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Rosenkrantz JL, Brandorff JE, Raghib S, Kapadia A, Vaine CA, Bragg DC, Farmiloe G, Jacobs FMJ. ZNF91 is an endogenous repressor of the molecular phenotype associated with X-linked dystonia-parkinsonism (XDP). Proc Natl Acad Sci U S A 2024; 121:e2401217121. [PMID: 39102544 PMCID: PMC11331120 DOI: 10.1073/pnas.2401217121] [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: 01/22/2024] [Accepted: 06/18/2024] [Indexed: 08/07/2024] Open
Abstract
X-linked dystonia-parkinsonism (XDP) is a severe neurodegenerative disorder resulting from an inherited intronic SINE-Alu-VNTR (SVA) retrotransposon in the TAF1 gene that causes dysregulation of TAF1 transcription. The specific mechanism underlying this dysregulation remains unclear, but it is hypothesized to involve the formation of G-quadruplexes (G4) structures within the XDP-SVA that impede transcription. In this study, we show that ZNF91, a critical repressor of SVA retrotransposons, specifically binds to G4-forming DNA sequences. Further, we found that genetic deletion of ZNF91 exacerbates the molecular phenotype associated with the XDP-SVA insertion in patient cells, while no difference was observed when ZNF91 was deleted from isogenic control cells. Additionally, we observed a significant age-related reduction in ZNF91 expression in whole blood and brain, indicating a progressive loss of repression of the XDP-SVA in XDP. These findings indicate that ZNF91 plays a crucial role in controlling the molecular phenotype associated with XDP. Since ZNF91 binds to G4-forming DNA sequences in SVAs, this suggests that interactions between ZNF91 and G4-forming sequences in the XDP-SVA minimize the severity of the molecular phenotype. Our results showing that ZNF91 expression levels significantly decrease with age provide a potential explanation for the age-related progressive neurodegenerative character of XDP. Collectively, our study provides important insights into the protective role of ZNF91 in XDP pathogenesis and suggests that restoring ZNF91 expression, destabilization of G4s, or targeted repression of the XDP-SVA could be future therapeutic strategies to prevent or treat XDP.
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Affiliation(s)
- Jimi L. Rosenkrantz
- Faculty of Science, Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam1098 XH, The Netherlands
| | - J. Elias Brandorff
- Faculty of Science, Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam1098 XH, The Netherlands
| | - Sanaz Raghib
- Faculty of Science, Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam1098 XH, The Netherlands
| | - Ashni Kapadia
- Faculty of Science, Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam1098 XH, The Netherlands
| | - Christine A. Vaine
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Boston, MA02129
| | - D. Cristopher Bragg
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Boston, MA02129
| | - Grace Farmiloe
- Faculty of Science, Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam1098 XH, The Netherlands
| | - Frank M. J. Jacobs
- Faculty of Science, Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam1098 XH, The Netherlands
- Faculty of Science, Amsterdam Neuroscience, Complex Trait Genetics, University of Amsterdam, Amsterdam1098 XH, The Netherlands
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2
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Roychaudhury A, Lee YR, Choi TI, Thomas MG, Khan TN, Yousaf H, Skinner C, Maconachie G, Crosier M, Horak H, Constantinescu CS, Kim TY, Lee KH, Kyung JJ, Wang T, Ku B, Chodirker BN, Hammer MF, Gottlob I, Norton WHJ, Gerlai R, Kim HG, Graziano C, Pippucci T, Iovino E, Montanari F, Severi G, Toro C, Boerkoel CF, Cha HS, Choi CY, Kim S, Yoon JH, Gilmore K, Vora NL, Davis EE, Chudley AE, Schwartz CE, Kim CH. SRPK3 Is Essential for Cognitive and Ocular Development in Humans and Zebrafish, Explaining X-Linked Intellectual Disability. Ann Neurol 2024. [PMID: 39073169 DOI: 10.1002/ana.27037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/07/2024] [Accepted: 07/08/2024] [Indexed: 07/30/2024]
Abstract
OBJECTIVE Intellectual disability is often the outcome of neurodevelopmental disorders and is characterized by significant impairments in intellectual and adaptive functioning. X-linked intellectual disability (XLID) is a subset of these disorders caused by genetic defects on the X chromosome, affecting about 2 out of 1,000 males. In syndromic form, it leads to a broad range of cognitive, behavioral, ocular, and physical disabilities. METHODS Employing exome or genome sequencing, here we identified 4 missense variants (c.475C > G; p.H159D, c.1373C > A; p.T458N, and c.1585G > A; p.E529K, c.953C > T; p.S318L) and a putative truncating variant (c.1413_1414del; p.Y471*) in the SRPK3 gene in 9 XLID patients from 5 unrelated families. To validate SRPK3 as a novel XLID gene, we established a knockout (KO) model of the SRPK3 orthologue in zebrafish. RESULTS The 8 patients ascertained postnatally shared common clinical features including intellectual disability, agenesis of the corpus callosum, abnormal eye movement, and ataxia. A ninth case, ascertained prenatally, had a complex structural brain phenotype. Together, these data indicate a pathological role of SRPK3 in neurodevelopmental disorders. In post-fertilization day 5 larvae (free swimming stage), KO zebrafish exhibited severe deficits in eye movement and swim bladder inflation, mimicking uncontrolled ocular movement and physical clumsiness observed in human patients. In adult KO zebrafish, cerebellar agenesis and behavioral abnormalities were observed, recapitulating human phenotypes of cerebellar atrophy and intellectual disability. INTERPRETATION Overall, these results suggest a crucial role of SRPK3 in the pathogenesis of syndromic X-linked intellectual disability and provide new insights into brain development, cognitive and ocular dysfunction in both humans and zebrafish. ANN NEUROL 2024.
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Affiliation(s)
| | - Yu-Ri Lee
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Tae-Ik Choi
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Mervyn G Thomas
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behavior, University of Leicester, Leicester, UK
| | - Tahir N Khan
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Hammad Yousaf
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | | | - Gail Maconachie
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behavior, University of Leicester, Leicester, UK
- Division of Ophthalmology and Orthoptics, Health Science School, University of Sheffield, Sheffield, UK
| | - Moira Crosier
- Human Developmental Biology Resource, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Holli Horak
- Department of Neurology, University of Arizona, Tucson, AZ, USA
| | - Cris S Constantinescu
- Academic Unit of Mental Health and Clinical Neuroscience, University of Nottingham, Nottingham, UK
- Cooper Neurological Institute and Cooper Medical School of Rowan University, Camden, NJ, USA
| | - Tae-Yoon Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Kang-Han Lee
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Jae-Jun Kyung
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Tao Wang
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Bernard N Chodirker
- Department of Pediatrics and Child Health, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | | | - Irene Gottlob
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behavior, University of Leicester, Leicester, UK
- Cooper Neurological Institute and Cooper Medical School of Rowan University, Camden, NJ, USA
| | - William H J Norton
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Robert Gerlai
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Tommaso Pippucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Emanuela Iovino
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | | | - Giulia Severi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, MD, USA
| | - Cornelius F Boerkoel
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, MD, USA
| | - Hyo Sun Cha
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Cheol Yong Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Sungjin Kim
- Department of Microbiology & Molecular Biology, Chungnam National University, Daejeon, South Korea
| | - Je-Hyun Yoon
- Department of Oncology Science, University of Oklahoma, Oklahoma City, OK, USA
| | - Kelly Gilmore
- Division of Maternal Fetal Medicine, Department of Ob/Gyn, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Neeta L Vora
- Division of Maternal Fetal Medicine, Department of Ob/Gyn, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Erica E Davis
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
- Department of Pediatrics, Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Albert E Chudley
- Department of Pediatrics and Child Health, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Charles E Schwartz
- Greenwood Genetic Center, Greenwood, SC, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
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3
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Honer MA, Ferman BI, Gray ZH, Bondarenko EA, Whetstine JR. Epigenetic modulators provide a path to understanding disease and therapeutic opportunity. Genes Dev 2024; 38:473-503. [PMID: 38914477 PMCID: PMC11293403 DOI: 10.1101/gad.351444.123] [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] [Indexed: 06/26/2024]
Abstract
The discovery of epigenetic modulators (writers, erasers, readers, and remodelers) has shed light on previously underappreciated biological mechanisms that promote diseases. With these insights, novel biomarkers and innovative combination therapies can be used to address challenging and difficult to treat disease states. This review highlights key mechanisms that epigenetic writers, erasers, readers, and remodelers control, as well as their connection with disease states and recent advances in associated epigenetic therapies.
