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V RP, Finnell RH, Ross ME, Alarcón P, Suazo J. Neural tube defects and epigenetics: role of histone post-translational histone modifications. Epigenomics 2024; 16:419-426. [PMID: 38410929 DOI: 10.2217/epi-2023-0357] [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] [Indexed: 02/28/2024] Open
Abstract
Neural tube defects (NTDs) are the most common congenital anomalies of the CNS. It is widely appreciated that both genetic and environmental factors contribute to their etiology. The inability to ascribe clear genetic patterns of inheritance to various NTD phenotypes suggests it is possible that epigenetic mechanisms are involved in the etiology of NTDs. In this context, the contribution of DNA methylation as an underlying contributing factor to the etiology of NTDs has been extensively reviewed. Here, an updated accounting of the evidence linking post-translational histone modifications to these birth defects, relying heavily upon studies in humans, and the possible molecular implications inferred from reports based on cellular and animal models, are presented.
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Affiliation(s)
- Rosa Pardo V
- Section of Genetics, Hospital Clínico Universidad de Chile, Dr. Carlos Lorca Tobar #999, Santiago, Chile
- Unit of Neonatology, Hospital Clínico Universidad de Chile, Dr. Carlos Lorca Tobar #999, Santiago, Chile
| | - Richard H Finnell
- Center for Precision Environmental Health, Department of Molecular & Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - M Elizabeth Ross
- Center for Neurogenetics, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, 407 East 61st Street, NY, USA
| | - Pablo Alarcón
- Section of Genetics, Hospital Clínico Universidad de Chile, Dr. Carlos Lorca Tobar #999, Santiago, Chile
- Section of Genetics, Hospital Sótero del Río, Avenida Concha y Toro #3459, Santiago, Chile
| | - José Suazo
- Institute for Research in Dental Sciences, School of Dentistry, Universidad de Chile, Olivos #943, Santiago, Chile
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Uyanga VA, Bello SF, Qian X, Chao N, Li H, Zhao J, Wang X, Jiao H, Onagbesan OM, Lin H. Transcriptomics analysis unveils key potential genes associated with brain development and feeding behavior in the hypothalamus of L-citrulline-fed broiler chickens. Poult Sci 2023; 102:103136. [PMID: 37844531 PMCID: PMC10585647 DOI: 10.1016/j.psj.2023.103136] [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: 07/10/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/18/2023] Open
Abstract
High ambient temperature is a major environmental stressor affecting poultry production, especially in the tropical and subtropical regions of the world. Nutritional interventions have been adopted to combat thermal stress in poultry, including the use of amino acids. L-citrulline is a nonessential amino acid that is involved in nitric oxide generation and thermoregulation, however, the molecular mechanisms behind L-citrulline's regulation of body temperature are still unascertained. This study investigated the global gene expression in the hypothalamus of chickens fed either basal diet or L-citrulline-supplemented diets under different housing temperatures. Ross 308 broilers were fed with basal diet (CON) or 1% L-citrulline diet (LCT) from day-old, and later subjected to 2 environmental temperatures in a 2 by 2 factorial arrangement as follows; basal diet-fed chickens housed at 24°C (CON-TN); L-citrulline diet-fed chickens housed at 24°C (LCT-TN); basal diet-fed chickens housed at 35°C (CON-HS), and L-citrulline diet-fed chickens housed at 35°C (LCT-HS) from 22 to 42 d of age. At 42-days old, hypothalamic tissues were collected for mRNA analyses and RNA sequencing. A total of 1,019 million raw reads were generated and about 82.59 to 82.96% were uniquely mapped to genes. The gene ontology (GO) term between the CON-TN and LCT-TN groups revealed significant enrichments of pathways such as central nervous system development, and Wnt signaling pathway. On the other hand, GO terms between the CON-HS and LCT-HS groups revealed enrichments in the regulation of corticosteroid release, regulation of feeding behavior, and regulation of inflammatory response. Several potential candidate genes were identified to be responsible for central nervous system development (EMX2, WFIKKN2, SLC6A4 Wnt10a, and PHOX2B), and regulation of feed intake (NPY, AgRP, GAL, POMC, and NMU) in chickens. Therefore, this study unveils that L-citrulline can influence transcripts associated with brain development, feeding behavior, energy metabolism, and thermoregulation in chickens raised under different ambient temperatures.
