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Morin A, Chu C, Pavlidis P. Identifying Reproducible Transcription Regulator Coexpression Patterns with Single Cell Transcriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580581. [PMID: 38559016 PMCID: PMC10979919 DOI: 10.1101/2024.02.15.580581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The proliferation of single cell transcriptomics has potentiated our ability to unveil patterns that reflect dynamic cellular processes, rather than cell type compositional effects that emerge from bulk tissue samples. In this study, we leverage a broad collection of single cell RNA-seq data to identify the gene partners whose expression is most coordinated with each human and mouse transcription regulator (TR). We assembled 120 human and 103 mouse scRNA-seq datasets from the literature (>28 million cells), constructing a single cell coexpression network for each. We aimed to understand the consistency of TR coexpression profiles across a broad sampling of biological contexts, rather than examine the preservation of context-specific signals. Our workflow therefore explicitly prioritizes the patterns that are most reproducible across cell types. Towards this goal, we characterize the similarity of each TR's coexpression within and across species. We create single cell coexpression rankings for each TR, demonstrating that this aggregated information recovers literature curated targets on par with ChIP-seq data. We then combine the coexpression and ChIP-seq information to identify candidate regulatory interactions supported across methods and species. Finally, we highlight interactions for the important neural TR ASCL1 to demonstrate how our compiled information can be adopted for community use.
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Affiliation(s)
- Alexander Morin
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | - Chingpan Chu
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
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Zhang J, Yang L, Sun Y, Zhang L, Wang Y, Liu M, Li X, Liang Y, Zhao H, Liu Z, Qiu Z, Zhang T, Xie J. Up-regulation of miR-10a-5p expression inhibits the proliferation and differentiation of neural stem cells by targeting Chl1. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 38841745 DOI: 10.3724/abbs.2024078] [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: 06/07/2024] Open
Abstract
Neural tube defects (NTDs) are characterized by the failure of neural tube closure during embryogenesis and are considered the most common and severe central nervous system anomalies during early development. Recent microRNA (miRNA) expression profiling studies have revealed that the dysregulation of several miRNAs plays an important role in retinoic acid (RA)-induced NTDs. However, the molecular functions of these miRNAs in NTDs remain largely unidentified. Here, we show that miR-10a-5p is significantly upregulated in RA-induced NTDs and results in reduced cell growth due to cell cycle arrest and dysregulation of cell differentiation. Moreover, the cell adhesion molecule L1-like ( Chl1) is identified as a direct target of miR-10a-5p in neural stem cells (NSCs) in vitro, and its expression is reduced in RA-induced NTDs. siRNA-mediated knockdown of intracellular Chl1 affects cell proliferation and differentiation similar to those of miR-10a-5p overexpression, which further leads to the inhibition of the expressions of downstream ERK1/2 MAPK signaling pathway proteins. These cellular responses are abrogated by either increased expression of the direct target of miR-10a-5p ( Chl1) or an ERK agonist such as honokiol. Overall, our study demonstrates that miR-10a-5p plays a major role in the process of NSC growth and differentiation by directly targeting Chl1, which in turn induces the downregulation of the ERK1/2 cascade, suggesting that miR-10a-5p and Chl1 are critical for NTD formation in the development of embryos.
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Affiliation(s)
- Juan Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
- Department of Cell Biology and Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan 030001, China
| | - Lihong Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Yuqing Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Li Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Yufei Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Ming Liu
- Department of Cell Biology and Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan 030001, China
| | - Xiujuan Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Yuxiang Liang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Hong Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Zhizhen Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Zhiyong Qiu
- 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, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
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Aranda S, Muntané G, Vilella E. Coexpression network analysis of the adult brain sheds light on the pathogenic mechanism of DDR1 in schizophrenia and bipolar disorder. Transl Psychiatry 2024; 14:112. [PMID: 38395959 PMCID: PMC10891045 DOI: 10.1038/s41398-024-02823-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
DDR1 has been linked to schizophrenia (SCZ) and bipolar disorder (BD) in association studies. DDR1 encodes 58 distinct transcripts, which can be translated into five isoforms (DDR1a-e) and are expressed in the brain. However, the transcripts expressed in each brain cell type, their functions and their involvement in SCZ and BD remain unknown. Here, to infer the processes in which DDR1 transcripts are involved, we used transcriptomic data from the human brain dorsolateral prefrontal cortex of healthy controls (N = 936) and performed weighted gene coexpression network analysis followed by enrichment analyses. Then, to explore the involvement of DDR1 transcripts in SCZ (N = 563) and BD (N = 222), we studied the association of coexpression modules with disease and performed differential expression and transcript significance analyses. Some DDR1 transcripts were distributed across five coexpression modules identified in healthy controls (MHC). MHC1 and MHC2 were enriched in the cell cycle and proliferation of astrocytes and OPCs; MHC3 and MHC4 were enriched in oligodendrocyte differentiation and myelination; and MHC5 was enriched in neurons and synaptic transmission. Most of the DDR1 transcripts associated with SCZ and BD pertained to MHC1 and MHC2. Altogether, our results suggest that DDR1 expression might be altered in SCZ and BD via the proliferation of astrocytes and OPCs, suggesting that these processes are relevant in psychiatric disorders.