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Affiliation(s)
- Madison A Honer
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Benjamin I Ferman
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Zach H Gray
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Elena A Bondarenko
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
| | - Johnathan R Whetstine
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA;
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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4
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Crombie EM, Korecki AJ, Cleverley K, Adair BA, Cunningham TJ, Lee WC, Lengyell TC, Maduro C, Mo V, Slade LM, Zouhair I, Fisher EMC, Simpson EM. Taf1 knockout is lethal in embryonic male mice and heterozygous females show weight and movement disorders. Dis Model Mech 2024; 17:dmm050741. [PMID: 38804708 PMCID: PMC11261634 DOI: 10.1242/dmm.050741] [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: 02/01/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024] Open
Abstract
The TATA box-binding protein-associated factor 1 (TAF1) is a ubiquitously expressed protein and the largest subunit of the basal transcription factor TFIID, which plays a key role in initiation of RNA polymerase II-dependent transcription. TAF1 missense variants in human males cause X-linked intellectual disability, a neurodevelopmental disorder, and TAF1 is dysregulated in X-linked dystonia-parkinsonism, a neurodegenerative disorder. However, this field has lacked a genetic mouse model of TAF1 disease to explore its mechanism in mammals and treatments. Here, we generated and validated a conditional cre-lox allele and the first ubiquitous Taf1 knockout mouse. We discovered that Taf1 deletion in male mice was embryonically lethal, which may explain why no null variants have been identified in humans. In the brains of Taf1 heterozygous female mice, no differences were found in gross structure, overall expression and protein localisation, suggesting extreme skewed X inactivation towards the non-mutant chromosome. Nevertheless, these female mice exhibited a significant increase in weight, weight with age, and reduced movement, suggesting that a small subset of neurons was negatively impacted by Taf1 loss. Finally, this new mouse model may be a future platform for the development of TAF1 disease therapeutics.
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Affiliation(s)
- Elisa M. Crombie
- Department of Neuromuscular Diseases, UCL Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Andrea J. Korecki
- Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Karen Cleverley
- Department of Neuromuscular Diseases, UCL Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Bethany A. Adair
- Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver V6T 1Z3, Canada
| | | | - Weaverly Colleen Lee
- Department of Neuromuscular Diseases, UCL Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Tess C. Lengyell
- Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Cheryl Maduro
- Department of Neuromuscular Diseases, UCL Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Victor Mo
- Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Liam M. Slade
- Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Ines Zouhair
- Department of Neuromuscular Diseases, UCL Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Elizabeth M. C. Fisher
- Department of Neuromuscular Diseases, UCL Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Elizabeth M. Simpson
- Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver V6T 1Z3, Canada
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5
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He XD, Phillips S, Hioki K, Majhi PD, Babbitt C, Tremblay KD, Pobezinsky LA, Mager J. TATA-binding associated factors have distinct roles during early mammalian development. Dev Biol 2024; 511:53-62. [PMID: 38593904 PMCID: PMC11143476 DOI: 10.1016/j.ydbio.2024.04.002] [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: 12/21/2023] [Revised: 03/06/2024] [Accepted: 04/04/2024] [Indexed: 04/11/2024]
Abstract
Early embryonic development is a finely orchestrated process that requires precise regulation of gene expression coordinated with morphogenetic events. TATA-box binding protein-associated factors (TAFs), integral components of transcription initiation coactivators like TFIID and SAGA, play a crucial role in this intricate process. Here we show that disruptions in TAF5, TAF12 and TAF13 individually lead to embryonic lethality in the mouse, resulting in overlapping yet distinct phenotypes. Taf5 and Taf12 mutant embryos exhibited a failure to implant post-blastocyst formation, and Taf5 mutants have aberrant lineage specification within the inner cell mass. In contrast, Taf13 mutant embryos successfully implant and form egg-cylinder stages but fail to initiate gastrulation. Strikingly, we observed a depletion of pluripotency factors in TAF13-deficient embryos, including OCT4, NANOG and SOX2, highlighting an indispensable role of TAF13 in maintaining pluripotency. Transcriptomic analysis revealed distinct gene targets affected by the loss of TAF5, TAF12 and TAF13. Thus, we propose that TAF5, TAF12 and TAF13 convey locus specificity to the TFIID complex throughout the mouse genome.
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Affiliation(s)
- Xinjian Doris He
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Shelby Phillips
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Kaito Hioki
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Prabin Dhangada Majhi
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Courtney Babbitt
- Department of Biology, University of Massachusetts, Amherst, MA, USA
| | - Kimberly D Tremblay
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Leonid A Pobezinsky
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA.
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6
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Zhang C, Yang L, Zhang H, Wu F, Zhang Y, Zhang K, Wu C, Li R, Dong M, Zhao S, Song H. TAF1 is needed for the proliferation and maturation of thyroid follicle cells via Notch signaling. Am J Physiol Endocrinol Metab 2024; 326:E832-E841. [PMID: 38656129 DOI: 10.1152/ajpendo.00403.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
Thyroid dysgenesis (TD) is the common pathogenic mechanism of congenital hypothyroidism (CH). In addition, known pathogenic genes are limited to those that are directly involved in thyroid development. To identify additional candidate pathogenetic genes, we performed forward genetic screening for TD in zebrafish, followed by positional cloning. The candidate gene was confirmed in vitro using the Nthy-ori 3.1 cell line and in vivo using a zebrafish model organism. We obtained a novel zebrafish line with thyroid dysgenesis and identified the candidate pathogenetic mutation TATA-box binding protein associated Factor 1 (taf1) by positional cloning. Further molecular studies revealed that taf1 was needed for the proliferation of thyroid follicular cells by binding to the NOTCH1 promoter region. Knockdown of TAF1 impaired the proliferation and maturation of thyroid cells, thereby leading to thyroid dysplasia. This study showed that TAF1 promoted Notch signaling and that this association played a pivotal role in thyroid development.NEW & NOTEWORTHY In our study, we obtained a novel zebrafish line with thyroid dysgenesis (TD) and identified the candidate pathogenetic mutation TATA-box binding protein associated Factor 1 (taf1). Further researches revealed that taf1 was required for thyroid follicular cells by binding to the NOTCH1 promoter region. Our findings revealed a novel role of TAF1 in thyroid morphogenesis.
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Affiliation(s)
- Caoxu Zhang
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Liu Yang
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Haiyang Zhang
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Fengyao Wu
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Yue Zhang
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Kaiwen Zhang
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Chenyang Wu
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Rui Li
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Mei Dong
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Shuangxia Zhao
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Huaidong Song
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
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7
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Thomsen M, Lange LM, Zech M, Lohmann K. Genetics and Pathogenesis of Dystonia. ANNUAL REVIEW OF PATHOLOGY 2024; 19:99-131. [PMID: 37738511 DOI: 10.1146/annurev-pathmechdis-051122-110756] [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: 09/24/2023]
Abstract
Dystonia is a clinically and genetically highly heterogeneous neurological disorder characterized by abnormal movements and postures caused by involuntary sustained or intermittent muscle contractions. A number of groundbreaking genetic and molecular insights have recently been gained. While they enable genetic testing and counseling, their translation into new therapies is still limited. However, we are beginning to understand shared pathophysiological pathways and molecular mechanisms. It has become clear that dystonia results from a dysfunctional network involving the basal ganglia, cerebellum, thalamus, and cortex. On the molecular level, more than a handful of, often intertwined, pathways have been linked to pathogenic variants in dystonia genes, including gene transcription during neurodevelopment (e.g., KMT2B, THAP1), calcium homeostasis (e.g., ANO3, HPCA), striatal dopamine signaling (e.g., GNAL), endoplasmic reticulum stress response (e.g., EIF2AK2, PRKRA, TOR1A), autophagy (e.g., VPS16), and others. Thus, different forms of dystonia can be molecularly grouped, which may facilitate treatment development in the future.
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Affiliation(s)
- Mirja Thomsen
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany;
| | - Lara M Lange
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany;
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany;
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8
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Johansson J, Lidéus S, Höijer I, Ameur A, Gudmundsson S, Annerén G, Bondeson ML, Wilbe M. A novel quantitative targeted analysis of X-chromosome inactivation (XCI) using nanopore sequencing. Sci Rep 2023; 13:12856. [PMID: 37553382 PMCID: PMC10409790 DOI: 10.1038/s41598-023-34413-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 04/29/2023] [Indexed: 08/10/2023] Open
Abstract
X-chromosome inactivation (XCI) analyses often assist in diagnostics of X-linked traits, however accurate assessment remains challenging with current methods. We developed a novel strategy using amplification-free Cas9 enrichment and Oxford nanopore technologies sequencing called XCI-ONT, to investigate and rigorously quantify XCI in human androgen receptor gene (AR) and human X-linked retinitis pigmentosa 2 gene (RP2). XCI-ONT measures methylation over 116 CpGs in AR and 58 CpGs in RP2, and separate parental X-chromosomes without PCR bias. We show the usefulness of the XCI-ONT strategy over the PCR-based golden standard XCI technique that only investigates one or two CpGs per gene. The results highlight the limitations of using the golden standard technique when the XCI pattern is partially skewed and the advantages of XCI-ONT to rigorously quantify XCI. This study provides a universal XCI-method on DNA, which is highly valuable in clinical and research framework of X-linked traits.
