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Kim SM, Cho SY, Kim MW, Roh SR, Shin HS, Suh YH, Geum D, Lee MA. Genome-Wide Analysis Identifies NURR1-Controlled Network of New Synapse Formation and Cell Cycle Arrest in Human Neural Stem Cells. Mol Cells 2020; 43:551-571. [PMID: 32522891 PMCID: PMC7332357 DOI: 10.14348/molcells.2020.0071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/01/2020] [Accepted: 05/09/2020] [Indexed: 02/07/2023] Open
Abstract
Nuclear receptor-related 1 (Nurr1) protein has been identified as an obligatory transcription factor in midbrain dopaminergic neurogenesis, but the global set of human NURR1 target genes remains unexplored. Here, we identified direct gene targets of NURR1 by analyzing genome-wide differential expression of NURR1 together with NURR1 consensus sites in three human neural stem cell (hNSC) lines. Microarray data were validated by quantitative PCR in hNSCs and mouse embryonic brains and through comparison to published human data, including genome-wide association study hits and the BioGPS gene expression atlas. Our analysis identified ~40 NURR1 direct target genes, many of them involved in essential protein modules such as synapse formation, neuronal cell migration during brain development, and cell cycle progression and DNA replication. Specifically, expression of genes related to synapse formation and neuronal cell migration correlated tightly with NURR1 expression, whereas cell cycle progression correlated negatively with it, precisely recapitulating midbrain dopaminergic development. Overall, this systematic examination of NURR1-controlled regulatory networks provides important insights into this protein's biological functions in dopamine-based neurogenesis.
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Affiliation(s)
- Soo Min Kim
- Department of Brain Science, Ajou University School of Medicine, Suwon 6499, Korea
- Neuroscience Graduate Program, Department of Biomedical Sciences, Graduate School of Ajou University, Suwon 16499, Korea
| | | | - Min Woong Kim
- Department of Brain Science, Ajou University School of Medicine, Suwon 6499, Korea
- Neuroscience Graduate Program, Department of Biomedical Sciences, Graduate School of Ajou University, Suwon 16499, Korea
| | - Seung Ryul Roh
- Department of Brain Science, Ajou University School of Medicine, Suwon 6499, Korea
- Neuroscience Graduate Program, Department of Biomedical Sciences, Graduate School of Ajou University, Suwon 16499, Korea
| | - Hee Sun Shin
- Department of Brain Science, Ajou University School of Medicine, Suwon 6499, Korea
- Neuroscience Graduate Program, Department of Biomedical Sciences, Graduate School of Ajou University, Suwon 16499, Korea
| | - Young Ho Suh
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Dongho Geum
- Department of Medical Science, Korea University Medical School, Seoul 02841, Korea
| | - Myung Ae Lee
- Department of Brain Science, Ajou University School of Medicine, Suwon 6499, Korea
- Neuroscience Graduate Program, Department of Biomedical Sciences, Graduate School of Ajou University, Suwon 16499, Korea
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Bianchi DW, Deprest J, Levy B, Chitty LS, Ghidini A, Hui L, van Mieghem T, George ST. The 2019 Malcolm Ferguson-Smith Young Investigator Award. Prenat Diagn 2020; 40:763-765. [PMID: 32597540 DOI: 10.1002/pd.5763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Diana W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Jan Deprest
- Departments of Obstetrics and Gynaecology, University Hospitals, Leuven, Belgium
| | - Brynn Levy
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Lyn S Chitty
- Genetic and Genomic Medicine, University College London, Great Ormond Street Institute of Child Health, London, UK
| | - Alessandro Ghidini
- Antenatal Testing Center, Inova Alexandria Hospital, Alexandria, VA, USA
| | - Lisa Hui
- Departments of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
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Bianchi DW, Ghidini A, Levy B, Deprest J, van Mieghem T, Chitty LS, Hui L, McLean-Inglis A. The 2018 Malcolm Ferguson-Smith Young Investigator Award. Prenat Diagn 2019; 39:835-837. [PMID: 31414475 DOI: 10.1002/pd.5533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Diana W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Alessandro Ghidini
- Department of Obstetrics and Gynecology, Inova Alexandria Hospital, Alexandria, VA, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Jan Deprest
- Academic Department of Development and Regeneration, Woman and Child, Biomedical Sciences, and Clinical Department of Obstetrics and Gynaecology, KU Leuven, Leuven, Belgium
| | - Tim van Mieghem
- Departments of Obstetrics and Gynaecology, Mount Sinai Hospital, Toronto, Canada
| | - Lyn S Chitty
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Lisa Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC, Australia
