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Jiao L, Junfang Z, Yanna L, Caixia J, Chen Z, Song J, Jie X, Xiaoli Y, Xin G, Libo X, Feng W, lixia L, Chunli X, Lei X. miR-153 promotes neural differentiation by activating the cell adhesion/Ca 2+ signaling pathway and targeting ion channel activity in HT-22 cells by bioinformatic analysis. Heliyon 2024; 10:e30204. [PMID: 38694121 PMCID: PMC11061740 DOI: 10.1016/j.heliyon.2024.e30204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024] Open
Abstract
MicroRNAs have been studied extensively in neurodegenerative diseases. In a previous study, miR-153 promoted neural differentiation and projection formation in mouse hippocampal HT-22 cells. However, the pathways and molecular mechanism underlying miR-153-induced neural differentiation remain unclear. To explore the molecular mechanism of miR-153 on neural differentiation, we performed RNA sequencing on miR-153-overexpressed HT-22 cells. Based on RNA sequencing, differentially expressed genes (DEGs) and pathways in miR-153-overexpressed cells were identified. The Database for Annotation, Visualization and Integrated Discovery and Gene Set Enrichment Analysis were used to perform functional annotation and enrichment analysis of DEGs. Targetscan predicted the targets of miR-153. The Search Tool for the Retrieval of Interacting Genes and Cytoscape, were used to construct protein-protein interaction networks and identify hub genes. Q-PCR was used to detect mRNA expression of the identified genes. The expression profiles of the identified genes were compared between embryonic days 9.5 (E9.5) and E11.5 in the embryotic mouse brain of the GDS3442 dataset. Cell Counting Kit-8 assay was used to determine cell proliferation and cellular susceptibility to amyloid β-protein (Aβ) toxicity in miR-153-overexpressed cells. The results indicated that miR-153 increased cell adhesion/Ca2+ (Cdh5, Nrcam, and P2rx4) and Bdnf/Ntrk2 neurotrophic signaling pathway, and decreased ion channel activity (Kcnc3, Kcna4, Clcn5, and Scn5a). The changes in the expression of the identified genes in miR-153-overexpressed cells were consistent with the expression profile of GDS3442 during neural differentiation. In addition, miR-153 overexpression decreased cellular susceptibility to Aβ toxicity in HT-22 cells. In conclusion, miR-153 overexpression may promote neural differentiation by inducing cell adhesion and the Bdnf/Ntrk2 pathway, and regulating electrophysiological maturity by targeting ion channels. MiR-153 may play an important role in neural differentiation; the findings provide a useful therapeutic direction for neurodegenerative diseases.
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Affiliation(s)
- Li Jiao
- Teaching Laboratory Center, Tongji University School of Medicine, Shanghai, China
| | - Zhang Junfang
- Teaching Laboratory Center, Tongji University School of Medicine, Shanghai, China
| | - Li Yanna
- Teaching Laboratory Center, Tongji University School of Medicine, Shanghai, China
| | - Jin Caixia
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Zhang Chen
- Department of Laboratory Research Center, Tongji University School of Medicine, Shanghai, China
| | - Jia Song
- Teaching Laboratory Center, Tongji University School of Medicine, Shanghai, China
| | - Xu Jie
- Teaching Laboratory Center, Tongji University School of Medicine, Shanghai, China
| | - Yan Xiaoli
- Teaching Laboratory Center, Tongji University School of Medicine, Shanghai, China
| | - Gui Xin
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Xing Libo
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Wang Feng
- Department of Neurology, The Seventh People's Hospital of Integrated Traditional Chinese and Western Medicine Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lu lixia
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Xu Chunli
- Department of Neurology, The Seventh People's Hospital of Integrated Traditional Chinese and Western Medicine Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xu Lei
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
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Zhang L, Zhou Q, Zhang J, Cao K, Fan C, Chen S, Jiang H, Wu F. Liver transcriptomic and proteomic analyses provide new insight into the pathogenesis of liver fibrosis in mice. Genomics 2023; 115:110738. [PMID: 37918454 DOI: 10.1016/j.ygeno.2023.110738] [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: 04/17/2023] [Revised: 09/25/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND Liver fibrosis (LF) is a kind of progressive liver injury reaction. The goal of this study was to achieve a more detailed understanding of the molecular changes in response to CCl4-induced LF through the identification of a differentially expressed liver transcriptomic and proteomic. RESULTS A total of 1224 differentially expressed genes (DEGs) and 302 differentially expressed proteins (DEPs) were significantly identified at the transcriptomic and proteomic level, respectively, and 69 genes (hereafter "cor-DEGs-DEPs" genes) were detected at both levels. Pathway enrichment analysis showed that these cor-DEGs-DEPs genes were significantly enriched in 133 pathways. Importantly, among the cor-DEGs-DEPs genes, Gstm1, Gstm3, Ephx1 and Gstp1 were shown to be associated with metabolic pathways, and confirmed by RT-qPCR and parallel reaction monitoring (PRM) verification. CONCLUSIONS Through the combined analysis of transcriptomic and proteomic data, this study provides valuable insights into the potential mechanism of the pathogenesis of LF, and lays a theoretical foundation for the further development of targeted therapy for LF.
