1
|
Lu G, Zhang Y, Xia H, He X, Xu P, Wu L, Li D, Ma L, Wu J, Peng Q. Identification of a de novo mutation of the FOXG1 gene and comprehensive analysis for molecular factors in Chinese FOXG1-related encephalopathies. Front Mol Neurosci 2022; 15:1039990. [PMID: 36568277 PMCID: PMC9768341 DOI: 10.3389/fnmol.2022.1039990] [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: 09/08/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Background FOXG1-related encephalopathy, also known as FOXG1 syndrome or FOXG1-related disorder, affects most aspects of development and causes microcephaly and brain malformations. This syndrome was previously considered to be the congenital variant of Rett syndrome. The abnormal function or expression of FOXG1, caused by intragenic mutations, microdeletions or microduplications, was considered to be crucial pathological factor for this disorder. Currently, most of the FOXG1-related encephalopathies have been identified in Europeans and North Americans, and relatively few Chinese cases were reported. Methods Array-Comparative Genomic Hybridization (Array-CGH) and whole-exome sequencing (WES) were carried out for the proband and her parent to detect pathogenic variants. Results A de novo nonsense mutation (c.385G>T, p.Glu129Ter) of FOXG1 was identified in a female child in a cohort of 73 Chinese children with neurodevelopmental disorders/intellectual disorders (NDDs/IDs). In order to have a comprehensive view of FOXG1-related encephalopathy in China, relevant published reports were browsed and twelve cases with mutations in FOXG1 or copy number variants (CNVs) involving FOXG1 gene were involved in the analysis eventually. Feeding difficulties, seizures, delayed speech, corpus callosum hypoplasia and underdevelopment of frontal and temporal lobes occurred in almost all cases. Out of the 12 cases, eight patients (66.67%) had single-nucleotide mutations of FOXG1 gene and four patients (33.33%) had CNVs involving FOXG1 (3 microdeletions and 1 microduplication). The expression of FOXG1 could also be potentially disturbed by deletions of several brain-active regulatory elements located in intergenic FOXG1-PRKD1 region. Further analysis indicated that PRKD1 might be a cooperating factor to regulate the expression of FOXG1, MECP2 and CDKL5 to contribute the RTT/RTT-like disorders. Discussion This re-analysis would broaden the existed knowledge about the molecular etiology and be helpful for diagnosis, treatment, and gene therapy of FOXG1-related disorders in the future.
Collapse
Affiliation(s)
- Guanting Lu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People's Hospital, Deyang, China
- Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China
| | - Yan Zhang
- Department of Obstetrics and Gynecology, Strategic Support Force Medical Center, Beijing, China
| | - Huiyun Xia
- Department of Child Healthcare, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | - Xiaoyan He
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People's Hospital, Deyang, China
- Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China
| | - Pei Xu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People's Hospital, Deyang, China
- Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China
| | - Lianying Wu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People's Hospital, Deyang, China
- Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China
| | - Ding Li
- Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China
| | - Liya Ma
- Department of Child Healthcare, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | - Jin Wu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People's Hospital, Deyang, China
- Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China
| | - Qiongling Peng
- Department of Child Healthcare, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| |
Collapse
|
2
|
Craig CP, Calamaro E, Fong CT, Iqbal AM, Paciorkowski AR, Zhang B. Diagnosis of FOXG1 syndrome caused by recurrent balanced chromosomal rearrangements: case study and literature review. Mol Cytogenet 2020; 13:40. [PMID: 33632291 PMCID: PMC7905679 DOI: 10.1186/s13039-020-00506-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/05/2020] [Indexed: 02/06/2023] Open
Abstract
Background The FOXG1 gene plays a vital role in mammalian brain differentiation and development. Intra- and intergenic mutations resulting in loss of function or altered expression of the FOXG1 gene cause FOXG1 syndrome. The hallmarks of this syndrome are severe developmental delay with absent verbal language, post-natal growth restriction, post-natal microcephaly, and a recognizable movement disorder characterized by chorea and dystonia.