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Affiliation(s)
- Josefin Johansson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden
| | - Sarah Lidéus
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden
| | - Ida Höijer
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden
| | - Sanna Gudmundsson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Göran Annerén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden
| | - Marie-Louise Bondeson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden
| | - Maria Wilbe
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden.
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9
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Bernardini A, Mukherjee P, Scheer E, Kamenova I, Antonova S, Mendoza Sanchez PK, Yayli G, Morlet B, Timmers HTM, Tora L. Hierarchical TAF1-dependent co-translational assembly of the basal transcription factor TFIID. Nat Struct Mol Biol 2023; 30:1141-1152. [PMID: 37386215 PMCID: PMC10442232 DOI: 10.1038/s41594-023-01026-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 05/31/2023] [Indexed: 07/01/2023]
Abstract
Large heteromeric multiprotein complexes play pivotal roles at every step of gene expression in eukaryotic cells. Among them, the 20-subunit basal transcription factor TFIID nucleates the RNA polymerase II preinitiation complex at gene promoters. Here, by combining systematic RNA-immunoprecipitation (RIP) experiments, single-molecule imaging, proteomics and structure-function analyses, we show that human TFIID biogenesis occurs co-translationally. We discovered that all protein heterodimerization steps happen during protein synthesis. We identify TAF1-the largest protein in the complex-as a critical factor for TFIID assembly. TAF1 acts as a flexible scaffold that drives the co-translational recruitment of TFIID submodules preassembled in the cytoplasm. Altogether, our data suggest a multistep hierarchical model for TFIID biogenesis that culminates with the co-translational assembly of the complex onto the nascent TAF1 polypeptide. We envision that this assembly strategy could be shared with other large heteromeric protein complexes.
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Affiliation(s)
- Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Pooja Mukherjee
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Ivanka Kamenova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Nature Protocols, London, UK
| | - Simona Antonova
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
- The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Paulina Karen Mendoza Sanchez
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Gizem Yayli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - H T Marc Timmers
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.
- Centre National de la Recherche Scientifique, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France.
- Université de Strasbourg, Illkirch, France.
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10
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Leid J, Gray R, Rakita P, Koenig AL, Tripathy R, Fitzpatrick JAJ, Kaufman C, Solnica-Krezel L, Lavine KJ. Deletion of taf1 and taf5 in zebrafish capitulate cardiac and craniofacial abnormalities associated with TAFopathies through perturbations in metabolism. Biol Open 2023; 12:bio059905. [PMID: 37746814 PMCID: PMC10354717 DOI: 10.1242/bio.059905] [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: 02/27/2023] [Accepted: 05/16/2023] [Indexed: 09/26/2023] Open
Abstract
Intellectual disability is a neurodevelopmental disorder that affects 2-3% of the general population. Syndromic forms of intellectual disability frequently have a genetic basis and are often accompanied by additional developmental anomalies. Pathogenic variants in components of TATA-binding protein associated factors (TAFs) have recently been identified in a subset of patients with intellectual disability, craniofacial hypoplasia, and congenital heart disease. This syndrome has been termed as a TAFopathy and includes mutations in TATA binding protein (TBP), TAF1, TAF2, and TAF6. The underlying mechanism by which TAFopathies give rise to neurodevelopmental, craniofacial, and cardiac abnormalities remains to be defined. Through a forward genetic screen in zebrafish, we have recovered a recessive mutant phenotype characterized by craniofacial hypoplasia, ventricular hypoplasia, heart failure at 96 h post-fertilization and lethality, and show it is caused by a nonsense mutation in taf5. CRISPR/CAS9 mediated gene editing revealed that these defects where phenocopied by mutations in taf1 and taf5. Mechanistically, taf5-/- zebrafish displayed misregulation in metabolic gene expression and metabolism as evidenced by RNA sequencing, respiration assays, and metabolite studies. Collectively, these findings suggest that the TAF complex may contribute to neurologic, craniofacial, and cardiac development through regulation of metabolism.
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Affiliation(s)
- Jamison Leid
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ryan Gray
- Departments of Nutritional Sciences, Dell Pediatrics Research Institute, University of Texas at Austin, Austin, TX 78723, USA
| | - Peter Rakita
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew L. Koenig
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rohan Tripathy
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - James A. J. Fitzpatrick
- Departments of Neuroscience and Cell Biology, Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Charles Kaufman
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kory J. Lavine
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Immunology and Pathology, Washington University School of Medicine, St. Louis, MO 63110, USA
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11
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Bernardini A, Mukherjee P, Scheer E, Kamenova I, Antonova S, Sanchez PKM, Yayli G, Morlet B, Timmers HM, Tora L. Hierarchical TAF1-dependent co-translational assembly of the basal transcription factor TFIID. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535704. [PMID: 37066372 PMCID: PMC10104070 DOI: 10.1101/2023.04.05.535704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Large heteromeric multiprotein complexes play pivotal roles at every step of gene expression in eukaryotic cells. Among them, the 20-subunit basal transcription factor TFIID nucleates RNA polymerase II preinitiation complex at gene promoters. Here, by combining systematic RNA-immunoprecipitation (RIP) experiments, single-molecule imaging, proteomics and structure-function analyses, we show that TFIID biogenesis occurs co-translationally. We discovered that all protein heterodimerization steps happen during protein synthesis. We identify TAF1 - the largest protein in the complex - as a critical factor for TFIID assembly. TAF1 acts as a flexible scaffold that drives the co-translational recruitment of TFIID submodules preassembled in the cytoplasm. Altogether, our data suggest a multistep hierarchical model for TFIID biogenesis that culminates with the co-translational assembly of the complex onto the nascent TAF1 polypeptide. We envision that this assembly strategy could be shared with other large heteromeric protein complexes.
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Affiliation(s)
- Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Pooja Mukherjee
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Ivanka Kamenova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Simona Antonova
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Germany
| | - Paulina Karen Mendoza Sanchez
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Germany
| | - Gizem Yayli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - H.T. Marc Timmers
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Germany
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
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12
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Wang L, Wang Y, Yu Y, Liu D, Zhao J, Zhang L. Deciphering Selectivity Mechanism of BRD9 and TAF1(2) toward Inhibitors Based on Multiple Short Molecular Dynamics Simulations and MM-GBSA Calculations. Molecules 2023; 28:molecules28062583. [PMID: 36985555 PMCID: PMC10052767 DOI: 10.3390/molecules28062583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
BRD9 and TAF1(2) have been regarded as significant targets of drug design for clinically treating acute myeloid leukemia, malignancies, and inflammatory diseases. In this study, multiple short molecular dynamics simulations combined with the molecular mechanics generalized Born surface area method were employed to investigate the binding selectivity of three ligands, 67B, 67C, and 69G, to BRD9/TAF1(2) with IC50 values of 230/59 nM, 1400/46 nM, and 160/410 nM, respectively. The computed binding free energies from the MM-GBSA method displayed good correlations with that provided by the experimental data. The results indicate that the enthalpic contributions played a critical factor in the selectivity recognition of inhibitors toward BRD9 and TAF1(2), indicating that 67B and 67C could more favorably bind to TAF1(2) than BRD9, while 69G had better selectivity toward BRD9 over TAF1(2). In addition, the residue-based free energy decomposition approach was adopted to calculate the inhibitor–residue interaction spectrum, and the results determined the gatekeeper (Y106 in BRD9 and Y1589 in TAF1(2)) and lipophilic shelf (G43, F44, and F45 in BRD9 and W1526, P1527, and F1528 in TAF1(2)), which could be identified as hotspots for designing efficient selective inhibitors toward BRD9 and TAF1(2). This work is also expected to provide significant theoretical guidance and insightful molecular mechanisms for the rational designs of efficient selective inhibitors targeting BRD9 and TAF1(2).
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13
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Mondia MWL, Kritselis MA, Donahue JE, Elinzano H, Sarangi S, Bryant D, Capelletti M, Korn WM, Yu E, Yan S, Toms SA, Wong ET. Dimorphic glioblastoma with glial and epithelioid phenotypes: Clonal evolution and immune selection. Front Neurol 2023; 13:1017087. [PMID: 36703629 PMCID: PMC9871816 DOI: 10.3389/fneur.2022.1017087] [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: 08/11/2022] [Accepted: 12/13/2022] [Indexed: 01/11/2023] Open
Abstract
Purpose Epithelioid glioblastoma is an unusual histologic variant of malignant glioma. The present study investigates both the genomic and transcriptomic determinants that may promote the development of this tumor. Methods Whole-exome sequencing (WES) and whole-transcriptome sequencing (WTS) were performed on an epithelioid glioblastoma, along with a specific bioinformatic pipeline to generate electronic karyotyping and investigate the tumor immune microenvironment. Microdissected sections containing typical glioblastoma features and epithelioid morphology were analyzed separately using the same methodologies. Results An epithelioid glioblastoma, with immunopositivity for GFAP, Olig-2, and ATRX but negative for IDH-1 and p53, was identified. The tumor cell content from microdissection was estimated to be 85-90% for both histologic tumor components. WES revealed that both glioma and epithelioid sections contained identical point mutations in PTEN, RB1, TERT promoter, and TP53. Electronic karyotype analysis also revealed similar chromosomal copy number alterations, but the epithelioid component showed additional abnormalities that were not found in the glioblastoma component. The tumor immune microenvironments were strikingly different and WTS revealed high levels of transcripts from myeloid cells as well as M1 and M2 macrophages in the glioma section, while transcripts from CD4+ lymphocytes and NK cells predominated in the epithelioid section. Conclusion Epithelioid glioblastoma may be genomically more unstable and oncogenically more advanced, harboring an increased number of mutations and karyotype abnormalities, compared to typical glioblastomas. The tumor immune microenvironment is also different.
