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Burgoyne T, Fassad MR, Schultz R, Elenius V, Lim JSY, Freke G, Rai R, Mohammed MA, Mitchison HM, Sironen AI. HYDIN variants cause primary ciliary dyskinesia in the Finnish population. Pediatr Pulmonol 2024. [PMID: 39291810 DOI: 10.1002/ppul.27267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 08/15/2024] [Accepted: 09/03/2024] [Indexed: 09/19/2024]
Abstract
INTRODUCTION Primary ciliary dyskinesia (PCD) is a rare genetic disorder characterized by chronic respiratory tract infections and in some cases laterality defects and infertility. The symptoms of PCD are caused by malfunction of motile cilia, hair-like organelles protruding out of the cell. Thus far, disease causing variants in over 50 genes have been identified and these variants explain around 70% of all known cases. Population specific genetics underlying PCD has been reported highlighting the importance of characterizing gene variants in different populations for development of gene-based diagnostics and management. METHODS Whole exome sequencing was used to identify disease causing variants in Finnish PCD cohort. The effect of the identified HYDIN variants on cilia structure and function was confirmed by high-speed video analysis, immunofluorescence and electron tomography. RESULTS In this study, we identified three Finnish PCD patients carrying homozygous loss-of-function variants and one patient with compound heterozygous variants within HYDIN. The functional studies showed defects in the axonemal central pair complex. All patients had clinical PCD symptoms including chronic wet cough and recurrent airway infections, associated with mostly static airway cilia. CONCLUSION Our results are consistent with the previously identified important role of HYDIN in the axonemal central pair complex and improve specific diagnostics of PCD in different national populations.
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Affiliation(s)
- Thomas Burgoyne
- Institute of Ophthalmology, University College London, London, UK
- PCD Diagnostic Team and Department of Paediatric Respiratory Medicine, Royal Brompton Hospital, London, UK
| | - Mahmoud R Fassad
- Great Ormond Street Institute of Child Health, University College London, London, UK
- Human Genetics Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Rüdiger Schultz
- Allergy Centre, Tampere University Hospital, Tampere, Finland
| | - Varpu Elenius
- Department of Pediatrics, Turku University Hospital, University of Turku, Turku, Finland
| | - Jacqueline S Y Lim
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Grace Freke
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Ranjit Rai
- PCD Diagnostic Team and Department of Paediatric Respiratory Medicine, Royal Brompton Hospital, London, UK
| | - Mai A Mohammed
- Great Ormond Street Institute of Child Health, University College London, London, UK
- Biochemistry Department, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Hannah M Mitchison
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Anu I Sironen
- Great Ormond Street Institute of Child Health, University College London, London, UK
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
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Jeong H, Dishuck PC, Yoo D, Harvey WT, Munson KM, Lewis AP, Kordosky J, Garcia GH, Yilmaz F, Hallast P, Lee C, Pastinen T, Eichler EE. Structural polymorphism and diversity of human segmental duplications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597452. [PMID: 38895457 PMCID: PMC11185583 DOI: 10.1101/2024.06.04.597452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Segmental duplications (SDs) contribute significantly to human disease, evolution, and diversity yet have been difficult to resolve at the sequence level. We present a population genetics survey of SDs by analyzing 170 human genome assemblies where the majority of SDs are fully resolved using long-read sequence assembly. Excluding the acrocentric short arms, we identify 173.2 Mbp of duplicated sequence (47.4 Mbp not present in the telomere-to-telomere reference) distinguishing fixed from structurally polymorphic events. We find that intrachromosomal SDs are among the most variable with rare events mapping near their progenitor sequences. African genomes harbor significantly more intrachromosomal SDs and are more likely to have recently duplicated gene families with higher copy number when compared to non-African samples. A comparison to a resource of 563 million full-length Iso-Seq reads identifies 201 novel, potentially protein-coding genes corresponding to these copy number polymorphic SDs.
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Affiliation(s)
- Hyeonsoo Jeong
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Altos Labs, San Diego, CA, USA
| | - Philip C. Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - William T. Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M. Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P. Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Jennifer Kordosky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Gage H. Garcia
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Feyza Yilmaz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Pille Hallast
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Tomi Pastinen
- Children’s Mercy Hospital and University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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Pollen AA, Kilik U, Lowe CB, Camp JG. Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution. Nat Rev Genet 2023; 24:687-711. [PMID: 36737647 PMCID: PMC9897628 DOI: 10.1038/s41576-022-00568-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 02/05/2023]
Abstract
Our ancestors acquired morphological, cognitive and metabolic modifications that enabled humans to colonize diverse habitats, develop extraordinary technologies and reshape the biosphere. Understanding the genetic, developmental and molecular bases for these changes will provide insights into how we became human. Connecting human-specific genetic changes to species differences has been challenging owing to an abundance of low-effect size genetic changes, limited descriptions of phenotypic differences across development at the level of cell types and lack of experimental models. Emerging approaches for single-cell sequencing, genetic manipulation and stem cell culture now support descriptive and functional studies in defined cell types with a human or ape genetic background. In this Review, we describe how the sequencing of genomes from modern and archaic hominins, great apes and other primates is revealing human-specific genetic changes and how new molecular and cellular approaches - including cell atlases and organoids - are enabling exploration of the candidate causal factors that underlie human-specific traits.
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Affiliation(s)
- Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
| | - Umut Kilik
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
| | - J Gray Camp
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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4
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Liang X, Heath LS. Towards understanding paleoclimate impacts on primate de novo genes. G3 (BETHESDA, MD.) 2023; 13:jkad135. [PMID: 37313728 PMCID: PMC10468307 DOI: 10.1093/g3journal/jkad135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/31/2023] [Accepted: 06/08/2023] [Indexed: 06/15/2023]
Abstract
De novo genes are genes that emerge as new genes in some species, such as primate de novo genes that emerge in certain primate species. Over the past decade, a great deal of research has been conducted regarding their emergence, origins, functions, and various attributes in different species, some of which have involved estimating the ages of de novo genes. However, limited by the number of species available for whole-genome sequencing, relatively few studies have focused specifically on the emergence time of primate de novo genes. Among those, even fewer investigate the association between primate gene emergence with environmental factors, such as paleoclimate (ancient climate) conditions. This study investigates the relationship between paleoclimate and human gene emergence at primate species divergence. Based on 32 available primate genome sequences, this study has revealed possible associations between temperature changes and the emergence of de novo primate genes. Overall, findings in this study are that de novo genes tended to emerge in the recent 13 MY when the temperature continues cooling, which is consistent with past findings. Furthermore, in the context of an overall trend of cooling temperature, new primate genes were more likely to emerge during local warming periods, where the warm temperature more closely resembled the environmental condition that preceded the cooling trend. Results also indicate that both primate de novo genes and human cancer-associated genes have later origins in comparison to random human genes. Future studies can be in-depth on understanding human de novo gene emergence from an environmental perspective as well as understanding species divergence from a gene emergence perspective.
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Affiliation(s)
- Xiao Liang
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Lenwood S Heath
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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5
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Huang TT, Xu HF, Wang SY, Lin WX, Tung YH, Khan KU, Zhang HH, Guo H, Zheng G, Zhang G. Identification of 1q21.1 microduplication in a family: A case report. World J Clin Cases 2023; 11:874-882. [PMID: 36818619 PMCID: PMC9928700 DOI: 10.12998/wjcc.v11.i4.874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/21/2022] [Accepted: 01/12/2023] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Copy number variation (CNV) has become widely recognized in recent years due to the extensive use of gene screening in developmental disorders and epilepsy research. 1q21.1 microduplication syndrome is a rare CNV disease that can manifest as multiple congenital developmental disorders, autism spectrum disorders, congenital malformations, and congenital heart defects with genetic heterogeneity.
CASE SUMMARY We reported a pediatric patient with 1q21.1 microduplication syndrome, and carried out a literature review to determine the correlation between 1q21.1 microduplication and its phenotypes. We summarized the patient’s medical history and clinical symptoms, and extracted genomic DNA from the patient, her parents, elder brother, and sister. The patient was an 8-mo-old girl who was hospitalized for recurrent convulsions over a 2-mo period. Whole exon sequencing and whole genome low-depth sequencing (CNV-seq) were then performed. Whole exon sequencing detected a 1.58-Mb duplication in the CHR1:145883867-147465312 region, which was located in the 1q21.1 region. Family analysis showed that the pathogenetic duplication fragment, which was also detected in her elder brother’s DNA originated from the mother.
