abnormal phenotype. These deletions and duplications are thought to be contributory, but not always sufficient, to elicit an abnormal outcome. Additional studies are necessary to further evaluate the penetrance and delineate the clinical spectrum associated with many of these newly described disorders.
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Affiliation(s)
- Kristen L Deak
- Department of Pathology, Duke University, Durham, NC, USA
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22
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Cooper DN, Bacolla A, Férec C, Vasquez KM, Kehrer-Sawatzki H, Chen JM. On the sequence-directed nature of human gene mutation: the role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease. Hum Mutat 2011; 32:1075-99. [PMID: 21853507 DOI: 10.1002/humu.21557] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Accepted: 06/17/2011] [Indexed: 12/21/2022]
Abstract
Different types of human gene mutation may vary in size, from structural variants (SVs) to single base-pair substitutions, but what they all have in common is that their nature, size and location are often determined either by specific characteristics of the local DNA sequence environment or by higher order features of the genomic architecture. The human genome is now recognized to contain "pervasive architectural flaws" in that certain DNA sequences are inherently mutation prone by virtue of their base composition, sequence repetitivity and/or epigenetic modification. Here, we explore how the nature, location and frequency of different types of mutation causing inherited disease are shaped in large part, and often in remarkably predictable ways, by the local DNA sequence environment. The mutability of a given gene or genomic region may also be influenced indirectly by a variety of noncanonical (non-B) secondary structures whose formation is facilitated by the underlying DNA sequence. Since these non-B DNA structures can interfere with subsequent DNA replication and repair and may serve to increase mutation frequencies in generalized fashion (i.e., both in the context of subtle mutations and SVs), they have the potential to serve as a unifying concept in studies of mutational mechanisms underlying human inherited disease.
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Affiliation(s)
- David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom.
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