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Affiliation(s)
- Selena Aranda
- Institut d'Investigació Sanitària Pere Virgili-CERCA, Reus, Spain
- Hospital Universitari Institut Pere Mata, Reus, Spain
- Universitat Rovira i Virgili, Reus, Spain
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM)-Instituto de Salud Carlos III, Madrid, Spain
| | - Gerard Muntané
- Institut d'Investigació Sanitària Pere Virgili-CERCA, Reus, Spain
- Hospital Universitari Institut Pere Mata, Reus, Spain
- Universitat Rovira i Virgili, Reus, Spain
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM)-Instituto de Salud Carlos III, Madrid, Spain
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Elisabet Vilella
- Institut d'Investigació Sanitària Pere Virgili-CERCA, Reus, Spain.
- Hospital Universitari Institut Pere Mata, Reus, Spain.
- Universitat Rovira i Virgili, Reus, Spain.
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM)-Instituto de Salud Carlos III, Madrid, Spain.
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Gharbi T, Liu C, Khan H, Zhang Z, Yang GY, Tang Y. Hypoxic Preconditioned Neural Stem Cell-Derived Extracellular Vesicles Contain Distinct Protein Cargo from Their Normal Counterparts. Curr Issues Mol Biol 2023; 45:1982-1997. [PMID: 36975497 PMCID: PMC10047917 DOI: 10.3390/cimb45030127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Hypoxic preconditioning has been demonstrated to increase the resistance of neural stem cells (NSCs) to hypoxic conditions, as well as to improve their capacity for differentiation and neurogenesis. Extracellular vesicles (EVs) have recently emerged as critical mediators of cell–cell communication, but their role in this hypoxic conditioning is presently unknown. Here, we demonstrated that three hours of hypoxic preconditioning triggers significant neural stem cell EV release. Proteomic profiling of EVs from normal and hypoxic preconditioned neural stem cells identified 20 proteins that were upregulated and 22 proteins that were downregulated after hypoxic preconditioning. We also found an upregulation of some of these proteins by qPCR, thus indicating differences also at the transcript level within the EVs. Among the upregulated proteins are CNP, Cyfip1, CASK, and TUBB5, which are well known to exhibit significant beneficial effects on neural stem cells. Thus, our results not only show a significant difference of protein cargo in EVs consequent to hypoxic exposure, but identify several candidate proteins that might play a pivotal role in the cell-to-cell mediated communication underlying neuronal differentiation, protection, maturation, and survival following exposure to hypoxic conditions.
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Zhang L, Lin S, Huang K, Chen A, Li N, Shen S, Zheng Z, Shi X, Sun J, Kong J, Chen M. Effects of HAR1 on cognitive function in mice and the regulatory network of HAR1 determined by RNA sequencing and applied bioinformatics analysis. Front Genet 2023; 14:947144. [PMID: 36968607 PMCID: PMC10030831 DOI: 10.3389/fgene.2023.947144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
Background: HAR1 is a 118-bp segment that lies in a pair of novel non-coding RNA genes. It shows a dramatic accelerated change with an estimated 18 substitutions in the human lineage since the human-chimpanzee ancestor, compared with the expected 0.27 substitutions based on the slow rate of change in this region in other amniotes. Mutations of HAR1 lead to a different HAR1 secondary structure in humans compared to that in chimpanzees. Methods: We cloned HAR1 into the EF-1α promoter vector to generate transgenic mice. Morris water maze tests and step-down passive avoidance tests were conducted to observe the changes in memory and cognitive abilities of mice. RNA-seq analysis was performed to identify differentially expressed genes (DEGs) between the experimental and control groups. Systematic bioinformatics analysis was used to confirm the pathways and functions that the DEGs were involved in. Results: Memory and cognitive abilities of the transgenic mice were significantly improved. The results of Gene Ontology (GO) analysis showed that Neuron differentiation, Dentate gyrus development, Nervous system development, Cerebral cortex neuron differentiation, Cerebral cortex development, Cerebral cortex development and Neurogenesis are all significant GO terms related to brain development. The DEGs enriched in these terms included Lhx2, Emx2, Foxg1, Nr2e1 and Emx1. All these genes play an important role in regulating the functioning of Cajal-Retzius cells (CRs). The DEGs were also enriched in glutamatergic synapses, synapses, memory, and the positive regulation of long-term synaptic potentiation. In addition, "cellular response to calcium ions" exhibited the second highest rich factor in the GO analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the DEGs showed that the neuroactive ligand-receptor interaction pathway was the most significantly enriched pathway, and DEGs also notably enriched in neuroactive ligand-receptor interaction, axon guidance, and cholinergic synapses. Conclusion: HAR1 overexpression led to improvements in memory and cognitive abilities of the transgenic mice. The possible mechanism for this was that the long non-coding RNA (lncRNA) HAR1A affected brain development by regulating the function of CRs. Moreover, HAR1A may be involved in ligand-receptor interaction, axon guidance, and synapse formation, all of which are important in brain development and evolution. Furthermore, cellular response to calcium may play an important role in those processes.