CONCLUSION Whole exon sequencing combined with quantitative polymerase chain reaction can provide an accurate molecular diagnosis in children with 1q21.1 microduplication syndrome, which is of great significance for genetic counseling and early intervention.
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Affiliation(s)
- Ting-Ting Huang
- Department of Neurology, Children’s Hospital of Nanjing Medical University, Nanjing 210000, Jiangsu Province, China
| | - Hai-Feng Xu
- Department of Neurology, Children’s Hospital of Nanjing Medical University, Nanjing 210000, Jiangsu Province, China
| | - Shang-Yu Wang
- Department of Neurology, Children’s Hospital of Nanjing Medical University, Nanjing 210000, Jiangsu Province, China
| | - Wen-Xin Lin
- Department of Neurology, Children’s Hospital of Nanjing Medical University, Nanjing 210000, Jiangsu Province, China
| | - Yie-Hen Tung
- Department of Neurology, Children’s Hospital of Nanjing Medical University, Nanjing 210000, Jiangsu Province, China
| | - Kaleem Ullah Khan
- Department of Neurology, Children’s Hospital of Nanjing Medical University, Nanjing 210000, Jiangsu Province, China
| | - Hui-Hui Zhang
- Nanjing Medical University, Nanjing 210000, Jiangsu Province, China
- Nanjing Xiaozhuang University Experimental Primary School, Nanjing 210000, Jiangsu Province, China
| | - Hu Guo
- Department of Neurology, Children’s Hospital of Nanjing Medical University, Nanjing 210000, Jiangsu Province, China
| | - Guo Zheng
- Department of Neurology, Children’s Hospital of Nanjing Medical University, Nanjing 210000, Jiangsu Province, China
| | - Gang Zhang
- Department of Neurology, Children’s Hospital of Nanjing Medical University, Nanjing 210000, Jiangsu Province, China
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6
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Sønderby IE, Ching CRK, Thomopoulos SI, van der Meer D, Sun D, Villalon‐Reina JE, Agartz I, Amunts K, Arango C, Armstrong NJ, Ayesa‐Arriola R, Bakker G, Bassett AS, Boomsma DI, Bülow R, Butcher NJ, Calhoun VD, Caspers S, Chow EWC, Cichon S, Ciufolini S, Craig MC, Crespo‐Facorro B, Cunningham AC, Dale AM, Dazzan P, de Zubicaray GI, Djurovic S, Doherty JL, Donohoe G, Draganski B, Durdle CA, Ehrlich S, Emanuel BS, Espeseth T, Fisher SE, Ge T, Glahn DC, Grabe HJ, Gur RE, Gutman BA, Haavik J, Håberg AK, Hansen LA, Hashimoto R, Hibar DP, Holmes AJ, Hottenga J, Hulshoff Pol HE, Jalbrzikowski M, Knowles EEM, Kushan L, Linden DEJ, Liu J, Lundervold AJ, Martin‐Brevet S, Martínez K, Mather KA, Mathias SR, McDonald‐McGinn DM, McRae AF, Medland SE, Moberget T, Modenato C, Monereo Sánchez J, Moreau CA, Mühleisen TW, Paus T, Pausova Z, Prieto C, Ragothaman A, Reinbold CS, Reis Marques T, Repetto GM, Reymond A, Roalf DR, Rodriguez‐Herreros B, Rucker JJ, Sachdev PS, Schmitt JE, Schofield PR, Silva AI, Stefansson H, Stein DJ, Tamnes CK, Tordesillas‐Gutiérrez D, Ulfarsson MO, Vajdi A, van 't Ent D, van den Bree MBM, Vassos E, Vázquez‐Bourgon J, Vila‐Rodriguez F, Walters GB, Wen W, Westlye LT, Wittfeld K, Zackai EH, Stefánsson K, Jacquemont S, Thompson PM, Bearden CE, Andreassen OA. Effects of copy number variations on brain structure and risk for psychiatric illness: Large-scale studies from the ENIGMA working groups on CNVs. Hum Brain Mapp 2022; 43:300-328. [PMID: 33615640 PMCID: PMC8675420 DOI: 10.1002/hbm.25354] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/07/2021] [Accepted: 01/13/2021] [Indexed: 01/21/2023] Open
Abstract
The Enhancing NeuroImaging Genetics through Meta-Analysis copy number variant (ENIGMA-CNV) and 22q11.2 Deletion Syndrome Working Groups (22q-ENIGMA WGs) were created to gain insight into the involvement of genetic factors in human brain development and related cognitive, psychiatric and behavioral manifestations. To that end, the ENIGMA-CNV WG has collated CNV and magnetic resonance imaging (MRI) data from ~49,000 individuals across 38 global research sites, yielding one of the largest studies to date on the effects of CNVs on brain structures in the general population. The 22q-ENIGMA WG includes 12 international research centers that assessed over 533 individuals with a confirmed 22q11.2 deletion syndrome, 40 with 22q11.2 duplications, and 333 typically developing controls, creating the largest-ever 22q11.2 CNV neuroimaging data set. In this review, we outline the ENIGMA infrastructure and procedures for multi-site analysis of CNVs and MRI data. So far, ENIGMA has identified effects of the 22q11.2, 16p11.2 distal, 15q11.2, and 1q21.1 distal CNVs on subcortical and cortical brain structures. Each CNV is associated with differences in cognitive, neurodevelopmental and neuropsychiatric traits, with characteristic patterns of brain structural abnormalities. Evidence of gene-dosage effects on distinct brain regions also emerged, providing further insight into genotype-phenotype relationships. Taken together, these results offer a more comprehensive picture of molecular mechanisms involved in typical and atypical brain development. This "genotype-first" approach also contributes to our understanding of the etiopathogenesis of brain disorders. Finally, we outline future directions to better understand effects of CNVs on brain structure and behavior.
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Affiliation(s)
- Ida E. Sønderby
- Department of Medical GeneticsOslo University HospitalOsloNorway
- Norwegian Centre for Mental Disorders Research (NORMENT), Division of Mental Health and AddictionOslo University Hospital and University of OsloOsloNorway
- KG Jebsen Centre for Neurodevelopmental DisordersUniversity of OsloOsloNorway
| | - Christopher R. K. Ching
- Imaging Genetics CenterMark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern CaliforniaMarina del ReyCaliforniaUSA
| | - Sophia I. Thomopoulos
- Imaging Genetics CenterMark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern CaliforniaMarina del ReyCaliforniaUSA
| | - Dennis van der Meer
- Norwegian Centre for Mental Disorders Research (NORMENT), Division of Mental Health and AddictionOslo University Hospital and University of OsloOsloNorway
- School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life SciencesMaastricht UniversityMaastrichtThe Netherlands
| | - Daqiang Sun
- Semel Institute for Neuroscience and Human Behavior, Departments of Psychiatry and Biobehavioral Sciences and PsychologyUniversity of California Los AngelesLos AngelesCaliforniaUSA
- Department of Mental HealthVeterans Affairs Greater Los Angeles Healthcare System, Los AngelesCaliforniaUSA
| | - Julio E. Villalon‐Reina
- Imaging Genetics CenterMark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern CaliforniaMarina del ReyCaliforniaUSA
| | - Ingrid Agartz
- NORMENT, Institute of Clinical PsychiatryUniversity of OsloOsloNorway
- Department of Psychiatric ResearchDiakonhjemmet HospitalOsloNorway
- Department of Clinical NeuroscienceKarolinska InstitutetStockholmSweden
| | - Katrin Amunts
- Institute of Neuroscience and Medicine (INM‐1)Research Centre JülichJülichGermany
- Cecile and Oskar Vogt Institute for Brain Research, Medical FacultyUniversity Hospital Düsseldorf, Heinrich‐Heine‐University DüsseldorfDüsseldorfGermany
| | - Celso Arango
- Department of Child and Adolescent PsychiatryInstitute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañon, IsSGM, Universidad Complutense, School of MedicineMadridSpain
- Centro Investigación Biomédica en Red de Salud Mental (CIBERSAM)MadridSpain
| | | | - Rosa Ayesa‐Arriola
- Centro Investigación Biomédica en Red de Salud Mental (CIBERSAM)MadridSpain
- Department of PsychiatryMarqués de Valdecilla University Hospital, Valdecilla Biomedical Research Institute (IDIVAL)SantanderSpain
| | - Geor Bakker
- Department of Psychiatry and NeuropsychologyMaastricht UniversityMaastrichtThe Netherlands
- Department of Radiology and Nuclear MedicineVU University Medical CenterAmsterdamThe Netherlands
| | - Anne S. Bassett
- Clinical Genetics Research ProgramCentre for Addiction and Mental HealthTorontoOntarioCanada
- Dalglish Family 22q Clinic for Adults with 22q11.2 Deletion Syndrome, Toronto General HospitalUniversity Health NetworkTorontoOntarioCanada
- Department of PsychiatryUniversity of TorontoTorontoOntarioCanada
| | - Dorret I. Boomsma
- Department of Biological PsychologyVrije Universiteit AmsterdamAmsterdamThe Netherlands