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Affiliation(s)
- Mark Willy L. Mondia
- Department of Neurosciences, College of Medicine and Philippine General Hospital, University of the Philippines Manila, Manila, Philippines
| | - Michael A. Kritselis
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI, United States
| | - John E. Donahue
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI, United States
| | - Heinrich Elinzano
- Department of Neurology, The Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI, United States
| | - Sasmit Sarangi
- Department of Neurology, The Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI, United States
| | | | | | | | - Esther Yu
- Department of Radiation Oncology, The Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI, United States
| | - Sherry Yan
- Department of Radiation Oncology, The Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI, United States
| | - Steven A. Toms
- Department of Neurosurgery, The Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI, United States
| | - Eric T. Wong
- Department of Neurology, The Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI, United States,Department of Radiation Oncology, The Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI, United States,Department of Neurosurgery, The Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI, United States,Division of Hematology/Oncology, Department of Medicine, The Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI, United States,*Correspondence: Eric T. Wong ✉
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14
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Janssen BDE, van den Boogaard MJH, Lichtenbelt K, Seaby EG, Stals K, Ellard S, Newbury-Ecob R, Dixit A, Roht L, Pajusalu S, Õunap K, Firth HV, Buckley M, Wilson M, Roscioli T, Tidwell T, Mao R, Ennis S, Holwerda SJ, van Gassen K, van Jaarsveld RH. De novo putative loss-of-function variants in TAF4 are associated with a neuro-developmental disorder. Hum Mutat 2022; 43:1844-1851. [PMID: 35904126 PMCID: PMC10087332 DOI: 10.1002/humu.24444] [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: 01/27/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 01/24/2023]
Abstract
TATA-binding protein associated factor 4 (TAF4) is a subunit of the Transcription Factor IID (TFIID) complex, a central player in transcription initiation. Other members of this multimeric complex have been implicated previously as monogenic disease genes in human developmental disorders. TAF4 has not been described to date as a monogenic disease gene. We here present a cohort of eight individuals, each carrying de novo putative loss-of-function (pLoF) variants in TAF4 and expressing phenotypes consistent with a neuro-developmental disorder (NDD). Common features include intellectual disability, abnormal behavior, and facial dysmorphisms. We propose TAF4 as a novel dominant disease gene for NDD, and coin this novel disorder "TAF4-related NDD" (T4NDD). We place T4NDD in the context of other disorders related to TFIID subunits, revealing shared features of T4NDD with other TAF-opathies.
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Affiliation(s)
- Beau D E Janssen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Klaske Lichtenbelt
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Eleanor G Seaby
- Genomic Informatics Group, University of Southampton, Southampton, UK
| | - Karen Stals
- Exeter Genomic Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | - Sian Ellard
- Exeter Genomic Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK.,Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Ruth Newbury-Ecob
- Clinical Genetics, St Michael's Hospital Bristol, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Abhijit Dixit
- Department of Clinical Genetics, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Laura Roht
- Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
| | | | - Michael Buckley
- Randwick Genomics laboratory, New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - Meredith Wilson
- Department of Clinical Genetics, Children's Hospital at Westmead, and Discipline of Genomic Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Tony Roscioli
- Randwick Genomics laboratory, New South Wales Health Pathology, Sydney, New South Wales, Australia.,Neurosciences Research Australia, University of NSW, Kensington, New South Wales, Australia.,Randwick Genomics laboratory, New South Wales Health Pathology, Sydney, New South Wales, Australia
| | | | - Rong Mao
- ARUP Laboratories, Salt Lake City, Utah, USA.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Sarah Ennis
- Genomic Informatics Group, University of Southampton, Southampton, UK
| | - Sjoerd J Holwerda
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Koen van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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15
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Di Fede E, Grazioli P, Lettieri A, Parodi C, Castiglioni S, Taci E, Colombo EA, Ancona S, Priori A, Gervasini C, Massa V. Epigenetic disorders: Lessons from the animals–animal models in chromatinopathies. Front Cell Dev Biol 2022; 10:979512. [PMID: 36225316 PMCID: PMC9548571 DOI: 10.3389/fcell.2022.979512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Chromatinopathies are defined as genetic disorders caused by mutations in genes coding for protein involved in the chromatin state balance. So far 82 human conditions have been described belonging to this group of congenital disorders, sharing some molecular features and clinical signs. For almost all of these conditions, no specific treatment is available. For better understanding the molecular cascade caused by chromatin imbalance and for envisaging possible therapeutic strategies it is fundamental to combine clinical and basic research studies. To this end, animal modelling systems represent an invaluable tool to study chromatinopathies. In this review, we focused on available data in the literature of animal models mimicking the human genetic conditions. Importantly, affected organs and abnormalities are shared in the different animal models and most of these abnormalities are reported as clinical manifestation, underlying the parallelism between clinics and translational research.
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Affiliation(s)
- Elisabetta Di Fede
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
| | - Paolo Grazioli
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
| | - Antonella Lettieri
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
| | - Chiara Parodi
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
| | - Silvia Castiglioni
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
| | - Esi Taci
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
| | - Elisa Adele Colombo
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
| | - Silvia Ancona
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
| | - Alberto Priori
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
- “Aldo Ravelli” Center for Neurotechnology and Experimental Brain Therapeutics, Università Degli Studi di Milano, Milan, Italy
| | - Cristina Gervasini
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
- “Aldo Ravelli” Center for Neurotechnology and Experimental Brain Therapeutics, Università Degli Studi di Milano, Milan, Italy
| | - Valentina Massa
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
- “Aldo Ravelli” Center for Neurotechnology and Experimental Brain Therapeutics, Università Degli Studi di Milano, Milan, Italy
- *Correspondence: Valentina Massa,
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16
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Bhuiyan P, Chuwdhury GS, Sun Z, Chen Y, Dong H, Ahmed FF, Nana L, Rahman MH, Qian Y. Network Biology Approaches to Uncover Therapeutic Targets Associated with Molecular Signaling Pathways from circRNA in Postoperative Cognitive Dysfunction Pathogenesis. J Mol Neurosci 2022; 72:1875-1901. [PMID: 35792980 DOI: 10.1007/s12031-022-02042-6] [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: 04/07/2022] [Accepted: 06/07/2022] [Indexed: 12/19/2022]
Abstract
Postoperative cognitive dysfunction (POCD) is a cognitive deterioration and dementia that arise after a surgical procedure, affecting up to 40% of surgery patients over the age of 60. The precise etiology and molecular mechanisms underlying POCD remain uncovered. These reasons led us to employ integrative bioinformatics and machine learning methodologies to identify several biological signaling pathways involved and molecular signatures to better understand the pathophysiology of POCD. A total of 223 differentially expressed genes (DEGs) comprising 156 upregulated and 67 downregulated genes were identified from the circRNA microarray dataset by comparing POCD and non-POCD samples. Gene ontology (GO) analyses of DEGs were significantly involved in neurogenesis, autophagy regulation, translation in the postsynapse, modulating synaptic transmission, regulation of the cellular catabolic process, macromolecule modification, and chromatin remodeling. Pathway enrichment analysis indicated some key molecular pathways, including mTOR signaling pathway, AKT phosphorylation of cytosolic targets, MAPK and NF-κB signaling pathway, PI3K/AKT signaling pathway, nitric oxide signaling pathway, chaperones that modulate interferon signaling pathway, apoptosis signaling pathway, VEGF signaling pathway, cellular senescence, RANKL/RARK signaling pathway, and AGE/RAGE pathway. Furthermore, seven hub genes were identified from the PPI network and also determined transcription factors and protein kinases. Finally, we identified a new predictive drug for the treatment of SCZ using the LINCS L1000, GCP, and P100 databases. Together, our results bring a new era of the pathogenesis of a deeper understanding of POCD, identified novel therapeutic targets, and predicted drug inhibitors in POCD.
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Affiliation(s)
- Piplu Bhuiyan
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, People's Republic of China
| | - G S Chuwdhury
- Department of Computer Science and Engineering, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Zhaochu Sun
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, People's Republic of China
| | - Yinan Chen
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, People's Republic of China
| | - Hongquan Dong
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, People's Republic of China
| | - Fee Faysal Ahmed
- Department of Mathematics, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Li Nana
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, People's Republic of China
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia, 7003, Bangladesh.
| | - Yanning Qian
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, People's Republic of China.