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Affiliation(s)
- Luting Zhang
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guang-Dong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shengmou Lin
- Department of Obstetrics and Gynecology, The University of Hong Kong—Shenzhen Hospital, Shenzhen, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Kailing Huang
- Guangzhou Mendel Genomics and Medical Technology Co., Ltd., Guangzhou, China
| | - Allen Chen
- Guangzhou Mendel Genomics and Medical Technology Co., Ltd., Guangzhou, China
| | - Nan Li
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guang-Dong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | | | - Zhouxia Zheng
- Guangzhou Mendel Genomics and Medical Technology Co., Ltd., Guangzhou, China
| | - Xiaoshun Shi
- Guangzhou Mendel Genomics and Medical Technology Co., Ltd., Guangzhou, China
| | - Jimei Sun
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guang-Dong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jingyin Kong
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guang-Dong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Min Chen
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guang-Dong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Min Chen,
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Yang J, Xu J, Zhang L, Li Y, Chen M. Identifying key m 6A-methylated lncRNAs and genes associated with neural tube defects via integrative MeRIP and RNA sequencing analyses. Front Genet 2022; 13:974357. [PMID: 36482889 PMCID: PMC9722945 DOI: 10.3389/fgene.2022.974357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/04/2022] [Indexed: 07/23/2023] Open
Abstract
Objective: N6-methyladenosine (m6A) is a common post-transcriptional modification of messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs). However, m6A-modified lncRNAs are still largely unexplored. This study aimed to investigate differentially m6A-modified lncRNAs and genes involved in neural tube defect (NTD) development. Methods: Pregnant Kunming mice (9-10 weeks of age) were treated with retinoic acid to construct NTD models. m6A levels and methyltransferase-like 3 (METTL3) expression were evaluated in brain tissues of the NTD models. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) were performed on the NovaSeq platform and Illumina HiSeq 2,500 platform, respectively. Differentially m6A-methylated differentially expressed lncRNAs (DElncRNAs) and differentially expressed genes (DEGs) were identified, followed by GO biological process and KEGG pathway functional enrichment analyses. Expression levels of several DElncRNAs and DEGs were evaluated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) for validation. Results: m6A levels and METTL3 expression levels were significantly lower in the brain tissues of the NTD mouse model than in controls. By integrating MeRIP-seq and RNA-seq data, 13 differentially m6A-methylated DElncRNAs and 170 differentially m6A-methylated DEGs were identified. They were significantly enriched in the Hippo signaling pathway and mannose-type O-glycan biosynthesis. The qRT-PCR results confirmed the decreased expression levels of lncRNAs, such as Mir100hg, Gm19265, Gm10544, and Malat1, and genes, such as Zfp236, Erc2, and Hmg20a, in the NTD group. Conclusion: METTL3-mediated m6A modifications may be involved in NTD development. In particular, decreased expression levels of Mir100hg, Gm19265, Gm10544, Malat1, Zfp236, Erc2, and Hmg20a may contribute to the development of NTD.