- Amsterdam Public Health (APH) Research InstituteAmsterdam UMCAmsterdamThe Netherlands
| | - Robin Bülow
- Institute of Diagnostic Radiology and NeuroradiologyUniversity Medicine GreifswaldGreifswaldGermany
| | - Nancy J. Butcher
- Department of PsychiatryUniversity of TorontoTorontoOntarioCanada
- Child Health Evaluative SciencesThe Hospital for Sick Children Research InstituteTorontoOntarioCanada
| | - Vince D. Calhoun
- Tri‐institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS)Georgia State, Georgia Tech, EmoryAtlantaGeorgiaUSA
| | - Svenja Caspers
- Institute of Neuroscience and Medicine (INM‐1)Research Centre JülichJülichGermany
- Institute for Anatomy IMedical Faculty & University Hospital Düsseldorf, University of DüsseldorfDüsseldorfGermany
| | - Eva W. C. Chow
- Clinical Genetics Research ProgramCentre for Addiction and Mental HealthTorontoOntarioCanada
- Department of PsychiatryUniversity of TorontoTorontoOntarioCanada
| | - Sven Cichon
- Institute of Neuroscience and Medicine (INM‐1)Research Centre JülichJülichGermany
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland
- Department of BiomedicineUniversity of BaselBaselSwitzerland
| | - Simone Ciufolini
- Department of Psychosis StudiesInstitute of Psychiatry, Psychology and Neuroscience, King's College LondonLondonUnited Kingdom
| | - Michael C. Craig
- Department of Forensic and Neurodevelopmental SciencesThe Sackler Institute for Translational Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King's CollegeLondonUnited Kingdom
| | | | - Adam C. Cunningham
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical NeurosciencesCardiff UniversityCardiffUnited Kingdom
| | - Anders M. Dale
- Center for Multimodal Imaging and GeneticsUniversity of California San DiegoLa JollaCaliforniaUSA
- Department RadiologyUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Paola Dazzan
- Department of Psychological MedicineInstitute of Psychiatry, Psychology and Neuroscience, King's College LondonLondonUnited Kingdom
| | - Greig I. de Zubicaray
- Faculty of HealthQueensland University of Technology (QUT)BrisbaneQueenslandAustralia
| | - Srdjan Djurovic
- Department of Medical GeneticsOslo University HospitalOsloNorway
- NORMENT, Department of Clinical ScienceUniversity of BergenBergenNorway
| | - Joanne L. Doherty
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical NeurosciencesCardiff UniversityCardiffUnited Kingdom
- Cardiff University Brain Research Imaging Centre (CUBRIC)CardiffUnited Kingdom
| | - Gary Donohoe
- Center for Neuroimaging, Genetics and GenomicsSchool of Psychology, NUI GalwayGalwayIreland
| | - Bogdan Draganski
- LREN, Centre for Research in Neuroscience, Department of NeuroscienceUniversity Hospital Lausanne and University LausanneLausanneSwitzerland
- Neurology DepartmentMax‐Planck Institute for Human Brain and Cognitive SciencesLeipzigGermany
| | - Courtney A. Durdle
- MIND Institute and Department of Psychiatry and Behavioral SciencesUniversity of California DavisDavisCaliforniaUSA
| | - Stefan Ehrlich
- Division of Psychological and Social Medicine and Developmental NeurosciencesFaculty of Medicine, TU DresdenDresdenGermany
| | - Beverly S. Emanuel
- Department of PediatricsPerelman School of Medicine at the University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Thomas Espeseth
- Department of PsychologyUniversity of OsloOsloNorway
- Department of PsychologyBjørknes CollegeOsloNorway
| | - Simon E. Fisher
- Language and Genetics DepartmentMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
- Donders Institute for Brain, Cognition and BehaviourRadboud UniversityNijmegenThe Netherlands
| | - Tian Ge
- Psychiatric and Neurodevelopmental Genetics UnitCenter for Genomic Medicine, Massachusetts General HospitalBostonMassachusettsUSA
- Department of Psychiatry, Massachusetts General HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | - David C. Glahn
- Tommy Fuss Center for Neuropsychiatric Disease ResearchBoston Children's HospitalBostonMassachusettsUSA
- Department of PsychiatryHarvard Medical SchoolBostonMassachusettsUSA
| | - Hans J. Grabe
- German Center for Neurodegenerative Diseases (DZNE)Site Rostock/GreifswaldGreifswaldGermany
- Department of Psychiatry and PsychotherapyUniversity Medicine GreifswaldGreifswaldGermany
| | - Raquel E. Gur
- Department of PsychiatryUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Youth Suicide Prevention, Intervention and Research CenterChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - Boris A. Gutman
- Medical Imaging Research Center, Department of Biomedical EngineeringIllinois Institute of TechnologyChicagoIllinoisUSA
| | - Jan Haavik
- Department of BiomedicineUniversity of BergenBergenNorway
- Division of PsychiatryHaukeland University HospitalBergenNorway
| | - Asta K. Håberg
- Department of Neuromedicine and Movement Science, Faculty of Medicine and Health SciencesNorwegian University of Science and TechnologyTrondheimNorway
- Department of Radiology and Nuclear MedicineSt. Olavs HospitalTrondheimNorway
| | - Laura A. Hansen
- Department of Psychiatry and Biobehavioral SciencesUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Ryota Hashimoto
- Department of Pathology of Mental DiseasesNational Institute of Mental Health, National Center of Neurology and PsychiatryTokyoJapan
- Department of PsychiatryOsaka University Graduate School of MedicineOsakaJapan
| | - Derrek P. Hibar
- Personalized Healthcare AnalyticsGenentech, Inc.South San FranciscoCaliforniaUSA
| | - Avram J. Holmes
- Department of PsychologyYale UniversityNew HavenConnecticutUSA
- Department of PsychiatryYale UniversityNew HavenConnecticutUSA
| | - Jouke‐Jan Hottenga
- Department of Biological PsychologyVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Hilleke E. Hulshoff Pol
- Department of Psychiatry, UMC Utrecht Brain Center, University Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | | | - Emma E. M. Knowles
- Department of Psychiatry, Massachusetts General HospitalHarvard Medical SchoolBostonMassachusettsUSA
- Department of PsychiatryBoston Children's HospitalBostonMassachusettsUSA
| | - Leila Kushan
- Semel Institute for Neuroscience and Human BehaviorUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - David E. J. Linden
- School for Mental Health and NeuroscienceMaastricht UniversityMaastrichtThe Netherlands
- Neuroscience and Mental Health Research InstituteCardiff UniversityCardiffUnited Kingdom
| | - Jingyu Liu
- Tri‐institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS)Georgia State, Georgia Tech, EmoryAtlantaGeorgiaUSA
- Computer ScienceGeorgia State UniversityAtlantaGeorgiaUSA
| | - Astri J. Lundervold
- Department of Biological and Medical PsychologyUniversity of BergenBergenNorway
| | - Sandra Martin‐Brevet
- LREN, Centre for Research in Neuroscience, Department of NeuroscienceUniversity Hospital Lausanne and University LausanneLausanneSwitzerland
| | - Kenia Martínez
- Department of Child and Adolescent PsychiatryInstitute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañon, IsSGM, Universidad Complutense, School of MedicineMadridSpain
- Centro Investigación Biomédica en Red de Salud Mental (CIBERSAM)MadridSpain
- Facultad de PsicologíaUniversidad Autónoma de MadridMadridSpain
| | - Karen A. Mather
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, Faculty of MedicineUniversity of New South WalesSydneyNew South WalesAustralia
- Neuroscience Research AustraliaSydneyNew South WalesAustralia
| | - Samuel R. Mathias
- Department of PsychiatryHarvard Medical SchoolBostonMassachusettsUSA
- Department of PsychiatryBoston Children's HospitalBostonMassachusettsUSA
| | - Donna M. McDonald‐McGinn
- Department of PediatricsPerelman School of Medicine at the University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Division of Human GeneticsChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
- Division of Human Genetics and 22q and You CenterChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - Allan F. McRae
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneQueenslandAustralia
| | - Sarah E. Medland
- Psychiatric GeneticsQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Torgeir Moberget
- Department of Psychology, Faculty of Social SciencesUniversity of OsloOsloNorway
| | - Claudia Modenato