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Affiliation(s)
- Victoria Anthony Uyanga
- Department of Animal Science, College of Animal Science and Veterinary Medicine, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control, Shandong Agricultural University, Tai'an City, Shandong Province 271018, China; Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Semiu Folaniyi Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Xin Qian
- Department of Animal Science, College of Animal Science and Veterinary Medicine, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control, Shandong Agricultural University, Tai'an City, Shandong Province 271018, China
| | - Ning Chao
- Department of Animal Science, College of Animal Science and Veterinary Medicine, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control, Shandong Agricultural University, Tai'an City, Shandong Province 271018, China
| | - Haifang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Jingpeng Zhao
- Department of Animal Science, College of Animal Science and Veterinary Medicine, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control, Shandong Agricultural University, Tai'an City, Shandong Province 271018, China
| | - Xiaojuan Wang
- Department of Animal Science, College of Animal Science and Veterinary Medicine, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control, Shandong Agricultural University, Tai'an City, Shandong Province 271018, China
| | - Hongchao Jiao
- Department of Animal Science, College of Animal Science and Veterinary Medicine, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control, Shandong Agricultural University, Tai'an City, Shandong Province 271018, China
| | - Okanlawon M Onagbesan
- Department of Animal Physiology, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Hai Lin
- Department of Animal Science, College of Animal Science and Veterinary Medicine, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control, Shandong Agricultural University, Tai'an City, Shandong Province 271018, China.
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Lin S, Wang C, Li Z, Qiu X. Distinct H3K27me3 and H3K27ac Modifications in Neural Tube Defects Induced by Benzo[a]pyrene. Brain Sci 2023; 13:brainsci13020334. [PMID: 36831877 PMCID: PMC9954656 DOI: 10.3390/brainsci13020334] [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: 12/17/2022] [Revised: 02/06/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023] Open
Abstract
The pathological mechanisms of neural tube defects (NTDs) are not yet fully understood. Although the dysregulation of histone modification in NTDs is recognized, it remains to be fully elucidated on a genome-wide level. We profiled genome-wide H3K27me3 and H3K27ac occupancy by CUT&Tag in neural tissues from ICR mouse embryos with benzo[a]pyrene (BaP)-induced NTDs (250 mg kg-1) at E9.5. Furthermore, we performed RNA sequencing (RNA-seq) to investigate the regulation of histone modifications on gene expressions. Gene ontology and KEGG analysis were conducted to predict pathways involved in the development of NTDs. Our analysis of histone 3 lysine 27 modification in BaP-NTD neural tissues compared to BaP-nonNTD revealed 6045 differentially trimethylated regions and 3104 acetylated regions throughout the genome, respectively. The functional analysis identified a number of pathways uniquely enriched for BaP-NTD embryos, including known neurodevelopment related pathways such as anterior/posterior pattern specification, ephrin receptor signaling pathway, neuron migration and neuron differentiation. RNA-seq identified 423 differentially expressed genes (DEGs) between BaP-NTD and BaP-nonNTD group. The combination analysis of CUT&Tag and RNA-seq found that 55 DEGs were modified by H3K27me3 and 25 by H3K27ac in BaP-NTD, respectively. In the transcriptional regulatory network, transcriptional factors including Srsf1, Ume6, Zbtb7b, and Cad were predicated to be involved in gene expression regulation. In conclusion, our results provide an overview of histone modifications during neural tube closure and demonstrate a key role of genome-wide alterations in H3K27me3 and H3K27ac in NTDs corresponding with changes in transcription profiles.
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Affiliation(s)
- Shanshan Lin
- Division of Birth Cohort Study, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Chengrui Wang
- Division of Birth Cohort Study, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Zhiwen Li
- Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, National Health Commission of the China, Beijing 100191, China
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
- Correspondence: (Z.L.); or (X.Q.); Tel.: +86-010-82801760 (Z.L.); Tel./Fax: +86-020-38367160 (X.Q.)
| | - Xiu Qiu
- Division of Birth Cohort Study, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
- Department of Women’s Health, Guangdong Provincial Key Clinical Specialty of Woman and Child Health, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
- Provincial Clinical Research Center for Child Health, Guangzhou 510623, China
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
- Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
- Correspondence: (Z.L.); or (X.Q.); Tel.: +86-010-82801760 (Z.L.); Tel./Fax: +86-020-38367160 (X.Q.)