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Affiliation(s)
- Lili Zhang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China; School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.
| | - Qiumei Zhou
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.
| | - Jiafu Zhang
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.
| | - Kefeng Cao
- Departments of Laboratory Medicine, Traditional Chinese Medical Hospital of Taihe County, Fuyang, China.
| | - Chang Fan
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China; School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.
| | - Sen Chen
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China; School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.
| | - Hui Jiang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China; School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.
| | - Furong Wu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
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Fidalgo da Silva E, Abu Khatir B, Drouillard C, Hinch I, Davis GO, Sameem M, Patel R, Fong J, Lubanska D, Porter LA. Tuberin levels during cellular differentiation in brain development. Differentiation 2023; 130:43-50. [PMID: 36608575 DOI: 10.1016/j.diff.2022.12.004] [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: 10/18/2021] [Revised: 12/13/2022] [Accepted: 12/21/2022] [Indexed: 12/26/2022]
Abstract
Tuberin is a member of a large protein complex, Tuberous Sclerosis Complex (TSC), and acts as a sensor for nutrient status regulating protein synthesis and cell cycle progression. Mutations in the Tuberin gene, TSC2, permits the formation of tumors that can lead to developmental defects in many organ systems, including the central nervous system. Tuberin is expressed in the brain throughout development and levels of Tuberin have been found to decrease during neuronal differentiation in cell lines in vitro. Our current work investigates the levels of Tuberin at two stages of embryonic development in vivo, and we study the mRNA and protein levels during a time course using immortalized cell lines in vitro. Our results show that total Tuberin levels are tightly regulated through developmental stages in the embryonic brain. At a cell biology level, we show that Tuberin levels are higher when cells are cultured as neurospheres, and knockdown of Tuberin results in a reduction in the number of neurospheres. This functional data supports the hypothesis that Tuberin is an important regulator of stemness and the reduction of Tuberin levels might support functional differentiation in the central nervous system. Understanding how Tuberin expression is regulated throughout neural development is essential to fully comprehend the role of this protein in several developmental and neural pathologies.
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Affiliation(s)
- Elizabeth Fidalgo da Silva
- Department of Biomedical Sciences, University of Windsor, 401 Sunset Ave. Windsor, Ontario, N9B 3P4, Canada
| | - Bashaer Abu Khatir
- Department of Biomedical Sciences, University of Windsor, 401 Sunset Ave. Windsor, Ontario, N9B 3P4, Canada
| | - Christopher Drouillard
- Department of Biomedical Sciences, University of Windsor, 401 Sunset Ave. Windsor, Ontario, N9B 3P4, Canada
| | - Isabelle Hinch
- Department of Biomedical Sciences, University of Windsor, 401 Sunset Ave. Windsor, Ontario, N9B 3P4, Canada
| | - Gordon Omar Davis
- Department of Biomedical Sciences, University of Windsor, 401 Sunset Ave. Windsor, Ontario, N9B 3P4, Canada
| | - Mariam Sameem
- Department of Biomedical Sciences, University of Windsor, 401 Sunset Ave. Windsor, Ontario, N9B 3P4, Canada
| | - Rutu Patel
- Department of Biomedical Sciences, University of Windsor, 401 Sunset Ave. Windsor, Ontario, N9B 3P4, Canada
| | - Jackie Fong
- Department of Biomedical Sciences, University of Windsor, 401 Sunset Ave. Windsor, Ontario, N9B 3P4, Canada
| | - Dorota Lubanska
- Department of Biomedical Sciences, University of Windsor, 401 Sunset Ave. Windsor, Ontario, N9B 3P4, Canada
| | - Lisa A Porter
- Department of Biomedical Sciences, University of Windsor, 401 Sunset Ave. Windsor, Ontario, N9B 3P4, Canada.