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Ghidini A, Bianchi DW, Levy B, Deprest J, van Mieghem T, Chitty LS, McLean-Inglis A. The 2015 Malcolm Ferguson-Smith Young Investigator Award. Prenat Diagn 2016; 36:599-600. [PMID: 27381265 DOI: 10.1002/pd.4855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Brynn Levy
- Clinical Cytogenetics Laboratory, Columbia University, New York, USA
| | | | | | - Lyn S Chitty
- University College London NHS Foundation Trust, London, United Kingdom
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Edlow AG, Hui L, Wick HC, Fried I, Bianchi DW. Assessing the fetal effects of maternal obesity via transcriptomic analysis of cord blood: a prospective case-control study. BJOG 2016; 123:180-9. [PMID: 26840378 DOI: 10.1111/1471-0528.13795] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2015] [Indexed: 01/25/2023]
Abstract
OBJECTIVE To analyse fetal gene expression at term using umbilical cord blood, in order to provide insights into the effects of maternal obesity on human development. DESIGN Prospective case-control study. SETTING Academic tertiary care centre. POPULATION Eight obese (body mass index ≥30 kg/m(2)) and eight lean (body mass index <25 kg/m(2)) pregnant women undergoing prelabour caesarean delivery at term. METHODS Women were matched for gestational age and fetal sex. Cord blood RNA was extracted and hybridised to gene expression arrays. Differentially regulated genes were identified using paired t-tests and the Benjamini-Hochberg correction. Functional analyses were performed using Ingenuity Pathway Analysis, BioGPS and Gene Set Enrichment Analysis with a fetal-specific annotation. Z-scores ≥2.0 or P-values <0.01 were considered significant. MAIN OUTCOME MEASURE Functions of differentially regulated genes in fetuses of obese women. RESULTS A total of 701 differentially regulated genes were identified, producing an expression profile implicating neurodegeneration, decreased survival of sensory neurons, and decreased neurogenesis in the fetuses of obese women. Upstream regulators related to inflammatory signalling were significantly activated; those related to insulin receptor signalling, lipid homeostasis, regulation of axonal guidance, and cellular response to oxidative stress were significantly inhibited. Of 26 tissue-specific genes that were differentially regulated in fetuses of obese women, six mapped to the fetal brain. CONCLUSION Maternal obesity affects fetal gene expression at term, implicating dysregulated brain development, inflammatory and immune signalling, glucose and lipid homeostasis, and oxidative stress. This may have implications for postnatal neurodevelopment and metabolism.
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Affiliation(s)
- A G Edlow
- Mother Infant Research Institute and Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, MA, USA
| | - L Hui
- Mother Infant Research Institute and Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, MA, USA.,Department of Perinatal Medicine, Mercy Hospital for Women, Heidelberg, Vic., Australia
| | - H C Wick
- Department of Computer Science, Tufts University, Medford, MA, USA
| | - I Fried
- Department of Computer Science, Tufts University, Medford, MA, USA
| | - D W Bianchi
- Mother Infant Research Institute and Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, MA, USA
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Predictive performance of a seven-plex antibody array in prenatal screening for Down Syndrome. DISEASE MARKERS 2015; 2015:519851. [PMID: 25983373 PMCID: PMC4423028 DOI: 10.1155/2015/519851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/17/2015] [Indexed: 12/27/2022]
Abstract
We evaluated the use of multiplex antibody array methodology for simultaneous measurement of serum protein markers for first trimester screening of Down Syndrome (DS) and other pregnancy outcomes such as preeclampsia. For this purpose, we constructed an antibody array for indirect (“sandwich”) measurement of seven serum proteins: pregnancy-associated plasma protein-A (PAPP-A), free beta subunit of human chorionic gonadotropin (fβ-hCG), alpha-fetoprotein (AFP), angiopoietin-like 3 (ANGPTL3), epidermal growth factor (EGF), insulin-like growth factor 2 (IGFII), and superoxide dismutase 1 (SOD1). This array was tested using 170 DS cases and 510 matched controls drawn during the 8th–13th weeks of pregnancy. Data were used for prediction modelling and compared to previously obtained AutoDELFIA immunoassay data for PAPP-A and fβ-hCG. PAPP-A and fβ-hCG serum concentrations obtained using antibody arrays were highly correlated with AutoDELFIA data. Moreover, DS prediction modeling using (log-MoMmed) antibody array and AutoDELFIA data gave comparable results. Of the other markers, AFP and IGFII showed significant changes in concentration, although adding these markers to a prediction model based on prior risk, PAPP-A and fβ-hCG did not improve the predictive performance. We conclude that implementation of antibody arrays in a prenatal screening setting is feasible but will require additional first trimester screening markers.