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Affiliation(s)
- Jing Yang
- Department of Obstetrics, Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jing Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Luting Zhang
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yingting Li
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Min Chen
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
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Bao N, Liu J, Peng Z, Zhang R, Ni R, Li R, Wu J, Liu Z, Pan B. Identification of circRNA-miRNA-mRNA networks to explore the molecular mechanism and immune regulation of postoperative neurocognitive disorder. Aging (Albany NY) 2022; 14:8374-8393. [PMID: 36279395 PMCID: PMC9648807 DOI: 10.18632/aging.204348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/14/2022] [Indexed: 11/25/2022]
Abstract
Postoperative neurocognitive disorder (PND) is a common complication in older patients. However, its pathogenesis has still remained elusive. Recent studies have shown that circular RNA (circRNA) plays an important role in the development of neurodegenerative diseases, such as PND after surgery. CircRNA, as a competitive endogenous RNA (ceRNA), mainly acts as a molecular sponge for miRNA to "adsorb" microRNA (miRNA) and to reduce the inhibitory effects of miRNAs on target mRNA. The sequencing data of circRNA were obtained from the Gene Expression Omnibus (GEO) database. By bioinformatic methods, circAtlas, miRDB, miRTarBase and miRwalk databases were applied to construct circRNA-miRNA-mRNA networks and screen differentially expressed mRNAs. To improve the accuracy of the data, we randomly divided aging mice into control (non-PND group) and PND groups, and used high-throughput sequencing to analyze their brain hippocampal tissue for analysis. Three key genes were cross-detected in the data of both groups, which were Unc13c, Tbx20 and St8sia2 (as hub genes), providing new targets for PND treatment. According to the results of the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, immune cell infiltration analysis, gene set enrichment analysis (GSEA), Connectivity Map (CMap) analysis, quantitative real-time polymerase chain reaction (qRT-PCR), the genes that were not related to the central nervous system were removed, and finally, mmu_circ_0000331/miR-1224-3p/Unc13c and mmu_circ_0000406/miR-24-3p/St8sia2 ceRNA networks were identified. In addition, the CMap method was used to select the top 4 active compounds with the largest negative correlation absolute values, including cimaterol, Rucaparib, FG-7142, and Hydrocortisone.
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Affiliation(s)
- Ning Bao
- Department of Anesthesiology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
- Department of Anesthesiology, Shenyang Women’s and Children’s Hospital, Shenyang, Liaoning, China
| | - Jiping Liu
- Department of Anesthesiology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Zhe Peng
- Department of Anesthesiology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Rong Zhang
- Department of Anesthesiology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Rufei Ni
- Department of Anesthesiology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Runzuan Li
- Department of Anesthesiology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Jian Wu
- Department of Anesthesiology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Zhenhua Liu
- Department of Anesthesiology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Botao Pan
- Department of Anesthesiology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
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Su T, Guan Q, Cheng H, Zhu Z, Jiang C, Guo P, Tai Y, Sun H, Wang M, Wei W, Wang Q. Functions of G protein-coupled receptor 56 in health and disease. Acta Physiol (Oxf) 2022; 236:e13866. [PMID: 35959520 DOI: 10.1111/apha.13866] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 01/29/2023]
Abstract
Human G protein-coupled receptor 56 (GPR56) is encoded by gene ADGRG1 from chromosome 16q21 and is homologously encoded in mice, at chromosome 8. Both 687 and 693 splice forms are present in humans and mice. GPR56 has a 381 amino acid-long N-terminal extracellular segment and a GPCR proteolysis site upstream from the first transmembrane domain. GPR56 is mainly expressed in the heart, brain, thyroid, platelets, and peripheral blood mononuclear cells. Accumulating evidence indicates that GPR56 promotes the formation of myelin sheaths and the development of oligodendrocytes in the cerebral cortex of the central nervous system. Moreover, GPR56 contributes to the development and differentiation of hematopoietic stem cells, induces adipogenesis, and regulates the function of immune cells. The lack of GPR56 leads to nervous system dysfunction, platelet disorders, and infertility. Abnormal expression of GPR56 is related to the malignant transformation and tumor metastasis of several cancers including melanoma, neuroglioma, and gastrointestinal cancer. Metabolic disorders and cardiovascular diseases are also associated with dysregulation of GPR56 expression, and GPR56 is involved in the pharmacological resistance to some antidepressant and cancer drug treatments. In this review, the molecular structure, expression profile, and signal transduction of GPR56 are introduced, and physiological and pathological functions of GRP56 are comprehensively summarized. Attributing to its significant biological functions and its long N-terminal extracellular region that interacts with multiple ligands, GPR56 is becoming an attractive therapeutic target in treating neurological and hematopoietic diseases.
