1
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Zha J, Chen Y, Cao F, Zhong J, Yu X, Wu H. Identification of novel BCL11A variant in a patient with developmental delay and behavioural differences. Int J Dev Neurosci 2024. [PMID: 39187446 DOI: 10.1002/jdn.10371] [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: 07/10/2024] [Revised: 08/11/2024] [Accepted: 08/14/2024] [Indexed: 08/28/2024] Open
Abstract
BACKGROUND The BCL11A gene is involved in disorders including intellectual disability syndrome (IDS), encodes a zinc finger protein highly expressed in haematopoietic and brain and acts as a transcriptional repressor of foetal haemoglobin (HbF). De novo variants in BCL11A have been associated with IDS, which is characterized by developmental delays, autism spectrum disorder (ASD) and speech and language delays. The reports of BCL11A gene variants are still limited worldwide, and additional cases are needed to expand the variant and phenotype spectrums. METHODS The patient is a 5-year-old girl who was hospitalized due to developmental delays. After analysing her clinical and pathological characterizations, whole-exome sequencing (WES) was performed for pathogenic genetic variants of developmental delay and behavioural differences. Candidate variant in BCL11A gene was identified and further validated by Sanger sequencing. RESULTS A heterozygous variant, c.1442delA (p.Glu481Glyfs*25), was identified in exon 4 of the BCL11A gene through WES. This variant results in a truncated expression of the encoded protein. This de novo variant was confirmed by Sanger sequencing. The language delay and behavioural differences were prominent in our patient. CONCLUSION Our finding demonstrates that BCL11A variant may cause developmental delay and behavioural differences, expanding the genetic spectrum of the BCL11A gene.
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Affiliation(s)
- Jian Zha
- Department of Neurology, Jiangxi Provincial Children's Hospital, Nanchang, People's Republic of China
| | - Yong Chen
- Department of Neurology, Jiangxi Provincial Children's Hospital, Nanchang, People's Republic of China
| | - Fangfang Cao
- Department of Neurology, Jiangxi Provincial Children's Hospital, Nanchang, People's Republic of China
| | - Jianmin Zhong
- Department of Neurology, Jiangxi Provincial Children's Hospital, Nanchang, People's Republic of China
| | - Xiongying Yu
- Department of Neurology, Jiangxi Provincial Children's Hospital, Nanchang, People's Republic of China
| | - Huaping Wu
- Department of Neurology, Jiangxi Provincial Children's Hospital, Nanchang, People's Republic of China
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Murthy S, Nongthomba U. Role of the BCL11A/B Homologue Chronophage (Cph) in Locomotor Behaviour of Drosophila melanogaster. Neuroscience 2024; 551:1-16. [PMID: 38763224 DOI: 10.1016/j.neuroscience.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/21/2024]
Abstract
Functioning of the nervous system requires proper formation and specification of neurons as well as accurate connectivity and signalling between them. Locomotor behaviour depends upon these events that occur during neural development, and any aberration in them could result in motor disorders. Transcription factors are believed to be master regulators that control these processes, but very few linked to behaviour have been identified so far. The Drosophila homologue of BCL11A (CTIP1) and BCL11B (CTIP2), Chronophage (Cph), was recently shown to be involved in temporal patterning of neural stem cells but its role in post-mitotic neurons is not known. We show that knockdown of Cph in neurons during development results in animals with locomotor defects at both larval and adult stages. The defects are more severe in adults, with inability to stand, uncoordinated behaviour and complete loss of ability to walk, climb, or fly. These defects are similar to the motor difficulties observed in some patients with mutations in BCL11A and BCL11B. Electrophysiological recordings showed reduced evoked activity and irregular neuronal firing. All Cph-expressing neurons in the ventral nerve cord are glutamatergic. Our results imply that Cph modulates primary locomotor activity through configuration of glutamatergic neurons. Thus, this study ascribes a hitherto unknown role to Cph in locomotor behaviour of Drosophila melanogaster.
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Affiliation(s)
- Smrithi Murthy
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru 560 012, India.
| | - Upendra Nongthomba
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru 560 012, India.
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3
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Laugwitz L, Cheng F, Collins SC, Hustinx A, Navarro N, Welsch S, Cox H, Hsieh TC, Vijayananth A, Buchert R, Bender B, Efthymiou S, Murphy D, Zafar F, Rana N, Grasshoff U, Falb RJ, Grimmel M, Seibt A, Zheng W, Ghaedi H, Thirion M, Couette S, Azizimalamiri R, Sadeghian S, Galehdari H, Zamani M, Zeighami J, Sedaghat A, Ramshe SM, Zare A, Alipoor B, Klee D, Sturm M, Ossowski S, Houlden H, Riess O, Wieczorek D, Gavin R, Maroofian R, Krawitz P, Yalcin B, Distelmaier F, Haack TB. ZSCAN10 deficiency causes a neurodevelopmental disorder with characteristic oto-facial malformations. Brain 2024; 147:2471-2482. [PMID: 38386308 PMCID: PMC11224597 DOI: 10.1093/brain/awae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 12/21/2023] [Accepted: 01/21/2024] [Indexed: 02/23/2024] Open
Abstract
Neurodevelopmental disorders are major indications for genetic referral and have been linked to more than 1500 loci including genes encoding transcriptional regulators. The dysfunction of transcription factors often results in characteristic syndromic presentations; however, at least half of these patients lack a genetic diagnosis. The implementation of machine learning approaches has the potential to aid in the identification of new disease genes and delineate associated phenotypes. Next generation sequencing was performed in seven affected individuals with neurodevelopmental delay and dysmorphic features. Clinical characterization included reanalysis of available neuroimaging datasets and 2D portrait image analysis with GestaltMatcher. The functional consequences of ZSCAN10 loss were modelled in mouse embryonic stem cells (mESCs), including a knockout and a representative ZSCAN10 protein truncating variant. These models were characterized by gene expression and western blot analyses, chromatin immunoprecipitation and quantitative PCR (ChIP-qPCR) and immunofluorescence staining. Zscan10 knockout mouse embryos were generated and phenotyped. We prioritized bi-allelic ZSCAN10 loss-of-function variants in seven affected individuals from five unrelated families as the underlying molecular cause. RNA-sequencing analyses in Zscan10-/- mESCs indicated dysregulation of genes related to stem cell pluripotency. In addition, we established in mESCs the loss-of-function mechanism for a representative human ZSCAN10 protein truncating variant by showing alteration of its expression levels and subcellular localization, interfering with its binding to DNA enhancer targets. Deep phenotyping revealed global developmental delay, facial asymmetry and malformations of the outer ear as consistent clinical features. Cerebral MRI showed dysplasia of the semicircular canals as an anatomical correlate of sensorineural hearing loss. Facial asymmetry was confirmed as a clinical feature by GestaltMatcher and was recapitulated in the Zscan10 mouse model along with inner and outer ear malformations. Our findings provide evidence of a novel syndromic neurodevelopmental disorder caused by bi-allelic loss-of-function variants in ZSCAN10.
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Affiliation(s)
- Lucia Laugwitz
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
- Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, University of Tübingen, Tübingen 72076, Germany
| | - Fubo Cheng
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
| | | | - Alexander Hustinx
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn 53127, Germany
| | - Nicolas Navarro
- Biogeosciences, UMR 6282 CNRS, EPHE, Université de Bourgogne, Dijon 2100, France
- EPHE, PSL University, Paris 75014, France
| | - Simon Welsch
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Helen Cox
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women’s and Children’s Hospitals NHS Foundation Trust, Birmingham B15 2TG, UK
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn 53127, Germany
| | - Aswinkumar Vijayananth
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn 53127, Germany
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
| | - Benjamin Bender
- Diagnostic and Interventional Neuroradiology, Radiologic Clinics, University of Tübingen, Tübingen 72076, Germany
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Faisal Zafar
- Pediatric Neurology, Children’s Hospital, Multan 60000, Pakistan
| | - Nuzhat Rana
- Pediatric Neurology, Children’s Hospital, Multan 60000, Pakistan
| | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
- Center for Rare Disease, University of Tübingen, Tübingen 72072, Germany
| | - Ruth J Falb
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
| | - Mona Grimmel
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
| | - Annette Seibt
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Wenxu Zheng
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
| | - Hamid Ghaedi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran
| | - Marie Thirion
- Inserm UMR1231, Université de Bourgogne, Dijon Cedex 21070, France
| | - Sébastien Couette
- Biogeosciences, UMR 6282 CNRS, EPHE, Université de Bourgogne, Dijon 2100, France
- EPHE, PSL University, Paris 75014, France
| | - Reza Azizimalamiri
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6135715794, Iran
| | - Saeid Sadeghian
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6135715794, Iran
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz 6135783151, Iran
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz 6135783151, Iran
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz 6155689467, Iran
| | - Jawaher Zeighami
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz 6155689467, Iran
| | - Alireza Sedaghat
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz 6155689467, Iran
- Diabetes Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6135715794, Iran
| | - Samira Molaei Ramshe
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran
| | - Ali Zare
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran
| | - Behnam Alipoor
- Department of Laboratory Sciences, Faculty of Paramedicine, Yasuj University of Medical Sciences, Yasuj 7591741417, Iran
| | - Dirk Klee
- Department of Pediatric Radiology, Medical Faculty, Institute of Radiology, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
- Genomics England, Queen Mary University of London, London EC1M 6BQ, UK
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen 72076, Germany
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
- Center for Rare Disease, University of Tübingen, Tübingen 72072, Germany
| | - Dagmar Wieczorek
- Medical Faculty and University Hospital Düsseldorf, Institute of Human Genetics, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Ryan Gavin
- West Midlands Regional Genetics Laboratory, Central and South Genomic Laboratory Hub, Birmingham B15 2TG, UK
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn 53127, Germany
| | - Binnaz Yalcin
- Inserm UMR1231, Université de Bourgogne, Dijon Cedex 21070, France
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
- Center for Rare Disease, University of Tübingen, Tübingen 72072, Germany
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4
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BenDavid E, Ramezanian S, Lu Y, Rousseau J, Schroeder A, Lavertu M, Tremblay JP. Emerging Perspectives on Prime Editor Delivery to the Brain. Pharmaceuticals (Basel) 2024; 17:763. [PMID: 38931430 PMCID: PMC11206523 DOI: 10.3390/ph17060763] [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: 05/09/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Prime editing shows potential as a precision genome editing technology, as well as the potential to advance the development of next-generation nanomedicine for addressing neurological disorders. However, turning in prime editors (PEs), which are macromolecular complexes composed of CRISPR/Cas9 nickase fused with a reverse transcriptase and a prime editing guide RNA (pegRNA), to the brain remains a considerable challenge due to physiological obstacles, including the blood-brain barrier (BBB). This review article offers an up-to-date overview and perspective on the latest technologies and strategies for the precision delivery of PEs to the brain and passage through blood barriers. Furthermore, it delves into the scientific significance and possible therapeutic applications of prime editing in conditions related to neurological diseases. It is targeted at clinicians and clinical researchers working on advancing precision nanomedicine for neuropathologies.
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Affiliation(s)
- Eli BenDavid
- Laboratory of Biomaterials and Tissue Engineering, Department of Chemical Engineering, Institute of Biomedical Engineering, Polytechnique Montréal, Montréal, QC H3C 3A7, Canada;
- Division of Human Genetics, Centre de Recherche du CHU de Québec—Université Laval, Québec, QC G1V 4G2, Canada
- Laboratory of Molecular Genetics and Gene Therapy, Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec, QC G1V 0A6, Canada
- Laboratory of Nanopharmacology and Pharmaceutical Nanoscience, Faculty of Pharmacy, Laval University, Québec, QC G1V 4G2, Canada
- Rappaport Faculty of Medicine, Technion—Israel Institute of Technology, Haifa 3525433, Israel
| | - Sina Ramezanian
- Division of Human Genetics, Centre de Recherche du CHU de Québec—Université Laval, Québec, QC G1V 4G2, Canada
- Laboratory of Molecular Genetics and Gene Therapy, Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec, QC G1V 0A6, Canada
| | - Yaoyao Lu
- Division of Human Genetics, Centre de Recherche du CHU de Québec—Université Laval, Québec, QC G1V 4G2, Canada
- Laboratory of Molecular Genetics and Gene Therapy, Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec, QC G1V 0A6, Canada
| | - Joël Rousseau
- Division of Human Genetics, Centre de Recherche du CHU de Québec—Université Laval, Québec, QC G1V 4G2, Canada
| | - Avi Schroeder
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion—Israel Institute of Technology, Haifa 3200003, Israel;
| | - Marc Lavertu
- Laboratory of Biomaterials and Tissue Engineering, Department of Chemical Engineering, Institute of Biomedical Engineering, Polytechnique Montréal, Montréal, QC H3C 3A7, Canada;
| | - Jacques P. Tremblay
- Division of Human Genetics, Centre de Recherche du CHU de Québec—Université Laval, Québec, QC G1V 4G2, Canada
- Laboratory of Molecular Genetics and Gene Therapy, Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec, QC G1V 0A6, Canada
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5
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Martins-Costa C, Wiegers A, Pham VA, Sidhaye J, Doleschall B, Novatchkova M, Lendl T, Piber M, Peer A, Möseneder P, Stuempflen M, Chow SYA, Seidl R, Prayer D, Höftberger R, Kasprian G, Ikeuchi Y, Corsini NS, Knoblich JA. ARID1B controls transcriptional programs of axon projection in an organoid model of the human corpus callosum. Cell Stem Cell 2024; 31:866-885.e14. [PMID: 38718796 DOI: 10.1016/j.stem.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 02/13/2024] [Accepted: 04/17/2024] [Indexed: 06/09/2024]
Abstract
Mutations in ARID1B, a member of the mSWI/SNF complex, cause severe neurodevelopmental phenotypes with elusive mechanisms in humans. The most common structural abnormality in the brain of ARID1B patients is agenesis of the corpus callosum (ACC), characterized by the absence of an interhemispheric white matter tract that connects distant cortical regions. Here, we find that neurons expressing SATB2, a determinant of callosal projection neuron (CPN) identity, show impaired maturation in ARID1B+/- neural organoids. Molecularly, a reduction in chromatin accessibility of genomic regions targeted by TCF-like, NFI-like, and ARID-like transcription factors drives the differential expression of genes required for corpus callosum (CC) development. Through an in vitro model of the CC tract, we demonstrate that this transcriptional dysregulation impairs the formation of long-range axonal projections, causing structural underconnectivity. Our study uncovers new functions of the mSWI/SNF during human corticogenesis, identifying cell-autonomous axonogenesis defects in SATB2+ neurons as a cause of ACC in ARID1B patients.