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Mangleburg CG, Wu T, Yalamanchili HK, Guo C, Hsieh YC, Duong DM, Dammer EB, De Jager PL, Seyfried NT, Liu Z, Shulman JM. Integrated analysis of the aging brain transcriptome and proteome in tauopathy. Mol Neurodegener 2020; 15:56. [PMID: 32993812 PMCID: PMC7526226 DOI: 10.1186/s13024-020-00405-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 09/18/2020] [Indexed: 01/09/2023] Open
Abstract
Background Tau neurofibrillary tangle pathology characterizes Alzheimer’s disease and other neurodegenerative tauopathies. Brain gene expression profiles can reveal mechanisms; however, few studies have systematically examined both the transcriptome and proteome or differentiated Tau- versus age-dependent changes. Methods Paired, longitudinal RNA-sequencing and mass-spectrometry were performed in a Drosophila model of tauopathy, based on pan-neuronal expression of human wildtype Tau (TauWT) or a mutant form causing frontotemporal dementia (TauR406W). Tau-induced, differentially expressed transcripts and proteins were examined cross-sectionally or using linear regression and adjusting for age. Hierarchical clustering was performed to highlight network perturbations, and we examined overlaps with human brain gene expression profiles in tauopathy. Results TauWT induced 1514 and 213 differentially expressed transcripts and proteins, respectively. TauR406W had a substantially greater impact, causing changes in 5494 transcripts and 697 proteins. There was a ~ 70% overlap between age- and Tau-induced changes and our analyses reveal pervasive bi-directional interactions. Strikingly, 42% of Tau-induced transcripts were discordant in the proteome, showing opposite direction of change. Tau-responsive gene expression networks strongly implicate innate immune activation. Cross-species analyses pinpoint human brain gene perturbations specifically triggered by Tau pathology and/or aging, and further differentiate between disease amplifying and protective changes. Conclusions Our results comprise a powerful, cross-species functional genomics resource for tauopathy, revealing Tau-mediated disruption of gene expression, including dynamic, age-dependent interactions between the brain transcriptome and proteome.
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Affiliation(s)
- Carl Grant Mangleburg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Timothy Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hari K Yalamanchili
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Caiwei Guo
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yi-Chen Hsieh
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology and Taub Institute for the study of Alzheimer's disease and the aging brain, Columbia University Medical Center, New York, NY, 10032, USA.,Cell Circuits Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Zhandong Liu
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, 1250 Moursund St., Suite N.1150, Houston, TX, 77030, USA
| | - Joshua M Shulman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA. .,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, 1250 Moursund St., Suite N.1150, Houston, TX, 77030, USA. .,Department of Neurology, Baylor College of Medicine, Houston, TX, 77030, USA.
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Deep Transcriptomic Analysis Reveals the Dynamic Developmental Progression during Early Development of Channel Catfish ( Ictalurus punctatus). Int J Mol Sci 2020; 21:ijms21155535. [PMID: 32748829 PMCID: PMC7432863 DOI: 10.3390/ijms21155535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/21/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022] Open
Abstract
The transition from fertilized egg to larva in fish is accompanied with various biological processes. We selected seven early developmental stages in channel catfish, Ictalurus punctatus, for transcriptome analysis, and covered 22,635 genes with 590 million high-quality RNA-sequencing (seq) reads. Differential expression analysis between neighboring developmental timepoints revealed significantly enriched biological categories associated with growth, development and morphogenesis, which was most evident at 2 vs. 5 days post fertilization (dpf) and 5 vs. 6 dpf. A gene co-expression network was constructed using the Weighted Gene Co-expression Network Analysis (WGCNA) approach and four critical modules were identified. Among candidate hub genes, GDF10, FOXA2, HCEA and SYCE3 were involved in head formation, egg development and the transverse central element of synaptonemal complexes. CK1, OAZ2, DARS1 and UBE2V2 were mainly associated with regulation of cell cycle, growth, brain development, differentiation and proliferation of enterocytes. IFI44L and ZIP10 were critical for the regulation of immune activity and ion transport. Additionally, TCK1 and TGFB1 were related to phosphate transport and regulating cell proliferation. All these genes play vital roles in embryogenesis and regulation of early development. These results serve as a rich dataset for functional genomic studies. Our work reveals new insights of the underlying mechanisms in channel catfish early development.
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Ahmed AF, de Bock CE, Sontag E, Hondermarck H, Lincz LF, Thorne RF. FAT1 cadherin controls neuritogenesis during NTera2 cell differentiation. Biochem Biophys Res Commun 2019; 514:625-631. [PMID: 31076104 DOI: 10.1016/j.bbrc.2019.04.197] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 04/29/2019] [Indexed: 02/09/2023]
Abstract
Fat1 cadherin is broadly expressed throughout the nervous system and has been implicated in neuronal differentiation. Here we examined the functional contribution of FAT1 during neuronal differentiation of the Ntera2 cell line model. FAT1 expression was increased during the retinoic acid (RA)-induced differentiation of NTera2 cells. Depletion of FAT1 with siRNA decreased the number of neurites produced after RA treatment. Moreover, FAT1 silencing also led to decreased Ser127-phosphorylation of YAP along with transcriptional increases in the Hippo target genes CTGF and ANKRD1, suggesting FAT1 alters Hippo signalling during differentiation. In the context of the Ntera2 model, FAT1 is required for efficient neuritogenesis, acting as a regulator of neurite formation during the early stages of differentiation.