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mafba and mafbb differentially regulate lymphatic endothelial cell migration in topographically distinct manners. Cell Rep 2022; 39:110982. [PMID: 35732122 DOI: 10.1016/j.celrep.2022.110982] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/11/2022] [Accepted: 05/27/2022] [Indexed: 11/24/2022] Open
Abstract
Lymphangiogenesis, formation of lymphatic vessels from pre-existing vessels, is a dynamic process that requires cell migration. Regardless of location, migrating lymphatic endothelial cell (LEC) progenitors probe their surroundings to form the lymphatic network. Lymphatic-development regulation requires the transcription factor MAFB in different species. Zebrafish Mafba, expressed in LEC progenitors, is essential for their migration in the trunk. However, the transcriptional mechanism that orchestrates LEC migration in different lymphatic endothelial beds remains elusive. Here, we uncover topographically different requirements of the two paralogs, Mafba and Mafbb, for LEC migration. Both mafba and mafbb are necessary for facial lymphatic development, but mafbb is dispensable for trunk lymphatic development. On the molecular level, we demonstrate a regulatory network where Vegfc-Vegfd-SoxF-Mafba-Mafbb is essential in facial lymphangiogenesis. We identify that mafba and mafbb tune the directionality of LEC migration and vessel morphogenesis that is ultimately necessary for lymphatic function.
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Eigenhuis KN, Somsen HB, van den Berg DLC. Transcription Pause and Escape in Neurodevelopmental Disorders. Front Neurosci 2022; 16:846272. [PMID: 35615272 PMCID: PMC9125161 DOI: 10.3389/fnins.2022.846272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Transcription pause-release is an important, highly regulated step in the control of gene expression. Modulated by various factors, it enables signal integration and fine-tuning of transcriptional responses. Mutations in regulators of pause-release have been identified in a range of neurodevelopmental disorders that have several common features affecting multiple organ systems. This review summarizes current knowledge on this novel subclass of disorders, including an overview of clinical features, mechanistic details, and insight into the relevant neurodevelopmental processes.
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Wang Y, Cheng Y, Yang Q, Kuang L, Liu G. Overexpression of FOXD2-AS1 enhances proliferation and impairs differentiation of glioma stem cells by activating the NOTCH pathway via TAF-1. J Cell Mol Med 2022; 26:2620-2632. [PMID: 35419917 PMCID: PMC9077300 DOI: 10.1111/jcmm.17268] [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: 05/15/2020] [Revised: 02/20/2022] [Accepted: 03/08/2022] [Indexed: 12/12/2022] Open
Abstract
Emerging data have highlighted the importance of long noncoding RNAs (lncRNAs) in exerting critical biological functions and roles in different forms of brain cancer, including gliomas. In this study, we sought to investigate the role of lncRNA FOXD2 adjacent opposite strand RNA 1 (FOXD2-AS1) in glioma cells. First, we used sphere formation assay and flow cytometry to select U251 glioma stem cells (GSCs). Then, we quantified the expression of lncRNA FOXD2-AS1, TATA-box binding protein associated factor 1 (TAF-1) and NOTCH1 in glioma tissues and GSCs, as well as the expression of GSC stem markers, OCT4, SOX2, Nanog, Nestin and CD133 in GSCs. Colony formation assay, sphere formation assay, and flow cytometry were used to evaluate GSC stemness. Next, the correlations among lncRNA FOXD2-AS1, TAF-1 and NOTCH1 were investigated. LncRNA FOXD2-AS1, TAF-1 and NOTCH1 were found to be elevated in glioma tissues and GSCs, and silencing lncRNA FOXD2-AS1 inhibited stemness and proliferation, while promoting apoptosis and differentiation of GSCs. LncRNA FOXD2-AS1 overexpression also led to increased NOTCH1 by recruiting TAF-1 to the NOTCH1 promoter region, thereby promoting stemness and proliferation, while impairing cell apoptosis and differentiation. Mechanistically, lncRNA FOXD2-AS1 elevation promoted glioma in vivo by activating the NOTCH signalling pathway via TAF-1 upregulation. Taken together, the key findings of our investigation support the proposition that downregulation of lncRNA FOXD2-AS1 presents a viable and novel molecular candidate for improving glioma treatment.
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Affiliation(s)
- Yang Wang
- Department of Neurotumor Disease Treatment Center, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yanli Cheng
- Department of Dermatology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Qi Yang
- Department of Orthopeadic Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Lei Kuang
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Guolei Liu
- Department of Otorhinolaryngology, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, China
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20
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Pozojevic J, Algodon SM, Cruz JN, Trinh J, Brüggemann N, Laß J, Grütz K, Schaake S, Tse R, Yumiceba V, Kruse N, Schulz K, Sreenivasan VKA, Rosales RL, Jamora RDG, Diesta CCE, Matschke J, Glatzel M, Seibler P, Händler K, Rakovic A, Kirchner H, Spielmann M, Kaiser FJ, Klein C, Westenberger A. Transcriptional Alterations in X-Linked Dystonia–Parkinsonism Caused by the SVA Retrotransposon. Int J Mol Sci 2022; 23:ijms23042231. [PMID: 35216353 PMCID: PMC8875906 DOI: 10.3390/ijms23042231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 02/05/2023] Open
Abstract
X-linked dystonia–parkinsonism (XDP) is a severe neurodegenerative disorder that manifests as adult-onset dystonia combined with parkinsonism. A SINE-VNTR-Alu (SVA) retrotransposon inserted in an intron of the TAF1 gene reduces its expression and alters splicing in XDP patient-derived cells. As a consequence, increased levels of the TAF1 intron retention transcript TAF1-32i can be found in XDP cells as compared to healthy controls. Here, we investigate the sequence of the deep intronic region included in this transcript and show that it is also present in cells from healthy individuals, albeit in lower amounts than in XDP cells, and that it undergoes degradation by nonsense-mediated mRNA decay. Furthermore, we investigate epigenetic marks (e.g., DNA methylation and histone modifications) present in this intronic region and the spanning sequence. Finally, we show that the SVA evinces regulatory potential, as demonstrated by its ability to repress the TAF1 promoter in vitro. Our results enable a better understanding of the disease mechanisms underlying XDP and transcriptional alterations caused by SVA retrotransposons.
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Affiliation(s)
- Jelena Pozojevic
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Shela Marie Algodon
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Joseph Neos Cruz
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Norbert Brüggemann
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
- Department of Neurology, University Hospital Schleswig Holstein, 23538 Lübeck, Germany
| | - Joshua Laß
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Karen Grütz
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Susen Schaake
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Ronnie Tse
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Veronica Yumiceba
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Nathalie Kruse
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Kristin Schulz
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Varun K. A. Sreenivasan
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Raymond L. Rosales
- The Hospital Neuroscience Institute, Department of Neurology and Psychiatry and The FMS-Research Center for Health Sciences, University of Santo Tomas, Manila 1008, Philippines;
| | - Roland Dominic G. Jamora
- Department of Neurosciences, College of Medicine-Philippine General Hospital, University of the Philippines Manila, Manila 1000, Philippines;
| | - Cid Czarina E. Diesta
- Department of Neurosciences, Movement Disorders Clinic, Makati Medical Center, Makati City 1229, Philippines;
| | - Jakob Matschke
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (J.M.); (M.G.)
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (J.M.); (M.G.)
| | - Philip Seibler
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Kristian Händler
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Aleksandar Rakovic
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Henriette Kirchner
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Malte Spielmann
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Lübeck/Kiel, 23538 Lübeck, Germany
| | - Frank J. Kaiser
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45147 Essen, Germany;
- Essener Zentrum für Seltene Erkrankungen, Universitätsmedizin Essen, 45147 Essen, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
- Correspondence: (C.K.); (A.W.)
| | - Ana Westenberger
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
- Correspondence: (C.K.); (A.W.)