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Affiliation(s)
- Catarina Martins-Costa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Andrea Wiegers
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Vincent A Pham
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Jaydeep Sidhaye
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Balint Doleschall
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Thomas Lendl
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Marielle Piber
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Angela Peer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Paul Möseneder
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Marlene Stuempflen
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
| | - Siu Yu A Chow
- Institute of Industrial Science, The University of Tokyo, 153-8505 Tokyo, Japan; Institute for AI and Beyond, The University of Tokyo, 113-0032 Tokyo, Japan
| | - Rainer Seidl
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Daniela Prayer
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
| | - Romana Höftberger
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
| | - Gregor Kasprian
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, 153-8505 Tokyo, Japan; Institute for AI and Beyond, The University of Tokyo, 113-0032 Tokyo, Japan
| | - Nina S Corsini
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria.
| | - Jürgen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria.
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García-Aznar JM, Alonso Alvarez S, Bernal Del Castillo T. Pivotal role of BCL11B in the immune, hematopoietic and nervous systems: a review of the BCL11B-associated phenotypes from the genetic perspective. Genes Immun 2024; 25:232-241. [PMID: 38472338 PMCID: PMC11178493 DOI: 10.1038/s41435-024-00263-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
The transcription factor BCL11B plays an essential role in the development of central nervous system and T cell differentiation by regulating the expression of numerous genes involved in several pathways. Monoallelic defects in the BCL11B gene leading to loss-of-function are associated with a wide spectrum of phenotypes, including neurological disorders with or without immunological features and susceptibility to hematological malignancies. From the genetic point of view, the landscape of BCL11B mutations reported so far does not fully explain the genotype-phenotype correlation. In this review, we sought to compile the phenotypic and genotypic variables associated with previously reported mutations in this gene in order to provide a better understanding of the consequences of deleterious variants. We also highlight the importance of a careful evaluation of the mutation type, its location and the pattern of inheritance of the variants in order to assign the most accurate pathogenicity and actionability of the genetic findings.
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Affiliation(s)
- José María García-Aznar
- Healthincode, A Coruña, Spain.
- Universitary Institute of Oncology of Principado de Asturias (IUOPA), Oviedo, Spain.
- Health Research Institute of Principado de Asturias, Oviedo, Spain.
| | - Sara Alonso Alvarez
- Universitary Institute of Oncology of Principado de Asturias (IUOPA), Oviedo, Spain
- Health Research Institute of Principado de Asturias, Oviedo, Spain
- Hematology Department, Hospital Universitario Clínico de Asturias, Oviedo, Spain
| | - Teresa Bernal Del Castillo
- Universitary Institute of Oncology of Principado de Asturias (IUOPA), Oviedo, Spain
- Health Research Institute of Principado de Asturias, Oviedo, Spain
- Hematology Department, Hospital Universitario Clínico de Asturias, Oviedo, Spain
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7
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Schrauwen I, Rajendran Y, Acharya A, Öhman S, Arvio M, Paetau R, Siren A, Avela K, Granvik J, Leal SM, Määttä T, Kokkonen H, Järvelä I. Optical genome mapping unveils hidden structural variants in neurodevelopmental disorders. Sci Rep 2024; 14:11239. [PMID: 38755281 PMCID: PMC11099145 DOI: 10.1038/s41598-024-62009-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024] Open
Abstract
While short-read sequencing currently dominates genetic research and diagnostics, it frequently falls short of capturing certain structural variants (SVs), which are often implicated in the etiology of neurodevelopmental disorders (NDDs). Optical genome mapping (OGM) is an innovative technique capable of capturing SVs that are undetectable or challenging-to-detect via short-read methods. This study aimed to investigate NDDs using OGM, specifically focusing on cases that remained unsolved after standard exome sequencing. OGM was performed in 47 families using ultra-high molecular weight DNA. Single-molecule maps were assembled de novo, followed by SV and copy number variant calling. We identified 7 variants of interest, of which 5 (10.6%) were classified as likely pathogenic or pathogenic, located in BCL11A, OPHN1, PHF8, SON, and NFIA. We also identified an inversion disrupting NAALADL2, a gene which previously was found to harbor complex rearrangements in two NDD cases. Variants in known NDD genes or candidate variants of interest missed by exome sequencing mainly consisted of larger insertions (> 1kbp), inversions, and deletions/duplications of a low number of exons (1-4 exons). In conclusion, in addition to improving molecular diagnosis in NDDs, this technique may also reveal novel NDD genes which may harbor complex SVs often missed by standard sequencing techniques.
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Affiliation(s)
- Isabelle Schrauwen
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA.
| | - Yasmin Rajendran
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA
| | - Anushree Acharya
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA
| | | | - Maria Arvio
- Päijät-Häme Wellbeing Services, Neurology, Lahti, Finland
| | - Ritva Paetau
- Department of Child Neurology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Auli Siren
- Kanta-Häme Central Hospital, Hämeenlinna, Finland
| | - Kristiina Avela
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Johanna Granvik
- The Wellbeing Services County of Ostrobothnia, Kokkola, Finland
| | - Suzanne M Leal
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Tuomo Määttä
- The Wellbeing Services County of Kainuu, Kajaani, Finland
| | - Hannaleena Kokkonen
- Northern Finland Laboratory Centre NordLab and Medical Research Centre, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Irma Järvelä
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
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8
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Fanelli G, Franke B, Fabbri C, Werme J, Erdogan I, De Witte W, Poelmans G, Ruisch IH, Reus LM, van Gils V, Jansen WJ, Vos SJ, Alam KA, Martinez A, Haavik J, Wimberley T, Dalsgaard S, Fóthi Á, Barta C, Fernandez-Aranda F, Jimenez-Murcia S, Berkel S, Matura S, Salas-Salvadó J, Arenella M, Serretti A, Mota NR, Bralten J. Local patterns of genetic sharing challenge the boundaries between neuropsychiatric and insulin resistance-related conditions. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.07.24303921. [PMID: 38496672 PMCID: PMC10942494 DOI: 10.1101/2024.03.07.24303921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The co-occurrence of insulin resistance (IR)-related metabolic conditions with neuropsychiatric disorders is a complex public health challenge. Evidence of the genetic links between these phenotypes is emerging, but little is currently known about the genomic regions and biological functions that are involved. To address this, we performed Local Analysis of [co]Variant Association (LAVA) using large-scale (N=9,725-933,970) genome-wide association studies (GWASs) results for three IR-related conditions (type 2 diabetes mellitus, obesity, and metabolic syndrome) and nine neuropsychiatric disorders. Subsequently, positional and expression quantitative trait locus (eQTL)-based gene mapping and downstream functional genomic analyses were performed on the significant loci. Patterns of negative and positive local genetic correlations (|rg|=0.21-1, pFDR<0.05) were identified at 109 unique genomic regions across all phenotype pairs. Local correlations emerged even in the absence of global genetic correlations between IR-related conditions and Alzheimer's disease, bipolar disorder, and Tourette's syndrome. Genes mapped to the correlated regions showed enrichment in biological pathways integral to immune-inflammatory function, vesicle trafficking, insulin signalling, oxygen transport, and lipid metabolism. Colocalisation analyses further prioritised 10 genetically correlated regions for likely harbouring shared causal variants, displaying high deleterious or regulatory potential. These variants were found within or in close proximity to genes, such as SLC39A8 and HLA-DRB1, that can be targeted by supplements and already known drugs, including omega-3/6 fatty acids, immunomodulatory, antihypertensive, and cholesterol-lowering drugs. Overall, our findings underscore the complex genetic landscape of IR-neuropsychiatric multimorbidity, advocating for an integrated disease model and offering novel insights for research and treatment strategies in this domain.
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Affiliation(s)
- Giuseppe Fanelli
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Barbara Franke
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Chiara Fabbri
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Josefin Werme
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Izel Erdogan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ward De Witte
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Geert Poelmans
- Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - I. Hyun Ruisch
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lianne Maria Reus
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- Center for Neurobehavioral Genetics, University of California, Los Angeles, Los Angeles, California, United States
| | - Veerle van Gils
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Center Limburg, Maastricht University, Maastricht, The Netherlands
| | - Willemijn J. Jansen
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Center Limburg, Maastricht University, Maastricht, The Netherlands
| | - Stephanie J.B. Vos
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Center Limburg, Maastricht University, Maastricht, The Netherlands
| | | | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Norway
- K.G. Jebsen Center for Translational Research in Parkinson’s Disease, University of Bergen, Norway
| | - Jan Haavik
- Department of Biomedicine, University of Bergen, Norway
- Division of Psychiatry, Haukeland University Hospital, Norway
| | - Theresa Wimberley
- National Centre for Register-based Research, School of Business and Social Sciences, Aarhus University, Aarhus, Denmark
- iPSYCH - The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Aarhus, Denmark
| | - Søren Dalsgaard
- National Centre for Register-based Research, School of Business and Social Sciences, Aarhus University, Aarhus, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Child and Adolescent Psychiatry Glostrup, Mental Health Services of the Capital Region, Hellerup, Denmark
| | - Ábel Fóthi
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Csaba Barta
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Fernando Fernandez-Aranda
- Clinical Psychology Department, University Hospital of Bellvitge, Barcelona, Spain
- Psychoneurobiology of Eating and Addictive Behaviors Group, Neurosciences Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- CIBER Fisiopatología Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Barcelona, Spain
- Department of Clinical Sciences, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Susana Jimenez-Murcia
- Clinical Psychology Department, University Hospital of Bellvitge, Barcelona, Spain
- Psychoneurobiology of Eating and Addictive Behaviors Group, Neurosciences Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- CIBER Fisiopatología Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Barcelona, Spain
- Department of Clinical Sciences, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Psychological Services, University of Barcelona, Spain
| | - Simone Berkel
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Silke Matura
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jordi Salas-Salvadó
- Universitat Rovira i Virgili, Biochemistry and biotechnology Department, Grup Alimentació, Nutrició, Desenvolupament i Salut Mental, Unitat de Nutrició Humana, Reus, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
- Institut d’Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
| | - Martina Arenella
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Forensic and Neurodevelopmental Science, Institute of Psychiatry, Psychology and Neuroscience, King’s College, London, UK
| | | | - Nina Roth Mota
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Janita Bralten
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
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9
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Huyghebaert J, Mateiu L, Elinck E, Van Rossem KE, Christiaenssen B, D'Incal CP, McCormack MK, Lazzarini A, Vandeweyer G, Kooy RF. Identification of a DLG3 stop mutation in the MRX20 family. Eur J Hum Genet 2024; 32:317-323. [PMID: 38273165 PMCID: PMC10923781 DOI: 10.1038/s41431-024-01537-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 01/27/2024] Open
Abstract
Here, we identified the causal mutation in the MRX20 family, one of the larger X-linked pedigrees that have been described in which no gene had been identified up till now. In 1995, the putative disease gene had been mapped to the pericentromeric region on the X chromosome, but no follow-up studies were performed. Here, whole exome sequencing (WES) on two affected and one unaffected family member revealed the c.195del/p.(Thr66ProfsTer55) mutation in the DLG3 gene (NM_021120.4) that segregated with the affected individuals in the family. DLG3 mutations have been consequently associated with intellectual disability and are a plausible explanation for the clinical abnormalities observed in this family. In addition, we identified two other variants co-segregating with the phenotype: a stop gain mutation in SSX1 (c.358G>T/p.(Glu120Ter)) (NM_001278691.2) and a nonsynonymous SNV in USP27X (c.56 A>G/p.(Gln19Arg)) (NM_001145073.3). RNA sequencing revealed 14 differentially expressed genes (p value < 0.1) in 7 affected males compared to 4 unaffected males of the family, including four genes known to be associated with neurological disorders. Thus, in this paper we identified the c.195del/p.(Thr66ProfsTer55) mutation in the DLG3 gene (NM_021120.4) as likely responsible for the phenotype observed in the MRX20 family.
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Affiliation(s)
| | - Ligia Mateiu
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Ellen Elinck
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | | | | | | | - Michael K McCormack
- Department of Psychiatry, Rutgers University-Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
- Department of Cell Biology and Neurosciences, Virtua Health College of Medicine and Life Sciences of Rowan University, Stratford, NJ, 08084, USA
| | - Alice Lazzarini
- Department of Neurology, Rutgers University-Robert Wood Johnson Medical School, New Brunswick, NJ, 08903, USA
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.
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10
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Seigfried FA, Britsch S. The Role of Bcl11 Transcription Factors in Neurodevelopmental Disorders. BIOLOGY 2024; 13:126. [PMID: 38392344 PMCID: PMC10886639 DOI: 10.3390/biology13020126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/05/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024]
Abstract
Neurodevelopmental disorders (NDDs) comprise a diverse group of diseases, including developmental delay, autism spectrum disorder (ASD), intellectual disability (ID), and attention-deficit/hyperactivity disorder (ADHD). NDDs are caused by aberrant brain development due to genetic and environmental factors. To establish specific and curative therapeutic approaches, it is indispensable to gain precise mechanistic insight into the cellular and molecular pathogenesis of NDDs. Mutations of BCL11A and BCL11B, two closely related, ultra-conserved zinc-finger transcription factors, were recently reported to be associated with NDDs, including developmental delay, ASD, and ID, as well as morphogenic defects such as cerebellar hypoplasia. In mice, Bcl11 transcription factors are well known to orchestrate various cellular processes during brain development, for example, neural progenitor cell proliferation, neuronal migration, and the differentiation as well as integration of neurons into functional circuits. Developmental defects observed in both, mice and humans display striking similarities, suggesting Bcl11 knockout mice provide excellent models for analyzing human disease. This review offers a comprehensive overview of the cellular and molecular functions of Bcl11a and b and links experimental research to the corresponding NDDs observed in humans. Moreover, it outlines trajectories for future translational research that may help to better understand the molecular basis of Bcl11-dependent NDDs as well as to conceive disease-specific therapeutic approaches.
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Affiliation(s)
- Franziska Anna Seigfried
- Institute of Molecular and Cellular Anatomy, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Stefan Britsch
- Institute of Molecular and Cellular Anatomy, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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11
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Wang N, Wan R, Tang K. Transcriptional regulation in the development and dysfunction of neocortical projection neurons. Neural Regen Res 2024; 19:246-254. [PMID: 37488873 PMCID: PMC10503610 DOI: 10.4103/1673-5374.379039] [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: 01/29/2023] [Revised: 04/10/2023] [Accepted: 05/17/2023] [Indexed: 07/26/2023] Open
Abstract
Glutamatergic projection neurons generate sophisticated excitatory circuits to integrate and transmit information among different cortical areas, and between the neocortex and other regions of the brain and spinal cord. Appropriate development of cortical projection neurons is regulated by certain essential events such as neural fate determination, proliferation, specification, differentiation, migration, survival, axonogenesis, and synaptogenesis. These processes are precisely regulated in a tempo-spatial manner by intrinsic factors, extrinsic signals, and neural activities. The generation of correct subtypes and precise connections of projection neurons is imperative not only to support the basic cortical functions (such as sensory information integration, motor coordination, and cognition) but also to prevent the onset and progression of neurodevelopmental disorders (such as intellectual disability, autism spectrum disorders, anxiety, and depression). This review mainly focuses on the recent progress of transcriptional regulations on the development and diversity of neocortical projection neurons and the clinical relevance of the failure of transcriptional modulations.