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Affiliation(s)
- Tiantian Su
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Centre of Anti-inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, Anhui Province, China
| | - Qiuyun Guan
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Centre of Anti-inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, Anhui Province, China
| | - Huijuan Cheng
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Centre of Anti-inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, Anhui Province, China
| | - Zhenduo Zhu
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Centre of Anti-inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, Anhui Province, China
| | - Chunru Jiang
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Centre of Anti-inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, Anhui Province, China
| | - Paipai Guo
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Centre of Anti-inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, Anhui Province, China
| | - Yu Tai
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Centre of Anti-inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, Anhui Province, China
| | - Hanfei Sun
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Centre of Anti-inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, Anhui Province, China
| | - Manman Wang
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Centre of Anti-inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, Anhui Province, China
| | - Wei Wei
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Centre of Anti-inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, Anhui Province, China
| | - Qingtong Wang
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Centre of Anti-inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, Anhui Province, China
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Martínez Traverso IM, Steimle JD, Zhao X, Wang J, Martin JF. LATS1/2 control TGFB-directed epithelial-to-mesenchymal transition in the murine dorsal cranial neuroepithelium through YAP regulation. Development 2022; 149:dev200860. [PMID: 36125128 PMCID: PMC9587805 DOI: 10.1242/dev.200860] [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: 04/22/2022] [Accepted: 08/12/2022] [Indexed: 11/20/2022]
Abstract
Hippo signaling, an evolutionarily conserved kinase cascade involved in organ size control, plays key roles in various tissue developmental processes, but its role in craniofacial development remains poorly understood. Using the transgenic Wnt1-Cre2 driver, we inactivated the Hippo signaling components Lats1 and Lats2 in the cranial neuroepithelium of mouse embryos and found that the double conditional knockout (DCKO) of Lats1/2 resulted in neural tube and craniofacial defects. Lats1/2 DCKO mutant embryos had microcephaly with delayed and defective neural tube closure. Furthermore, neuroepithelial cell shape and architecture were disrupted within the cranial neural tube in Lats1/2 DCKO mutants. RNA sequencing of embryonic neural tubes revealed increased TGFB signaling in Lats1/2 DCKO mutants. Moreover, markers of epithelial-to-mesenchymal transition (EMT) were upregulated in the cranial neural tube. Inactivation of Hippo signaling downstream effectors, Yap and Taz, suppressed neuroepithelial defects, aberrant EMT and TGFB upregulation in Lats1/2 DCKO embryos, indicating that LATS1/2 function via YAP and TAZ. Our findings reveal important roles for Hippo signaling in modulating TGFB signaling during neural crest EMT.
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Affiliation(s)
- Idaliz M. Martínez Traverso
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
- Interdepartmental Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey D. Steimle
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiaolei Zhao
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jun Wang
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center and The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - James F. Martin
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
- Interdepartmental Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Cardiomyocyte Renewal Laboratory, Texas Heart Institute, Houston, TX 77030, USA
- Center for Organ Repair and Renewal, Baylor College of Medicine, Houston, TX 77030 , USA
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10
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Zhao D, Liu Y, Jia S, He Y, Wei X, Liu D, Ma W, Luo W, Gu H, Yuan Z. Influence of maternal obesity on the multi-omics profiles of the maternal body, gestational tissue, and offspring. Biomed Pharmacother 2022; 151:113103. [PMID: 35605294 DOI: 10.1016/j.biopha.2022.113103] [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: 03/28/2022] [Revised: 04/25/2022] [Accepted: 05/10/2022] [Indexed: 11/28/2022] Open
Abstract
Epidemiological studies show that obesity during pregnancy affects more than half of the pregnancies in the developed countries and is associated with obstetric problems and poor outcomes. Obesity tends to increase the incidence of complications. Furthermore, the resulting offspring are also adversely affected. However, the molecular mechanisms of obesity leading to poor pregnancy outcomes remain unclear. Omics methods are used for genetic diagnosis and marker discovery. The aim of this review was to summarize the maternal and fetal pathophysiological alterations induced by gestational obesity,identified using multi-omics detection techniques, and to generalize the biological functions and potential mechanisms of the differentially expressed molecules.
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Affiliation(s)
- Duan Zhao
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang 110004, China.
| | - Yusi Liu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang 110004, China.
| | - Shanshan Jia
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang 110004, China.
| | - Yiwen He
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang 110004, China.
| | - Xiaowei Wei
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang 110004, China.
| | - Dan Liu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang 110004, China.
| | - Wei Ma
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang 110004, China.
| | - Wenting Luo
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang 110004, China.
| | - Hui Gu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang 110004, China.
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang 110004, China.
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11
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Meng X, Wang W, Wang X. MicroRNA-34a and microRNA-146a target CELF3 and suppress the osteogenic differentiation of periodontal ligament stem cells under cyclic mechanical stretch. J Dent Sci 2021; 17:1281-1291. [PMID: 35784124 PMCID: PMC9236897 DOI: 10.1016/j.jds.2021.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/17/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
| | | | - Xueling Wang
- Corresponding author. Department of Stomatology, Aerospace Center Hospital, 15 Yuquan Road, Haidian District, Beijing 100049, PR China.