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Huang W, Yuan Z, Gu H. Exploring epigenomic mechanisms of neural tube defects using multi-omics methods and data. Ann N Y Acad Sci 2022; 1515:50-60. [PMID: 35666948 DOI: 10.1111/nyas.14802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Neural tube defects (NTDs) are a heterogeneous set of malformations attributed to disruption in normal neural tube closure during early embryogenesis. An in-depth understanding of NTD etiology and mechanisms remains elusive, however. Among the proposed mechanisms, epigenetic changes are thought to play an important role in the formation of NTDs. Epigenomics covers a wide spectrum of genomic DNA sequence modifications that can be investigated via high-throughput techniques. Recent advances in epigenomic technologies have enabled epigenetic studies of congenital malformations and facilitated the integration of big data into the understanding of NTDs. Herein, we review clinical epigenomic data that focuses on DNA methylation, histone modification, and miRNA alterations in human neural tissues, placental tissues, and leukocytes to explore potential mechanisms by which candidate genes affect human NTD pathogenesis. We discuss the links between epigenomics and gene regulatory mechanisms, and the effects of epigenetic alterations in human tissues on neural tube closure.
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Affiliation(s)
- Wanqi Huang
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, China
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, China
| | - Hui Gu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, China
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Gray de Cristoforis A, Ferrari F, Clotman F, Vogel T. Differentiation and localization of interneurons in the developing spinal cord depends on DOT1L expression. Mol Brain 2020; 13:85. [PMID: 32471461 PMCID: PMC7260853 DOI: 10.1186/s13041-020-00623-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/18/2020] [Indexed: 11/12/2022] Open
Abstract
Genetic and epigenetic factors contribute to the development of the spinal cord. Failure in correct exertion of the developmental programs, including neurulation, neural tube closure and neurogenesis of the diverse spinal cord neuronal subtypes results in defects of variable severity. We here report on the histone methyltransferase Disruptor of Telomeric 1 Like (DOT1L), which mediates histone H3 lysine 79 (H3K79) methylation. Conditional inactivation of DOT1L using Wnt1-cre as driver (Dot1l-cKO) showed that DOT1L expression is essential for spinal cord neurogenesis and localization of diverse neuronal subtypes, similar to its function in the development of the cerebral cortex and cerebellum. Transcriptome analysis revealed that DOT1L deficiency favored differentiation over progenitor proliferation. Dot1l-cKO mainly decreased the numbers of dI1 interneurons expressing Lhx2. In contrast, Lhx9 expressing dI1 interneurons did not change in numbers but localized differently upon Dot1l-cKO. Similarly, loss of DOT1L affected localization but not generation of dI2, dI3, dI5, V0 and V1 interneurons. The resulting derailed interneuron patterns might be responsible for increased cell death, occurrence of which was restricted to the late developmental stage E18.5. Together our data indicate that DOT1L is essential for subtype-specific neurogenesis, migration and localization of dorsal and ventral interneurons in the developing spinal cord, in part by regulating transcriptional activation of Lhx2.
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Affiliation(s)
- Angelica Gray de Cristoforis
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
| | - Francesco Ferrari
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Frédéric Clotman
- Laboratory of Neural Differentiation, Institute of Neuroscience, Université catholique de Louvain, Brussels, Belgium
| | - Tanja Vogel
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany.
- Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany.
- Centre for Basics in Neuromodulation (Neuromodul Basics), Freiburg, Germany.
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Yu J, Wang L, Pei P, Li X, Wu J, Qiu Z, Zhang J, Ao R, Wang S, Zhang T, Xie J. Reduced H3K27me3 leads to abnormal Hox gene expression in neural tube defects. Epigenetics Chromatin 2019; 12:76. [PMID: 31856916 PMCID: PMC6921514 DOI: 10.1186/s13072-019-0318-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 12/03/2019] [Indexed: 12/15/2022] Open
Abstract
Background Neural tube defects (NTDs) are severe, common birth defects that result from failure of normal neural tube closure during early embryogenesis. Accumulating strong evidence indicates that genetic factors contribute to NTDs etiology, among them, HOX genes play a key role in neural tube closure. Although abnormal HOX gene expression can lead to NTDs, the underlying pathological mechanisms have not fully been understood. Method We detected that H3K27me3 and expression of the Hox genes in a retinoic acid (RA) induced mouse NTDs model on E8.5, E9.5 and E10.5 using RNA-sequencing and chromatin immunoprecipitation sequencing assays. Furthermore, we quantified 10 Hox genes using NanoString nCounter in brain tissue of fetuses with 39 NTDs patients including anencephaly, spina bifida, hydrocephaly and encephalocele. Results Here, our results showed differential expression in 26 genes with a > 20-fold change in the level of expression, including 10 upregulated Hox genes. RT-qPCR revealed that these 10 Hox genes were all upregulated in RA-induced mouse NTDs as well as RA-treated embryonic stem cells (ESCs). Using ChIP-seq assays, we demonstrate that a decrease in H3K27me3 level upregulates the expression of Hox cluster A–D in RA-induced mouse NTDs model on E10.5. Interestingly, RA treatment led to attenuation of H3K27me3 due to cooperate between UTX and Suz12, affecting Hox gene regulation. Further analysis, in human anencephaly cases, upregulation of 10 HOX genes was observed, along with aberrant levels of H3K27me3. Notably, HOXB4, HOXC4 and HOXD1 expression was negatively correlated with H3K27me3 levels. Conclusion Our results indicate that abnormal HOX gene expression induced by aberrant H3K27me3 levels may be a risk factor for NTDs and highlight the need for further analysis of genome-wide epigenetic modification in NTDs.