- LREN, Centre for Research in Neuroscience, Department of NeuroscienceUniversity Hospital Lausanne and University LausanneLausanneSwitzerland
- University of LausanneLausanneSwitzerland
| | - Jennifer Monereo Sánchez
- School for Mental Health and NeuroscienceMaastricht UniversityMaastrichtThe Netherlands
- Faculty of Health, Medicine and Life SciencesMaastricht UniversityMaastrichtThe Netherlands
- Department of Radiology and Nuclear MedicineMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Clara A. Moreau
- Sainte Justine Hospital Research CenterUniversity of Montreal, MontrealQCCanada
| | - Thomas W. Mühleisen
- Institute of Neuroscience and Medicine (INM‐1)Research Centre JülichJülichGermany
- Cecile and Oskar Vogt Institute for Brain Research, Medical FacultyUniversity Hospital Düsseldorf, Heinrich‐Heine‐University DüsseldorfDüsseldorfGermany
- Department of BiomedicineUniversity of BaselBaselSwitzerland
| | - Tomas Paus
- Bloorview Research InstituteHolland Bloorview Kids Rehabilitation HospitalTorontoOntarioCanada
- Departments of Psychology and PsychiatryUniversity of TorontoTorontoOntarioCanada
| | - Zdenka Pausova
- Translational Medicine, The Hospital for Sick ChildrenTorontoOntarioCanada
| | - Carlos Prieto
- Bioinformatics Service, NucleusUniversity of SalamancaSalamancaSpain
| | | | - Céline S. Reinbold
- Department of BiomedicineUniversity of BaselBaselSwitzerland
- Centre for Lifespan Changes in Brain and Cognition, Department of PsychologyUniversity of OsloOsloNorway
| | - Tiago Reis Marques
- Department of Psychosis StudiesInstitute of Psychiatry, Psychology and Neuroscience, King's College LondonLondonUnited Kingdom
- Psychiatric Imaging Group, MRC London Institute of Medical Sciences (LMS), Hammersmith HospitalImperial College LondonLondonUnited Kingdom
| | - Gabriela M. Repetto
- Center for Genetics and GenomicsFacultad de Medicina, Clinica Alemana Universidad del DesarrolloSantiagoChile
| | - Alexandre Reymond
- Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
| | - David R. Roalf
- Department of PsychiatryUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | | | - James J. Rucker
- Department of Psychological MedicineInstitute of Psychiatry, Psychology and Neuroscience, King's College LondonLondonUnited Kingdom
| | - Perminder S. Sachdev
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, Faculty of MedicineUniversity of New South WalesSydneyNew South WalesAustralia
- Neuropsychiatric InstituteThe Prince of Wales HospitalSydneyNew South WalesAustralia
| | - James E. Schmitt
- Department of Radiology and PsychiatryUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Peter R. Schofield
- Neuroscience Research AustraliaSydneyNew South WalesAustralia
- School of Medical SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Ana I. Silva
- Neuroscience and Mental Health Research InstituteCardiff UniversityCardiffUnited Kingdom
- School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life SciencesMaastricht UniversityMaastrichtThe Netherlands
| | | | - Dan J. Stein
- SA MRC Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Neuroscience InstituteUniversity of Cape TownCape TownSouth Africa
| | - Christian K. Tamnes
- Norwegian Centre for Mental Disorders Research (NORMENT), Division of Mental Health and AddictionOslo University Hospital and University of OsloOsloNorway
- Department of Psychiatric ResearchDiakonhjemmet HospitalOsloNorway
- PROMENTA Research Center, Department of PsychologyUniversity of OsloOsloNorway
| | - Diana Tordesillas‐Gutiérrez
- Centro Investigación Biomédica en Red de Salud Mental (CIBERSAM)MadridSpain
- Neuroimaging Unit, Technological FacilitiesValdecilla Biomedical Research Institute (IDIVAL), SantanderSpain
| | - Magnus O. Ulfarsson
- Population Genomics, deCODE genetics/AmgenReykjavikIceland
- Faculty of Electrical and Computer EngineeringUniversity of Iceland, ReykjavikIceland
| | - Ariana Vajdi
- Semel Institute for Neuroscience and Human BehaviorUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Dennis van 't Ent
- Department of Biological PsychologyVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Marianne B. M. van den Bree
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical NeurosciencesCardiff UniversityCardiffUnited Kingdom
| | - Evangelos Vassos
- Social, Genetic and Developmental Psychiatry CentreInstitute of Psychiatry, Psychology & Neuroscience, King's College LondonLondonUnited Kingdom
| | - Javier Vázquez‐Bourgon
- Centro Investigación Biomédica en Red de Salud Mental (CIBERSAM)MadridSpain
- Department of PsychiatryMarqués de Valdecilla University Hospital, Valdecilla Biomedical Research Institute (IDIVAL)SantanderSpain
- School of MedicineUniversity of CantabriaSantanderSpain
| | - Fidel Vila‐Rodriguez
- Department of PsychiatryThe University of British ColumbiaVancouverBritish ColumbiaCanada
| | - G. Bragi Walters
- Population Genomics, deCODE genetics/AmgenReykjavikIceland
- Faculty of MedicineUniversity of IcelandReykjavikIceland
| | - Wei Wen
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, Faculty of MedicineUniversity of New South WalesSydneyNew South WalesAustralia
| | - Lars T. Westlye
- KG Jebsen Centre for Neurodevelopmental DisordersUniversity of OsloOsloNorway
- Department of PsychologyUniversity of OsloOsloNorway
- NORMENT, Division of Mental Health and AddictionOslo University HospitalOsloNorway
| | - Katharina Wittfeld
- German Center for Neurodegenerative Diseases (DZNE)Site Rostock/GreifswaldGreifswaldGermany
- Department of Psychiatry and PsychotherapyUniversity Medicine GreifswaldGreifswaldGermany
| | - Elaine H. Zackai
- Department of PediatricsPerelman School of Medicine at the University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Division of Human GeneticsChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - Kári Stefánsson
- Population Genomics, deCODE genetics/AmgenReykjavikIceland
- Faculty of MedicineUniversity of IcelandReykjavikIceland
| | - Sebastien Jacquemont
- Sainte Justine Hospital Research CenterUniversity of Montreal, MontrealQCCanada
- Department of PediatricsUniversity of Montreal, MontrealQCCanada
| | - Paul M. Thompson
- Imaging Genetics CenterMark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern CaliforniaMarina del ReyCaliforniaUSA
| | - Carrie E. Bearden
- Semel Institute for Neuroscience and Human Behavior, Departments of Psychiatry and Biobehavioral Sciences and PsychologyUniversity of California Los AngelesLos AngelesCaliforniaUSA
- Center for Neurobehavioral GeneticsUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Ole A. Andreassen
- Norwegian Centre for Mental Disorders Research (NORMENT), Division of Mental Health and AddictionOslo University Hospital and University of OsloOsloNorway
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7
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Salama SR. The Complexity of the Mammalian Transcriptome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1363:11-22. [PMID: 35220563 DOI: 10.1007/978-3-030-92034-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Draft genome assemblies for multiple mammalian species combined with new technologies to map transcripts from diverse RNA samples to these genomes developed in the early 2000s revealed that the mammalian transcriptome was vastly larger and more complex than previously anticipated. Efforts to comprehensively catalog the identity and features of transcripts present in a variety of species, tissues and cell lines revealed that a large fraction of the mammalian genome is transcribed in at least some settings. A large number of these transcripts encode long non-coding RNAs (lncRNAs). Many lncRNAs overlap or are anti-sense to protein coding genes and others overlap small RNAs. However, a large number are independent of any previously known mRNA or small RNA. While the functions of a majority of these lncRNAs are unknown, many appear to play roles in gene regulation. Many lncRNAs have species-specific and cell type specific expression patterns and their evolutionary origins are varied. While technological challenges have hindered getting a full picture of the diversity and transcript structure of all of the transcripts arising from lncRNA loci, new technologies including single molecule nanopore sequencing and single cell RNA sequencing promise to generate a comprehensive picture of the mammalian transcriptome.