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12
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Tian Y, Zhan Y, Jiang Q, Lu W, Li X. Expression and function of PDGF-C in development and stem cells. Open Biol 2021; 11:210268. [PMID: 34847773 PMCID: PMC8633783 DOI: 10.1098/rsob.210268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Platelet-derived growth factor C (PDGF-C) is a relatively new member of the PDGF family, discovered nearly 20 years after the finding of platelet-derived growth factor A (PDGF-A) and platelet-derived growth factor B (PDGF-B). PDGF-C is generally expressed in most organs and cell types. Studies from the past 20 years have demonstrated critical roles of PDGF-C in numerous biological, physiological and pathological processes, such as development, angiogenesis, tumour growth, tissue remodelling, wound healing, atherosclerosis, fibrosis, stem/progenitor cell regulation and metabolism. Understanding PDGF-C expression and activities thus will be of great importance to various research disciplines. In this review, however, we mainly discuss the expression and functions of PDGF-C and its receptors in development and stem cells.
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Affiliation(s)
- Yi Tian
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, People’s Republic of China
| | - Ying Zhan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, People’s Republic of China
| | - Qin Jiang
- Ophthalmic Department, Affiliated Eye Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Weisi Lu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, People’s Republic of China
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, People’s Republic of China
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13
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Aberrant Gcm1 expression mediates Wnt/β-catenin pathway activation in folate deficiency involved in neural tube defects. Cell Death Dis 2021; 12:234. [PMID: 33664222 PMCID: PMC7933360 DOI: 10.1038/s41419-020-03313-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 02/07/2023]
Abstract
Wnt signaling plays a major role in early neural development. An aberrant activation in Wnt/β-catenin pathway causes defective anteroposterior patterning, which results in neural tube closure defects (NTDs). Changes in folate metabolism may participate in early embryo fate determination. We have identified that folate deficiency activated Wnt/β-catenin pathway by upregulating a chorion-specific transcription factor Gcm1. Specifically, folate deficiency promoted formation of the Gcm1/β-catenin/T-cell factor (TCF4) complex formation to regulate the Wnt targeted gene transactivation through Wnt-responsive elements. Moreover, the transcription factor Nanog upregulated Gcm1 transcription in mESCs under folate deficiency. Lastly, in NTDs mouse models and low-folate NTDs human brain samples, Gcm1 and Wnt/β-catenin targeted genes related to neural tube closure are specifically overexpressed. These results indicated that low-folate level promoted Wnt/β-catenin signaling via activating Gcm1, and thus leaded into aberrant vertebrate neural development.
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14
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Jia S, Zhang L, Zhang K, Wang L, Khan A, Zhang J, Sun Y, Wang Y, Song M, Lyu Y, Li M, Lu X, Niu B, Liu Z, Xie J. Nkx2.1 downregulation is involved in brain abnormality induced by excess retinoic acid. Acta Biochim Biophys Sin (Shanghai) 2020; 52:683-690. [PMID: 32445470 DOI: 10.1093/abbs/gmaa037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 03/12/2020] [Accepted: 03/29/2020] [Indexed: 11/13/2022] Open
Abstract
Abnormal development of central nervous system (CNS) caused by neural tube defects is not only a major contributor in the prevalence of stillbirths and neonatal deaths but also causes lifelong physical disability in surviving infants. Due to insufficient known investigated causes, CNS developmental abnormality has brought sever burden on health around the world. From previous results of high throughput transcriptome sequencing, we selected transcription factor Nkx2.1 as a candidate to investigate its role on brain abnormalities induced by excessive retinoic acid. The result of in situ hybridization showed that Nkx2.1 was mainly expressed in mouse brain. After the Nkx2.1 gene was silenced, retarded proliferation and accelerated apoptosis were found in mouse Neuro-2a (N2a) cells. Furthermore, our results indicated that the main components of sonic hedgehog (Shh) signaling pathway were affected in Nkx2.1-silenced cells, implying that Nkx2.1 plays an important role in the development of mouse brain by regulating Shh signaling pathway.