Case presentation Here we describe a case of a 7-year-old male patient found to have a de novo balanced translocation between chromosome 3 at band 3q14.1 and chromosome 14 at band 14q12 via G-banding chromosome and Fluorescence In Situ Hybridization (FISH) analyses. This rearrangement disrupts the proximity of FOXG1 to a previously described smallest region of deletion overlap (SRO), likely resulting in haploinsufficiency. Conclusions This case adds to the growing body of literature implicating chromosomal structural variants in the manifestation of this disorder and highlights the vital role of cis-acting regulatory elements in the normal expression of this gene. Finally, we propose a protocol for reflex FISH analysis to improve diagnostic efficiency for patients with suspected FOXG1 syndrome.
Collapse
Affiliation(s)
- Connor P Craig
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Ave, Box 608, Rochester, NY, 14642, USA.,School of Medicine and Dentistry, University of Rochester, 601 Elmwood Ave, Rochester, NY, 14642, USA
| | - Emily Calamaro
- Department of Pediatrics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA
| | - Chin-To Fong
- Department of Pediatrics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA
| | - Anwar M Iqbal
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Ave, Box 608, Rochester, NY, 14642, USA
| | - Alexander R Paciorkowski
- Department of Pediatrics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA.,Department of Neurology, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA.,Center for Neural Development and Disease, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA.,Departments of Neuroscience and Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA
| | - Bin Zhang
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Ave, Box 608, Rochester, NY, 14642, USA. .,Department of Pediatrics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA.
| |
Collapse
|
3
|
Abstract
Structural and quantitative chromosomal rearrangements, collectively referred to as structural variation (SV), contribute to a large extent to the genetic diversity of the human genome and thus are of high relevance for cancer genetics, rare diseases and evolutionary genetics. Recent studies have shown that SVs can not only affect gene dosage but also modulate basic mechanisms of gene regulation. SVs can alter the copy number of regulatory elements or modify the 3D genome by disrupting higher-order chromatin organization such as topologically associating domains. As a result of these position effects, SVs can influence the expression of genes distant from the SV breakpoints, thereby causing disease. The impact of SVs on the 3D genome and on gene expression regulation has to be considered when interpreting the pathogenic potential of these variant types.
Collapse
Affiliation(s)
- Malte Spielmann
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Darío G Lupiáñez
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, Germany. .,Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany.
| |
Collapse
|
4
|
Coban N, Gokcen C, Akbayram S, Calisgan B. Evaluation of Platelet Parameters in Children with Autism Spectrum Disorder: Elongated Collagen-Adenosine Diphosphate and Collagen-Epinephrine Closure Times. Autism Res 2019; 12:1069-1076. [PMID: 31077574 DOI: 10.1002/aur.2122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 01/01/2019] [Accepted: 04/22/2019] [Indexed: 12/20/2022]
Abstract
Changes related to the serotonin system play a key role in the etiology of autism spectrum disorder (ASD). Although we know that platelets are associated with the serotonin system, their relation to ASD has not yet been elucidated. In this study, we aim to investigate platelet parameters in children with ASD. Forty patients with ASD according to Diagnostic and Statistical Manual of Mental Disorders 5 (DSM-5) and 30 healthy controls were included in the study. A complete blood count was done to measure parameters relating to platelet morphology. Moreover, prothrombin time (PT) and activated partial thromboplastin time (aPTT) were evaluated. Lastly, platelet functions were assessed with a platelet functions analyzer 100 (PFA-100) device by measuring collagen-ADP and collagen-epinephrine (EPI) closure times. There was not a significant difference between the groups in terms of platelet count, mean platelet volume (MPV), platelet distribution width, plateletcrit, PT, or aPTT parameters for ASD patients when compared to the control group (P > 0.05). However, MPV in severe ASD, as quantified by the Childhood Autism Rating Scale, was found to be significantly lower when compared to mild to moderate ASD (P = 0.047). Moreover, in terms of platelet functions, the elongation in collagen-ADP and collagen-EPI closure times were significantly higher for the ASD group (P = 0.044). These results may suggest an impairment in platelet functions rather than in platelet morphology for children with ASD. Considering these results, further investigation of thrombocyte functions in the ASD may lead to a better understanding of the pathogenesis of ASD and to the development of our limited knowledge of this disorder. Autism Res 2019, 12: 1069-1076. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Serotonin is a chemical that is found in brain as wells as in blood cells that function in blood clotting in the human body. There are problems related to serotonin in brains of people who have autism. Thus, blood clotting cells may also be affected in people who have autism. In this study, we compare blood clotting functions of children with autism with that of healthy controls.