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Affiliation(s)
- Abdulrzag F Ahmed
- Department of Pharmacology, Faculty of Pharmacy, Elmergib University, Alkhoms, Libya; School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Charles E de Bock
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Australia, Randwick, NSW 2031, Australia
| | - Estelle Sontag
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia; Hunter Medical Research Institute, New Lambton, New South Wales, 2305, Australia
| | - Hubert Hondermarck
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia; Hunter Medical Research Institute, New Lambton, New South Wales, 2305, Australia
| | - Lisa F Lincz
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia; Hunter Medical Research Institute, New Lambton, New South Wales, 2305, Australia; Hunter Haematology Research Group, Calvary Mater Newcastle Hospital, Waratah, NSW, 2298, Australia
| | - Rick F Thorne
- Translational Research Institute, Henan Provincial People's Hospital, Zhengzhou University, 450053, Zhengzhou, China; School of Environmental and Life Sciences, University of Newcastle, NSW, 2258, Australia.
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Hasna J, Bohic S, Lemoine S, Blugeon C, Bouron A. Zinc Uptake and Storage During the Formation of the Cerebral Cortex in Mice. Mol Neurobiol 2019; 56:6928-6940. [DOI: 10.1007/s12035-019-1581-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/20/2019] [Indexed: 12/17/2022]
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Radziejewska A, Chmurzynska A. Folate and choline absorption and uptake: Their role in fetal development. Biochimie 2018; 158:10-19. [PMID: 30529042 DOI: 10.1016/j.biochi.2018.12.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/04/2018] [Indexed: 12/29/2022]
Abstract
SCOPE In this review, we attempt to assess how choline and folate transporters affect fetal development. We focus on how the expression of these transporters in response to choline and folate intake affects transport effectiveness. We additionally describe allelic variants of the genes encoding these transporters and their phenotypic effects. METHODS AND RESULTS We made an extensive review of recent articles describing role of choline and folate - with particularly emphasize on their transporters - in fetal development. Folate and choline are necessary for the proper functioning of the cell and body. During pregnancy, the requirements of these nutrients increase because of elevated maternal demand and the rapid division of fetal cells. The concentrations of folate and choline in cells depend on food intake, the absorption of nutrients, and the cellular transport system, which is tissue-specific and developmentally regulated. Relatively few studies have investigated the role of choline transporters in fetal development. CONCLUSIONS In this review we show relations between functioning of folate and choline transporters and fetal development.
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Affiliation(s)
- Anna Radziejewska
- Institute of Human Nutrition and Dietetics, Poznań University of Life Sciences, Poland
| | - Agata Chmurzynska
- Institute of Human Nutrition and Dietetics, Poznań University of Life Sciences, Poland.
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Ding J, Hagood JS, Ambalavanan N, Kaminski N, Bar-Joseph Z. iDREM: Interactive visualization of dynamic regulatory networks. PLoS Comput Biol 2018. [PMID: 29538379 PMCID: PMC5868853 DOI: 10.1371/journal.pcbi.1006019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Dynamic Regulatory Events Miner (DREM) software reconstructs dynamic regulatory networks by integrating static protein-DNA interaction data with time series gene expression data. In recent years, several additional types of high-throughput time series data have been profiled when studying biological processes including time series miRNA expression, proteomics, epigenomics and single cell RNA-Seq. Combining all available time series and static datasets in a unified model remains an important challenge and goal. To address this challenge we have developed a new version of DREM termed interactive DREM (iDREM). iDREM provides support for all data types mentioned above and combines them with existing interaction data to reconstruct networks that can lead to novel hypotheses on the function and timing of regulators. Users can interactively visualize and query the resulting model. We showcase the functionality of the new tool by applying it to microglia developmental data from multiple labs.
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Affiliation(s)
- Jun Ding
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - James S. Hagood
- Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego and Rady Children’s Hospital, La Jolla, California, United States of America
| | - Namasivayam Ambalavanan
- Division of Neonatology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Zhang P, Luo X, Guo Z, Xiong A, Dong H, Zhang Q, Liu C, Zhu J, Wang H, Yu N, Zhang J, Hong Y, Yang L, Huang J. Neuritin Inhibits Notch Signaling through Interacted with Neuralized to Promote the Neurite Growth. Front Mol Neurosci 2017. [PMID: 28642682 PMCID: PMC5462965 DOI: 10.3389/fnmol.2017.00179] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Neuritin plays a key role in neural development and regeneration by promoting neurite outgrowth and synapse maturation. However, the mechanism of neuritin in modulating neurite growth has not been elucidated. Here, using yeast two-hybrid we screened and discovered the interaction of neuritin and neuralized (NEURL1), which is an important regulator that can activate Notch signaling through promoting endocytosis of Notch ligand. And then we identified the interaction of neuritin and neuralized by co-immunoprecipitation (IP) assays, and clarified that neuritin and NEURL1 were co-localized on the cell membrane of SH-SY5Y cells. Moreover, neuritin significantly suppressed Notch ligand Jagged1 (JAG1) endocytosis promoted by NEURL1, and then inhibited the activation of Notch receptor Notch intracellular domain (NICD) and decreased the expression of downstream gene hairy and enhancer of split-1 (HES1). Importantly, the effect of neuritin on inhibiting Notch signaling was rescued by NEURL1, which indicated that neuritin is an upstream and negative regulator of NEURL1 to inhibit Notch signaling through interaction with NEURL1. Notably, recombinant neuritin restored the retraction of neurites caused by activation of Notch, and neurite growth stimulated by neuritin was partially blocked by NEURL1. These findings establish neuritin as an upstream and negative regulator of NEURL1 that inhibits Notch signaling to promote neurite growth. This mechanism connects neuritin with Notch signaling, and provides a valuable foundation for further investigation of neuritin's role in neurodevelopment and neural plasticity.