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Affiliation(s)
- Sansan Jia
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan 030001, China
- State Key Laboratory of Military Stomatology, Department of Oral & Maxillofacial Surgery, The Fourth Military Medical University, Xi’an 710032, China
| | - Li Zhang
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan 030001, China
| | - Kaili Zhang
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan 030001, China
| | - Lei Wang
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan 030001, China
| | - Ajab Khan
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan 030001, China
| | - Juan Zhang
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan 030001, China
| | - Yuqing Sun
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan 030001, China
| | - Yufei Wang
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan 030001, China
| | - Meiyan Song
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan 030001, China
| | - Yi Lyu
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan 030001, China
| | - Meining Li
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan 030001, China
| | - Xin Lu
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan 030001, China
| | - Bo Niu
- Department of Biotechnology, Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Zhizhen Liu
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan 030001, China
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan 030001, China
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15
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Cheng X, Pei P, Yu J, Zhang Q, Li D, Xie X, Wu J, Wang S, Zhang T. F-box protein FBXO30 mediates retinoic acid receptor γ ubiquitination and regulates BMP signaling in neural tube defects. Cell Death Dis 2019; 10:551. [PMID: 31320612 PMCID: PMC6639381 DOI: 10.1038/s41419-019-1783-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/11/2019] [Accepted: 06/24/2019] [Indexed: 02/06/2023]
Abstract
Retinoic acid (RA), an active derivative of vitamin A, is critical for the neural system development. During the neural development, the RA/RA receptor (RAR) pathway suppresses BMP signaling-mediated proliferation and differentiation of neural progenitor cells. However, how the stability of RAR is regulated during neural system development and how BMP pathway genes expression in neural tissue from human fetuses affected with neural tube defects (NTDs) remain elusive. Here, we report that FBXO30 acts as an E3 ubiquitin ligase and targets RARγ for ubiquitination and proteasomal degradation. In this way, FBXO30 positively regulates BMP signaling in mammalian cells. Moreover, RA treatment leads to suppression of BMP signaling by reducing the level of FBXO30 in mammalian cells and in mouse embryos with NTDs. In samples from human NTDs with high levels of retinol, downregulation of BMP target genes was observed, along with aberrant FBXO30 levels. Collectively, our results demonstrate that RARγ levels are controlled by FBXO30-mediated ubiquitination and that FBXO30 is a key regulator of BMP signaling. Furthermore, we suggest a novel mechanism by which high-retinol levels affect the level of FBXO30, which antagonizes BMP signaling during early stage development.
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Affiliation(s)
- Xiyue Cheng
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China
- Graduate School of Peking Union Medical College, 100730, Beijing, China
| | - Pei Pei
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China
| | - Juan Yu
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, 030001, Taiyuan, Shanxi, China
| | - Qin Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China
| | - Dan Li
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China
| | - Xiaolu Xie
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China
| | - Jianxin Wu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China
| | - Shan Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China.
- Institute of Basic Medical Sciences, Chinese Academy of Medical Science, 100730, Beijing, China.
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, 100020, Beijing, China.
- Graduate School of Peking Union Medical College, 100730, Beijing, China.
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16
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Zhang J, Yang L, Yu J, Yang Q, Mu J, Xie J. Alteration of the microRNA expression profile and identification of miRNA/mRNA negative regulation pairs in neural tube defects. Acta Biochim Biophys Sin (Shanghai) 2019; 51:761-765. [PMID: 31169880 DOI: 10.1093/abbs/gmz050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Indexed: 11/14/2022] Open
Affiliation(s)
- Juan Zhang
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, China
| | - Lihong Yang
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, China
| | - Juan Yu
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, China
| | - Qiaoyan Yang
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, China
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, China
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17
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Vilella E, Gas C, Garcia-Ruiz B, Rivera FJ. Expression of DDR1 in the CNS and in myelinating oligodendrocytes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118483. [PMID: 31108116 DOI: 10.1016/j.bbamcr.2019.04.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/15/2022]
Abstract
Discoidin domain receptor 1 (DDR1) is a tyrosine kinase receptor that is activated by fibrillar collagens. Here, we review the expression and role of DDR1 in the central nervous system (CNS). In a murine model, DDR1 is expressed in oligodendrocytes in the developing brain and during remyelination. In human adult brain tissue, DDR1 is detected in a similar pattern as other classical myelin proteins such as myelin basic protein (MBP). Up to 50 transcripts of DDR1 have been detected in human tissues, of which 5 isoforms have been identified. In the human brain, all 5 isoforms are detectable, but DDR1b is the most highly expressed, and DDR1c is coexpressed with myelin genes. DDR1 sequence variants have been associated with psychiatric disorders, and upregulation of this gene occurs in gliomas. Moreover, mutations in DDR1 have been found in tumors of Schwann cells, which are the myelinating cells of the peripheral nervous system. All these data suggest that DDR1 plays a role in myelination and is relevant to neuropsychiatric diseases.
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Affiliation(s)
- Elisabet Vilella
- Hospital Universitari Institut Pere Mata, Ctra de l'Institut Pere Mata, s/n, 43206 Reus, Spain; Institut d'Investigació Sanitària Pere Virgili, Avda. Josep Laporte, 1, 43204 Reus, Spain; Universitat Rovira i Virgili, C/ Sant Llorenç, 21, 43201 Reus, Spain; Centro de investigaciòn biomedical en red en Salud Mental (CIBERSAM), Spain.
| | - Cinta Gas
- Institut d'Investigació Sanitària Pere Virgili, Avda. Josep Laporte, 1, 43204 Reus, Spain; Universitat Rovira i Virgili, C/ Sant Llorenç, 21, 43201 Reus, Spain.