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Affiliation(s)
- Ningxin Wang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong Province, China
| | - Rong Wan
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong Province, China
| | - Ke Tang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong Province, China
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12
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Zheng G, Orkin SH. Transcriptional Repressor BCL11A in Erythroid Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:199-215. [PMID: 39017845 DOI: 10.1007/978-3-031-62731-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
BCL11A, a zinc finger repressor, is a stage-specific transcription factor that controls the switch from fetal (HbF, α2γ2) to adult (HbA, α2β2) hemoglobin in erythroid cells. While BCL11A was known as a factor critical for B-lymphoid cell development, its relationship to erythroid cells and HbF arose through genome-wide association studies (GWAS). Subsequent work validated its role as a silencer of γ-globin gene expression in cultured cells and mice. Erythroid-specific loss of BCL11A rescues the phenotype of engineered sickle cell disease (SCD) mice, thereby suggesting that downregulation of BCL11A expression might be beneficial in patients with SCD and β-thalassemia. Common genetic variation in GWAS resides in an erythroid-specific enhancer within the BCL11A gene that is required for its own expression. CRISPR/Cas9 gene editing of the enhancer revealed a GATA-binding site that confers a large portion of its regulatory function. Disruption of the GATA site leads to robust HbF reactivation. Advancement of a guide RNA targeting the GATA-binding site in clinical trials has recently led to approval of first-in-man use of ex vivo CRISPR editing of hematopoietic stem/progenitor cells (HSPCs) as therapy of SCD and β-thalassemia. Future challenges include expanding access and infrastructure for delivery of genetic therapy to eligible patients, reducing potential toxicity and costs, exploring prospects for in vivo targeting of hematopoietic stem cells (HSCs), and developing small molecule drugs that impair function of BCL11A protein as an alternative option.
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Affiliation(s)
- Ge Zheng
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Harvard Medical School and HHMI, Boston, MA, USA
| | - Stuart H Orkin
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
- Harvard Medical School and HHMI, Boston, MA, USA.
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13
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Ward SK, Wadley A, Tsai CHA, Benke PJ, Emrick L, Fisher K, Houck KM, Dai H, Guillen Sacoto MJ, Craigen W, Glaser K, Murdock DR, Rohena L, Diderich KEM, Bruggenwirth HT, Lee B, Bacino C, Burrage LC, Rosenfeld JA. De novo missense variants in ZBTB47 are associated with developmental delays, hypotonia, seizures, gait abnormalities, and variable movement abnormalities. Am J Med Genet A 2024; 194:17-30. [PMID: 37743782 PMCID: PMC11221546 DOI: 10.1002/ajmg.a.63399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/26/2023]
Abstract
The collection of known genetic etiologies of neurodevelopmental disorders continues to increase, including several syndromes associated with defects in zinc finger protein transcription factors (ZNFs) that vary in clinical severity from mild learning disabilities and developmental delay to refractory seizures and severe autism spectrum disorder. Here we describe a new neurodevelopmental disorder associated with variants in ZBTB47 (also known as ZNF651), which encodes zinc finger and BTB domain-containing protein 47. Exome sequencing (ES) was performed for five unrelated patients with neurodevelopmental disorders. All five patients are heterozygous for a de novo missense variant in ZBTB47, with p.(Glu680Gly) (c.2039A>G) detected in one patient and p.(Glu477Lys) (c.1429G>A) identified in the other four patients. Both variants impact conserved amino acid residues. Bioinformatic analysis of each variant is consistent with pathogenicity. We present five unrelated patients with de novo missense variants in ZBTB47 and a phenotype characterized by developmental delay with intellectual disability, seizures, hypotonia, gait abnormalities, and variable movement abnormalities. We propose that these variants in ZBTB47 are the basis of a new neurodevelopmental disorder.
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Affiliation(s)
- Scott K Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, USA
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alexandrea Wadley
- Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Chun-Hui Anne Tsai
- Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Paul J Benke
- Joe DiMaggio Children's Hospital, Hollywood, Florida, USA
| | - Lisa Emrick
- Department of Pediatrics, Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, Texas, USA
| | - Kristen Fisher
- Department of Pediatrics, Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, Texas, USA
| | - Kimberly M Houck
- Department of Pediatrics, Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, Texas, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, USA
| | | | - William Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, USA
| | - Kimberly Glaser
- Joe DiMaggio Children's Hospital, Hollywood, Florida, USA
- Invitae, San Francisco, California, USA
| | - David R Murdock
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, USA
- The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Luis Rohena
- Department of Pediatrics, Division of Medical Genetics, San Antonio Military Medical Center, San Antonio, Texas, USA
- Department of Pediatrics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Hennie T Bruggenwirth
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, USA
| | - Carlos Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, USA
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14
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Yamaguchi M, Huynh MA, Chiyonobu T, Yoshida H. Knockdown of Chronophage in the nervous system mimics features of neurodevelopmental disorders caused by BCL11A/B variants. Exp Cell Res 2023; 433:113827. [PMID: 37926342 DOI: 10.1016/j.yexcr.2023.113827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
Neurodevelopmental disorders (NDD) are a group of disorders that include intellectual disability. Although several genes have been implicated in NDD, the molecular mechanisms underlying its pathogenesis remain unclear. Therefore, it is important to develop novel models to analyze the functions of NDD-causing genes in vivo. Recently, rare pathogenic variants of the B-cell lymphoma/leukemia11A/B (BCL11A/B) gene have been identified in several patients with NDD. Drosophila carries the Chronophage (Cph) gene, which has been predicted to be a homolog of BCL11A/B based on the conservation of the amino acid sequence. In the present study, we investigated whether nervous system-specific knockdown of Cph mimics NDD phenotypes in Drosophila. Nervous system-specific knockdown of Cph induced learning and locomotor defects in larvae and epilepsy-like behaviors in adults. The number of synaptic branches was also elevated in the larval neuromuscular junction without a corresponding increase in the number of boutons. Furthermore, the expression levels of putative target genes that are Drosophila homologs of the mammalian BCL11 target genes were decreased in Cph knockdown flies. These results suggest that Cph knockdown flies are a promising model for investigating the pathology of NDD-induced BCL11A/B dysfunction.
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Affiliation(s)
- Mizuki Yamaguchi
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.
| | - Man Anh Huynh
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Tomohiro Chiyonobu
- Department of Molecular Diagnostics and Therapeutics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachi-hirokoji, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Hideki Yoshida
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan; Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.
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15
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Sun Y, Wiese M, Hmadi R, Karayol R, Seyfferth J, Martinez Greene JA, Erdogdu NU, Deboutte W, Arrigoni L, Holz H, Renschler G, Hirsch N, Foertsch A, Basilicata MF, Stehle T, Shvedunova M, Bella C, Pessoa Rodrigues C, Schwalb B, Cramer P, Manke T, Akhtar A. MSL2 ensures biallelic gene expression in mammals. Nature 2023; 624:173-181. [PMID: 38030723 PMCID: PMC10700137 DOI: 10.1038/s41586-023-06781-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
In diploid organisms, biallelic gene expression enables the production of adequate levels of mRNA1,2. This is essential for haploinsufficient genes, which require biallelic expression for optimal function to prevent the onset of developmental disorders1,3. Whether and how a biallelic or monoallelic state is determined in a cell-type-specific manner at individual loci remains unclear. MSL2 is known for dosage compensation of the male X chromosome in flies. Here we identify a role of MSL2 in regulating allelic expression in mammals. Allele-specific bulk and single-cell analyses in mouse neural progenitor cells revealed that, in addition to the targets showing biallelic downregulation, a class of genes transitions from biallelic to monoallelic expression after MSL2 loss. Many of these genes are haploinsufficient. In the absence of MSL2, one allele remains active, retaining active histone modifications and transcription factor binding, whereas the other allele is silenced, exhibiting loss of promoter-enhancer contacts and the acquisition of DNA methylation. Msl2-knockout mice show perinatal lethality and heterogeneous phenotypes during embryonic development, supporting a role for MSL2 in regulating gene dosage. The role of MSL2 in preserving biallelic expression of specific dosage-sensitive genes sets the stage for further investigation of other factors that are involved in allelic dosage compensation in mammalian cells, with considerable implications for human disease.
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Affiliation(s)
- Yidan Sun
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Meike Wiese
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Raed Hmadi
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Remzi Karayol
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Janine Seyfferth
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Juan Alfonso Martinez Greene
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Niyazi Umut Erdogdu
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ward Deboutte
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Laura Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Herbert Holz
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Gina Renschler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Naama Hirsch
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Arion Foertsch
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Thomas Stehle
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Maria Shvedunova
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Chiara Bella
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Bjoern Schwalb
- Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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16
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Wang X, Zhang Z, Zuo W, Wang D, Yang F, Liu Q, Xiao Y. Case Report: Identification of microduplication in the chromosomal 2p16.1p15 region in an infant suffering from pulmonary arterial hypertension. Front Cardiovasc Med 2023; 10:1219480. [PMID: 37937284 PMCID: PMC10626460 DOI: 10.3389/fcvm.2023.1219480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 10/03/2023] [Indexed: 11/09/2023] Open
Abstract
This study reports the first case of a patient with chromosomal 2p16.1p15 microduplication syndrome complicated by pulmonary arterial hypertension (PAH). A female infant was admitted to the hospital suffering from dyskinesia and developmental delay, and conventional echocardiography revealed an atrial septal defect (ASD), which was not taken seriously or treated at that time. Two years later, preoperative right heart catheterization for ASD closure revealed a mean pulmonary artery pressure (mPAP) of 45 mmHg. The mPAP was reduced, and the condition was stabilized after drug therapy. A genomic copy number duplication (3×) of at least 2.58 Mb in the 2p16.1p15 region on the paternal chromosome was revealed. Multiple Online Mendelian Inheritance in Man (OMIM) genes are involved in this genomic region, such as BCL11A, EHBP1, FAM161A, PEX13, and REL. EHBP1 promotes a molecular phenotypic transformation of pulmonary vascular endothelial cells and is thought to be involved in the rapidly developing PAH of this infant. Collectively, our findings contribute to the knowledge of the genes involved and the clinical manifestations of the 2p16.1p15 microduplication syndrome. Moreover, clinicians should be alert to the possibility of PAH and take early drug intervention when facing patients with 2p16.1p15 microduplications.
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Affiliation(s)
- Xun Wang
- Department of Cardiology, Hunan Children’s Hospital, Changsha, China
| | - Zeying Zhang
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Wanyun Zuo
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Dan Wang
- Department of Cardiology, Hunan Children’s Hospital, Changsha, China
| | - Fan Yang
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Qiming Liu
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yunbin Xiao
- Department of Cardiology, Hunan Children’s Hospital, Changsha, China
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17
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Wiegreffe C, Ehricke S, Schmid L, Andratschke J, Britsch S. Using i-GONAD for Cell-Type-Specific and Systematic Analysis of Developmental Transcription Factors In Vivo. BIOLOGY 2023; 12:1236. [PMID: 37759634 PMCID: PMC10526018 DOI: 10.3390/biology12091236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
Transcription factors (TFs) regulate gene expression via direct DNA binding together with cofactors and in chromatin remodeling complexes. Their function is thus regulated in a spatiotemporal and cell-type-specific manner. To analyze the functions of TFs in a cell-type-specific context, genome-wide DNA binding, as well as the identification of interacting proteins, is required. We used i-GONAD (improved genome editing via oviductal nucleic acids delivery) in mice to genetically modify TFs by adding fluorescent reporter and affinity tags that can be exploited for the imaging and enrichment of target cells as well as chromatin immunoprecipitation and pull-down assays. As proof-of-principle, we showed the functional genetic modification of the closely related developmental TFs, Bcl11a and Bcl11b, in defined cell types of newborn mice. i-GONAD is a highly efficient procedure for modifying TF-encoding genes via the integration of small insertions, such as reporter and affinity tags. The novel Bcl11a and Bcl11b mouse lines, described in this study, will be used to improve our understanding of the Bcl11 family's function in neurodevelopment and associated disease.
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Affiliation(s)
- Christoph Wiegreffe
- Medical Faculty, Institute of Molecular and Cellular Anatomy, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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18
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Miceli M, Failla P, Saccuzzo L, Galesi O, Amata S, Romano C, Bonaglia MC, Fichera M. Trait - driven analysis of the 2p15p16.1 microdeletion syndrome suggests a complex pattern of interactions between candidate genes. Genes Genomics 2023; 45:491-505. [PMID: 36807877 PMCID: PMC10027778 DOI: 10.1007/s13258-023-01369-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/27/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND Individuals with the 2p15p16.1 microdeletion syndrome share a complex phenotype including neurodevelopmental delay, brain malformations, microcephaly, and autistic behavior. The analysis of the shortest region of overlap (SRO) between deletions in ~ 40 patients has led to the identification of two critical regions and four strongly candidate genes (BCL11A, REL, USP34 and XPO1). However, the delineation of their role in the occurrence of specific traits is hampered by their incomplete penetrance. OBJECTIVE To better delineate the role of hemizygosity of specific regions in selected traits by leveraging information both from penetrant and non - penetrant deletions. METHODS Deletions in patients that do not present a specific trait cannot contribute to delineate the SROs. We recently developed a probabilistic model that, by considering also the non - penetrant deletions, allows a more reliable assignment of peculiar traits to specific genomic segments. We apply this method adding two new patients to the published cases. RESULTS Our results delineate an intricate pattern of genotype - phenotype correlation where BCL11A emerges as the main gene for autistic behavior while USP34 and/or XPO1 haploinsufficiency are mainly associated with microcephaly, hearing loss and IUGR. BCL11A, USP34 and XPO1 genes are broadly related with brain malformations albeit with distinct patterns of brain damage. CONCLUSIONS The observed penetrance of deletions encompassing different SROs and that predicted when considering each single SRO as acting independently, may reflect a more complex model than the additive one. Our approach may improve the genotype/phenotype correlation and may help to identify specific pathogenic mechanisms in contiguous gene syndromes.
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Affiliation(s)
- Martina Miceli
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy
| | | | - Lucia Saccuzzo
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy
| | | | | | - Corrado Romano
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy
| | - Maria Clara Bonaglia
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Marco Fichera
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy.
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy.
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19
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Lu HY, Orkin SH, Sankaran VG. Fetal Hemoglobin Regulation in Beta-Thalassemia. Hematol Oncol Clin North Am 2023; 37:301-312. [PMID: 36907604 DOI: 10.1016/j.hoc.2022.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
β-thalassemia is caused by mutations that reduce β-globin production, causing globin chain imbalance, ineffective erythropoiesis, and consequent anemia. Increased fetal hemoglobin (HbF) levels can ameliorate the severity of β-thalassemia by compensating for the globin chain imbalance. Careful clinical observations paired with population studies and advances in human genetics have enabled the discovery of major regulators of HbF switching (i.e. BCL11A, ZBTB7A) and led to pharmacological and genetic therapies for treating β-thalassemia patients. Recent functional screens using genome editing and other emerging tools have identified many new HbF regulators, which may improve therapeutic HbF induction in the future.