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Affiliation(s)
- Pan Zhang
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Department of Biochemistry, Shihezi University School of MedicineShihezi, China
| | - Xing Luo
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Department of Biochemistry, Shihezi University School of MedicineShihezi, China
| | - Zheng Guo
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Department of Biochemistry, Shihezi University School of MedicineShihezi, China
| | - Anying Xiong
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Department of Biochemistry, Shihezi University School of MedicineShihezi, China
| | - Hongchang Dong
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Department of Biochemistry, Shihezi University School of MedicineShihezi, China
| | - Qiao Zhang
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Department of Biochemistry, Shihezi University School of MedicineShihezi, China
| | - Chunyan Liu
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Department of Biochemistry, Shihezi University School of MedicineShihezi, China
| | - Jingling Zhu
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Department of Biochemistry, Shihezi University School of MedicineShihezi, China
| | - Haiyan Wang
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Department of Biochemistry, Shihezi University School of MedicineShihezi, China
| | - Na Yu
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Department of Biochemistry, Shihezi University School of MedicineShihezi, China
| | - Jinli Zhang
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Department of Biochemistry, Shihezi University School of MedicineShihezi, China
| | - Yu Hong
- School of Medicine, Hangzhou Normal UniversityHangzhou, China
| | - Lei Yang
- School of Medicine, Hangzhou Normal UniversityHangzhou, China
| | - Jin Huang
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Department of Biochemistry, Shihezi University School of MedicineShihezi, China
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Namjoshi SV, Raab-Graham KF. Screening the Molecular Framework Underlying Local Dendritic mRNA Translation. Front Mol Neurosci 2017; 10:45. [PMID: 28286470 PMCID: PMC5323403 DOI: 10.3389/fnmol.2017.00045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/10/2017] [Indexed: 12/13/2022] Open
Abstract
In the last decade, bioinformatic analyses of high-throughput proteomics and transcriptomics data have enabled researchers to gain insight into the molecular networks that may underlie lasting changes in synaptic efficacy. Development and utilization of these techniques have advanced the field of learning and memory significantly. It is now possible to move from the study of activity-dependent changes of a single protein to modeling entire network changes that require local protein synthesis. This data revolution has necessitated the development of alternative computational and statistical techniques to analyze and understand the patterns contained within. Thus, the focus of this review is to provide a synopsis of the journey and evolution toward big data techniques to address still unanswered questions regarding how synapses are modified to strengthen neuronal circuits. We first review the seminal studies that demonstrated the pivotal role played by local mRNA translation as the mechanism underlying the enhancement of enduring synaptic activity. In the interest of those who are new to the field, we provide a brief overview of molecular biology and biochemical techniques utilized for sample preparation to identify locally translated proteins using RNA sequencing and proteomics, as well as the computational approaches used to analyze these data. While many mRNAs have been identified, few have been shown to be locally synthesized. To this end, we review techniques currently being utilized to visualize new protein synthesis, a task that has proven to be the most difficult aspect of the field. Finally, we provide examples of future applications to test the physiological relevance of locally synthesized proteins identified by big data approaches.