| | - Beatriz Garcia-Ruiz
- Hospital Universitari Institut Pere Mata, Ctra de l'Institut Pere Mata, s/n, 43206 Reus, Spain; Universitat Rovira i Virgili, C/ Sant Llorenç, 21, 43201 Reus, Spain.
| | - Francisco J Rivera
- Laboratory of Stem Cells and Neuroregeneration, Institute of Anatomy, Histology and Pathology, Faculty of Medicine, Universidad Austral de Chile, 5090000 Valdivia, Chile; Center for Interdisciplinary Studies on the Nervous System (CISNe), Universidad Austral de Chile, 5090000 Valdivia, Chile; Institute of Molecular Regenerative Medicine, Paracelsus Medical University, 5020 Salzburg, Austria; Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, 5020 Salzburg, Austria.
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18
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Santander N, Lizama C, Murgas L, Contreras S, Martin AJM, Molina P, Quiroz A, Rivera K, Salas-Pérez F, Godoy A, Rigotti A, Busso D. Transcriptional profiling of embryos lacking the lipoprotein receptor SR-B1 reveals a regulatory circuit governing a neurodevelopmental or metabolic decision during neural tube closure. BMC Genomics 2018; 19:731. [PMID: 30290792 PMCID: PMC6173885 DOI: 10.1186/s12864-018-5110-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/24/2018] [Indexed: 12/20/2022] Open
Abstract
Background The high-density lipoprotein receptor SR-B1 mediates cellular uptake of several lipid species, including cholesterol and vitamin E. During early mouse development, SR-B1 is located in the maternal-fetal interface, where it facilitates vitamin E transport towards the embryo. Consequently, mouse embryos lacking SR-B1 are vitamin E-deficient, and around half of them fail to close the neural tube and show cephalic neural tube defects (NTD). Here, we used transcriptomic profiling to identify the molecular determinants of this phenotypic difference between SR-B1 deficient embryos with normal morphology or with NTD. Results We used RNA-Seq to compare the transcriptomic profile of three groups of embryos retrieved from SR-B1 heterozygous intercrosses: wild-type E9.5 embryos (WT), embryos lacking SR-B1 that are morphologically normal, without NTD (KO-N) and SR-B1 deficient embryos with this defect (KO-NTD). We identified over 1000 differentially expressed genes: down-regulated genes in KO-NTD embryos were enriched for functions associated to neural development, while up-regulated genes in KO-NTD embryos were enriched for functions related to lipid metabolism. Feeding pregnant dams a vitamin E-enriched diet, which prevents NTD in SR-B1 KO embryos, resulted in mRNA levels for those differentially expressed genes that were more similar to KO-N than to KO-NTD embryos. We used gene regulatory network analysis to identify putative transcriptional regulators driving the different embryonic expression profiles, and identified a regulatory circuit controlled by the androgen receptor that may contribute to this dichotomous expression profile in SR-B1 embryos. Supporting this possibility, the expression level of the androgen receptor correlated strongly with the expression of several genes involved in neural development and lipid metabolism. Conclusions Our analysis shows that normal and defective embryos lacking SR-B1 have divergent expression profiles, explained by a defined set of transcription factors that may explain their divergent phenotype. We propose that distinct expression profiles may be relevant during early development to support embryonic nutrition and neural tube closure. Electronic supplementary material The online version of this article (10.1186/s12864-018-5110-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicolás Santander
- Department of Nutrition, Diabetes, and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Marcoleta 367, 83300024, Santiago, CP, Chile
| | - Carlos Lizama
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Leandro Murgas
- Network Biology Laboratory, Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Sebastián Contreras
- Network Biology Laboratory, Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Alberto J M Martin
- Network Biology Laboratory, Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Paz Molina
- Department of Nutrition, Diabetes, and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Marcoleta 367, 83300024, Santiago, CP, Chile
| | - Alonso Quiroz
- Department of Nutrition, Diabetes, and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Marcoleta 367, 83300024, Santiago, CP, Chile
| | - Katherine Rivera
- Department of Nutrition, Diabetes, and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Marcoleta 367, 83300024, Santiago, CP, Chile
| | - Francisca Salas-Pérez
- Department of Nutrition, Diabetes, and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Marcoleta 367, 83300024, Santiago, CP, Chile
| | - Alejandro Godoy
- Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.,Department of Urology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Attilio Rigotti
- Department of Nutrition, Diabetes, and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Marcoleta 367, 83300024, Santiago, CP, Chile.,Center of Molecular Nutrition and Chronic Diseases, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Dolores Busso
- Department of Nutrition, Diabetes, and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Marcoleta 367, 83300024, Santiago, CP, Chile.
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