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OUP accepted manuscript. Brain 2022; 145:3022-3034. [DOI: 10.1093/brain/awac154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/14/2022] [Accepted: 04/03/2022] [Indexed: 11/12/2022] Open
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22
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Yu X, Bai Y, Han B, Ju M, Tang T, Shen L, Li M, Yang L, Zhang Z, Hu G, Chao J, Zhang Y, Yao H. Extracellular vesicle-mediated delivery of circDYM alleviates CUS-induced depressive-like behaviours. J Extracell Vesicles 2022; 11:e12185. [PMID: 35029057 PMCID: PMC8758833 DOI: 10.1002/jev2.12185] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 11/25/2021] [Accepted: 12/29/2021] [Indexed: 12/16/2022] Open
Abstract
Major depressive disorder (MDD) is the most prevalent psychiatric disorder worldwide and severely limits psychosocial function and quality of life, but no effective medication is currently available. Circular RNAs (circRNAs) have been revealed to participate in the MDD pathological process. Targeted delivery of circRNAs without blood-brain barrier (BBB) restriction for remission of MDD represents a promising approach for antidepressant therapy. In this study, RVG-circDYM-extracellular vesicles (RVG-circDYM-EVs) were engineered to target and preferentially transfer circDYM to the brain, and the effect on the pathological process in a chronic unpredictable stress (CUS) mouse model of depression was investigated. The results showed that RVG-circDYM-EVs were successfully purified by ultracentrifugation from overexpressed circDYM HEK 293T cells, and the characterization of RVG-circDYM-EVs was successfully demonstrated in terms of size, morphology and specific markers. Beyond demonstrating proof-of-concept for an RNA drug delivery technology, we observed that systemic administration of RVG-circDYM-EVs efficiently delivered circDYM to the brain, and alleviated CUS-induced depressive-like behaviours, and we discovered that RVG-circDYM-EVs notably inhibited microglial activation, BBB leakiness and peripheral immune cells infiltration, and attenuated astrocyte disfunction induced by CUS. CircDYM can bind mechanistically to the transcription factor TAF1 (TATA-box binding protein associated factor 1), resulting in the decreased expression of its downstream target genes with consequently suppressed neuroinflammation. Taken together, our findings suggest that extracellular vesicle-mediated delivery of circDYM is effective for MDD treatment and promising for clinical applications.
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Affiliation(s)
- Xiaoyu Yu
- Department of PharmacologySchool of MedicineSoutheast UniversityNanjingJiangsuChina
| | - Ying Bai
- Department of PharmacologySchool of MedicineSoutheast UniversityNanjingJiangsuChina
| | - Bing Han
- Department of PharmacologySchool of MedicineSoutheast UniversityNanjingJiangsuChina
| | - Minzi Ju
- Department of PharmacologySchool of MedicineSoutheast UniversityNanjingJiangsuChina
| | - Tianci Tang
- Department of PharmacologySchool of MedicineSoutheast UniversityNanjingJiangsuChina
| | - Ling Shen
- Department of PharmacologySchool of MedicineSoutheast UniversityNanjingJiangsuChina
| | - Mingyue Li
- Department of PharmacologySchool of MedicineSoutheast UniversityNanjingJiangsuChina
| | - Li Yang
- Department of PharmacologySchool of MedicineSoutheast UniversityNanjingJiangsuChina
| | - Zhao Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural MedicinesInstitute of Materia Medica & Neuroscience CenterChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Guoku Hu
- Department of Pharmacology and Experimental NeuroscienceUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Jie Chao
- Department of PhysiologySchool of MedicineSoutheast UniversityNanjingJiangsuChina
| | - Yuan Zhang
- Department of PharmacologySchool of MedicineSoutheast UniversityNanjingJiangsuChina
| | - Honghong Yao
- Department of PharmacologySchool of MedicineSoutheast UniversityNanjingJiangsuChina
- Jiangsu Provincial Key Laboratory of Critical Care MedicineSoutheast UniversityNanjingJiangsuChina
- Co‐innovation Center of NeuroregenerationNantong UniversityNantongJiangsuChina
- Institute of Life SciencesKey Laboratory of Developmental Genes and Human DiseaseSoutheast UniversityNanjingJiangsuChina
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Pozojevic J, Cruz JN, Westenberger A. X-linked dystonia-parkinsonism: over and above a repeat disorder. MED GENET-BERLIN 2021; 33:319-324. [PMID: 38835428 PMCID: PMC11006257 DOI: 10.1515/medgen-2021-2105] [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: 04/29/2021] [Accepted: 11/24/2021] [Indexed: 06/06/2024]
Abstract
X-linked dystonia-parkinsonism (XDP) is an adult-onset neurodegenerative movement disorder, caused by a founder retrotransposon insertion in an intron of the TAF1 gene. This insertion contains a polymorphic hexanucleotide repeat (CCCTCT)n, the length of which inversely correlates with the age at disease onset (AAO) and other clinical parameters, aligning XDP with repeat expansion disorders. Nevertheless, many other pathogenic mechanisms are conceivably at play in XDP, indicating that in contrast to other repeat disorders, the (CCCTCT)n repeat may not be the actual (or only) disease cause. Here, we summarize and discuss genetic and molecular aspects of XDP, highlighting the role of the hexanucleotide repeat in age-related disease penetrance and expressivity.
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Affiliation(s)
- Jelena Pozojevic
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Joseph Neos Cruz
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
- Disease Molecular Biology and Epigenetics Laboratory, University of the Philippines Diliman, Quezon City, Philippines
| | - Ana Westenberger
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
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24
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Cirnaru MD, Creus-Muncunill J, Nelson S, Lewis TB, Watson J, Ellerby LM, Gonzalez-Alegre P, Ehrlich ME. Striatal Cholinergic Dysregulation after Neonatal Decrease in X-Linked Dystonia Parkinsonism-Related TAF1 Isoforms. Mov Disord 2021; 36:2780-2794. [PMID: 34403156 DOI: 10.1002/mds.28750] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/24/2021] [Accepted: 07/12/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND X-linked dystonia parkinsonism is a generalized, progressive dystonia followed by parkinsonism with onset in adulthood and accompanied by striatal neurodegeneration. Causative mutations are located in a noncoding region of the TATA-box binding protein-associated factor 1 (TAF1) gene and result in aberrant splicing. There are 2 major TAF1 isoforms that may be decreased in symptomatic patients, including the ubiquitously expressed canonical cTAF1 and the neuronal-specific nTAF1. OBJECTIVE The objective of this study was to determine the behavioral and transcriptomic effects of decreased cTAF1 and/or nTAF1 in vivo. METHODS We generated adeno-associated viral (AAV) vectors encoding microRNAs targeting Taf1 in a splice-isoform selective manner. We performed intracerebroventricular viral injections in newborn mice and rats and intrastriatal infusions in 3-week-old rats. The effects of Taf1 knockdown were assayed at 4 months of age with evaluation of motor function, histology, and RNA sequencing of the striatum, followed by its validation. RESULTS We report motor deficits in all cohorts, more pronounced in animals injected at P0, in which we also identified transcriptomic alterations in multiple neuronal pathways, including the cholinergic synapse. In both species, we show a reduced number of striatal cholinergic interneurons and their marker mRNAs after Taf1 knockdown in the newborn. CONCLUSION This study provides novel information regarding the requirement for TAF1 in the postnatal maintenance of striatal cholinergic neurons, the dysfunction of which is involved in other inherited forms of dystonia. © 2021 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Maria-Daniela Cirnaru
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jordi Creus-Muncunill
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shareen Nelson
- Raymond G. Perelman Center for Cellular & Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Travis B Lewis
- Raymond G. Perelman Center for Cellular & Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jaime Watson
- Raymond G. Perelman Center for Cellular & Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lisa M Ellerby
- Buck Institute for Research on Aging, Novato, California, USA
| | - Pedro Gonzalez-Alegre
- Raymond G. Perelman Center for Cellular & Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michelle E Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Dhanalakshmi C, Janakiraman U, Moutal A, Fukunaga K, Khanna R, Nelson MA. Evaluation of the effects of the T-type calcium channel enhancer SAK3 in a rat model of TAF1 deficiency. Neurobiol Dis 2021; 149:105224. [PMID: 33359140 PMCID: PMC8230513 DOI: 10.1016/j.nbd.2020.105224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/03/2020] [Accepted: 12/16/2020] [Indexed: 11/18/2022] Open
Abstract
The TATA-box binding protein associated factor 1 (TAF1) is part of the TFIID complex that plays a key role during the initiation of transcription. Variants of TAF1 are associated with neurodevelopmental disorders. Previously, we found that CRISPR/Cas9 based editing of the TAF1 gene disrupts the morphology of the cerebral cortex and blunts the expression as well as the function of the CaV3.1 (T-type) voltage gated calcium channel. Here, we tested the efficacy of SAK3 (ethyl 8'-methyl-2', 4-dioxo-2-(piperidin-1-yl)-2'H-spiro [cyclopentane-1, 3'-imidazo [1, 2-a] pyridine]-2-ene-3-carboxylate), a T-type calcium channel enhancer, in an animal model of TAF1 intellectual disability (ID) syndrome. At post-natal day 3, rat pups were subjected to intracerebroventricular (ICV) injection of either gRNA-control or gRNA-TAF1 CRISPR/Cas9 viruses. At post-natal day 21, the rat pups were given SAK3 (0.25 mg/kg, p.o.) or vehicle for 14 days (i.e. till post-natal day 35) and then subjected to behavioral, morphological, and molecular studies. Oral administration of SAK3 (0.25 mg/kg, p.o.) significantly rescued locomotion abnormalities associated with TAF1 gene editing. SAK3 treatment prevented the loss of cortical neurons and GFAP-positive astrocytes observed after TAF1 gene editing. In addition, SAK3 protected cells from apoptosis. SAK3 also restored the Brain-derived neurotrophic factor/protein kinase B/Glycogen Synthase Kinase 3 Beta (BDNF/AKT/GSK3β) signaling axis in TAF1 edited animals. Finally, SAK3 normalized the levels of three GSK3β substrates - CaV3.1, FOXP2, and CRMP2. We conclude that the T-type calcium channel enhancer SAK3 is beneficial against the deleterious effects of TAF1 gene-editing, in part, by stimulating the BDNF/AKT/GSK3β signaling pathway.