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Affiliation(s)
- Sanjeev V Namjoshi
- Center for Learning and Memory, The University of Texas at Austin, AustinTX, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, AustinTX, USA
| | - Kimberly F Raab-Graham
- Center for Learning and Memory, The University of Texas at Austin, AustinTX, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, AustinTX, USA; Department of Physiology and Pharmacology, Wake Forest Health Sciences, Medical Center Boulevard, Winston-SalemNC, USA
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Analysis of gene expression in the nervous system identifies key genes and novel candidates for health and disease. Neurogenetics 2017; 18:81-95. [PMID: 28190221 PMCID: PMC5359387 DOI: 10.1007/s10048-017-0509-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 01/20/2017] [Indexed: 01/09/2023]
Abstract
The incidence of neurodegenerative diseases in the developed world has risen over the last century, concomitant with an increase in average human lifespan. A major challenge is therefore to identify genes that control neuronal health and viability with a view to enhancing neuronal health during ageing and reducing the burden of neurodegeneration. Analysis of gene expression data has recently been used to infer gene functions for a range of tissues from co-expression networks. We have now applied this approach to transcriptomic datasets from the mammalian nervous system available in the public domain. We have defined the genes critical for influencing neuronal health and disease in different neurological cell types and brain regions. The functional contribution of genes in each co-expression cluster was validated using human disease and knockout mouse phenotypes, pathways and gene ontology term annotation. Additionally a number of poorly annotated genes were implicated by this approach in nervous system function. Exploiting gene expression data available in the public domain allowed us to validate key nervous system genes and, importantly, to identify additional genes with minimal functional annotation but with the same expression pattern. These genes are thus novel candidates for a role in neurological health and disease and could now be further investigated to confirm their function and regulation during ageing and neurodegeneration.
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13
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Incorporation of non-canonical amino acids into the developing murine proteome. Sci Rep 2016; 6:32377. [PMID: 27572480 PMCID: PMC5004113 DOI: 10.1038/srep32377] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 08/09/2016] [Indexed: 12/25/2022] Open
Abstract
Analysis of the developing proteome has been complicated by a lack of tools that can be easily employed to label and identify newly synthesized proteins within complex biological mixtures. Here, we demonstrate that the methionine analogs azidohomoalanine and homopropargylglycine can be globally incorporated into the proteome of mice through facile intraperitoneal injections. These analogs contain bio-orthogonal chemical handles to which fluorescent tags can be conjugated to identify newly synthesized proteins. We show these non-canonical amino acids are incorporated into various tissues in juvenile mice and in a concentration dependent manner. Furthermore, administration of these methionine analogs to pregnant dams during a critical stage of murine development, E10.5-12.5 when many tissues are assembling, does not overtly disrupt development as assessed by proteomic analysis and normal parturition and growth of pups. This successful demonstration that non-canonical amino acids can be directly administered in vivo will enable future studies that seek to characterize the murine proteome during growth, disease and repair.
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Not just a colourful metaphor: modelling the landscape of cellular development using Hopfield networks. NPJ Syst Biol Appl 2016; 2:16001. [PMID: 28725466 PMCID: PMC5516853 DOI: 10.1038/npjsba.2016.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 11/05/2015] [Accepted: 12/15/2015] [Indexed: 01/12/2023] Open
Abstract
The epigenetic landscape was introduced by Conrad Waddington as a metaphor of cellular development. Like a ball rolling down a hillside is channelled through a succession of valleys until it reaches the bottom, cells follow specific trajectories from a pluripotent state to a committed state. Transcription factors (TFs) interacting as a network (the gene regulatory network (GRN)) orchestrate this developmental process within each cell. Here, we quantitatively model the epigenetic landscape using a kind of artificial neural network called the Hopfield network (HN). An HN is composed of nodes (genes/TFs) and weighted undirected edges, resulting in a weight matrix (W) that stores interactions among the nodes over the entire network. We used gene co-expression to compute the edge weights. Through W, we then associate an energy score (E) to each input pattern (pattern of co-expression for a specific developmental stage) such that each pattern has a specific E. We propose that, based on the co-expression values stored in W, HN associates lower E values to stable phenotypic states and higher E to transient states. We validate our model using time course gene-expression data sets representing stages of development across 12 biological processes including differentiation of human embryonic stem cells into specialized cells, differentiation of THP1 monocytes to macrophages during immune response and trans-differentiation of epithelial to mesenchymal cells in cancer. We observe that transient states have higher energy than the stable phenotypic states, yielding an arc-shaped trajectory. This relationship was confirmed by perturbation analysis. HNs offer an attractive framework for quantitative modelling of cell differentiation (as a landscape) from empirical data. Using HNs, we identify genes and TFs that drive cell-fate transitions, and gain insight into the global dynamics of GRNs.
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15
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Ahmed AF, de Bock CE, Lincz LF, Pundavela J, Zouikr I, Sontag E, Hondermarck H, Thorne RF. FAT1 cadherin acts upstream of Hippo signalling through TAZ to regulate neuronal differentiation. Cell Mol Life Sci 2015; 72:4653-69. [PMID: 26104008 PMCID: PMC11113810 DOI: 10.1007/s00018-015-1955-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 06/09/2015] [Accepted: 06/10/2015] [Indexed: 12/19/2022]
Abstract
The Hippo pathway is emerging as a critical nexus that balances self-renewal of progenitors against differentiation; however, upstream elements in vertebrate Hippo signalling are poorly understood. High expression of Fat1 cadherin within the developing neuroepithelium and the manifestation of severe neurological phenotypes in Fat1-knockout mice suggest roles in neurogenesis. Using the SH-SY5Y model of neuronal differentiation and employing gene silencing techniques, we show that FAT1 acts to control neurite outgrowth, also driving cells towards terminal differentiation via inhibitory effects on proliferation. FAT1 actions were shown to be mediated through Hippo signalling where it activated core Hippo kinase components and antagonised functions of the Hippo effector TAZ. Suppression of FAT1 promoted the nucleocytoplasmic shuttling of TAZ leading to enhanced transcription of the Hippo target gene CTGF together with accompanying increases in nuclear levels of Smad3. Silencing of TAZ reversed the effects of FAT1 depletion thus connecting inactivation of TAZ-TGFbeta signalling with Hippo signalling mediated through FAT1. These findings establish FAT1 as a new upstream Hippo element regulating early stages of differentiation in neuronal cells.