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Affiliation(s)
- Juan Yu
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Lei Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Pei Pei
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Xue Li
- School of Clinical Medical, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Jianxin Wu
- Department of Biochemistry, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Zhiyong Qiu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Juan Zhang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Ruifang Ao
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Shan Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
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Craenen K, Verslegers M, Craeghs L, Quintens R, Janssen A, Coolkens A, Baatout S, Moons L, Benotmane MA. Abnormal retinal pigment epithelium melanogenesis as a major determinant for radiation-induced congenital eye defects. Reprod Toxicol 2019; 91:59-73. [PMID: 31705956 DOI: 10.1016/j.reprotox.2019.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/30/2019] [Accepted: 10/07/2019] [Indexed: 01/26/2023]
Abstract
Recent studies highlighted a link between ionizing radiation exposure during neurulation and birth defects such as microphthalmos and anophthalmos. Because the mechanisms underlying these defects remain largely unexplored, we irradiated pregnant C57BL/6J mice (1.0 Gy, X-rays) at embryonic day (E)7.5, followed by histological and gene/protein expression analyses at defined days. Irradiation impaired embryonic development at E9 and we observed a delayed pigmentation of the retinal pigment epithelium (RPE) at E11. In addition, a reduced RNA expression and protein abundance of critical eye-development genes (e.g. Pax6 and Lhx2) was observed. Furthermore, a decreased expression of Mitf, Tyr and Tyrp1 supported the radiation-induced perturbation in RPE pigmentation. Finally, via immunostainings for proliferation (Ki67) and mitosis (phosphorylated histone 3), a decreased mitotic index was observed in the E18 retina after exposure at E7.5. Overall, we propose a plausible etiological model for radiation-induced eye-size defects, with RPE melanogenesis as a major determining factor.
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Affiliation(s)
- Kai Craenen
- Radiobiology Unit, Interdisciplinary Biosciences, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre SCK-CEN, Boeretang 200, Mol 2400, Belgium; Laboratory of Neural Circuit Development and Regeneration, Animal Physiology and Neurobiology section, Department of Biology, Faculty of Science, KU Leuven, Naamsestraat 61 bus 2464, Leuven 3000, Belgium
| | - Mieke Verslegers
- Radiobiology Unit, Interdisciplinary Biosciences, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre SCK-CEN, Boeretang 200, Mol 2400, Belgium
| | - Livine Craeghs
- Radiobiology Unit, Interdisciplinary Biosciences, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre SCK-CEN, Boeretang 200, Mol 2400, Belgium; Laboratory of Neural Circuit Development and Regeneration, Animal Physiology and Neurobiology section, Department of Biology, Faculty of Science, KU Leuven, Naamsestraat 61 bus 2464, Leuven 3000, Belgium
| | - Roel Quintens
- Radiobiology Unit, Interdisciplinary Biosciences, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre SCK-CEN, Boeretang 200, Mol 2400, Belgium
| | - Ann Janssen
- Radiobiology Unit, Interdisciplinary Biosciences, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre SCK-CEN, Boeretang 200, Mol 2400, Belgium
| | - Amelie Coolkens
- Radiobiology Unit, Interdisciplinary Biosciences, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre SCK-CEN, Boeretang 200, Mol 2400, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Interdisciplinary Biosciences, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre SCK-CEN, Boeretang 200, Mol 2400, Belgium
| | - Lieve Moons
- Laboratory of Neural Circuit Development and Regeneration, Animal Physiology and Neurobiology section, Department of Biology, Faculty of Science, KU Leuven, Naamsestraat 61 bus 2464, Leuven 3000, Belgium
| | - Mohammed Abderrafi Benotmane
- Radiobiology Unit, Interdisciplinary Biosciences, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre SCK-CEN, Boeretang 200, Mol 2400, Belgium.