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Affiliation(s)
- Henry Y Lu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Karp Family Research Laboratories, Boston Children's Hospital, 1 Blackfan Street, Boston, MA 02115, USA. https://twitter.com/realhenrylu
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Karp Family Research Laboratories, Boston Children's Hospital, 1 Blackfan Street, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Karp Family Research Laboratories, Boston Children's Hospital, 1 Blackfan Street, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA, USA.
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20
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Cato LD, Li R, Lu HY, Yu F, Wissman M, Mkumbe BS, Ekwattanakit S, Deelen P, Mwita L, Sangeda R, Suksangpleng T, Riolueang S, Bronson PG, Paul DS, Kawabata E, Astle WJ, Aguet F, Ardlie K, de Lapuente Portilla AL, Kang G, Zhang Y, Nouraie SM, Gordeuk VR, Gladwin MT, Garrett ME, Ashley-Koch A, Telen MJ, Custer B, Kelly S, Dinardo CL, Sabino EC, Loureiro P, Carneiro-Proietti AB, Maximo C, Méndez A, Hammerer-Lercher A, Sheehan VA, Weiss MJ, Franke L, Nilsson B, Butterworth AS, Viprakasit V, Nkya S, Sankaran VG. Genetic regulation of fetal hemoglobin across global populations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.24.23287659. [PMID: 36993312 PMCID: PMC10055601 DOI: 10.1101/2023.03.24.23287659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Human genetic variation has enabled the identification of several key regulators of fetal-to-adult hemoglobin switching, including BCL11A, resulting in therapeutic advances. However, despite the progress made, limited further insights have been obtained to provide a fuller accounting of how genetic variation contributes to the global mechanisms of fetal hemoglobin (HbF) gene regulation. Here, we have conducted a multi-ancestry genome-wide association study of 28,279 individuals from several cohorts spanning 5 continents to define the architecture of human genetic variation impacting HbF. We have identified a total of 178 conditionally independent genome-wide significant or suggestive variants across 14 genomic windows. Importantly, these new data enable us to better define the mechanisms by which HbF switching occurs in vivo. We conduct targeted perturbations to define BACH2 as a new genetically-nominated regulator of hemoglobin switching. We define putative causal variants and underlying mechanisms at the well-studied BCL11A and HBS1L-MYB loci, illuminating the complex variant-driven regulation present at these loci. We additionally show how rare large-effect deletions in the HBB locus can interact with polygenic variation to influence HbF levels. Our study paves the way for the next generation of therapies to more effectively induce HbF in sickle cell disease and β-thalassemia.
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Affiliation(s)
- Liam D. Cato
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rick Li
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Henry Y. Lu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Fulong Yu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mariel Wissman
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Baraka S. Mkumbe
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Biochemistry, Muhimbili University of Health and Allied Science, Dar es Salaam, Tanzania
- Department of Artificial Intelligence and Innovative Medicine, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Supachai Ekwattanakit
- Siriraj Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Patrick Deelen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Liberata Mwita
- Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Raphael Sangeda
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Thidarat Suksangpleng
- Siriraj Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Suchada Riolueang
- Siriraj Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Paola G. Bronson
- R&D Translational Biology, Biogen, Cambridge, Massachusetts, USA
| | - Dirk S. Paul
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
| | - Emily Kawabata
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - William J. Astle
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Francois Aguet
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kristin Ardlie
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Guolian Kang
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yingze Zhang
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Seyed Mehdi Nouraie
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Victor R. Gordeuk
- Division of Hematology and Oncology, Department of Medicine, Comprehensive Sickle Cell Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Mark T. Gladwin
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Melanie E. Garrett
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Marilyn J. Telen
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, UCSF, San Francisco, California, USA
| | - Shannon Kelly
- Vitalant Research Institute, San Francisco, California, USA
- Division of Pediatric Hematology, UCSF Benioff Children's Hospital, Oakland, California, USA
| | - Carla Luana Dinardo
- Fundacao Pro-Sangue Hemocentro de Sao Paulo, Sao Paulo, Brazil
- Institute of Tropical Medicine, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Ester C. Sabino
- Institute of Tropical Medicine, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | | | | | | | | | - Adriana Méndez
- Institute of Laboratory Medicine, Cantonal Hospital Aarau, 5000 Aarau, Switzerland
| | | | - Vivien A. Sheehan
- Aflac Cancer & Blood Disorders Center, Children's Healthcare of Atlanta & Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Lude Franke
- Oncode Institute, Amsterdam, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Björn Nilsson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
- Department of Laboratory Medicine, Lund University, 221 84 Lund, Sweden
| | - Adam S. Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Vip Viprakasit
- Siriraj Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Siana Nkya
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Biochemistry, Muhimbili University of Health and Allied Science, Dar es Salaam, Tanzania
- Tanzania Human Genetics Organisation, Tanzania
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Biochemistry, Muhimbili University of Health and Allied Science
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21
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Wang S, Cai X, Liu S, Zhou Q, Wang T, Du S, Wang D, Yang F, Wu Q, Han Y. A novel BCL11A polymorphism influences gene expression, therapeutic response and epilepsy risk: A multicenter study. Front Mol Neurosci 2022; 15:1010101. [PMID: 36568279 PMCID: PMC9780294 DOI: 10.3389/fnmol.2022.1010101] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Background Genetic factors have been found to be associated with the efficacy and adverse reactions of antiseizure medications. BCL11A is an important regulator of the development of neuronal networks. However, the role of BCL11A in epilepsy remains unclear. This study aimed to evaluate the genetic association of BCL11A with the susceptibility to develop epileptic seizures and therapeutic response of patients with epilepsy in Han Chinese. Methods We matched 450 epilepsy cases with 550 healthy controls and 131 drug-resistant epilepsy patients with 319 drug-responsive epilepsy patients from two different centers. Genetic association analysis, genetic interaction analysis, expression quantitative trait loci analysis and protein-protein interaction analysis were conducted. Results Our results showed that rs2556375 not only increases susceptibility to develop epileptic seizures (OR = 2.700, 95% = 1.366-5.338, p = 0.004 and OR = 2.984, 95% = 1.401-6.356, p = 0.005, respectively), but also increases the risk of drug resistance(OR = 21.336, 95%CI =2.489-183.402, p = 0.005). The interaction between rs2556375 and rs12477097 results in increased risk for pharma coresistant. In addition, rs2556375 regulated BCL11A expression in human brain tissues (p = 0.0096 and p = 0.033, respectively). Furthermore, the protein encoded by BCL11A interacted with targets of approved antiepileptic drugs. Conclusion BCL11A may be a potential therapeutic target for epilepsy. Rs2556375 may increase the risks of epilepsy and drug resistance by regulating BCL11A expression in human brain tissues. Moreover, the interaction between rs2556375 and rs12477097 results in increased risk for drug resistance.
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Affiliation(s)
- Shitao Wang
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China,Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, China
| | - Xuemei Cai
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Shiyong Liu
- Department of Neurosurgery, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Qixin Zhou
- Laboratory of Learning and Memory, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ting Wang
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Sunbing Du
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Dan Wang
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Fei Yang
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Qian Wu
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yanbing Han
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China,*Correspondence: Yanbing Han,
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22
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Differential Regulation of the BDNF Gene in Cortical and Hippocampal Neurons. J Neurosci 2022; 42:9110-9128. [PMID: 36316156 PMCID: PMC9761680 DOI: 10.1523/jneurosci.2535-21.2022] [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: 12/27/2021] [Revised: 09/18/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) is a widely expressed neurotrophin that supports the survival, differentiation, and signaling of various neuronal populations. Although it has been well described that expression of BDNF is strongly regulated by neuronal activity, little is known whether regulation of BDNF expression is similar in different brain regions. Here, we focused on this fundamental question using neuronal populations obtained from rat cerebral cortices and hippocampi of both sexes. First, we thoroughly characterized the role of the best-described regulators of BDNF gene - cAMP response element binding protein (CREB) family transcription factors, and show that activity-dependent BDNF expression depends more on CREB and the coactivators CREB binding protein (CBP) and CREB-regulated transcriptional coactivator 1 (CRTC1) in cortical than in hippocampal neurons. Our data also reveal an important role of CREB in the early induction of BDNF mRNA expression after neuronal activity and only modest contribution after prolonged neuronal activity. We further corroborated our findings at BDNF protein level. To determine the transcription factors regulating BDNF expression in these rat brain regions in addition to CREB family, we used in vitro DNA pulldown assay coupled with mass spectrometry, chromatin immunoprecipitation (ChIP), and bioinformatics, and propose a number of neurodevelopmentally important transcription factors, such as FOXP1, SATB2, RAI1, BCL11A, and TCF4 as brain region-specific regulators of BDNF expression. Together, our data reveal complicated brain region-specific fine-tuning of BDNF expression.SIGNIFICANCE STATEMENT To date, majority of the research has focused on the regulation of brain-derived neurotrophic factor (BDNF) in the brain but much less is known whether the regulation of BDNF expression is universal in different brain regions and neuronal populations. Here, we report that the best described regulators of BDNF gene from the cAMP-response element binding protein (CREB) transcription factor family have a more profound role in the activity-dependent regulation of BDNF in cortex than in hippocampus. Our results indicate a brain region-specific fine tuning of BDNF expression. Moreover, we have used unbiased determination of novel regulators of the BDNF gene and report a number of neurodevelopmentally important transcription factors as novel potential regulators of the BDNF expression.
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23
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Bruce L, Peter B. Three children with different de novo BCL11A variants and diverse developmental phenotypes, but shared global motor discoordination and apraxic speech: Evidence for a functional gene network influencing the developing cerebellum and motor and auditory cortices. Am J Med Genet A 2022; 188:3401-3415. [PMID: 35856171 DOI: 10.1002/ajmg.a.62904] [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: 09/15/2021] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 01/31/2023]
Abstract
BCL11A is implicated in BCL11A-Related Intellectual Development Disorder (BCL11A-IDD). Previously reported cases had various types of BCL11A variants (copy-number variations [CNVs], singlenucleotide variants [SNVs]). Phenotypes included global, cognitive, and motor delays, autism spectrum disorder (ASD), craniofacial dysmorphology, and speech and language delays described generally, with only two reports specifying childhood apraxia of speech (CAS). Here, we present three additional children with CAS and de novo BCL11A variants, a p.Ala182Thr nonconservative missense and a p.GLu611.Ter nonsense variant, both in exon 4, and a 106 kb deletion harboring exons 1 and 2. All three children have fine and gross motor discoordination, feeding difficulties, and visual motor disorders. Intellectual and learning disabilities and disordered language skills were seen only in the child with the missense variant and the child with the deletion. These findings align with, and expand, previous findings in that BCL11A variants have significant and highly penetrant apraxic effects across motor systems, consistent with cerebellar involvement. The deletion of exons 1 and 2 is the smallest BCL11A CNV with the full phenotypic expression reported to date. The present results support previous findings in that BCL11A-IDD can result from BCL11A variants regardless of type (deletion, SNVs). A gene expression study shows that BCL11 is expressed highly in the early developing cerebellum and primary motor and auditory cortices. Significant co-expression rates in these regions with genes previously implicated in disorders of spoken language and in ASD support the phenotypic overlaps in children with BCL11A-IDD, CAS, and ASD.
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Affiliation(s)
- Laurel Bruce
- College of Health Solutions, Arizona State University, Tempe, Arizona, USA
| | - Beate Peter
- College of Health Solutions, Arizona State University, Tempe, Arizona, USA
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24
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Mees I, Li S, Tran H, Ang CS, Williamson NA, Hannan AJ, Renoir T. Phosphoproteomic dysregulation in Huntington's disease mice is rescued by environmental enrichment. Brain Commun 2022; 4:fcac305. [PMID: 36523271 PMCID: PMC9746689 DOI: 10.1093/braincomms/fcac305] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 09/05/2022] [Accepted: 11/21/2022] [Indexed: 09/05/2023] Open
Abstract
Huntington's disease is a fatal autosomal-dominant neurodegenerative disorder, characterized by neuronal cell dysfunction and loss, primarily in the striatum, cortex and hippocampus, causing motor, cognitive and psychiatric impairments. Unfortunately, no treatments are yet available to modify the progression of the disease. Recent evidence from Huntington's disease mouse models suggests that protein phosphorylation (catalysed by kinases and hydrolysed by phosphatases) might be dysregulated, making this major post-translational modification a potential area of interest to find novel therapeutic targets. Furthermore, environmental enrichment, used to model an active lifestyle in preclinical models, has been shown to alleviate Huntington's disease-related motor and cognitive symptoms. However, the molecular mechanisms leading to these therapeutic effects are still largely unknown. In this study, we applied a phosphoproteomics approach combined with proteomic analyses on brain samples from pre-motor symptomatic R6/1 Huntington's disease male mice and their wild-type littermates, after being housed either in environmental enrichment conditions, or in standard housing conditions from 4 to 8 weeks of age (n = 6 per group). We hypothesized that protein phosphorylation dysregulations occur prior to motor onset in this mouse model, in two highly affected brain regions, the striatum and hippocampus. Furthermore, we hypothesized that these phosphoproteome alterations are rescued by environmental enrichment. When comparing 8-week-old Huntington's disease mice and wild-type mice in standard housing conditions, our analysis revealed 229 differentially phosphorylated peptides in the striatum, compared with only 15 differentially phosphorylated peptides in the hippocampus (statistical thresholds fold discovery rate 0.05, fold change 1.5). At the same disease stage, minor differences were found in protein levels, with 24 and 22 proteins dysregulated in the striatum and hippocampus, respectively. Notably, we found no differences in striatal protein phosphorylation and protein expression when comparing Huntington's disease mice and their wild-type littermates in environmentally enriched conditions. In the hippocampus, only four peptides were differentially phosphorylated between the two genotypes under environmentally enriched conditions, and 22 proteins were differentially expressed. Together, our data indicates that protein phosphorylation dysregulations occur in the striatum of Huntington's disease mice, prior to motor symptoms, and that the kinases and phosphatases leading to these changes in protein phosphorylation might be viable drug targets to consider for this disorder. Furthermore, we show that an early environmental intervention was able to rescue the changes observed in protein expression and phosphorylation in the striatum of Huntington's disease mice and might underlie the beneficial effects of environmental enrichment, thus identifying novel therapeutic targets.