Collapse
Affiliation(s)
- Nurdan Coban
- Department of Child and Adolescent Psychiatry, Gaziantep University, Gaziantep, Turkey
| | - Cem Gokcen
- Department of Child and Adolescent Psychiatry, Gaziantep University, Gaziantep, Turkey
| | - Sinan Akbayram
- Department of Pediatric Hematology, Gaziantep University, Gaziantep, Turkey
| | - Baran Calisgan
- Department of Child and Adolescent Psychiatry, Gaziantep University, Gaziantep, Turkey
| |
Collapse
|
5
|
Laugsch M, Bartusel M, Rehimi R, Alirzayeva H, Karaolidou A, Crispatzu G, Zentis P, Nikolic M, Bleckwehl T, Kolovos P, van Ijcken WFJ, Šarić T, Koehler K, Frommolt P, Lachlan K, Baptista J, Rada-Iglesias A. Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs. Cell Stem Cell 2019; 24:736-752.e12. [PMID: 30982769 DOI: 10.1016/j.stem.2019.03.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 01/03/2019] [Accepted: 03/06/2019] [Indexed: 11/18/2022]
Abstract
The pathological consequences of structural variants disrupting 3D genome organization can be difficult to elucidate in vivo due to differences in gene dosage sensitivity between mice and humans. This is illustrated by branchiooculofacial syndrome (BOFS), a rare congenital disorder caused by heterozygous mutations within TFAP2A, a neural crest regulator for which humans, but not mice, are haploinsufficient. Here, we present a BOFS patient carrying a heterozygous inversion with one breakpoint located within a topologically associating domain (TAD) containing enhancers essential for TFAP2A expression in human neural crest cells (hNCCs). Using patient-specific hiPSCs, we show that, although the inversion shuffles the TFAP2A hNCC enhancers with novel genes within the same TAD, this does not result in enhancer adoption. Instead, the inversion disconnects one TFAP2A allele from its cognate enhancers, leading to monoallelic and haploinsufficient TFAP2A expression in patient hNCCs. Our work illustrates the power of hiPSC differentiation to unveil long-range pathomechanisms.
Collapse
Affiliation(s)
- Magdalena Laugsch
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Institute of Human Genetics, CMMC, University Hospital Cologne, Cologne, Germany
| | - Michaela Bartusel
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Rizwan Rehimi
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Hafiza Alirzayeva
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Agathi Karaolidou
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Giuliano Crispatzu
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Peter Zentis
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Milos Nikolic
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Tore Bleckwehl
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Petros Kolovos
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | | | - Tomo Šarić
- Center for Physiology and Pathophysiology, Institute for Neurophysiology, Medical Faculty, University of Cologne, Cologne, Germany
| | - Katrin Koehler
- Department of Pediatrics, University Clinic Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Peter Frommolt
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Katherine Lachlan
- Human Genetics & Genomic Medicine, University of Southampton, Southampton General Hospital, Southampton, UK; Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Princess Anne Hospital, Southampton, UK
| | - Julia Baptista
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK; Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.
| | - Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Cantabria, Spain.