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Dahiya S, Saini V, Kumar P, Kumar A. Protein-Protein interaction network analyses of human WNT proteins involved in neural development. Bioinformation 2019; 15:307-314. [PMID: 31249432 PMCID: PMC6589473 DOI: 10.6026/97320630015307] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 04/09/2019] [Indexed: 11/23/2022] Open
Abstract
WNT proteins are involved from initial of neural tissue specification to the end of cell fate determination and organ development. The
present work was carried out to understand the involvement of different WNT isoforms (WNT3a, WNT5a and WNT7b) in neural
development. A total of 718, 546 and 1004 PPIs for WNT3a, WNT5a and WNT7b respectively, were predicted by STRING database with
confidence score more than 0.400. A network carrying all the selected PPIs of targeted proteins was constructed by using Cytoscape by
assigning source node, target node and combined score as edge attribute. A total 2268 interactions of WNT3a, WNT5a and WNT7b were
predicted to be involved in multiple signaling pathways and developmental processes. 43 of 2268 PPIs were refined after analyzing role of
targeted proteins specifically in brain and neural development. WNT3a, WNT5a and WNT7a were predicted to be interacting with 18, 17
and 11 proteins, respectively, with average node degree score of 1.89, 2.12 and 1.82 respectively. The CytoHubba algorithm identified
WNT3a, WNT5a, and WNT7b as hub proteins in neural development ranked on the basis of EPC (Edge Percolated Component) score of
9.352, 9.258 and 8.387.
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Affiliation(s)
- Sween Dahiya
- Toxicology and Computational Biology Group, Centre for Bioinformatics, M. D. University, Rohtak, Haryana 124001 India
| | - Vandana Saini
- Toxicology and Computational Biology Group, Centre for Bioinformatics, M. D. University, Rohtak, Haryana 124001 India
| | - Pawan Kumar
- Toxicology and Computational Biology Group, Centre for Bioinformatics, M. D. University, Rohtak, Haryana 124001 India
| | - Ajit Kumar
- Toxicology and Computational Biology Group, Centre for Bioinformatics, M. D. University, Rohtak, Haryana 124001 India
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Ma FF, Cao DD, Ouyang S, Tang R, Liu Z, Li Y, Wu J. Hypermethylation of AKT2 gene is associated with neural-tube defects in fetus. Placenta 2016; 48:80-86. [PMID: 27871477 DOI: 10.1016/j.placenta.2016.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 09/26/2016] [Accepted: 10/17/2016] [Indexed: 01/18/2023]
Abstract
INTRODUCTION Neural-tube defects (NTDs) are common birth defects of complex etiology. Although many studies have confirmed a genetic component, the exact mechanism between DNA methylation and NTDs remains unclear. METHODS In this work, we investigated the alteration of methylation from placental tissues obtained from 152 normal infants or with NTDs in 130 children with neural-tube defects. Genome-wide changes in DNA methylation were measured using the NimbleGen microarray. The expression levels of 12 genes were also determined, and two genes (AKT2 and CDC25C) showed low expression in NTDs by quantitative real-time PCR analysis. Then, the methyhlated region of AKT2 promoter sequences were confirmed by massARRAY. RESULTS A total of 150 differentially methylated regions (81 low methylated regions and 69 high methylated regions) were selected by microarray. The expression levels of AKT2 and CDC25C showed lower expression in NTDs. And the percentage of methyhlated region of AKT2 promoter were increased in NTDs. CONCLUSIONS DNA mythelation was one of the possible epigenetic variations correlated with the occurrence of NTDs, and AKT2 may be a candidate gene for NTDs.
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Affiliation(s)
- Fei Fei Ma
- Dept. of Biochemistry, Capital Institute of Pediatrics, Beijing 100020, China
| | - Ding Ding Cao
- Dept. of Biochemistry, Capital Institute of Pediatrics-Peking University Teaching Hospital, Beijing 100020, China
| | - Shengrong Ouyang
- Dept. of Biochemistry, Capital Institute of Pediatrics, Beijing 100020, China
| | - Renqiao Tang
- Graduate School, Chinese Academy of Medical Science, Beijing 100730, China
| | - Zhuo Liu
- Dept. of Biochemistry, Capital Institute of Pediatrics, Beijing 100020, China
| | - Yuanyuan Li
- Dept. of Biochemistry, Capital Institute of Pediatrics, Beijing 100020, China
| | - Jianxin Wu
- Dept. of Biochemistry, Capital Institute of Pediatrics, Beijing 100020, China; Dept. of Biochemistry, Capital Institute of Pediatrics-Peking University Teaching Hospital, Beijing 100020, China.
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