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Affiliation(s)
- Isaline Mees
- Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, VIC 3010, Australia
| | - Shanshan Li
- Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, VIC 3010, Australia
| | - Harvey Tran
- Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, University of Melbourne, Parkville, VIC 3010, Australia
| | - Nicholas A Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, University of Melbourne, Parkville, VIC 3010, Australia
| | - Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, VIC 3010, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Thibault Renoir
- Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, VIC 3010, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
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25
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Du H, Wang Z, Guo R, Yang L, Liu G, Zhang Z, Xu Z, Tian Y, Yang Z, Li X, Chen B. Transcription factors Bcl11a and Bcl11b are required for the production and differentiation of cortical projection neurons. Cereb Cortex 2022; 32:3611-3632. [PMID: 34963132 PMCID: PMC9433425 DOI: 10.1093/cercor/bhab437] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/02/2021] [Indexed: 12/31/2022] Open
Abstract
The generation and differentiation of cortical projection neurons are extensively regulated by interactive programs of transcriptional factors. Here, we report the cooperative functions of transcription factors Bcl11a and Bcl11b in regulating the development of cortical projection neurons. Among the cells derived from the cortical neural stem cells, Bcl11a is expressed in the progenitors and the projection neurons, while Bcl11b expression is restricted to the projection neurons. Using conditional knockout mice, we show that deficiency of Bcl11a leads to reduced proliferation and precocious differentiation of cortical progenitor cells, which is exacerbated when Bcl11b is simultaneously deleted. Besides defective neuronal production, the differentiation of cortical projection neurons is blocked in the absence of both Bcl11a and Bcl11b: Expression of both pan-cortical and subtype-specific genes is reduced or absent; axonal projections to the thalamus, hindbrain, spinal cord, and contralateral cortical hemisphere are reduced or absent. Furthermore, neurogenesis-to-gliogenesis switch is accelerated in the Bcl11a-CKO and Bcl11a/b-DCKO mice. Bcl11a likely regulates neurogenesis through repressing the Nr2f1 expression. These results demonstrate that Bcl11a and Bcl11b jointly play critical roles in the generation and differentiation of cortical projection neurons and in controlling the timing of neurogenesis-to-gliogenesis switch.
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Affiliation(s)
- Heng Du
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Ziwu Wang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Rongliang Guo
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Lin Yang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Guoping Liu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Zhuangzhi Zhang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Zhejun Xu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Yu Tian
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Zhengang Yang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Xiaosu Li
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Bin Chen
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
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26
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van der Meer D, Shadrin AA, O'Connell K, Bettella F, Djurovic S, Wolfers T, Alnæs D, Agartz I, Smeland OB, Melle I, Sánchez JM, Linden DEJ, Dale AM, Westlye LT, Andreassen OA, Frei O, Kaufmann T. Boosting Schizophrenia Genetics by Utilizing Genetic Overlap With Brain Morphology. Biol Psychiatry 2022; 92:291-298. [PMID: 35164939 DOI: 10.1016/j.biopsych.2021.12.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Schizophrenia is a complex polygenic disorder with subtle, distributed abnormalities in brain morphology. There are indications of shared genetic architecture between schizophrenia and brain measures despite low genetic correlations. Through the use of analytical methods that allow for mixed directions of effects, this overlap may be leveraged to improve our understanding of underlying mechanisms of schizophrenia and enrich polygenic risk prediction outcome. METHODS We ran a multivariate genome-wide analysis of 175 brain morphology measures using data from 33,735 participants of the UK Biobank and analyzed the results in a conditional false discovery rate together with schizophrenia genome-wide association study summary statistics of the Psychiatric Genomics Consortium (PGC) Wave 3. We subsequently created a pleiotropy-enriched polygenic score based on the loci identified through the conditional false discovery rate approach and used this to predict schizophrenia in a nonoverlapping sample of 743 individuals with schizophrenia and 1074 healthy controls. RESULTS We found that 20% of the loci and 50% of the genes significantly associated with schizophrenia were also associated with brain morphology. The conditional false discovery rate analysis identified 428 loci, including 267 novel loci, significantly associated with brain-linked schizophrenia risk, with functional annotation indicating high relevance for brain tissue. The pleiotropy-enriched polygenic score explained more variance in liability than conventional polygenic scores across several scenarios. CONCLUSIONS Our results indicate strong genetic overlap between schizophrenia and brain morphology with mixed directions of effect. The results also illustrate the potential of exploiting polygenetic overlap between brain morphology and mental disorders to boost discovery of brain tissue-specific genetic variants and its use in polygenic risk frameworks.
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Affiliation(s)
- Dennis van der Meer
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway; School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands.
| | - Alexey A Shadrin
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kevin O'Connell
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Francesco Bettella
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Thomas Wolfers
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Dag Alnæs
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ingrid Agartz
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Olav B Smeland
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ingrid Melle
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jennifer Monereo Sánchez
- School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands; Department of Radiology and Nuclear Medicine, Maastricht University Medical Center, Maastricht, the Netherlands
| | - David E J Linden
- School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands
| | - Anders M Dale
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, California
| | - Lars T Westlye
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Psychology, University of Oslo, Oslo, Norway
| | - Ole A Andreassen
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Oleksandr Frei
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Tobias Kaufmann
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Psychiatry and Psychotherapy, University of Tübingen, Tübingen, Germany
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27
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Christensen MB, Levy AM, Mohammadi NA, Niceta M, Kaiyrzhanov R, Dentici ML, Alam CA, Alesi V, Benoit V, Bhatia KP, Bierhals T, Boßelmann CM, Buratti J, Callewaert B, Ceulemans B, Charles P, De Wachter M, Dehghani M, D'haenens E, Doco-Fenzy M, Geßner M, Gobert C, Guliyeva U, Haack TB, Hammer TB, Heinrich T, Hempel M, Herget T, Hoffmann U, Horvath J, Houlden H, Keren B, Kresge C, Kumps C, Lederer D, Lermine A, Magrinelli F, Maroofian R, Mehrjardi MYV, Moudi M, Müller AJ, Oostra AJ, Pletcher BA, Ros-Pardo D, Samarasekera S, Tartaglia M, Van Schil K, Vogt J, Wassmer E, Winkelmann J, Zaki MS, Zech M, Lerche H, Radio FC, Gomez-Puertas P, Møller RS, Tümer Z. Biallelic variants in ZNF142 lead to a syndromic neurodevelopmental disorder. Clin Genet 2022; 102:98-109. [PMID: 35616059 PMCID: PMC9546172 DOI: 10.1111/cge.14165] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 11/28/2022]
Abstract
Biallelic variants of the gene encoding for the zinc-finger protein 142 (ZNF142) have recently been associated with intellectual disability (ID), speech impairment, seizures, and movement disorders in nine individuals from five families. In this study, we obtained phenotype and genotype information of 26 further individuals from 16 families. Among the 27 different ZNF142 variants identified in the total of 35 individuals only four were missense. Missense variants may give a milder phenotype by changing the local structure of ZF motifs as suggested by protein modelling; but this correlation should be validated in larger cohorts and pathogenicity of the missense variants should be investigated with functional studies. Clinical features of the 35 individuals suggest that biallelic ZNF142 variants lead to a syndromic neurodevelopmental disorder with mild to moderate ID, varying degrees of delay in language and gross motor development, early onset seizures, hypotonia, behavioral features, movement disorders, and facial dysmorphism. The differences in symptom frequencies observed in the unpublished individuals compared to those of published, and recognition of previously underemphasized facial features are likely to be due to the small sizes of the previous cohorts, which underlines the importance of larger cohorts for the phenotype descriptions of rare genetic disorders. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Maria B Christensen
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Amanda M Levy
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Nazanin A Mohammadi
- Department of Epilepsy Genetics and Personalized Treatment, The Danish Epilepsy Centre, Dianalund, Denmark.,Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Disorders, University College London Institute of Neurology, London, United Kingdom
| | - Maria Lisa Dentici
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy.,Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chadi Al Alam
- Pediatric Neurology department, American center for Psychiatry and Neurology, Abu Dhabi and Al Ain, United Arab Emirates.,Pediatric Neurology department, Haykel Hospital, El Koura, Lebanon
| | - Viola Alesi
- Translational Cytogenomics Research Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | - Kailash P Bhatia
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian M Boßelmann
- Department of Neurology and Epileptology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Julien Buratti
- Department of Medical Genetics, Pitié-Salpêtrière Hospital, AP- HP, Sorbonne Université, Paris, France
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Berten Ceulemans
- Department of Pediatric Neurology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Perrine Charles
- Department of Medical Genetics, Pitié-Salpêtrière Hospital, AP- HP, Sorbonne Université, Paris, France
| | - Matthias De Wachter
- Department of Pediatric Neurology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Mohammadreza Dehghani
- Medical Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Erika D'haenens
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Martine Doco-Fenzy
- SFR CAP SANTE, HMB2 CHU, Reims, France.,CHU de Nantes, service de génétique médicale, Nantes, France
| | - Michaela Geßner
- KfH-Board of Trustees for Dialysis and Kidney Transplantation (KfH-Kuratorium für Dialyse und Nierentransplantation e.V.), Neu Isenburg, Germany
| | - Cyrielle Gobert
- Neuropediatric department, Centre Hospitalier Neurologique William Lennox, Ottignies, Belgium
| | | | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Trine B Hammer
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.,Department of Epilepsy Genetics and Personalized Treatment, The Danish Epilepsy Centre, Dianalund, Denmark
| | - Tilman Heinrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,MVZ Humangenetik und Molekularpathologie GmbH, Rostock, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Theresia Herget
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Judit Horvath
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - Henry Houlden
- Department of Neuromuscular Disorders, University College London Institute of Neurology, London, United Kingdom
| | - Boris Keren
- Department of Medical Genetics, Pitié-Salpêtrière Hospital, AP- HP, Sorbonne Université, Paris, France
| | | | - Candy Kumps
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | | | - Francesca Magrinelli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Reza Maroofian
- Department of Neuromuscular Disorders, University College London Institute of Neurology, London, United Kingdom
| | | | - Mahdiyeh Moudi
- Department of Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Amelie J Müller
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Anna J Oostra
- Neuropediatric department, Ghent University Hospital, Ghent, Belgium.,Centre for Developmental disorders, Ghent, Belgium
| | | | - David Ros-Pardo
- Molecular Modeling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), Madrid, Spain
| | | | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Kristof Van Schil
- Department of Medical Genetics, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Julie Vogt
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Birmingham, United Kingdom
| | - Evangeline Wassmer
- Birmingham Women and Children's Hospital, Birmingham, United Kingdom.,Institute of Health and Neurodevelopment, Aston University, Birmingham, United Kingdom
| | - Juliane Winkelmann
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt.,Genetics Department, Armed Forces College of Medicine (AFCM), Cairo, Egypt
| | - Michael Zech
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | | | - Paulino Gomez-Puertas
- Molecular Modeling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), Madrid, Spain
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Treatment, The Danish Epilepsy Centre, Dianalund, Denmark.,Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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28
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Hamanaka K, Miyake N, Mizuguchi T, Miyatake S, Uchiyama Y, Tsuchida N, Sekiguchi F, Mitsuhashi S, Tsurusaki Y, Nakashima M, Saitsu H, Yamada K, Sakamoto M, Fukuda H, Ohori S, Saida K, Itai T, Azuma Y, Koshimizu E, Fujita A, Erturk B, Hiraki Y, Ch'ng GS, Kato M, Okamoto N, Takata A, Matsumoto N. Large-scale discovery of novel neurodevelopmental disorder-related genes through a unified analysis of single-nucleotide and copy number variants. Genome Med 2022; 14:40. [PMID: 35468861 PMCID: PMC9040275 DOI: 10.1186/s13073-022-01042-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/25/2022] [Indexed: 12/12/2022] Open
Abstract
Background Previous large-scale studies of de novo variants identified a number of genes associated with neurodevelopmental disorders (NDDs); however, it was also predicted that many NDD-associated genes await discovery. Such genes can be discovered by integrating copy number variants (CNVs), which have not been fully considered in previous studies, and increasing the sample size. Methods We first constructed a model estimating the rates of de novo CNVs per gene from several factors such as gene length and number of exons. Second, we compiled a comprehensive list of de novo single-nucleotide variants (SNVs) in 41,165 individuals and de novo CNVs in 3675 individuals with NDDs by aggregating our own and publicly available datasets, including denovo-db and the Deciphering Developmental Disorders study data. Third, summing up the de novo CNV rates that we estimated and SNV rates previously established, gene-based enrichment of de novo deleterious SNVs and CNVs were assessed in the 41,165 cases. Significantly enriched genes were further prioritized according to their similarity to known NDD genes using a deep learning model that considers functional characteristics (e.g., gene ontology and expression patterns). Results We identified a total of 380 genes achieving statistical significance (5% false discovery rate), including 31 genes affected by de novo CNVs. Of the 380 genes, 52 have not previously been reported as NDD genes, and the data of de novo CNVs contributed to the significance of three genes (GLTSCR1, MARK2, and UBR3). Among the 52 genes, we reasonably excluded 18 genes [a number almost identical to the theoretically expected false positives (i.e., 380 × 0.05 = 19)] given their constraints against deleterious variants and extracted 34 “plausible” candidate genes. Their validity as NDD genes was consistently supported by their similarity in function and gene expression patterns to known NDD genes. Quantifying the overall similarity using deep learning, we identified 11 high-confidence (> 90% true-positive probabilities) candidate genes: HDAC2, SUPT16H, HECTD4, CHD5, XPO1, GSK3B, NLGN2, ADGRB1, CTR9, BRD3, and MARK2. Conclusions We identified dozens of new candidates for NDD genes. Both the methods and the resources developed here will contribute to the further identification of novel NDD-associated genes. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01042-w.
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Affiliation(s)
- Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Futoshi Sekiguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satomi Mitsuhashi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yoshinori Tsurusaki
- Faculty of Nutritional Science, Sagami Women's University, Sagamihara, Japan
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kohei Yamada
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Masamune Sakamoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiromi Fukuda
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Sachiko Ohori
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Toshiyuki Itai
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yoshiteru Azuma
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Pediatrics, Aichi Medical University, Nagakute, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Biray Erturk
- Department of Medical Genetics, Ege University Faculty of Medicine, Izmir, Turkey.,Current affiliation: Department of Medical Genetics, Prof. Dr. Cemil Tascioglu City Hospital, Istanbul, Turkey
| | - Yoko Hiraki
- Hiroshima Municipal Center for Child Health and Development, Hiroshima, Japan
| | | | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan. .,Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Wako, Japan.
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
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Caulier AL, Sankaran VG. Molecular and cellular mechanisms that regulate human erythropoiesis. Blood 2022; 139:2450-2459. [PMID: 34936695 PMCID: PMC9029096 DOI: 10.1182/blood.2021011044] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/15/2021] [Indexed: 12/03/2022] Open
Abstract
To enable effective oxygen transport, ∼200 billion red blood cells (RBCs) need to be produced every day in the bone marrow through the fine-tuned process of erythropoiesis. Erythropoiesis is regulated at multiple levels to ensure that defective RBC maturation or overproduction can be avoided. Here, we provide an overview of different layers of this control, ranging from cytokine signaling mechanisms that enable extrinsic regulation of RBC production to intrinsic transcriptional pathways necessary for effective erythropoiesis. Recent studies have also elucidated the importance of posttranscriptional regulation and highlighted additional gatekeeping mechanisms necessary for effective erythropoiesis. We additionally discuss the insights gained by studying human genetic variation affecting erythropoiesis and highlight the discovery of BCL11A as a regulator of hemoglobin switching through genetic studies. Finally, we provide an outlook of how our ability to measure multiple facets of this process at single-cell resolution, while accounting for the impact of human variation, will continue to refine our knowledge of erythropoiesis and how this process is perturbed in disease. As we learn more about this intricate and important process, additional opportunities to modulate erythropoiesis for therapeutic purposes will undoubtedly emerge.