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Affiliation(s)
- Sofie R Salama
- UC Santa Cruz Genomics Institute, Department of Biomolecular Engineering and Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
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8
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Abstract
The human brain is characterized by the large size and intricate folding of its cerebral cortex, which are fundamental for our higher cognitive function and frequently altered in pathological dysfunction. Cortex folding is not unique to humans, nor even to primates, but is common across mammals. Cortical growth and folding are the result of complex developmental processes that involve neural stem and progenitor cells and their cellular lineages, the migration and differentiation of neurons, and the genetic programs that regulate and fine-tune these processes. All these factors combined generate mechanical stress and strain on the developing neural tissue, which ultimately drives orderly cortical deformation and folding. In this review we examine and summarize the current knowledge on the molecular, cellular, histogenic and mechanical mechanisms that are involved in and influence folding of the cerebral cortex, and how they emerged and changed during mammalian evolution. We discuss the main types of pathological malformations of human cortex folding, their specific developmental origin, and how investigating their genetic causes has illuminated our understanding of key events involved. We close our review by presenting the state-of-the-art animal and in vitro models of cortex folding that are currently used to study these devastating developmental brain disorders in children, and what are the main challenges that remain ahead of us to fully understand brain folding.
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Affiliation(s)
- Lucia Del Valle Anton
- Instituto de Neurociencias, Agencia Estatal Consejo Superior de Investigaciones Científicas, San Juan de Alicante, Alicante, Spain
| | - Victor Borrell
- Instituto de Neurociencias, Agencia Estatal Consejo Superior de Investigaciones Científicas, San Juan de Alicante, Alicante, Spain
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9
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Vervoort L, Dierckxsens N, Pereboom Z, Capozzi O, Rocchi M, Shaikh TH, Vermeesch JR. 22q11.2 Low Copy Repeats Expanded in the Human Lineage. Front Genet 2021; 12:706641. [PMID: 34335701 PMCID: PMC8320366 DOI: 10.3389/fgene.2021.706641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/23/2021] [Indexed: 11/13/2022] Open
Abstract
Segmental duplications or low copy repeats (LCRs) constitute duplicated regions interspersed in the human genome, currently neglected in standard analyses due to their extreme complexity. Recent functional studies have indicated the potential of genes within LCRs in synaptogenesis, neuronal migration, and neocortical expansion in the human lineage. One of the regions with the highest proportion of duplicated sequence is the 22q11.2 locus, carrying eight LCRs (LCR22-A until LCR22-H), and rearrangements between them cause the 22q11.2 deletion syndrome. The LCR22-A block was recently reported to be hypervariable in the human population. It remains unknown whether this variability also exists in non-human primates, since research is strongly hampered by the presence of sequence gaps in the human and non-human primate reference genomes. To chart the LCR22 haplotypes and the associated inter- and intra-species variability, we de novo assembled the region in non-human primates by a combination of optical mapping techniques. A minimal and likely ancient haplotype is present in the chimpanzee, bonobo, and rhesus monkey without intra-species variation. In addition, the optical maps identified assembly errors and closed gaps in the orthologous chromosome 22 reference sequences. These findings indicate the LCR22 expansion to be unique to the human population, which might indicate involvement of the region in human evolution and adaptation. Those maps will enable LCR22-specific functional studies and investigate potential associations with the phenotypic variability in the 22q11.2 deletion syndrome.
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Affiliation(s)
| | | | - Zjef Pereboom
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
- Evolutionary Ecology Group, Department of Biology, Antwerp University, Antwerp, Belgium
| | | | | | - Tamim H. Shaikh
- Section of Genetics and Metabolism, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States
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10
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Wu J, Liu Y, Zhao Y. Systematic Review on Local Ancestor Inference From a Mathematical and Algorithmic Perspective. Front Genet 2021; 12:639877. [PMID: 34108987 PMCID: PMC8181461 DOI: 10.3389/fgene.2021.639877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/12/2021] [Indexed: 11/20/2022] Open
Abstract
Genotypic data provide deep insights into the population history and medical genetics. The local ancestry inference (LAI) (also termed local ancestry deconvolution) method uses the hidden Markov model (HMM) to solve the mathematical problem of ancestry reconstruction based on genomic data. HMM is combined with other statistical models and machine learning techniques for particular genetic tasks in a series of computer tools. In this article, we surveyed the mathematical structure, application characteristics, historical development, and benchmark analysis of the LAI method in detail, which will help researchers better understand and further develop LAI methods. Firstly, we extensively explore the mathematical structure of each model and its characteristic applications. Next, we use bibliometrics to show detailed model application fields and list articles to elaborate on the historical development. LAI publications had experienced a peak period during 2006-2016 and had kept on moving in the following years. The efficiency, accuracy, and stability of the existing models were evaluated by the benchmark. We find that phased data had higher accuracy in comparison with unphased data. We summarize these models with their distinct advantages and disadvantages. The Loter model uses dynamic programming to obtain a globally optimal solution with its parameter-free advantage. Aligned bases can be used directly in the Seqmix model if the genotype is hard to call. This research may help model developers to realize current challenges, develop more advanced models, and enable scholars to select appropriate models according to given populations and datasets.
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Affiliation(s)
- Jie Wu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yangxiu Liu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
| | - Yiqiang Zhao
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
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11
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Shew CJ, Carmona-Mora P, Soto DC, Mastoras M, Roberts E, Rosas J, Jagannathan D, Kaya G, O'Geen H, Dennis MY. Diverse Molecular Mechanisms Contribute to Differential Expression of Human Duplicated Genes. Mol Biol Evol 2021; 38:3060-3077. [PMID: 34009325 PMCID: PMC8321529 DOI: 10.1093/molbev/msab131] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 04/08/2021] [Accepted: 04/28/2021] [Indexed: 12/24/2022] Open
Abstract
Emerging evidence links genes within human-specific segmental duplications (HSDs) to traits and diseases unique to our species. Strikingly, despite being nearly identical by sequence (>98.5%), paralogous HSD genes are differentially expressed across human cell and tissue types, though the underlying mechanisms have not been examined. We compared cross-tissue mRNA levels of 75 HSD genes from 30 families between humans and chimpanzees and found expression patterns consistent with relaxed selection on or neofunctionalization of derived paralogs. In general, ancestral paralogs exhibited greatest expression conservation with chimpanzee orthologs, though exceptions suggest certain derived paralogs may retain or supplant ancestral functions. Concordantly, analysis of long-read isoform sequencing data sets from diverse human tissues and cell lines found that about half of derived paralogs exhibited globally lower expression. To understand mechanisms underlying these differences, we leveraged data from human lymphoblastoid cell lines (LCLs) and found no relationship between paralogous expression divergence and post-transcriptional regulation, sequence divergence, or copy-number variation. Considering cis-regulation, we reanalyzed ENCODE data and recovered hundreds of previously unidentified candidate CREs in HSDs. We also generated large-insert ChIP-sequencing data for active chromatin features in an LCL to better distinguish paralogous regions. Some duplicated CREs were sufficient to drive differential reporter activity, suggesting they may contribute to divergent cis-regulation of paralogous genes. This work provides evidence that cis-regulatory divergence contributes to novel expression patterns of recent gene duplicates in humans.
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Affiliation(s)
- Colin J Shew
- Genome Center, University of California Davis, CA, USA.,Integrative Genetics and Genomics Graduate Group, University of California Davis, CA, USA
| | - Paulina Carmona-Mora
- Genome Center, University of California Davis, CA, USA.,MIND Institute, University of California, Davis, CA, USA.,Autism Research Training Program, University of California, Davis, CA, USA
| | - Daniela C Soto
- Genome Center, University of California Davis, CA, USA.,Integrative Genetics and Genomics Graduate Group, University of California Davis, CA, USA
| | - Mira Mastoras
- Genome Center, University of California Davis, CA, USA
| | | | - Joseph Rosas
- Genome Center, University of California Davis, CA, USA.,Postbaccalaureate Research Education Program, University of California, Davis, CA, USA
| | | | - Gulhan Kaya
- Genome Center, University of California Davis, CA, USA
| | | | - Megan Y Dennis
- Genome Center, University of California Davis, CA, USA.,Integrative Genetics and Genomics Graduate Group, University of California Davis, CA, USA.,MIND Institute, University of California, Davis, CA, USA.,Autism Research Training Program, University of California, Davis, CA, USA.,Postbaccalaureate Research Education Program, University of California, Davis, CA, USA.,Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
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12
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Murphy WJ, Foley NM, Bredemeyer KR, Gatesy J, Springer MS. Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation. Annu Rev Anim Biosci 2020; 9:29-53. [PMID: 33228377 DOI: 10.1146/annurev-animal-061220-023149] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genomes of placental mammals are being sequenced at an unprecedented rate. Alignments of hundreds, and one day thousands, of genomes spanning the rich living and extinct diversity of species offer unparalleled power to resolve phylogenetic controversies, identify genomic innovations of adaptation, and dissect the genetic architecture of reproductive isolation. We highlight outstanding questions about the earliest phases of placental mammal diversification and the promise of newer methods, as well as remaining challenges, toward using whole genome data to resolve placental mammal phylogeny. The next phase of mammalian comparative genomics will see the completion and application of finished-quality, gapless genome assemblies from many ordinal lineages and closely related species. Interspecific comparisons between the most hypervariable genomic loci will likely reveal large, but heretofore mostly underappreciated, effects on population divergence, morphological innovation, and the origin of new species.