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Maternal obesity affects fetal neurodevelopmental and metabolic gene expression: a pilot study. PLoS One 2014; 9:e88661. [PMID: 24558408 PMCID: PMC3928248 DOI: 10.1371/journal.pone.0088661] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/11/2014] [Indexed: 11/19/2022] Open
Abstract
Objective One in three pregnant women in the United States is obese. Their offspring are at increased risk for neurodevelopmental and metabolic morbidity. Underlying molecular mechanisms are poorly understood. We performed a global gene expression analysis of mid-trimester amniotic fluid cell-free fetal RNA in obese versus lean pregnant women. Methods This prospective pilot study included eight obese (BMI≥30) and eight lean (BMI<25) women undergoing clinically indicated mid-trimester genetic amniocentesis. Subjects were matched for gestational age and fetal sex. Fetuses with abnormal karyotype or structural anomalies were excluded. Cell-free fetal RNA was extracted from amniotic fluid and hybridized to whole genome expression arrays. Genes significantly differentially regulated in 8/8 obese-lean pairs were identified using paired t-tests with the Benjamini-Hochberg correction (false discovery rate of <0.05). Biological interpretation was performed with Ingenuity Pathway Analysis and the BioGPS gene expression atlas. Results In fetuses of obese pregnant women, 205 genes were significantly differentially regulated. Apolipoprotein D, a gene highly expressed in the central nervous system and integral to lipid regulation, was the most up-regulated gene (9-fold). Apoptotic cell death was significantly down-regulated, particularly within nervous system pathways involving the cerebral cortex. Activation of the transcriptional regulators estrogen receptor, FOS, and STAT3 was predicted in fetuses of obese women, suggesting a pro-estrogenic, pro-inflammatory milieu. Conclusion Maternal obesity affects fetal neurodevelopmental and metabolic gene expression as early as the second trimester. These findings may have implications for postnatal neurodevelopmental and metabolic abnormalities described in the offspring of obese women.
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Abstract
OBJECTIVE To identify the tissue expression patterns and biological pathways enriched in term amniotic fluid cell-free fetal RNA by comparing functional genomic analyses of term and second-trimester amniotic fluid supernatants. METHODS This was a prospective whole genome microarray study comparing eight amniotic fluid samples collected from women at term who underwent prelabor cesarean delivery and eight second-trimester amniotic fluid samples from routine amniocenteses. A functional annotation tool was used to compare tissue expression patterns in term and second-trimester samples. Pathways analysis software identified physiologic systems, molecular and cellular functions, and upstream regulators that were significantly overrepresented in term amniotic fluid. RESULTS There were 2,871 significantly differentially regulated genes. In term amniotic fluid, tissue expression analysis showed enrichment of salivary gland, tracheal, and renal transcripts as compared with brain and embryonic neural cells in the second trimester. Functional analysis of genes upregulated at term revealed pathways that were highly specific for postnatal adaptation such as immune function, digestion, respiration, carbohydrate metabolism, and adipogenesis. Inflammation and prostaglandin synthesis, two key processes involved in normal labor, were also activated in term amniotic fluid. CONCLUSIONS Transcriptomic analysis of amniotic fluid cell-free fetal RNA detects fetal maturation processes activated in term pregnancy. These findings further develop the concept of amniotic fluid supernatant as a real-time gene expression "summary fluid" and support its potential for future studies of fetal development.
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