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Affiliation(s)
- Chinnasamy Dhanalakshmi
- Department of Pathology, University of Arizona College of Medicine and College of Pharmacy, Tucson, AZ, USA
| | - Udaiyappan Janakiraman
- Department of Pathology, University of Arizona College of Medicine and College of Pharmacy, Tucson, AZ, USA
| | - Aubin Moutal
- Department of Pharmacology, University of Arizona College of Medicine and College of Pharmacy, Tucson, AZ, USA; The Center for Innovation in Brain Sciences, The University of Arizona Health Sciences, Tucson, AZ, United States; The BIO5 Institute, University of Arizona, United States
| | - Kohji Fukunaga
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Rajesh Khanna
- Department of Pharmacology, University of Arizona College of Medicine and College of Pharmacy, Tucson, AZ, USA; The Center for Innovation in Brain Sciences, The University of Arizona Health Sciences, Tucson, AZ, United States; The BIO5 Institute, University of Arizona, United States
| | - Mark A Nelson
- Department of Pathology, University of Arizona College of Medicine and College of Pharmacy, Tucson, AZ, USA.
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Al Ali J, Vaine CA, Shah S, Campion L, Hakoum A, Supnet ML, Acuña P, Aldykiewicz G, Multhaupt-Buell T, Ganza NGM, Lagarde JBB, De Guzman JK, Go C, Currall B, Trombetta B, Webb PK, Talkowski M, Arnold SE, Cheah PS, Ito N, Sharma N, Bragg DC, Ozelius L, Breakefield XO. TAF1 Transcripts and Neurofilament Light Chain as Biomarkers for X-linked Dystonia-Parkinsonism. Mov Disord 2020; 36:206-215. [PMID: 32975318 PMCID: PMC7891430 DOI: 10.1002/mds.28305] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/24/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
Background X‐linked dystonia‐parkinsonism is a rare neurological disease endemic to the Philippines. Dystonic symptoms appear in males at the mean age of 40 years and progress to parkinsonism with degenerative pathology in the striatum. A retrotransposon inserted in intron 32 of the TAF1 gene leads to alternative splicing in the region and a reduction of the full‐length mRNA transcript. Objectives The objective of this study was to discover cell‐based and biofluid‐based biomarkers for X‐linked dystonia‐parkinsonism. Methods RNA from patient‐derived neural progenitor cells and their secreted extracellular vesicles were used to screen for dysregulation of TAF1 expression. Droplet‐digital polymerase chain reaction was used to quantify the expression of TAF1 mRNA fragments 5′ and 3′ to the retrotransposon insertion and the disease‐specific splice variant TAF1‐32i in whole‐blood RNA. Plasma levels of neurofilament light chain were measured using single‐molecule array. Results In neural progenitor cells and their extracellular vesicles, we confirmed that the TAF1‐3′/5′ ratio was lower in patient samples, whereas TAF1‐32i expression is higher relative to controls. In whole‐blood RNA, both TAF1‐3′/5′ ratio and TAF1‐32i expression can differentiate patient (n = 44) from control samples (n = 18) with high accuracy. Neurofilament light chain plasma levels were significantly elevated in patients (n = 43) compared with both carriers (n = 16) and controls (n = 21), with area under the curve of 0.79. Conclusions TAF1 dysregulation in blood serves as a disease‐specific biomarker that could be used as a readout for monitoring therapies targeting TAF1 splicing. Neurofilament light chain could be used in monitoring neurodegeneration and disease progression in patients. © 2020 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Jamal Al Ali
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Christine A Vaine
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Shivangi Shah
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Lindsey Campion
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Ahmad Hakoum
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Melanie L Supnet
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Patrick Acuña
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Sunshine Care Foundation, Roxas City, Philippines
| | - Gabrielle Aldykiewicz
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Trisha Multhaupt-Buell
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | | | | | - Jan K De Guzman
- Sunshine Care Foundation, Roxas City, Philippines.,Department of Neurology, Jose R. Reyes Memorial Medical Center, Metro Manila, Philippines
| | - Criscely Go
- Department of Neurology, Jose R. Reyes Memorial Medical Center, Metro Manila, Philippines
| | - Benjamin Currall
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Center for Genomic Medicine, Mass General Research Institute, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Bianca Trombetta
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, Alzheimer's Clinical & Translational Research Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Pia K Webb
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, Alzheimer's Clinical & Translational Research Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Michael Talkowski
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Genomic Medicine, Mass General Research Institute, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Steven E Arnold
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, Alzheimer's Clinical & Translational Research Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Pike S Cheah
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Naoto Ito
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Nutan Sharma
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - D Cristopher Bragg
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Laurie Ozelius
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Xandra O Breakefield
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
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Janakiraman U, Dhanalakshmi C, Yu J, Moutal A, Boinon L, Fukunaga K, Khanna R, Nelson MA. The investigation of the T-type calcium channel enhancer SAK3 in an animal model of TAF1 intellectual disability syndrome. Neurobiol Dis 2020; 143:105006. [PMID: 32622085 PMCID: PMC7422587 DOI: 10.1016/j.nbd.2020.105006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/17/2020] [Accepted: 06/27/2020] [Indexed: 01/21/2023] Open
Abstract
T-type calcium channels, in the central nervous system, are involved in the pathogenesis of many neurodegenerative diseases, including TAF1 intellectual disability syndrome (TAF1 ID syndrome). Here, we evaluated the efficacy of a novel T-type Ca2+ channel enhancer, SAK3 (ethyl 8'-methyl-2', 4-dioxo-2-(piperidin-1-yl)-2'H-spiro [cyclopentane-1, 3'-imidazo [1, 2-a] pyridine]-2-ene-3-carboxylate) in an animal model of TAF1 ID syndrome. At post-natal day 3, rat pups were subjected to intracerebroventricular (ICV) injection of either gRNA-control or gRNA-TAF1 CRISPR/Cas9 viruses. At post-natal day 21 animals were given SAK3 (0.25 mg/kg, p.o.) or vehicle up to post-natal day 35 (i.e. 14 days). Rats were subjected to behavioral, morphological, electrophysiological, and molecular studies. Oral administration of SAK3 (0.25 mg/kg, p.o.) significantly rescued the behavior abnormalities in beam walking test and open field test caused by TAF1 gene editing. We observed an increase in calbindin-positive Purkinje cells and GFAP-positive astrocytes as well as a decrease in IBA1-positive microglia cells in SAK3-treated animals. In addition, SAK3 protected the Purkinje and granule cells from apoptosis induced by TAF-1 gene editing. SAK3 also restored the excitatory post synaptic current (sEPSCs) in TAF1 edited Purkinje cells. Finally, SAK3 normalized the BDNF/AKT signaling axis in TAF1 edited animals. Altogether, these observations suggest that SAK3 could be a novel therapeutic agent for TAF1 ID syndrome.
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Affiliation(s)
- Udaiyappan Janakiraman
- Department of Pathology, University of Arizona College of Medicine, College of Pharmacy, Tucson, AZ, USA
| | - Chinnasamy Dhanalakshmi
- Department of Pathology, University of Arizona College of Medicine, College of Pharmacy, Tucson, AZ, USA
| | - Jie Yu
- Department of Pharmacology, University of Arizona College of Medicine, College of Pharmacy, Tucson, AZ, USA; College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou 310058, China
| | - Aubin Moutal
- Department of Pharmacology, University of Arizona College of Medicine, College of Pharmacy, Tucson, AZ, USA
| | - Lisa Boinon
- Department of Pharmacology, University of Arizona College of Medicine, College of Pharmacy, Tucson, AZ, USA
| | - Kohji Fukunaga
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Rajesh Khanna
- Department of Pathology, University of Arizona College of Medicine, College of Pharmacy, Tucson, AZ, USA; Department of Pharmacology, University of Arizona College of Medicine, College of Pharmacy, Tucson, AZ, USA; The Center for Innovation in Brain Sciences, The University of Arizona Health Sciences, Tucson, AZ, USA; The BIO5 Institute, University of Arizona, USA
| | - Mark A Nelson
- Department of Pathology, University of Arizona College of Medicine, College of Pharmacy, Tucson, AZ, USA.