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Affiliation(s)
- William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
| | - Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Mark S Springer
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, California 92521, USA
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13
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Lodewijk GA, Fernandes DP, Vretzakis I, Savage JE, Jacobs FMJ. Evolution of Human Brain Size-Associated NOTCH2NL Genes Proceeds toward Reduced Protein Levels. Mol Biol Evol 2020; 37:2531-2548. [PMID: 32330268 PMCID: PMC7475042 DOI: 10.1093/molbev/msaa104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ever since the availability of genomes from Neanderthals, Denisovans, and ancient humans, the field of evolutionary genomics has been searching for protein-coding variants that may hold clues to how our species evolved over the last ∼600,000 years. In this study, we identify such variants in the human-specific NOTCH2NL gene family, which were recently identified as possible contributors to the evolutionary expansion of the human brain. We find evidence for the existence of unique protein-coding NOTCH2NL variants in Neanderthals and Denisovans which could affect their ability to activate Notch signaling. Furthermore, in the Neanderthal and Denisovan genomes, we find unusual NOTCH2NL configurations, not found in any of the modern human genomes analyzed. Finally, genetic analysis of archaic and modern humans reveals ongoing adaptive evolution of modern human NOTCH2NL genes, identifying three structural variants acting complementary to drive our genome to produce a lower dosage of NOTCH2NL protein. Because copy-number variations of the 1q21.1 locus, encompassing NOTCH2NL genes, are associated with severe neurological disorders, this seemingly contradicting drive toward low levels of NOTCH2NL protein indicates that the optimal dosage of NOTCH2NL may have not yet been settled in the human population.
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Affiliation(s)
- Gerrald A Lodewijk
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Diana P Fernandes
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Iraklis Vretzakis
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeanne E Savage
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Complex Trait Genetics
| | - Frank M J Jacobs
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Complex Trait Genetics
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14
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di Porzio U. A bigger brain for a more complex environment. Rev Neurosci 2020; 31:/j/revneuro.ahead-of-print/revneuro-2020-0041/revneuro-2020-0041.xml. [PMID: 32924383 DOI: 10.1515/revneuro-2020-0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/04/2020] [Indexed: 11/15/2022]
Abstract
The environment increased complexity required more neural functions to develop in the hominin brains, and the hominins adapted to the complexity by developing a bigger brain with a greater interconnection between its parts. Thus, complex environments drove the growth of the brain. In about two million years during hominin evolution, the brain increased three folds in size, one of the largest and most complex amongst mammals, relative to body size. The size increase has led to anatomical reorganization and complex neuronal interactions in a relatively small skull. At birth, the human brain is only about 20% of its adult size. That facilitates the passage through the birth canal. Therefore, the human brain, especially cortex, develops postnatally in a rich stimulating environment with continuous brain wiring and rewiring and insertion of billions of new neurons. One of the consequence is that in the newborn brain, neuroplasticity is always turned "on" and it remains active throughout life, which gave humans the ability to adapt to complex and often hostile environments, integrate external experiences, solve problems, elaborate abstract ideas and innovative technologies, store a lot of information. Besides, hominins acquired unique abilities as music, language, and intense social cooperation. Overwhelming ecological, social, and cultural challenges have made the human brain so unique. From these events, as well as the molecular genetic changes that took place in those million years, under the pressure of natural selection, derive the distinctive cognitive abilities that have led us to complex social organizations and made our species successful.
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Affiliation(s)
- Umberto di Porzio
- Developmental Neurobiology Laboratory, Institute of Genetics and Biophysics, CNR, Via Pietro Castellino 111, 80128 Naples, Italy
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15
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Cantsilieris S, Sunkin SM, Johnson ME, Anaclerio F, Huddleston J, Baker C, Dougherty ML, Underwood JG, Sulovari A, Hsieh P, Mao Y, Catacchio CR, Malig M, Welch AE, Sorensen M, Munson KM, Jiang W, Girirajan S, Ventura M, Lamb BT, Conlon RA, Eichler EE. An evolutionary driver of interspersed segmental duplications in primates. Genome Biol 2020; 21:202. [PMID: 32778141 PMCID: PMC7419210 DOI: 10.1186/s13059-020-02074-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 06/08/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The complex interspersed pattern of segmental duplications in humans is responsible for rearrangements associated with neurodevelopmental disease, including the emergence of novel genes important in human brain evolution. We investigate the evolution of LCR16a, a putative driver of this phenomenon that encodes one of the most rapidly evolving human-ape gene families, nuclear pore interacting protein (NPIP). RESULTS Comparative analysis shows that LCR16a has independently expanded in five primate lineages over the last 35 million years of primate evolution. The expansions are associated with independent lineage-specific segmental duplications flanking LCR16a leading to the emergence of large interspersed duplication blocks at non-orthologous chromosomal locations in each primate lineage. The intron-exon structure of the NPIP gene family has changed dramatically throughout primate evolution with different branches showing characteristic gene models yet maintaining an open reading frame. In the African ape lineage, we detect signatures of positive selection that occurred after a transition to more ubiquitous expression among great ape tissues when compared to Old World and New World monkeys. Mouse transgenic experiments from baboon and human genomic loci confirm these expression differences and suggest that the broader ape expression pattern arose due to mutational changes that emerged in cis. CONCLUSIONS LCR16a promotes serial interspersed duplications and creates hotspots of genomic instability that appear to be an ancient property of primate genomes. Dramatic changes to NPIP gene structure and altered tissue expression preceded major bouts of positive selection in the African ape lineage, suggestive of a gene undergoing strong adaptive evolution.
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Affiliation(s)
- Stuart Cantsilieris
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Present Address: Centre for Eye Research Australia, Department of Surgery (Ophthalmology), University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | | | - Matthew E Johnson
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Fabio Anaclerio
- Department of Biology-Genetics, University of Bari, Bari, Italy
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, 98195, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Max L Dougherty
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Jason G Underwood
- Pacific Biosciences (PacBio) of California, Incorporated, Menlo Park, CA, 94025, USA
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - PingHsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Yafei Mao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | | | - Maika Malig
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Present Address: Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616, USA
- Present Address: Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, 95616, USA
| | - AnneMarie E Welch
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Present Address: Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Melanie Sorensen
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Weihong Jiang
- Case Transgenic and Targeting Facility, Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, Department of Anthropology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Mario Ventura
- Department of Biology-Genetics, University of Bari, Bari, Italy
| | - Bruce T Lamb
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Ronald A Conlon
- Case Transgenic and Targeting Facility, Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
- Howard Hughes Medical Institute, University of Washington School of Medicine, 3720 15th Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA.
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16
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Shen F, Kidd JM. Rapid, Paralog-Sensitive CNV Analysis of 2457 Human Genomes Using QuicK-mer2. Genes (Basel) 2020; 11:genes11020141. [PMID: 32013076 PMCID: PMC7073954 DOI: 10.3390/genes11020141] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 12/22/2022] Open
Abstract
Gene duplication is a major mechanism for the evolution of gene novelty, and copy-number variation makes a major contribution to inter-individual genetic diversity. However, most approaches for studying copy-number variation rely upon uniquely mapping reads to a genome reference and are unable to distinguish among duplicated sequences. Specialized approaches to interrogate specific paralogs are comparatively slow and have a high degree of computational complexity, limiting their effective application to emerging population-scale data sets. We present QuicK-mer2, a self-contained, mapping-free approach that enables the rapid construction of paralog-specific copy-number maps from short-read sequence data. This approach is based on the tabulation of unique k-mer sequences from short-read data sets, and is able to analyze a 20X coverage human genome in approximately 20 min. We applied our approach to newly released sequence data from the 1000 Genomes Project, constructed paralog-specific copy-number maps from 2457 unrelated individuals, and uncovered copy-number variation of paralogous genes. We identify nine genes where none of the analyzed samples have a copy number of two, 92 genes where the majority of samples have a copy number other than two, and describe rare copy number variation effecting multiple genes at the APOBEC3 locus.