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Affiliation(s)
- Alexis L Caulier
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA; and
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA; and
- Broad Institute of MIT and Harvard, Cambridge, MA
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30
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Molecular Diagnostic Outcomes from 700 Cases: What Can We Learn from a Retrospective Analysis of Clinical Exome Sequencing? J Mol Diagn 2022; 24:274-286. [PMID: 35065284 PMCID: PMC9904168 DOI: 10.1016/j.jmoldx.2021.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 11/29/2021] [Accepted: 12/10/2021] [Indexed: 01/19/2023] Open
Abstract
Clinical exome sequencing (CES) aids in the diagnosis of rare genetic disorders. Herein, we report the molecular diagnostic yield and spectrum of genetic alterations contributing to disease in 700 pediatric cases analyzed at the Children's Hospital of Philadelphia. The overall diagnostic yield was 23%, with three cases having more than one molecular diagnosis and 2.6% having secondary/additional findings. A candidate gene finding was reported in another 8.4% of cases. The clinical indications with the highest diagnostic yield were neurodevelopmental disorders (including seizures), whereas immune- and oncology-related indications were negatively associated with molecular diagnosis. The rapid expansion of knowledge regarding the genome's role in human disease necessitates reanalysis of CES samples. To capture these new discoveries, a subset of cases (n = 240) underwent reanalysis, with an increase in diagnostic yield. We describe our experience reporting CES results in a pediatric setting, including reporting of secondary findings, reporting newly discovered genetic conditions, and revisiting negative test results. Finally, we highlight the challenges associated with implementing critical updates to the CES workflow. Although these updates are necessary, they demand an investment of time and resources from the laboratory. In summary, these data demonstrate the clinical utility of exome sequencing and reanalysis, while highlighting the critical considerations for continuous improvement of a CES test in a clinical laboratory.
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31
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Chen CA, Lattier J, Zhu W, Rosenfeld J, Wang L, Scott TM, Du H, Patel V, Dang A, Magoulas P, Streff H, Sebastian J, Svihovec S, Curry K, Delgado MR, Hanchard N, Lalani S, Marom R, Madan-Khetarpal S, Saenz M, Dai H, Meng L, Xia F, Bi W, Liu P, Posey JE, Scott DA, Lupski JR, Eng CM, Xiao R, Yuan B. Retrospective analysis of a clinical exome sequencing cohort reveals the mutational spectrum and identifies candidate disease-associated loci for BAFopathies. Genet Med 2022; 24:364-373. [PMID: 34906496 PMCID: PMC8957292 DOI: 10.1016/j.gim.2021.09.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/19/2021] [Accepted: 06/19/2021] [Indexed: 02/03/2023] Open
Abstract
PURPOSE BRG1/BRM-associated factor (BAF) complex is a chromatin remodeling complex that plays a critical role in gene regulation. Defects in the genes encoding BAF subunits lead to BAFopathies, a group of neurodevelopmental disorders with extensive locus and phenotypic heterogeneity. METHODS We retrospectively analyzed data from 16,243 patients referred for clinical exome sequencing (ES) with a focus on the BAF complex. We applied a genotype-first approach, combining predicted genic constraints to propose candidate BAFopathy genes. RESULTS We identified 127 patients carrying pathogenic variants, likely pathogenic variants, or de novo variants of unknown clinical significance in 11 known BAFopathy genes. Those include 34 patients molecularly diagnosed using ES reanalysis with new gene-disease evidence (n = 21) or variant reclassifications in known BAFopathy genes (n = 13). We also identified de novo or predicted loss-of-function variants in 4 candidate BAFopathy genes, including ACTL6A, BICRA (implicated in Coffin-Siris syndrome during this study), PBRM1, and SMARCC1. CONCLUSION We report the mutational spectrum of BAFopathies in an ES cohort. A genotype-driven and pathway-based reanalysis of ES data identified new evidence for candidate genes involved in BAFopathies. Further mechanistic and phenotypic characterization of additional patients are warranted to confirm their roles in human disease and to delineate their associated phenotypic spectrums.
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Affiliation(s)
- Chun-An Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | | | | | - Jill Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Lei Wang
- Baylor Genetics Laboratory, Houston, TX
| | - Tiana M. Scott
- Texas Children’s Hospital, Houston, TX, Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | | | - Anh Dang
- Baylor Genetics Laboratory, Houston, TX
| | - Pilar Magoulas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | | | - Shayna Svihovec
- University of Colorado Anschutz Medical Campus; Children’s Hospital Colorado, Aurora, CO
| | - Kathryn Curry
- Genetics and Metabolic Department, St. Luke’s Health System
| | - Mauricio R. Delgado
- Texas Scottish Rite Hospital for Children, Dallas, TX, USA, Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Neil Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | - Seema Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | | | - Margarita Saenz
- University of Colorado Anschutz Medical Campus; Children’s Hospital Colorado, Aurora, CO
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX, Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Christine M. Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX, Current address: Department of Laboratories, Seattle Children’s Hospital, Seattle, WA
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Demirci S, Leonard A, Essawi K, Tisdale JF. CRISPR-Cas9 to induce fetal hemoglobin for the treatment of sickle cell disease. Mol Ther Methods Clin Dev 2021; 23:276-285. [PMID: 34729375 PMCID: PMC8526756 DOI: 10.1016/j.omtm.2021.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Genome editing is potentially a curative technique available to all individuals with β-hemoglobinopathies, including sickle cell disease (SCD). Fetal hemoglobin (HbF) inhibits sickle hemoglobin (HbS) polymerization, and it is well described that naturally occurring hereditary persistence of HbF (HPFH) alleviates disease symptoms; therefore, reawakening of developmentally silenced HbF in adult red blood cells (RBCs) has long been of interest as a therapeutic strategy. Recent advances in genome editing platforms, particularly with the use of CRISPR-Cas9, have paved the way for efficient HbF induction through the creation of artificial HPFH mutations, editing of transcriptional HbF silencers, and modulating epigenetic intermediates that govern HbF expression. Clinical trials investigating BCL11A enhancer editing in patients with β-hemoglobinopathies have demonstrated promising results, although follow-up is short and the number of patients treated to date is low. While practical, economic, and clinical challenges of genome editing are well recognized by the scientific community, potential solutions to overcome these hurdles are in development. Here, we review the recent progress and obstacles yet to be overcome for the most effective and feasible HbF reactivation practice using CRISPR-Cas9 genome editing as a curative strategy for patients with SCD.
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Affiliation(s)
- Selami Demirci
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20814, USA
| | - Alexis Leonard
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20814, USA
| | - Khaled Essawi
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20814, USA
- Department of Medical Laboratory Science, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - John F. Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20814, USA
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Rosanwo TO, Bauer DE. Editing outside the body: Ex vivo gene-modification for β-hemoglobinopathy cellular therapy. Mol Ther 2021; 29:3163-3178. [PMID: 34628053 PMCID: PMC8571174 DOI: 10.1016/j.ymthe.2021.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/01/2021] [Accepted: 10/02/2021] [Indexed: 12/26/2022] Open
Abstract
Genome editing produces genetic modifications in somatic cells, offering novel curative possibilities for sickle cell disease and β-thalassemia. These opportunities leverage clinical knowledge of hematopoietic stem cell transplant and gene transfer. Advantages to this mode of ex vivo therapy include locus-specific alteration of patient hematopoietic stem cell genomes, lack of allogeneic immune response, and avoidance of insertional mutagenesis. Despite exciting progress, many aspects of this approach remain to be optimized for ideal clinical implementation, including the efficiency and specificity of gene modification, delivery to hematopoietic stem cells, and robust and nontoxic engraftment of gene-modified cells. This review highlights genome editing as compared to other genetic therapies, the differences between editing strategies, and the clinical prospects and challenges of implementing genome editing as a novel treatment. As the world's most common monogenic disorders, the β-hemoglobinopathies are at the forefront of bringing genome editing to the clinic and hold promise for molecular medicine to address human disease at its root.
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Affiliation(s)
- Tolulope O Rosanwo
- Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston MA, USA; Department of Pediatrics, Boston Medical Center, Boston, MA, USA
| | - Daniel E Bauer
- Department of Pediatrics, Harvard Medical School, Boston MA, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA; Broad Institute, Cambridge, MA, USA.
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BAF45b Is Required for Efficient Zika Virus Infection of HAP1 Cells. Viruses 2021; 13:v13102007. [PMID: 34696437 PMCID: PMC8540262 DOI: 10.3390/v13102007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 01/10/2023] Open
Abstract
The 2016 Zika virus (ZIKV) epidemic illustrates the impact of flaviviruses as emerging human pathogens. For unknown reasons, ZIKV replicates more efficiently in neural progenitor cells (NPCs) than in postmitotic neurons. Here, we identified host factors used by ZIKV using the NCI-60 library of cell lines and COMPARE analysis, and cross-analyzed this library with two other libraries of host factors with importance for ZIKV infection. We identified BAF45b, a subunit of the BAF (Brg1/Brm-associated factors) protein complexes that regulate differentiation of NPCs to post-mitotic neurons. ZIKV (and other flaviviruses) infected HAP1 cells deficient in expression of BAF45b and other BAF subunits less efficiently than wildtype (WT) HAP1 cells. We concluded that subunits of the BAF complex are important for infection of ZIKV and other flavivirus. Given their function in cell and tissue differentiation, such regulators may be important determinants of tropism and pathogenesis of arthropod-borne flaviviruses.
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Shen Y, Li R, Teichert K, Montbleau KE, Verboon JM, Voit RA, Sankaran VG. Pathogenic BCL11A variants provide insights into the mechanisms of human fetal hemoglobin silencing. PLoS Genet 2021; 17:e1009835. [PMID: 34634037 PMCID: PMC8530301 DOI: 10.1371/journal.pgen.1009835] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 10/21/2021] [Accepted: 09/24/2021] [Indexed: 11/18/2022] Open
Abstract
Increased production of fetal hemoglobin (HbF) can ameliorate the severity of sickle cell disease and β-thalassemia. BCL11A has been identified as a key regulator of HbF silencing, although its precise mechanisms of action remain incompletely understood. Recent studies have identified pathogenic mutations that cause heterozygous loss-of-function of BCL11A and result in a distinct neurodevelopmental disorder that is characterized by persistent HbF expression. While the majority of cases have deletions or null mutations causing haploinsufficiency of BCL11A, several missense variants have also been identified. Here, we perform functional studies on these variants to uncover specific liabilities for BCL11A's function in HbF silencing. We find several mutations in an N-terminal C2HC zinc finger that increase proteasomal degradation of BCL11A. We also identify a distinct C-terminal missense variant in the fifth zinc finger domain that we demonstrate causes loss-of-function through disruption of DNA binding. Our analysis of missense variants causing loss-of-function in vivo illuminates mechanisms by which BCL11A silences HbF and also suggests potential therapeutic avenues for HbF induction to treat sickle cell disease and β-thalassemia.
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Affiliation(s)
- Yong Shen
- Division of Hematology/Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Rick Li
- Division of Hematology/Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Kristian Teichert
- Division of Hematology/Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Kara E. Montbleau
- Division of Hematology/Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jeffrey M. Verboon
- Division of Hematology/Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Richard A. Voit
- Division of Hematology/Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States of America
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Li X, Chen M, Liu B, Lu P, Lv X, Zhao X, Cui S, Xu P, Nakamura Y, Kurita R, Chen B, Huang DCS, Liu DP, Liu M, Zhao Q. Transcriptional silencing of fetal hemoglobin expression by NonO. Nucleic Acids Res 2021; 49:9711-9723. [PMID: 34379783 PMCID: PMC8464040 DOI: 10.1093/nar/gkab671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/19/2021] [Accepted: 07/23/2021] [Indexed: 12/21/2022] Open
Abstract
Human fetal globin (γ-globin) genes are developmentally silenced after birth, and reactivation of γ-globin expression in adulthood ameliorates symptoms of hemoglobin disorders, such as sickle cell disease (SCD) and β-thalassemia. However, the mechanisms by which γ-globin expression is precisely regulated are still incompletely understood. Here, we found that NonO (non-POU domain-containing octamer-binding protein) interacted directly with SOX6, and repressed the expression of γ-globin gene in human erythroid cells. We showed that NonO bound to the octamer binding motif, ATGCAAAT, of the γ-globin proximal promoter, resulting in inhibition of γ-globin transcription. Depletion of NonO resulted in significant activation of γ-globin expression in K562, HUDEP-2, and primary human erythroid progenitor cells. To confirm the role of NonO in vivo, we further generated a conditional knockout of NonO by using IFN-inducible Mx1-Cre transgenic mice. We found that induced NonO deletion reactivated murine embryonic globin and human γ-globin gene expression in adult β-YAC mice, suggesting a conserved role for NonO during mammalian evolution. Thus, our data indicate that NonO acts as a novel transcriptional repressor of γ-globin gene expression through direct promoter binding, and is essential for γ-globin gene silencing.
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Affiliation(s)
- Xinyu Li
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and Urology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Mengxia Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and Urology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Biru Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and Urology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Peifen Lu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and Urology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xiang Lv
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiang Zhao
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuaiying Cui
- Section of Hematology-Medical Oncology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Peipei Xu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and Urology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Bing Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and Urology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - David C S Huang
- The Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - De-Pei Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ming Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and Urology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Quan Zhao
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and Urology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing, China
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Tolve M, Ulusoy A, Patikas N, Islam KUS, Bodea GO, Öztürk E, Broske B, Mentani A, Wagener A, van Loo KMJ, Britsch S, Liu P, Khaled WT, Metzakopian E, Baader SL, Di Monte DA, Blaess S. The transcription factor BCL11A defines distinct subsets of midbrain dopaminergic neurons. Cell Rep 2021; 36:109697. [PMID: 34525371 DOI: 10.1016/j.celrep.2021.109697] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 07/08/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022] Open
Abstract
Midbrain dopaminergic (mDA) neurons are diverse in their projection targets, effect on behavior, and susceptibility to neurodegeneration. Little is known about the molecular mechanisms establishing this diversity during development. We show that the transcription factor BCL11A is expressed in a subset of mDA neurons in the developing and adult murine brain and in a subpopulation of pluripotent-stem-cell-derived human mDA neurons. By combining intersectional labeling and viral-mediated tracing, we demonstrate that Bcl11a-expressing mDA neurons form a highly specific subcircuit within the murine dopaminergic system. In the substantia nigra, the Bcl11a-expressing mDA subset is particularly vulnerable to neurodegeneration upon α-synuclein overexpression or oxidative stress. Inactivation of Bcl11a in murine mDA neurons increases this susceptibility further, alters the distribution of mDA neurons, and results in deficits in skilled motor behavior. In summary, BCL11A defines mDA subpopulations with highly distinctive characteristics and is required for establishing and maintaining their normal physiology.