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Affiliation(s)
- Abdulrzag F Ahmed
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Charles E de Bock
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Lisa F Lincz
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
- Hunter Haematology Research Group, Calvary Mater Newcastle Hospital, Waratah, NSW, 2298, Australia
| | - Jay Pundavela
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Ihssane Zouikr
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Estelle Sontag
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia
- Priority Research Centre for Translational Neuroscience and Mental Health, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Hubert Hondermarck
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Rick F Thorne
- Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia.
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, NSW, 2258, Australia.
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16
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Investigation of heart proteome of different consomic mouse strains. Testing the effect of polymorphisms on the proteome-wide trans-variation of proteins. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Santiago FE, Almeida MC, Carrettiero DC. BAG2 Is Repressed by NF-κB Signaling, and Its Overexpression Is Sufficient to Shift Aβ1-42 from Neurotrophic to Neurotoxic in Undifferentiated SH-SY5Y Neuroblastoma. J Mol Neurosci 2015; 57:83-9. [PMID: 25985852 DOI: 10.1007/s12031-015-0579-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 05/05/2015] [Indexed: 12/26/2022]
Abstract
Amyloid-beta (Aβ) binds to various neuronal receptors and elicits a context- and dose-dependent toxic or trophic response from neurons. The molecular mechanisms for this phenomenon are presently unknown. The cochaperone BAG2 has been shown to mediate important cellular responses to stress, including cell cycle arrest and apoptosis. Here, we use SH-SY5Y neuroblastoma cells to characterize BAG2 expression and regulation and investigate the involvement of BAG2 in Aβ1-42-mediated neurotrophism or neurotoxicity in the context of differentiation. We report that BAG2 is upregulated on differentiation of SH-SY5Y cells into neuron-like cells. This increase in BAG2 expression is accompanied by a change in response to treatment with Aβ1-42 from neurotrophic to neurotoxic. Further, overexpression of BAG2 in undifferentiated SH-SY5Y cells was sufficient to induce the change from neurotrophic to neurotoxic response. Of several transcription factors queried, the putative BAG2 promoter had a higher-than-expected occurrence of response elements (RE) for nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). Treatment with JSH-23, a potent inhibitor of NF-κB, caused a marked increase in BAG2 mRNA expression, suggesting that NF-κB is a repressor of BAG2 transcription in undifferentiated SH-SY5Y cells. Together, these data suggest that NF-κB-mediated modulation of BAG2 expression constitutes a "switch" that regulates the shift between the neurotrophic and neurotoxic effects of Aβ1-42.
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Affiliation(s)
- Fernando E Santiago
- Pós-graduação em Neurociência e Cognição, Universidade Federal do ABC, São Bernardo do Campo, Brazil,
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18
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Kobus K, Hartl D, Ott CE, Osswald M, Huebner A, von der Hagen M, Emmerich D, Kühnisch J, Morreau H, Hes FJ, Mautner VF, Harder A, Tinschert S, Mundlos S, Kolanczyk M. Double NF1 inactivation affects adrenocortical function in NF1Prx1 mice and a human patient. PLoS One 2015; 10:e0119030. [PMID: 25775093 PMCID: PMC4361563 DOI: 10.1371/journal.pone.0119030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 01/12/2015] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Neurofibromatosis type I (NF1, MIM#162200) is a relatively frequent genetic condition, which predisposes to tumor formation. Apart from tumors, individuals with NF1 often exhibit endocrine abnormalities such as precocious puberty (2,5-5% of NF1 patients) and some cases of hypertension (16% of NF1 patients). Several cases of adrenal cortex adenomas have been described in NF1 individuals supporting the notion that neurofibromin might play a role in adrenal cortex homeostasis. However, no experimental data were available to prove this hypothesis. MATERIALS AND METHODS We analysed Nf1Prx1 mice and one case of adrenal cortical hyperplasia in a NF1patient. RESULTS In Nf1Prx1 mice Nf1 is inactivated in the developing limbs, head mesenchyme as well as in the adrenal gland cortex, but not the adrenal medulla or brain. We show that adrenal gland size is increased in NF1Prx1 mice. Nf1Prx1 female mice showed corticosterone and aldosterone overproduction. Molecular analysis of Nf1 deficient adrenals revealed deregulation of multiple proteins, including steroidogenic acute regulatory protein (StAR), a vital mitochondrial factor promoting transfer of cholesterol into steroid making mitochondria. This was associated with a marked upregulation of MAPK pathway and a female specific increase of cAMP concentration in murine adrenal lysates. Complementarily, we characterized a patient with neurofibromatosis type I with macronodular adrenal hyperplasia with ACTH-independent cortisol overproduction. Comparison of normal control tissue- and adrenal hyperplasia- derived genomic DNA revealed loss of heterozygosity (LOH) of the wild type NF1 allele, showing that biallelic NF1 gene inactivation occurred in the hyperplastic adrenal gland. CONCLUSIONS Our data suggest that biallelic loss of Nf1 induces autonomous adrenal hyper-activity. We conclude that Nf1 is involved in the regulation of adrenal cortex function in mice and humans.