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Affiliation(s)
- Feichen Shen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Jeffrey M. Kidd
- Department of Human Genetics and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence:
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17
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The human-specific paralogs SRGAP2B and SRGAP2C differentially modulate SRGAP2A-dependent synaptic development. Sci Rep 2019; 9:18692. [PMID: 31822692 PMCID: PMC6904453 DOI: 10.1038/s41598-019-54887-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023] Open
Abstract
Human-specific gene duplications (HSGDs) have recently emerged as key modifiers of brain development and evolution. However, the molecular mechanisms underlying the function of HSGDs remain often poorly understood. In humans, a truncated duplication of SRGAP2A led to the emergence of two human-specific paralogs: SRGAP2B and SRGAP2C. The ancestral copy SRGAP2A limits synaptic density and promotes maturation of both excitatory (E) and inhibitory (I) synapses received by cortical pyramidal neurons (PNs). SRGAP2C binds to and inhibits all known functions of SRGAP2A leading to an increase in E and I synapse density and protracted synapse maturation, traits characterizing human cortical neurons. Here, we demonstrate how the evolutionary changes that led to the emergence of SRGAP2 HSGDs generated proteins that, in neurons, are intrinsically unstable and, upon hetero-dimerization with SRGAP2A, reduce SRGAP2A levels in a proteasome-dependent manner. Moreover, we show that, despite only a few non-synonymous mutations specifically targeting arginine residues, SRGAP2C is unique compared to SRGAP2B in its ability to induce long-lasting changes in synaptic density throughout adulthood. These mutations led to the ability of SRGAP2C to inhibit SRGAP2A function and thereby contribute to the emergence of human-specific features of synaptic development during evolution.
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18
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Suzuki IK. Molecular drivers of human cerebral cortical evolution. Neurosci Res 2019; 151:1-14. [PMID: 31175883 DOI: 10.1016/j.neures.2019.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 01/10/2023]
Abstract
One of the most important questions in human evolutionary biology is how our ancestor has acquired an expanded volume of the cerebral cortex, which may have significantly impacted on improving our cognitive abilities. Recent comparative approaches have identified developmental features unique to the human or hominid cerebral cortex, not shared with other animals including conventional experimental models. In addition, genomic, transcriptomic, and epigenomic signatures associated with human- or hominid-specific processes of the cortical development are becoming identified by virtue of technical progress in the deep nucleotide sequencing. This review discusses ontogenic and phylogenetic processes of the human cerebral cortex, followed by the introduction of recent comprehensive approaches identifying molecular mechanisms potentially driving the evolutionary changes in the cortical development.
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Affiliation(s)
- Ikuo K Suzuki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan; VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences, Leuven Brain Institute, KULeuven, 3000 Leuven, Belgium; Université Libre de Bruxelles (U.L.B.), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), ULB Neuroscience Institute (UNI), 1070 Brussels, Belgium.
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19
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Press MO, Hall AN, Morton EA, Queitsch C. Substitutions Are Boring: Some Arguments about Parallel Mutations and High Mutation Rates. Trends Genet 2019; 35:253-264. [PMID: 30797597 PMCID: PMC6435258 DOI: 10.1016/j.tig.2019.01.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/20/2018] [Accepted: 01/14/2019] [Indexed: 12/31/2022]
Abstract
Extant genomes are largely shaped by global transposition, copy-number fluctuation, and rearrangement of DNA sequences rather than by substitutions of single nucleotides. Although many of these large-scale mutations have low probabilities and are unlikely to repeat, others are recurrent or predictable in their effects, leading to stereotyped genome architectures and genetic variation in both eukaryotes and prokaryotes. Such recurrent, parallel mutation modes can profoundly shape the paths taken by evolution and undermine common models of evolutionary genetics. Similar patterns are also evident at the smaller scales of individual genes or short sequences. The scale and extent of this 'non-substitution' variation has recently come into focus through the advent of new genomic technologies; however, it is still not widely considered in genotype-phenotype association studies. In this review we identify common features of these disparate mutational phenomena and comment on the importance and interpretation of these mutational patterns.
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Affiliation(s)
| | - Ashley N Hall
- Department of Genome Sciences, University of Washington, Seattle, WA 91895, USA; Department of Molecular and Cellular Biology, University of Washington, Seattle, WA 91895, USA
| | - Elizabeth A Morton
- Department of Genome Sciences, University of Washington, Seattle, WA 91895, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 91895, USA.
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20
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Llinares-Benadero C, Borrell V. Deconstructing cortical folding: genetic, cellular and mechanical determinants. Nat Rev Neurosci 2019; 20:161-176. [DOI: 10.1038/s41583-018-0112-2] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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21
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Dougherty ML, Underwood JG, Nelson BJ, Tseng E, Munson KM, Penn O, Nowakowski TJ, Pollen AA, Eichler EE. Transcriptional fates of human-specific segmental duplications in brain. Genome Res 2018; 28:1566-1576. [PMID: 30228200 PMCID: PMC6169893 DOI: 10.1101/gr.237610.118] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/07/2018] [Indexed: 01/27/2023]
Abstract
Despite the importance of duplicate genes for evolutionary adaptation, accurate gene annotation is often incomplete, incorrect, or lacking in regions of segmental duplication. We developed an approach combining long-read sequencing and hybridization capture to yield full-length transcript information and confidently distinguish between nearly identical genes/paralogs. We used biotinylated probes to enrich for full-length cDNA from duplicated regions, which were then amplified, size-fractionated, and sequenced using single-molecule, long-read sequencing technology, permitting us to distinguish between highly identical genes by virtue of multiple paralogous sequence variants. We examined 19 gene families as expressed in developing and adult human brain, selected for their high sequence identity (average >99%) and overlap with human-specific segmental duplications (SDs). We characterized the transcriptional differences between related paralogs to better understand the birth-death process of duplicate genes and particularly how the process leads to gene innovation. In 48% of the cases, we find that the expressed duplicates have changed substantially from their ancestral models due to novel sites of transcription initiation, splicing, and polyadenylation, as well as fusion transcripts that connect duplication-derived exons with neighboring genes. We detect unannotated open reading frames in genes currently annotated as pseudogenes, while relegating other duplicates to nonfunctional status. Our method significantly improves gene annotation, specifically defining full-length transcripts, isoforms, and open reading frames for new genes in highly identical SDs. The approach will be more broadly applicable to genes in structurally complex regions of other genomes where the duplication process creates novel genes important for adaptive traits.
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Affiliation(s)
- Max L Dougherty
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Jason G Underwood
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Pacific Biosciences (PacBio) of California, Incorporated, Menlo Park, California 94025, USA
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Elizabeth Tseng
- Pacific Biosciences (PacBio) of California, Incorporated, Menlo Park, California 94025, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Osnat Penn
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Tomasz J Nowakowski
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94158, USA.,Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Alex A Pollen
- Department of Neurology, University of California, San Francisco, San Francisco, California 94158, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
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22
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1q21.1 microduplication: large verbal-nonverbal performance discrepancy and ddPCR assays of HYDIN/HYDIN2 copy number. NPJ Genom Med 2018; 3:24. [PMID: 30155272 PMCID: PMC6105585 DOI: 10.1038/s41525-018-0059-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 06/22/2018] [Accepted: 06/22/2018] [Indexed: 02/04/2023] Open
Abstract
Microduplication of chromosome 1q21.1 is observed in ~0.03% of adults. It has a highly variable, incompletely penetrant phenotype that can include intellectual disability, global developmental delay, specific learning disabilities, autism, schizophrenia, heart anomalies and dysmorphic features. We evaluated a 10-year-old-male with a 1q21.1 duplication by CGH microarray. He presented with major attention deficits, phonological dysphasia, poor fine motor skills, dysmorphia and mild autistic features, but not the typical macrocephaly. Neuropsychiatric evaluation demonstrated a novel phenotype: an unusually large discrepancy between non-verbal capacities (borderline-impaired WISC-IV index scores of 70 for Working Memory and 68 for Processing Speed) vs. strong verbal skills - scores of 126 for Verbal Comprehension (superior) and 111 for Perceptual Reasoning (normal). HYDIN2 has been hypothesized to underlie macrocephaly and perhaps cognitive deficits in this syndrome, but assessment of HYDIN2 copy number by microarray is difficult because of extensive segmental duplications. We performed whole-genome sequencing which supported HYDIN2 duplication (chr1:146,370,001-148,590,000, 2.22 Mb, hg38). To evaluate copy number more rigorously we developed droplet digital PCR assays of HYDIN2 (targeting unique 1 kb and 6 kb insertions) and its paralog HYDIN (targeting a unique 154 bp segment outside the HYDIN2 overlap). In an independent cohort, ddPCR was concordant with previous microarray data. Duplication of HYDIN2 was confirmed in the patient by ddPCR. This case demonstrates that a large discrepancy of verbal and non-verbal abilities can occur in 1q21.1 duplication syndrome, but it remains unclear whether this has a specific genomic basis. These ddPCR assays may be useful for future research on HYDIN2 copy number.