| |
Collapse
|
6
|
Zhu W, Zhang B, Li M, Mo F, Mi T, Wu Y, Teng Z, Zhou Q, Li W, Hu B. Precisely controlling endogenous protein dosage in hPSCs and derivatives to model FOXG1 syndrome. Nat Commun 2019; 10:928. [PMID: 30804331 PMCID: PMC6389984 DOI: 10.1038/s41467-019-08841-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 01/23/2019] [Indexed: 01/25/2023] Open
Abstract
Dosage of key regulators impinge on developmental disorders such as FOXG1 syndrome. Since neither knock-out nor knock-down strategy assures flexible and precise protein abundance control, to study hypomorphic or haploinsufficiency expression remains challenging. We develop a system in human pluripotent stem cells (hPSCs) using CRISPR/Cas9 and SMASh technology, with which we can target endogenous proteins for precise dosage control in hPSCs and at multiple stages of neural differentiation. We also reveal FOXG1 dose-dependently affect the cellular constitution of human brain, with 60% mildly affect GABAergic interneuron development while 30% thresholds the production of MGE derived neurons. Abnormal interneuron differentiation accounts for various neurological defects such as epilepsy or seizures, which stimulates future innovative cures of FOXG1 syndrome. By means of its robustness and easiness, dosage-control of proteins in hPSCs and their derivatives will update the understanding and treatment of additional diseases caused by abnormal protein dosage. Altered dosage of developmental regulators such as transcription factors can result in disorders, such as FOXG1 syndrome. Here, the authors demonstrate the utility of SMASh technology for modulating protein dosage by modeling FOXG1 syndrome using human pluripotent stem cell-derived neurons and neural organoids.
Collapse
Affiliation(s)
- Wenliang Zhu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Boya Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Mengqi Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Fan Mo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Tingwei Mi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yihui Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Zhaoqian Teng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China. .,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China. .,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
| | - Baoyang Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China. .,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
7
|
Zepeda-Mendoza CJ, Bardon A, Kammin T, Harris DJ, Cox H, Redin C, Ordulu Z, Talkowski ME, Morton CC. Phenotypic interpretation of complex chromosomal rearrangements informed by nucleotide-level resolution and structural organization of chromatin. Eur J Hum Genet 2018; 26:374-381. [PMID: 29321672 DOI: 10.1038/s41431-017-0068-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 09/20/2017] [Accepted: 10/31/2017] [Indexed: 01/06/2023] Open
Abstract
Molecular characterization of balanced chromosomal abnormalities constitutes a powerful tool in understanding the pathogenic mechanisms of complex genetic disorders. Here we report a male with severe global developmental delay in the presence of a complex karyotype and normal microarray and exome studies. The subject, referred to as DGAP294, has two de novo apparently balanced translocations involving chromosomes 1 and 14, and chromosomes 4 and 10, disrupting several different transcripts of adhesion G protein-coupled receptor L2 (ADGRL2) and protocadherin 15 (PCDH15). In addition, a maternally inherited inversion disrupts peptidyl arginine deiminase types 3 and 4 (PADI3 and PADI4) on chromosome 1. None of these gene disruptions explain the patient's phenotype. Using genome regulatory annotations and chromosome conformation data, we predict a position effect ~370 kb upstream of a translocation breakpoint located at 14q12. The position effect involves forkhead box G1 (FOXG1), mutations in which are associated with the congenital form of Rett syndrome and FOXG1 syndrome. We believe the FOXG1 position effect largely accounts for the clinical phenotype in DGAP294, which can be classified as FOXG1 syndrome like. Our findings emphasize the significance of not only analyzing disrupted genes by chromosomal rearrangements, but also evaluating potential long-range position effects in clinical diagnoses.