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Affiliation(s)
- Marianna Tolve
- Neurodevelopmental Genetics, Institute of Reconstructive Neurobiology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Ayse Ulusoy
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Nikolaos Patikas
- UK Dementia Research Institute, Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AH, UK
| | - K Ushna S Islam
- Neurodevelopmental Genetics, Institute of Reconstructive Neurobiology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Gabriela O Bodea
- Neurodevelopmental Genetics, Institute of Reconstructive Neurobiology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Ece Öztürk
- Neurodevelopmental Genetics, Institute of Reconstructive Neurobiology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Bianca Broske
- Neurodevelopmental Genetics, Institute of Reconstructive Neurobiology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Astrid Mentani
- Neurodevelopmental Genetics, Institute of Reconstructive Neurobiology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Antonia Wagener
- Neurodevelopmental Genetics, Institute of Reconstructive Neurobiology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Karen M J van Loo
- Section for Translational Epilepsy Research, Department of Neuropathology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Stefan Britsch
- Institute of Molecular and Cellular Anatomy, Ulm University, 89081 Ulm, Germany
| | - Pengtao Liu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Walid T Khaled
- Department of Pharmacology, University of Cambridge, Cambridge, CB 21PD, UK; Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
| | - Emmanouil Metzakopian
- UK Dementia Research Institute, Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Stephan L Baader
- Institute of Anatomy, Anatomy and Cell Biology, Medical Faculty, University of Bonn, 53115 Bonn, Germany
| | - Donato A Di Monte
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Sandra Blaess
- Neurodevelopmental Genetics, Institute of Reconstructive Neurobiology, Medical Faculty, University of Bonn, 53127 Bonn, Germany.
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Shen Y, Verboon JM, Zhang Y, Liu N, Kim YJ, Marglous S, Nandakumar SK, Voit RA, Fiorini C, Ejaz A, Basak A, Orkin SH, Xu J, Sankaran VG. A unified model of human hemoglobin switching through single-cell genome editing. Nat Commun 2021; 12:4991. [PMID: 34404810 PMCID: PMC8371164 DOI: 10.1038/s41467-021-25298-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/02/2021] [Indexed: 12/17/2022] Open
Abstract
Key mechanisms of fetal hemoglobin (HbF) regulation and switching have been elucidated through studies of human genetic variation, including mutations in the HBG1/2 promoters, deletions in the β-globin locus, and variation impacting BCL11A. While this has led to substantial insights, there has not been a unified understanding of how these distinct genetically-nominated elements, as well as other key transcription factors such as ZBTB7A, collectively interact to regulate HbF. A key limitation has been the inability to model specific genetic changes in primary isogenic human hematopoietic cells to uncover how each of these act individually and in aggregate. Here, we describe a single-cell genome editing functional assay that enables specific mutations to be recapitulated individually and in combination, providing insights into how multiple mutation-harboring functional elements collectively contribute to HbF expression. In conjunction with quantitative modeling and chromatin capture analyses, we illustrate how these genetic findings enable a comprehensive understanding of how distinct regulatory mechanisms can synergistically modulate HbF expression. Genetic mechanisms underlying fetal hemoglobin (HbF) regulation and switching are not fully understood. Here, the authors develop a single-cell genome editing functional assay to model how effects of mutation-harbouring functional elements contribute to HbF expression.
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Affiliation(s)
- Yong Shen
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeffrey M Verboon
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nan Liu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yoon Jung Kim
- Children's Medical Center Research Institute, Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Samantha Marglous
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Satish K Nandakumar
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard A Voit
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Claudia Fiorini
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ayesha Ejaz
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anindita Basak
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Howard Hughes Medical Institute, Boston, MA, USA
| | - Jian Xu
- Children's Medical Center Research Institute, Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. .,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Harvard Stem Cell Institute, Cambridge, MA, USA.
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Janowski M, Milewska M, Zare P, Pękowska A. Chromatin Alterations in Neurological Disorders and Strategies of (Epi)Genome Rescue. Pharmaceuticals (Basel) 2021; 14:765. [PMID: 34451862 PMCID: PMC8399958 DOI: 10.3390/ph14080765] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/26/2022] Open
Abstract
Neurological disorders (NDs) comprise a heterogeneous group of conditions that affect the function of the nervous system. Often incurable, NDs have profound and detrimental consequences on the affected individuals' lives. NDs have complex etiologies but commonly feature altered gene expression and dysfunctions of the essential chromatin-modifying factors. Hence, compounds that target DNA and histone modification pathways, the so-called epidrugs, constitute promising tools to treat NDs. Yet, targeting the entire epigenome might reveal insufficient to modify a chosen gene expression or even unnecessary and detrimental to the patients' health. New technologies hold a promise to expand the clinical toolkit in the fight against NDs. (Epi)genome engineering using designer nucleases, including CRISPR-Cas9 and TALENs, can potentially help restore the correct gene expression patterns by targeting a defined gene or pathway, both genetically and epigenetically, with minimal off-target activity. Here, we review the implication of epigenetic machinery in NDs. We outline syndromes caused by mutations in chromatin-modifying enzymes and discuss the functional consequences of mutations in regulatory DNA in NDs. We review the approaches that allow modifying the (epi)genome, including tools based on TALENs and CRISPR-Cas9 technologies, and we highlight how these new strategies could potentially change clinical practices in the treatment of NDs.
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Affiliation(s)
| | | | | | - Aleksandra Pękowska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteur Street, 02-093 Warsaw, Poland; (M.J.); (M.M.); (P.Z.)
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40
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D'Souza L, Channakkar AS, Muralidharan B. Chromatin remodelling complexes in cerebral cortex development and neurodevelopmental disorders. Neurochem Int 2021; 147:105055. [PMID: 33964373 PMCID: PMC7611358 DOI: 10.1016/j.neuint.2021.105055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 04/11/2021] [Accepted: 04/24/2021] [Indexed: 12/19/2022]
Abstract
The diverse number of neurons in the cerebral cortex are generated during development by neural stem cells lining the ventricle, and they continue maturing postnatally. Dynamic chromatin regulation in these neural stem cells is a fundamental determinant of the emerging property of the functional neural network, and the chromatin remodellers are critical determinants of this process. Chromatin remodellers participate in several steps of this process from proliferation, differentiation, migration leading to complex network formation which forms the basis of higher-order functions of cognition and behaviour. Here we review the role of these ATP-dependent chromatin remodellers in cortical development in health and disease and highlight several key mouse mutants of the subunits of the complexes which have revealed how the remodelling mechanisms control the cortical stem cell chromatin landscape for expression of stage-specific transcripts. Consistent with their role in cortical development, several putative risk variants in the subunits of the remodelling complexes have been identified as the underlying causes of several neurodevelopmental disorders. A basic understanding of the detailed molecular mechanism of their action is key to understating how mutations in the same networks lead to disease pathologies and perhaps pave the way for therapeutic development for these complex multifactorial disorders.
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Affiliation(s)
- Leora D'Souza
- Brain Development and Disease Mechanisms, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore Life Science Cluster, Bangalore, India
| | - Asha S Channakkar
- Brain Development and Disease Mechanisms, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore Life Science Cluster, Bangalore, India
| | - Bhavana Muralidharan
- Brain Development and Disease Mechanisms, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore Life Science Cluster, Bangalore, India.
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41
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Whole-genome sequencing identifies functional noncoding variation in SEMA3C that cosegregates with dyslexia in a multigenerational family. Hum Genet 2021; 140:1183-1200. [PMID: 34076780 PMCID: PMC8263547 DOI: 10.1007/s00439-021-02289-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/27/2021] [Indexed: 12/11/2022]
Abstract
Dyslexia is a common heritable developmental disorder involving impaired reading abilities. Its genetic underpinnings are thought to be complex and heterogeneous, involving common and rare genetic variation. Multigenerational families segregating apparent monogenic forms of language-related disorders can provide useful entrypoints into biological pathways. In the present study, we performed a genome-wide linkage scan in a three-generational family in which dyslexia affects 14 of its 30 members and seems to be transmitted with an autosomal dominant pattern of inheritance. We identified a locus on chromosome 7q21.11 which cosegregated with dyslexia status, with the exception of two cases of phenocopy (LOD = 2.83). Whole-genome sequencing of key individuals enabled the assessment of coding and noncoding variation in the family. Two rare single-nucleotide variants (rs144517871 and rs143835534) within the first intron of the SEMA3C gene cosegregated with the 7q21.11 risk haplotype. In silico characterization of these two variants predicted effects on gene regulation, which we functionally validated for rs144517871 in human cell lines using luciferase reporter assays. SEMA3C encodes a secreted protein that acts as a guidance cue in several processes, including cortical neuronal migration and cellular polarization. We hypothesize that these intronic variants could have a cis-regulatory effect on SEMA3C expression, making a contribution to dyslexia susceptibility in this family.
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Abstract
Behavioral genetics and cultural evolution have both revolutionized our understanding of human behavior-largely independent of each other. Here we reconcile these two fields under a dual inheritance framework, offering a more nuanced understanding of the interaction between genes and culture. Going beyond typical analyses of gene-environment interactions, we describe the cultural dynamics that shape these interactions by shaping the environment and population structure. A cultural evolutionary approach can explain, for example, how factors such as rates of innovation and diffusion, density of cultural sub-groups, and tolerance for behavioral diversity impact heritability estimates, thus yielding predictions for different social contexts. Moreover, when cumulative culture functionally overlaps with genes, genetic effects become masked, unmasked, or even reversed, and the causal effects of an identified gene become confounded with features of the cultural environment. The manner of confounding is specific to a particular society at a particular time, but a WEIRD (Western, educated, industrialized, rich, democratic) sampling problem obscures this boundedness. Cultural evolutionary dynamics are typically missing from models of gene-to-phenotype causality, hindering generalizability of genetic effects across societies and across time. We lay out a reconciled framework and use it to predict the ways in which heritability should differ between societies, between socioeconomic levels and other groupings within some societies but not others, and over the life course. An integrated cultural evolutionary behavioral genetic approach cuts through the nature-nurture debate and helps resolve controversies in topics such as IQ.
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43
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Wessels MW, Cnossen MH, van Dijk TB, Gillemans N, Schmidt KLJ, van Lom K, Vinjamur DS, Coyne S, Kurita R, Nakamura Y, de Man SA, Pfundt R, Azmani Z, Brouwer RWW, Bauer DE, van den Hout MCGN, van IJcken WFJ, Philipsen S. Molecular analysis of the erythroid phenotype of a patient with BCL11A haploinsufficiency. Blood Adv 2021; 5:2339-2349. [PMID: 33938942 PMCID: PMC8114548 DOI: 10.1182/bloodadvances.2020003753] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/12/2021] [Indexed: 12/29/2022] Open
Abstract
The BCL11A gene encodes a transcriptional repressor with essential functions in multiple tissues during human development. Haploinsufficiency for BCL11A causes Dias-Logan syndrome (OMIM 617101), an intellectual developmental disorder with hereditary persistence of fetal hemoglobin (HPFH). Due to the severe phenotype, disease-causing variants in BCL11A occur de novo. We describe a patient with a de novo heterozygous variant, c.1453G>T, in the BCL11A gene, resulting in truncation of the BCL11A-XL protein (p.Glu485X). The truncated protein lacks the 3 C-terminal DNA-binding zinc fingers and the nuclear localization signal, rendering it inactive. The patient displayed high fetal hemoglobin (HbF) levels (12.1-18.7% of total hemoglobin), in contrast to the parents who had HbF levels of 0.3%. We used cultures of patient-derived erythroid progenitors to determine changes in gene expression and chromatin accessibility. In addition, we investigated DNA methylation of the promoters of the γ-globin genes HBG1 and HBG2. HUDEP1 and HUDEP2 cells were used as models for fetal and adult human erythropoiesis, respectively. Similar to HUDEP1 cells, the patient's cells displayed Assay for Transposase-Accessible Chromatin (ATAC) peaks at the HBG1/2 promoters and significant expression of HBG1/2 genes. In contrast, HBG1/2 promoter methylation and genome-wide gene expression profiling were consistent with normal adult erythropoiesis. We conclude that HPFH is the major erythroid phenotype of constitutive BCL11A haploinsufficiency. Given the essential functions of BCL11A in other hematopoietic lineages and the neuronal system, erythroid-specific targeting of the BCL11A gene has been proposed for reactivation of γ-globin expression in β-hemoglobinopathy patients. Our data strongly support this approach.
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Affiliation(s)
| | - Marjon H Cnossen
- Department of Pediatric Hematology
- Academic Center for Hemoglobinopathies and Rare Anemias
| | - Thamar B van Dijk
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
| | - Nynke Gillemans
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
| | - K L Juliëtte Schmidt
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
| | - Kirsten van Lom
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Hematology, Erasmus MC, Rotterdam, The Netherlands
| | - Divya S Vinjamur
- Division of Hematology/Oncology, Department of Pediatric Oncology, Boston Children's Hospital, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Boston, MA
- Broad Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Steven Coyne
- Division of Hematology/Oncology, Department of Pediatric Oncology, Boston Children's Hospital, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Boston, MA
- Broad Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN, BioResource Center, Tsukuba, Japan
| | - Stella A de Man
- Department of Pediatrics, Amphia Hospital, Breda, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; and
| | - Zakia Azmani
- Department of Cell Biology, and
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
| | - Rutger W W Brouwer
- Department of Cell Biology, and
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
| | - Daniel E Bauer
- Division of Hematology/Oncology, Department of Pediatric Oncology, Boston Children's Hospital, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Boston, MA
- Broad Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | | | - Wilfred F J van IJcken
- Department of Cell Biology, and
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
| | - Sjaak Philipsen
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
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Li D, Wang Q, Gong NN, Kurolap A, Feldman HB, Boy N, Brugger M, Grand K, McWalter K, Guillen Sacoto MJ, Wakeling E, Hurst J, March ME, Bhoj EJ, Nowaczyk MJM, Gonzaga-Jauregui C, Mathew M, Dava-Wala A, Siemon A, Bartholomew D, Huang Y, Lee H, Martinez-Agosto JA, Schwaibold EMC, Brunet T, Choukair D, Pais LS, White SM, Christodoulou J, Brown D, Lindstrom K, Grebe T, Tiosano D, Kayser MS, Tan TY, Deardorff MA, Song Y, Hakonarson H. Pathogenic variants in SMARCA5, a chromatin remodeler, cause a range of syndromic neurodevelopmental features. SCIENCE ADVANCES 2021; 7:7/20/eabf2066. [PMID: 33980485 PMCID: PMC8115915 DOI: 10.1126/sciadv.abf2066] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/23/2021] [Indexed: 05/17/2023]
Abstract
Intellectual disability encompasses a wide spectrum of neurodevelopmental disorders, with many linked genetic loci. However, the underlying molecular mechanism for more than 50% of the patients remains elusive. We describe pathogenic variants in SMARCA5, encoding the ATPase motor of the ISWI chromatin remodeler, as a cause of a previously unidentified neurodevelopmental disorder, identifying 12 individuals with de novo or dominantly segregating rare heterozygous variants. Accompanying phenotypes include mild developmental delay, frequent postnatal short stature and microcephaly, and recurrent dysmorphic features. Loss of function of the SMARCA5 Drosophila ortholog Iswi led to smaller body size, reduced sensory dendrite complexity, and tiling defects in larvae. In adult flies, Iswi neural knockdown caused decreased brain size, aberrant mushroom body morphology, and abnormal locomotor function. Iswi loss of function was rescued by wild-type but not mutant SMARCA5. Our results demonstrate that SMARCA5 pathogenic variants cause a neurodevelopmental syndrome with mild facial dysmorphia.