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Understanding the Landscape of X-linked Variants Causing Intellectual Disability in Females Through Extreme X Chromosome Inactivation Skewing. Mol Neurobiol 2020; 57:3671-3684. [DOI: 10.1007/s12035-020-01981-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/08/2020] [Indexed: 12/14/2022]
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Ilyas M, Mir A, Efthymiou S, Houlden H. The genetics of intellectual disability: advancing technology and gene editing. F1000Res 2020; 9. [PMID: 31984132 PMCID: PMC6966773 DOI: 10.12688/f1000research.16315.1] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/10/2020] [Indexed: 12/22/2022] Open
Abstract
Intellectual disability (ID) is a neurodevelopmental condition affecting 1–3% of the world’s population. Genetic factors play a key role causing the congenital limitations in intellectual functioning and adaptive behavior. The heterogeneity of ID makes it more challenging for genetic and clinical diagnosis, but the advent of large-scale genome sequencing projects in a trio approach has proven very effective. However, many variants are still difficult to interpret. A combined approach of next-generation sequencing and functional, electrophysiological, and bioinformatics analysis has identified new ways to understand the causes of ID and help to interpret novel ID-causing genes. This approach offers new targets for ID therapy and increases the efficiency of ID diagnosis. The most recent functional advancements and new gene editing techniques involving the use of CRISPR–Cas9 allow for targeted editing of DNA in
in vitro and more effective mammalian and human tissue-derived disease models. The expansion of genomic analysis of ID patients in diverse and ancient populations can reveal rare novel disease-causing genes.
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Affiliation(s)
- Muhammad Ilyas
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan.,Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Asif Mir
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
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30
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Cheng H, Capponi S, Wakeling E, Marchi E, Li Q, Zhao M, Weng C, Piatek SG, Ahlfors H, Kleyner R, Rope A, Lumaka A, Lukusa P, Devriendt K, Vermeesch J, Posey JE, Palmer EE, Murray L, Leon E, Diaz J, Worgan L, Mallawaarachchi A, Vogt J, de Munnik SA, Dreyer L, Baynam G, Ewans L, Stark Z, Lunke S, Gonçalves AR, Soares G, Oliveira J, Fassi E, Willing M, Waugh JL, Faivre L, Riviere JB, Moutton S, Mohammed S, Payne K, Walsh L, Begtrup A, Sacoto MJG, Douglas G, Alexander N, Buckley MF, Mark PR, Adès LC, Sandaradura SA, Lupski JR, Roscioli T, Agrawal PB, Kline AD, Wang K, Timmers HTM, Lyon GJ. Missense variants in TAF1 and developmental phenotypes: challenges of determining pathogenicity. Hum Mutat 2019; 41:10.1002/humu.23936. [PMID: 31646703 PMCID: PMC7187541 DOI: 10.1002/humu.23936] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/16/2019] [Indexed: 12/26/2022]
Abstract
We recently described a new neurodevelopmental syndrome (TAF1/MRXS33 intellectual disability syndrome) (MIM# 300966) caused by pathogenic variants involving the X-linked gene TAF1, which participates in RNA polymerase II transcription. The initial study reported eleven families, and the syndrome was defined as presenting early in life with hypotonia, facial dysmorphia, and developmental delay that evolved into intellectual disability (ID) and/or autism spectrum disorder (ASD). We have now identified an additional 27 families through a genotype-first approach. Familial segregation analysis, clinical phenotyping, and bioinformatics were capitalized on to assess potential variant pathogenicity, and molecular modelling was performed for those variants falling within structurally characterized domains of TAF1. A novel phenotypic clustering approach was also applied, in which the phenotypes of affected individuals were classified using 51 standardized Human Phenotype Ontology (HPO) terms. Phenotypes associated with TAF1 variants show considerable pleiotropy and clinical variability, but prominent among previously unreported effects were brain morphological abnormalities, seizures, hearing loss, and heart malformations. Our allelic series broadens the phenotypic spectrum of TAF1/MRXS33 intellectual disability syndrome and the range of TAF1 molecular defects in humans. It also illustrates the challenges for determining the pathogenicity of inherited missense variants, particularly for genes mapping to chromosome X. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hanyin Cheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Simona Capponi
- German Cancer Consortium (DKTK), Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Urology, Medical Faculty-University of Freiburg, Freiburg, Germany
| | - Emma Wakeling
- North West Thames Regional Genetics Service, London North West University Healthcare NHS Trust, Harrow, UK
| | - Elaine Marchi
- Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, New York
| | - Quan Li
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Mengge Zhao
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Medical Center, New York, New York
| | - Stefan G. Piatek
- North East Thames Regional Genetics Laboratory, Great Ormond Street Hospital, London, UK
| | - Helena Ahlfors
- North East Thames Regional Genetics Laboratory, Great Ormond Street Hospital, London, UK
| | - Robert Kleyner
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Alan Rope
- Kaiser Permanente Center for Health Research, Portland, Oregon
- Genome Medical, South San Francisco, California
| | - Aimé Lumaka
- Department of Biomedical and Preclinical Sciences, GIGA-R, Laboratory of Human Genetics, University of Liège, Liège, Belgium
- Institut National de Recherche Biomédicale, Kinshasa, DR Congo
- Centre for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR Congo
| | - Prosper Lukusa
- Institut National de Recherche Biomédicale, Kinshasa, DR Congo
- Centre for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR Congo
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Koenraad Devriendt
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Joris Vermeesch
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Elizabeth E. Palmer
- Genetics of Learning Disability Service, Newcastle, New South Wales, Australia
- School of Women’s and Children’s Health, University of New South Wales, Randwick, New South Wales, Australia
| | - Lucinda Murray
- Genetics of Learning Disability Service, Newcastle, New South Wales, Australia
| | - Eyby Leon
- Rare Disease Institute, Children’s National Health System, Washington, District of Columbia
| | - Jullianne Diaz
- Rare Disease Institute, Children’s National Health System, Washington, District of Columbia
| | - Lisa Worgan
- Department of Clinical Genetics, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Amali Mallawaarachchi
- Department of Clinical Genetics, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Julie Vogt
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women’s and Children’s Hospitals NHS Foundation Trust, Birmingham, UK
| | - Sonja A. de Munnik
- Department of Human Genetics, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lauren Dreyer
- Genetic Services of Western Australia, Undiagnosed Diseases Program, Perth, Western Australia, Australia
| | - Gareth Baynam
- Genetic Services of Western Australia, Undiagnosed Diseases Program, Perth, Western Australia, Australia
- Western Australian Register of Developmental Anomalies, Perth, Western Australia, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
- Telethon Kids Institute, Perth, Western Australia, Australia
- Division of Paediatrics, School of Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Lisa Ewans
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
| | - Ana R. Gonçalves
- Center for Medical Genetics Dr. Jacinto de Magalhāes, Hospital and University Center of Porto, Porto, Portugal
| | - Gabriela Soares
- Center for Medical Genetics Dr. Jacinto de Magalhāes, Hospital and University Center of Porto, Porto, Portugal
| | - Jorge Oliveira
- Center for Medical Genetics Dr. Jacinto de Magalhāes, Hospital and University Center of Porto, Porto, Portugal
- unIGENe, and Center for Predictive and Preventive Genetics (CGPP), Institute for Molecular and Cell Biology (IBMC), Institute of Health Research and Innovation (i3S), University of Porto, Porto, Portugal
| | - Emily Fassi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, Michigan
| | - Marcia Willing
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, Michigan
| | - Jeff L. Waugh
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Pediatrics, Division of Pediatric Neurology, University of Texas Southwestern, Dallas, Texas
| | - Laurence Faivre
- INSERM U1231, LNC UMR1231 GAD, Burgundy University, Dijon, France
| | | | - Sebastien Moutton
- INSERM U1231, LNC UMR1231 GAD, Burgundy University, Dijon, France
- Department of Medical Genetics, Reference Center for Developmental Anomalies, Bordeaux University Hospital, Bordeaux, France
| | | | - Katelyn Payne
- Department of Neurology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Laurence Walsh
- Department of Neurology, Indiana University School of Medicine, Indianapolis, Indiana
| | | | | | | | | | - Michael F. Buckley
- New South Wales Health Pathology Genomic Laboratory, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Paul R. Mark
- Spectrum Health Division of Medical and Molecular Genetics, Grand Rapids, Michigan
| | - Lesley C. Adès
- Department of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales, Australia
- Department of Genetics, The Children’s Hospital at Westmead, Sydney, New South Wales, Australia
| | - Sarah A. Sandaradura
- Department of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales, Australia
- Department of Genetics, The Children’s Hospital at Westmead, Sydney, New South Wales, Australia
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Texas Children’s Hospital, Houston, Texas
| | - Tony Roscioli
- New South Wales Health Pathology Genomic Laboratory, Prince of Wales Hospital, Randwick, New South Wales, Australia
- Centre for Clinical Genetics, Sydney Children’s Hospital, Randwick, New South Wales, Australia
- Neuroscience Research Australia, University of New South Wales, Sydney, New South Wales, Australia
| | - Pankaj B. Agrawal
- Divisions of Newborn Medicine and Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, Maryland
| | - Antonie D. Kline
- Harvey Institute for Human Genetics, Greater Baltimore Medical Center, Baltimore, Maryland
| | | | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - H. T. Marc Timmers
- German Cancer Consortium (DKTK), Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Urology, Medical Faculty-University of Freiburg, Freiburg, Germany
| | - Gholson J. Lyon
- Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, New York
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
- The Graduate Center, The City University of New York, New York, New York
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