Collapse
Affiliation(s)
- Cinthya J Zepeda-Mendoza
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | - Tammy Kammin
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, USA
| | - David J Harris
- Harvard Medical School, Boston, MA, USA.,Boston Children's Hospital, Boston, MA, USA
| | - Helen Cox
- West Midlands Regional Clinical Genetics Unit, Birmingham Women's Hospital, Edgbaston, Birmingham, UK
| | - Claire Redin
- Harvard Medical School, Boston, MA, USA.,Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Zehra Ordulu
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Michael E Talkowski
- Harvard Medical School, Boston, MA, USA.,Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.,Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA.,Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Cynthia C Morton
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA. .,Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA. .,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA. .,Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
| |
Collapse
|
8
|
Regulatory variants of FOXG1 in the context of its topological domain organisation. Eur J Hum Genet 2017; 26:186-196. [PMID: 29289958 DOI: 10.1038/s41431-017-0011-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 02/02/2023] Open
Abstract
FOXG1 syndrome is caused by FOXG1 intragenic point mutations, or by long-range position effects (LRPE) of intergenic structural variants. However, the size of the FOXG1 regulatory landscape is uncertain, because the associated topologically associating domain (TAD) in fibroblasts is split into two domains in embryonic stem cells (hESC). Indeed, it has been suggested that the pathogenetic mechanism of deletions that remove the stem-cell-specific TAD boundary may be enhancer adoption due to ectopic activity of enhancer(s) located in the distal hESC-TAD. Herein we map three de novo translocation breakpoints to the proximal regulatory domain of FOXG1. The classical FOXG1 syndrome in these and in other translocation patients, and in a patient with an intergenic deletion that removes the hESC-specific TAD boundary, do not support the hypothesised enhancer adoption as a main contributor to the FOXG1 syndrome. Also, virtual 4 C and HiC-interaction data suggest that the hESC-specific TAD boundary may not be critical for FOXG1 regulation in a majority of human cells and tissues, including brain tissues and a neuronal progenitor cell line. Our data support the importance of a critical regulatory region (SRO) proximal to the hESC-specific TAD boundary. We further narrow this critical region by a deletion distal to the hESC-specific boundary, associated with a milder clinical phenotype. The distance from FOXG1 to the SRO ( > 500 kb) highlight a limitation of ENCODE DNase hypersensitivity data for functional prediction of LRPE. Moreover, the SRO has little overlap with a cluster of frequently associating regions (FIREs) located in the proximal hESC-TAD.
Collapse
|
9
|
Zhan R, Wang F, Wu Y, Wang Y, Qian W, Liu M, Liu T, He W, Ren H, Luo G. Nitric oxide promotes epidermal stem cell proliferation via FOXG1-c-Myc signalling. Nitric Oxide 2017; 73:1-8. [PMID: 29248687 DOI: 10.1016/j.niox.2017.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/14/2017] [Accepted: 12/11/2017] [Indexed: 10/18/2022]
Abstract
OBJECTIVE Epidermal stem cells (ESCs) play a critical role in wound repair, but the mechanism underlying ESC proliferation is unclear. Here, we explored the effects of nitric oxide (NO) on ESC proliferation and the possible underlying mechanism. METHODS The effect of NO (two NO donors, SNAP and spermine NONOate, were used) on cell proliferation was detected using cell proliferation and DNA synthesis assays. Thereafter, expression of FOXG1 and c-Myc induced by NO was determined by immunoblot analysis. pAdEasy-FOXG1 adenovirus and c-Myc siRNA plasmids were infected or transfected, respectively, into human ESCs to detect the effect of FOXG1 and c-Myc on NO-induced cell proliferation. Additionally, NO-induced ESC proliferation in vivo was detected by BrdU incorporation and a superficial second-degree mouse burn model. Moreover, the relationships among NO, FOXG1 and c-Myc were detected by western blotting, real-time PCR and dual luciferase assay. RESULTS NO exerted a biphasic effect on ESC proliferation, and 100 μM SNAP and 10 μM spermine NONOate were the optimal concentrations to promote cell proliferation. Additionally, NO-promoted human ESC proliferation was mediated by FOXG1 and c-Myc in vitro and vivo. Furthermore, NO regulated FOXG1 expression through cGMP signalling, and NO-induced transcription of c-Myc was regulated by FOXG1-mediated c-Myc promoter activity. CONCLUSION This study showed that the biphasic effect of NO on ESC proliferation as well as NO induced ESC proliferation were regulated by the cGMP/FOXG1/c-Myc signalling pathway, suggesting that NO may serve as a new disparate target for wound healing.