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23
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Brain organoids as models to study human neocortex development and evolution. Curr Opin Cell Biol 2018; 55:8-16. [PMID: 30006054 DOI: 10.1016/j.ceb.2018.06.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 06/11/2018] [Accepted: 06/14/2018] [Indexed: 11/20/2022]
Abstract
Since their recent development, organoids that emulate human brain tissue have allowed in vitro neural development studies to go beyond the limits of monolayer culture systems, such as neural rosettes. We present here a review of organoid studies that focuses on cortical wall development, starting with a technical comparison between pre-patterning and self-patterning brain organoid protocols. We then follow neocortex development in space and time and list those aspects where organoids have succeeded in emulating in vivo development, as well as those aspects that continue to be pending tasks. Finally, we present a summary of medical and evolutionary insight made possible by organoid technology.
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24
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Fiddes IT, Lodewijk GA, Mooring M, Bosworth CM, Ewing AD, Mantalas GL, Novak AM, van den Bout A, Bishara A, Rosenkrantz JL, Lorig-Roach R, Field AR, Haeussler M, Russo L, Bhaduri A, Nowakowski TJ, Pollen AA, Dougherty ML, Nuttle X, Addor MC, Zwolinski S, Katzman S, Kriegstein A, Eichler EE, Salama SR, Jacobs FMJ, Haussler D. Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis. Cell 2018; 173:1356-1369.e22. [PMID: 29856954 DOI: 10.1016/j.cell.2018.03.051] [Citation(s) in RCA: 311] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/16/2018] [Accepted: 03/21/2018] [Indexed: 12/12/2022]
Abstract
Genetic changes causing brain size expansion in human evolution have remained elusive. Notch signaling is essential for radial glia stem cell proliferation and is a determinant of neuronal number in the mammalian cortex. We find that three paralogs of human-specific NOTCH2NL are highly expressed in radial glia. Functional analysis reveals that different alleles of NOTCH2NL have varying potencies to enhance Notch signaling by interacting directly with NOTCH receptors. Consistent with a role in Notch signaling, NOTCH2NL ectopic expression delays differentiation of neuronal progenitors, while deletion accelerates differentiation into cortical neurons. Furthermore, NOTCH2NL genes provide the breakpoints in 1q21.1 distal deletion/duplication syndrome, where duplications are associated with macrocephaly and autism and deletions with microcephaly and schizophrenia. Thus, the emergence of human-specific NOTCH2NL genes may have contributed to the rapid evolution of the larger human neocortex, accompanied by loss of genomic stability at the 1q21.1 locus and resulting recurrent neurodevelopmental disorders.
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Affiliation(s)
- Ian T Fiddes
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Gerrald A Lodewijk
- University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
| | | | | | - Adam D Ewing
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Gary L Mantalas
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA; Molecular, Cell and Developmental Biology Department, UC Santa Cruz, Santa Cruz, CA, USA
| | - Adam M Novak
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Anouk van den Bout
- University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
| | - Alex Bishara
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Jimi L Rosenkrantz
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA; Howard Hughes Medical Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | | | - Andrew R Field
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA; Molecular, Cell and Developmental Biology Department, UC Santa Cruz, Santa Cruz, CA, USA
| | | | - Lotte Russo
- University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
| | - Aparna Bhaduri
- Department of Neurology and the Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at the University of California, San Francisco, San Francisco, CA, USA
| | - Tomasz J Nowakowski
- Department of Neurology and the Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at the University of California, San Francisco, San Francisco, CA, USA
| | - Alex A Pollen
- Department of Neurology and the Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at the University of California, San Francisco, San Francisco, CA, USA
| | - Max L Dougherty
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Xander Nuttle
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | | | - Simon Zwolinski
- Department of Cytogenetics, Northern Genetics Service, Institute of Genetic Medicine, Newcastle upon Tyne, UK
| | - Sol Katzman
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Arnold Kriegstein
- Department of Neurology and the Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at the University of California, San Francisco, San Francisco, CA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Sofie R Salama
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA; Howard Hughes Medical Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Frank M J Jacobs
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA; University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands.
| | - David Haussler
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA; Howard Hughes Medical Institute, UC Santa Cruz, Santa Cruz, CA, USA.
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25
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Florio M, Heide M, Pinson A, Brandl H, Albert M, Winkler S, Wimberger P, Huttner WB, Hiller M. Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex. eLife 2018; 7:32332. [PMID: 29561261 PMCID: PMC5898914 DOI: 10.7554/elife.32332] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/09/2018] [Indexed: 01/21/2023] Open
Abstract
Understanding the molecular basis that underlies the expansion of the neocortex during primate, and notably human, evolution requires the identification of genes that are particularly active in the neural stem and progenitor cells of the developing neocortex. Here, we have used existing transcriptome datasets to carry out a comprehensive screen for protein-coding genes preferentially expressed in progenitors of fetal human neocortex. We show that 15 human-specific genes exhibit such expression, and many of them evolved distinct neural progenitor cell-type expression profiles and levels compared to their ancestral paralogs. Functional studies on one such gene, NOTCH2NL, demonstrate its ability to promote basal progenitor proliferation in mice. An additional 35 human genes with progenitor-enriched expression are shown to have orthologs only in primates. Our study provides a resource of genes that are promising candidates to exert specific, and novel, roles in neocortical development during primate, and notably human, evolution.
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Affiliation(s)
- Marta Florio
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Michael Heide
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Anneline Pinson
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Holger Brandl
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Mareike Albert
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Pauline Wimberger
- Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
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26
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Gourari I, Schubert R, Prasad A. 1q21.1 Duplication syndrome and epilepsy: Case report and review. NEUROLOGY-GENETICS 2018; 4:e219. [PMID: 29379884 PMCID: PMC5773857 DOI: 10.1212/nxg.0000000000000219] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 11/09/2017] [Indexed: 02/04/2023]
Affiliation(s)
- Ioulia Gourari
- Department of Pediatrics (I.G.), New York Presbyterian Brooklyn Methodist Hospital, Brooklyn; Center for Neurological and Neurodevelopmental Health (R.S.), Voorhees Township, NJ; and Lineagen (A.P.), Salt Lake City, UT
| | - Romaine Schubert
- Department of Pediatrics (I.G.), New York Presbyterian Brooklyn Methodist Hospital, Brooklyn; Center for Neurological and Neurodevelopmental Health (R.S.), Voorhees Township, NJ; and Lineagen (A.P.), Salt Lake City, UT
| | - Aparna Prasad
- Department of Pediatrics (I.G.), New York Presbyterian Brooklyn Methodist Hospital, Brooklyn; Center for Neurological and Neurodevelopmental Health (R.S.), Voorhees Township, NJ; and Lineagen (A.P.), Salt Lake City, UT
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27
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Heide M, Long KR, Huttner WB. Novel gene function and regulation in neocortex expansion. Curr Opin Cell Biol 2017; 49:22-30. [PMID: 29227861 DOI: 10.1016/j.ceb.2017.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/18/2017] [Accepted: 11/26/2017] [Indexed: 01/01/2023]
Abstract
The expansion of the neocortex during human evolution is due to changes in our genome that result in increased and prolonged proliferation of neural stem and progenitor cells during neocortex development. Three principal types of such genomic changes can be distinguished, first, novel gene regulation in human, second, novel function in human of genes existing in both human and non-human species, and third, novel, human-specific genes. The latter comprise both, increases in the copy number of genes existing also in non-human species, and the emergence of genes giving rise to unique, human-specific gene products. Examples of all these types of changes in the human genome have been identified, with ARHGAP11B constituting a paradigmatic example of a unique, human-specific protein.
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Affiliation(s)
- Michael Heide
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, D-01307 Dresden, Germany
| | - Katherine R Long
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, D-01307 Dresden, Germany
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, D-01307 Dresden, Germany.
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