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Affiliation(s)
- Dong Li
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Qin Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Naihua N Gong
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Alina Kurolap
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Hagit Baris Feldman
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nikolas Boy
- Division of Child Neurology and Metabolic Medicine, Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Melanie Brugger
- Institute of Human Genetics, Technical University Munich, Munich, Germany
- Institute of Human Genetics, University Hospital LMU Munich, Goethestr. 29, Munich, Germany
| | - Katheryn Grand
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | - Emma Wakeling
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Jane Hurst
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Michael E March
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elizabeth J Bhoj
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Małgorzata J M Nowaczyk
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | | | - Mariam Mathew
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Ashita Dava-Wala
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Amy Siemon
- Department of Pediatrics and Clinical Genetics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Dennis Bartholomew
- Department of Pediatrics and Clinical Genetics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Yue Huang
- Department of Human Genetics; Division of Medical Genetics, Department of Pediatrics; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine; Department of Human Genetics; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics; Division of Medical Genetics, Department of Pediatrics; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Eva M C Schwaibold
- Department of Pathology and Laboratory Medicine; Department of Human Genetics; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Theresa Brunet
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Daniela Choukair
- Division of Paediatric Endocrinology and Diabetes, Department of Paediatrics, University Hospital Heidelberg, Heidelberg, Germany
| | - Lynn S Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - John Christodoulou
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Dana Brown
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Kristin Lindstrom
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Theresa Grebe
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ, USA
- College of Medicine, University of Arizona, Phoenix, 475 N. 5th Street, Phoenix, AZ, USA
| | - Dov Tiosano
- Pediatric Endocrinology Unit, Ruth Rappaport Children's Hospital, Rambam Healthcare Campus, Haifa, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Matthew S Kayser
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Matthew A Deardorff
- Departments of Pathology and Pediatrics, Children's Hospital Los Angeles, and University of Southern California, Los Angeles, CA, USA
| | - Yuanquan Song
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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45
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Salem NA, Mahnke AH, Konganti K, Hillhouse AE, Miranda RC. Cell-type and fetal-sex-specific targets of prenatal alcohol exposure in developing mouse cerebral cortex. iScience 2021; 24:102439. [PMID: 33997709 PMCID: PMC8105653 DOI: 10.1016/j.isci.2021.102439] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/07/2021] [Accepted: 04/13/2021] [Indexed: 11/17/2022] Open
Abstract
Prenatal alcohol exposure (PAE) results in cerebral cortical dysgenesis. Single-cell RNA sequencing was performed on murine fetal cerebral cortical cells from six timed pregnancies, to decipher persistent cell- and sex-specific effects of an episode of PAE during early neurogenesis. We found, in an analysis of 38 distinct neural subpopulations across 8 lineage subtypes, that PAE altered neural maturation and cell cycle and disrupted gene co-expression networks. Whereas most differentially regulated genes were inhibited, particularly in females, PAE also induced sex-independent neural expression of fetal hemoglobin, a presumptive epigenetic stress adaptation. PAE inhibited Bcl11a, Htt, Ctnnb1, and other upstream regulators of differentially expressed genes and inhibited several autism-linked genes, suggesting that neurodevelopmental disorders share underlying mechanisms. PAE females exhibited neural loss of X-inactivation, with correlated activation of autosomal genes and evidence for spliceosome dysfunction. Thus, episodic PAE persistently alters the developing neural transcriptome, contributing to sex- and cell-type-specific teratology. The neurogenic murine fetal cortex contains about 33 distinct cell subtypes Prenatal Alcohol Exposure (PAE) resulted in sex-specific alterations in developmental trajectory and cell cycle PAE females exhibited neural loss of X-inactivation and spliceosomal dysfunction PAE induced sex-independent neural expression of fetal hemoglobin gene transcripts
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Affiliation(s)
- Nihal A. Salem
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University Health Science Center, Medical Research and Education Building, 8447 Riverside Parkway, Bryan, TX 77807-3260, USA
- Texas A&M Institute for Neuroscience, Texas A&M University, College Station, TX, USA
| | - Amanda H. Mahnke
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University Health Science Center, Medical Research and Education Building, 8447 Riverside Parkway, Bryan, TX 77807-3260, USA
- Women's Health in Neuroscience Program, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Kranti Konganti
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX 77843, USA
| | - Andrew E. Hillhouse
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX 77843, USA
| | - Rajesh C. Miranda
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University Health Science Center, Medical Research and Education Building, 8447 Riverside Parkway, Bryan, TX 77807-3260, USA
- Texas A&M Institute for Neuroscience, Texas A&M University, College Station, TX, USA
- Women's Health in Neuroscience Program, Texas A&M University Health Science Center, Bryan, TX, USA
- Corresponding author
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46
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Frati G, Miccio A. Genome Editing for β-Hemoglobinopathies: Advances and Challenges. J Clin Med 2021; 10:482. [PMID: 33525591 PMCID: PMC7865242 DOI: 10.3390/jcm10030482] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/19/2021] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
β-hemoglobinopathies are the most common genetic disorders worldwide and are caused by mutations affecting the production or the structure of adult hemoglobin. Patients affected by these diseases suffer from anemia, impaired oxygen delivery to tissues, and multi-organ damage. In the absence of a compatible donor for allogeneic bone marrow transplantation, the lifelong therapeutic options are symptomatic care, red blood cell transfusions and pharmacological treatments. The last decades of research established lentiviral-mediated gene therapy as an efficacious therapeutic strategy. However, this approach is highly expensive and associated with a variable outcome depending on the effectiveness of the viral vector and the quality of the cell product. In the last years, genome editing emerged as a valuable tool for the development of curative strategies for β-hemoglobinopathies. Moreover, due to the wide range of its applications, genome editing has been extensively used to study regulatory mechanisms underlying globin gene regulation allowing the identification of novel genetic and pharmacological targets. In this work, we review the current advances and challenges of genome editing approaches to β-hemoglobinopathies. Special focus has been directed towards strategies aimed at correcting the defective β-globin gene or at inducing fetal hemoglobin (HbF), which are in an advanced state of clinical development.
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Affiliation(s)
- Giacomo Frati
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, Université de Paris, INSERM UMR 1163, F-75015 Paris, France
| | - Annarita Miccio
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, Université de Paris, INSERM UMR 1163, F-75015 Paris, France
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47
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Papizan JB, Porter SN, Sharma A, Pruett-Miller SM. Therapeutic gene editing strategies using CRISPR-Cas9 for the β-hemoglobinopathies. J Biomed Res 2021; 35:115-134. [PMID: 33349624 PMCID: PMC8038529 DOI: 10.7555/jbr.34.20200096] [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] [Indexed: 12/26/2022] Open
Abstract
With advancements in gene editing technologies, our ability to make precise and efficient modifications to the genome is increasing at a remarkable rate, paving the way for scientists and clinicians to uniquely treat a multitude of previously irremediable diseases. CRISPR-Cas9, short for clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9, is a gene editing platform with the ability to alter the nucleotide sequence of the genome in living cells. This technology is increasing the number and pace at which new gene editing treatments for genetic disorders are moving toward the clinic. The β-hemoglobinopathies are a group of monogenic diseases, which despite their high prevalence and chronic debilitating nature, continue to have few therapeutic options available. In this review, we will discuss our existing comprehension of the genetics and current state of treatment for β-hemoglobinopathies, consider potential genome editing therapeutic strategies, and provide an overview of the current state of clinical trials using CRISPR-Cas9 gene editing.
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Affiliation(s)
- James B Papizan
- Department of Cellular and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shaina N Porter
- Department of Cellular and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Akshay Sharma
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shondra M Pruett-Miller
- Department of Cellular and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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48
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Garcia-Forn M, Boitnott A, Akpinar Z, De Rubeis S. Linking Autism Risk Genes to Disruption of Cortical Development. Cells 2020; 9:cells9112500. [PMID: 33218123 PMCID: PMC7698947 DOI: 10.3390/cells9112500] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/10/2020] [Accepted: 11/15/2020] [Indexed: 02/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a prevalent neurodevelopmental disorder characterized by impairments in social communication and social interaction, and the presence of repetitive behaviors and/or restricted interests. In the past few years, large-scale whole-exome sequencing and genome-wide association studies have made enormous progress in our understanding of the genetic risk architecture of ASD. While showing a complex and heterogeneous landscape, these studies have led to the identification of genetic loci associated with ASD risk. The intersection of genetic and transcriptomic analyses have also begun to shed light on functional convergences between risk genes, with the mid-fetal development of the cerebral cortex emerging as a critical nexus for ASD. In this review, we provide a concise summary of the latest genetic discoveries on ASD. We then discuss the studies in postmortem tissues, stem cell models, and rodent models that implicate recently identified ASD risk genes in cortical development.
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Affiliation(s)
- Marta Garcia-Forn
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.G.-F.); (A.B.); (Z.A.)
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrea Boitnott
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.G.-F.); (A.B.); (Z.A.)
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zeynep Akpinar
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.G.-F.); (A.B.); (Z.A.)
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychology, College of Arts and Sciences, New York University, New York, NY 10003, USA
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.G.-F.); (A.B.); (Z.A.)
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Correspondence: ; Tel.: +1-212-241-0179
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49
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Parker KR, Migliorini D, Perkey E, Yost KE, Bhaduri A, Bagga P, Haris M, Wilson NE, Liu F, Gabunia K, Scholler J, Montine TJ, Bhoj VG, Reddy R, Mohan S, Maillard I, Kriegstein AR, June CH, Chang HY, Posey AD, Satpathy AT. Single-Cell Analyses Identify Brain Mural Cells Expressing CD19 as Potential Off-Tumor Targets for CAR-T Immunotherapies. Cell 2020; 183:126-142.e17. [PMID: 32961131 PMCID: PMC7640763 DOI: 10.1016/j.cell.2020.08.022] [Citation(s) in RCA: 269] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 05/26/2020] [Accepted: 08/12/2020] [Indexed: 12/18/2022]
Abstract
CD19-directed immunotherapies are clinically effective for treating B cell malignancies but also cause a high incidence of neurotoxicity. A subset of patients treated with chimeric antigen receptor (CAR) T cells or bispecific T cell engager (BiTE) antibodies display severe neurotoxicity, including fatal cerebral edema associated with T cell infiltration into the brain. Here, we report that mural cells, which surround the endothelium and are critical for blood-brain-barrier integrity, express CD19. We identify CD19 expression in brain mural cells using single-cell RNA sequencing data and confirm perivascular staining at the protein level. CD19 expression in the brain begins early in development alongside the emergence of mural cell lineages and persists throughout adulthood across brain regions. Mouse mural cells demonstrate lower levels of Cd19 expression, suggesting limitations in preclinical animal models of neurotoxicity. These data suggest an on-target mechanism for neurotoxicity in CD19-directed therapies and highlight the utility of human single-cell atlases for designing immunotherapies.
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MESH Headings
- Animals
- Antibodies, Bispecific/immunology
- Antigens, CD19/immunology
- B-Lymphocytes/immunology
- Blood-Brain Barrier/immunology
- Blood-Brain Barrier/metabolism
- Brain/immunology
- Brain/metabolism
- Cell Line, Tumor
- Cytotoxicity, Immunologic
- Epithelial Cells/metabolism
- Humans
- Immunotherapy/adverse effects
- Immunotherapy/methods
- Immunotherapy, Adoptive/adverse effects
- Immunotherapy, Adoptive/methods
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Muscle, Smooth, Vascular/metabolism
- Neoplasms
- Receptors, Antigen, T-Cell/immunology
- Receptors, Chimeric Antigen/immunology
- Single-Cell Analysis/methods
- T-Lymphocytes/immunology
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Kevin R Parker
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Denis Migliorini
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Translational Research in Onco-Hematology and Department of Oncology, Geneva University Hospitals and University of Geneva, Geneva, Switzerland.
| | - Eric Perkey
- Graduate Program in Cellular and Molecular Biology and Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA; Division of Hematology-Oncology, Department of Medicine and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Aparna Bhaduri
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Puneet Bagga
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mohammad Haris
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Functional and Molecular Imaging Laboratory, Research Branch, Sidra Medicine, Doha, Qatar; Laboratory Animal Research Center, Qatar University, Doha, Qatar
| | - Neil E Wilson
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Fang Liu
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Khatuna Gabunia
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John Scholler
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Vijay G Bhoj
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ravinder Reddy
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Suyash Mohan
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ivan Maillard
- Division of Hematology-Oncology, Department of Medicine and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arnold R Kriegstein
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Carl H June
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Avery D Posey
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Ansuman T Satpathy
- Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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50
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Demirci S, Leonard A, Tisdale JF. Genome editing strategies for fetal hemoglobin induction in beta-hemoglobinopathies. Hum Mol Genet 2020; 29:R100-R106. [PMID: 32406490 PMCID: PMC7673473 DOI: 10.1093/hmg/ddaa088] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 04/28/2020] [Accepted: 05/11/2020] [Indexed: 12/26/2022] Open
Abstract
Genome editing to correct a defective β-globin gene or induce fetal globin (HbF) for patients with beta-hemoglobinopathies has the potential to be a curative strategy available to all. HbF reactivation has long been an area of intense interest given the HbF inhibition of sickle hemoglobin (HbS) polymerization. Patients with HbS who also have high HbF tend to have less severe or even minimal clinical manifestations. Approaches to genetically engineer high HbF include de novo generation of naturally occurring hereditary persistence of fetal hemoglobin (HPFH) mutations, editing of transcriptional HbF repressors or their binding sites and/or regulating epigenetic intermediates controlling HbF expression. Recent preclinical and early clinical trial data show encouraging results; however, long-term follow-up is lacking, and the safety and efficacy concerns of genome editing remain.
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Affiliation(s)
- Selami Demirci
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes, National Institutes of Health, Bethesda, MD, USA
| | - Alexis Leonard
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes, National Institutes of Health, Bethesda, MD, USA
| | - John F Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes, National Institutes of Health, Bethesda, MD, USA
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