Collapse
Affiliation(s)
- Rixing Zhan
- Institute of Burn Research, State Key Laboratory of Trauma, Burn and Combined Injury, Key Laboratory of Proteomics of Chongqing, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China; School of Nursing, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Fan Wang
- Department of Plastic and Reconstructive Surgery, Southwestern Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Ying Wu
- The Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China.
| | - Ying Wang
- Institute of Burn Research, State Key Laboratory of Trauma, Burn and Combined Injury, Key Laboratory of Proteomics of Chongqing, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Wei Qian
- Institute of Burn Research, State Key Laboratory of Trauma, Burn and Combined Injury, Key Laboratory of Proteomics of Chongqing, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Menglong Liu
- Institute of Burn Research, State Key Laboratory of Trauma, Burn and Combined Injury, Key Laboratory of Proteomics of Chongqing, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Tengfei Liu
- Institute of Burn Research, State Key Laboratory of Trauma, Burn and Combined Injury, Key Laboratory of Proteomics of Chongqing, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Weifeng He
- Institute of Burn Research, State Key Laboratory of Trauma, Burn and Combined Injury, Key Laboratory of Proteomics of Chongqing, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Hui Ren
- School of Nursing, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Gaoxing Luo
- Institute of Burn Research, State Key Laboratory of Trauma, Burn and Combined Injury, Key Laboratory of Proteomics of Chongqing, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| |
Collapse
|
10
|
Pacheco NL, Heaven MR, Holt LM, Crossman DK, Boggio KJ, Shaffer SA, Flint DL, Olsen ML. RNA sequencing and proteomics approaches reveal novel deficits in the cortex of Mecp2-deficient mice, a model for Rett syndrome. Mol Autism 2017; 8:56. [PMID: 29090078 PMCID: PMC5655833 DOI: 10.1186/s13229-017-0174-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/02/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by mutations in the transcriptional regulator MeCP2. Much of our understanding of MeCP2 function is derived from transcriptomic studies with the general assumption that alterations in the transcriptome correlate with proteomic changes. Advances in mass spectrometry-based proteomics have facilitated recent interest in the examination of global protein expression to better understand the biology between transcriptional and translational regulation. METHODS We therefore performed the first comprehensive transcriptome-proteome comparison in a RTT mouse model to elucidate RTT pathophysiology, identify potential therapeutic targets, and further our understanding of MeCP2 function. The whole cortex of wild-type and symptomatic RTT male littermates (n = 4 per genotype) were analyzed using RNA-sequencing and data-independent acquisition liquid chromatography tandem mass spectrometry. Ingenuity® Pathway Analysis was used to identify significantly affected pathways in the transcriptomic and proteomic data sets. RESULTS Our results indicate these two "omics" data sets supplement one another. In addition to confirming previous works regarding mRNA expression in Mecp2-deficient animals, the current study identified hundreds of novel protein targets. Several selected protein targets were validated by Western blot analysis. These data indicate RNA metabolism, proteostasis, monoamine metabolism, and cholesterol synthesis are disrupted in the RTT proteome. Hits common to both data sets indicate disrupted cellular metabolism, calcium signaling, protein stability, DNA binding, and cytoskeletal cell structure. Finally, in addition to confirming disrupted pathways and identifying novel hits in neuronal structure and synaptic transmission, our data indicate aberrant myelination, inflammation, and vascular disruption. Intriguingly, there is no evidence of reactive gliosis, but instead, gene, protein, and pathway analysis suggest astrocytic maturation and morphological deficits. CONCLUSIONS This comparative omics analysis supports previous works indicating widespread CNS dysfunction and may serve as a valuable resource for those interested in cellular dysfunction in RTT.
Collapse
Affiliation(s)
- Natasha L. Pacheco
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd, Birmingham, AL 35294 USA
| | - Michael R. Heaven
- Vulcan Analytical, LLC, 1500 1st Ave. North, Birmingham, AL 35203 USA
| | - Leanne M. Holt
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd, Birmingham, AL 35294 USA
- School of Neuroscience, Virginia Polytechnic and State University, Life Sciences Building Room 213, 970 Washington St. SW, Blacksburg, VA 24061 USA
| | - David K. Crossman
- UAB Heflin Center for Genomic Science, Department of Genetics, University of Alabama at Birmingham, Kaul 424A, 1720 2nd Ave. South, Birmingham, AL 35294 USA
| | - Kristin J. Boggio
- Proteomics and Mass Spectrometry Facility, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 222 Maple Ave., Fuller Building, Shrewsbury, MA 01545 USA
| | - Scott A. Shaffer
- Proteomics and Mass Spectrometry Facility, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 222 Maple Ave., Fuller Building, Shrewsbury, MA 01545 USA
| | - Daniel L. Flint
- Luxumbra Strategic Research, LLC, 1331 South Eads St, Arlington, VA 22202 USA
| | - Michelle L. Olsen
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd, Birmingham, AL 35294 USA
- School of Neuroscience, Virginia Polytechnic and State University, Life Sciences Building Room 213, 970 Washington St. SW, Blacksburg, VA 24061 USA
| |
Collapse
|
11
|
Bijl N, Thys C, Wittevrongel C, De la Marche W, Devriendt K, Peeters H, Van Geet C, Freson K. Platelet studies in autism spectrum disorder patients and first-degree relatives. Mol Autism 2015; 6:57. [PMID: 26500752 PMCID: PMC4619313 DOI: 10.1186/s13229-015-0051-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 10/16/2015] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Platelets have been proven to be a useful cellular model to study some neuropathologies, due to the overlapping biological features between neurons and platelets as granule secreting cells. Altered platelet dense granule morphology was previously reported in three autism spectrum disorder (ASD) patients with chromosomal translocations that disrupted ASD candidate genes NBEA, SCAMP5, and AMYSIN, but a systematic analysis of platelet function in ASD is lacking in contrast to numerous reports of elevated serotonin levels in platelets and blood as potential biomarker for ASD. METHODS We explored platelet count, size, epinephrine-induced activation, and dense granule ATP secretion in a cohort of 159 ASD patients, their 289 first-degree relatives (103 unaffected siblings, 99 mothers, and 87 fathers), 45 adult controls, and 65 pediatric controls. For each of the responses separately, a linear mixed model with gender as a covariate was used to compare the level between groups. We next investigated the correlation between platelet function outcomes and severity of impairments in social behavior (social responsiveness score (SRS)). RESULTS The average platelet count was increased in ASD patients and siblings vs. controls (ASD 320.3 × 10(9)/L, p = 0.003; siblings 332.0 × 10(9)/L, p < 0.001; controls 283.0 × 10(9)/L). The maximal platelet secretion-dependent aggregation response to epinephrine was not significantly lower for ASD patients. However, secondary wave responses following stimulation with epinephrine were more frequently delayed or absent compared to controls (ASD 52 %, siblings 45 %, parents 53 %, controls 22 %, p = 0.002). In addition, stimulated release of ATP from dense granules was reduced in ASD patients, siblings, and parents vs. controls following activation of platelets with either collagen (ASD 1.54 μM, p = 0.001; siblings 1.51 μM, p < 0.001; parents 1.67 μM, p = 0.021; controls 2.03 μM) or ADP (ASD 0.96 μM, p = 0.003; siblings 1.00 μM, p = 0.012; parents 1.17 μM, p = 0.21; controls 1.40 μM). Plasma serotonin levels were increased for ASD patients (n = 20, p = 0.005) and siblings (n = 20, p = 0.0001) vs. controls (n = 16). No significant correlations were found in the different groups between SRS scores and count, size, epinephrine aggregation, or ATP release. CONCLUSIONS We report increased platelet counts, decreased platelet ATP dense granule secretion, and increased serotonin plasma levels not only in ASD patients but also in their first-degree relatives. This suggests that potential genetic factors associated with platelet counts and granule secretion can be associated with, but are not fully penetrant for ASD.
Collapse
Affiliation(s)
- Nora Bijl
- Department of Cardiovascular Sciences, Centre for Molecular and Vascular Biology, KU Leuven, Gasthuisberg Campus, O & N I, Herestraat 49-b911, 3000 Leuven, Belgium ; The LAuRes Consortium, KU Leuven, Leuven, Belgium
| | - Chantal Thys
- Department of Cardiovascular Sciences, Centre for Molecular and Vascular Biology, KU Leuven, Gasthuisberg Campus, O & N I, Herestraat 49-b911, 3000 Leuven, Belgium
| | - Christine Wittevrongel
- Department of Cardiovascular Sciences, Centre for Molecular and Vascular Biology, KU Leuven, Gasthuisberg Campus, O & N I, Herestraat 49-b911, 3000 Leuven, Belgium
| | - Wouter De la Marche
- Department of Neurosciences, Research Group Psychiatry, KU Leuven, Leuven, Belgium ; The LAuRes Consortium, KU Leuven, Leuven, Belgium
| | | | - Hilde Peeters
- Department of Human Genetics, KU Leuven, Leuven, Belgium ; The LAuRes Consortium, KU Leuven, Leuven, Belgium
| | - Chris Van Geet
- Department of Cardiovascular Sciences, Centre for Molecular and Vascular Biology, KU Leuven, Gasthuisberg Campus, O & N I, Herestraat 49-b911, 3000 Leuven, Belgium ; The LAuRes Consortium, KU Leuven, Leuven, Belgium
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Centre for Molecular and Vascular Biology, KU Leuven, Gasthuisberg Campus, O & N I, Herestraat 49-b911, 3000 Leuven, Belgium ; The LAuRes Consortium, KU Leuven, Leuven, Belgium
| |
Collapse
|
12
|
Goubau C, Buyse GM, Van Geet C, Freson K. The contribution of platelet studies to the understanding of disease mechanisms in complex and monogenetic neurological disorders. Dev Med Child Neurol 2014; 56:724-31. [PMID: 24579816 DOI: 10.1111/dmcn.12421] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/05/2014] [Indexed: 01/03/2023]
Abstract
Platelets, known for their role in primary haemostasis, prevent excessive bleeding after injury. The study of platelets has, therefore, traditionally focused on bleeding disorders. It has recently become evident, however, that platelet research can contribute to unravelling the disease mechanisms that underlie neuropathological disorders that have a subtle subclinical platelet phenotype. Platelets and neurosecretory cells have common gene expression profiles and share several biological features. This review provides a literature update on the use of platelets as easily accessible cells to study neurological disorders. We provide examples of the use of different platelet-based tests to understand the underlying pathophysiological mechanisms for both complex and monogenetic neuropathological disorders. In addition to the well-studied regulated granule secretion and serotonin metabolism, more recent studies have shown that defects in transcription factors, membrane transporters, G-protein signal transduction, and cytoskeletal proteins can be investigated using platelets to gain information on their role in neuropathology.
Collapse
Affiliation(s)
- Christophe Goubau
- Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium; Department of Child Neurology, University Hospitals Leuven, Leuven, Belgium
| | | | | | | |
Collapse
|