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Affiliation(s)
- Karolina Kobus
- Institute for Medical Genetics and Human Genetics, Charité, Universitätsmedizin Berlin, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development & Disease, Berlin, Germany
| | - Daniela Hartl
- Institute for Medical Genetics and Human Genetics, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Claus Eric Ott
- Max Planck Institute for Molecular Genetics, FG Development & Disease, Berlin, Germany
| | - Monika Osswald
- Max Planck Institute for Molecular Genetics, FG Development & Disease, Berlin, Germany
| | - Angela Huebner
- Klinik für Kinder- und Jugendmedizin, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Maja von der Hagen
- Abteilung Neuropädiatrie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Denise Emmerich
- Max Planck Institute for Molecular Genetics, FG Development & Disease, Berlin, Germany
| | - Jirko Kühnisch
- Institute for Medical Genetics and Human Genetics, Charité, Universitätsmedizin Berlin, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development & Disease, Berlin, Germany
| | - Hans Morreau
- Department of Pathology, Leiden University Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands
| | - Frederik J. Hes
- Department of Clinical Genetics, Leiden University Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands
| | - Victor F. Mautner
- Department of Maxillofacial Surgery, University Hospital Eppendorf, Hamburg, Germany
| | - Anja Harder
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Sigrid Tinschert
- Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University Innsbruck, Innsbruck, Austria
| | - Stefan Mundlos
- Institute for Medical Genetics and Human Genetics, Charité, Universitätsmedizin Berlin, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development & Disease, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin, Germany
| | - Mateusz Kolanczyk
- Institute for Medical Genetics and Human Genetics, Charité, Universitätsmedizin Berlin, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development & Disease, Berlin, Germany
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19
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Horstick EJ, Jordan DC, Bergeron SA, Tabor KM, Serpe M, Feldman B, Burgess HA. Increased functional protein expression using nucleotide sequence features enriched in highly expressed genes in zebrafish. Nucleic Acids Res 2015; 43:e48. [PMID: 25628360 PMCID: PMC4402511 DOI: 10.1093/nar/gkv035] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/12/2015] [Indexed: 12/18/2022] Open
Abstract
Many genetic manipulations are limited by difficulty in obtaining adequate levels of protein expression. Bioinformatic and experimental studies have identified nucleotide sequence features that may increase expression, however it is difficult to assess the relative influence of these features. Zebrafish embryos are rapidly injected with calibrated doses of mRNA, enabling the effects of multiple sequence changes to be compared in vivo. Using RNAseq and microarray data, we identified a set of genes that are highly expressed in zebrafish embryos and systematically analyzed for enrichment of sequence features correlated with levels of protein expression. We then tested enriched features by embryo microinjection and functional tests of multiple protein reporters. Codon selection, releasing factor recognition sequence and specific introns and 3′ untranslated regions each increased protein expression between 1.5- and 3-fold. These results suggested principles for increasing protein yield in zebrafish through biomolecular engineering. We implemented these principles for rational gene design in software for codon selection (CodonZ) and plasmid vectors incorporating the most active non-coding elements. Rational gene design thus significantly boosts expression in zebrafish, and a similar approach will likely elevate expression in other animal models.
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Affiliation(s)
- Eric J Horstick
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Diana C Jordan
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Sadie A Bergeron
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Kathryn M Tabor
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Mihaela Serpe
- Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Benjamin Feldman
- Zebrafish Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Harold A Burgess
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
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20
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carboxypeptidase E-ΔN, a neuroprotein transiently expressed during development protects embryonic neurons against glutamate neurotoxicity. PLoS One 2014; 9:e112996. [PMID: 25426952 PMCID: PMC4245097 DOI: 10.1371/journal.pone.0112996] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 10/17/2014] [Indexed: 12/04/2022] Open
Abstract
Neuroprotective proteins expressed in the fetus play a critical role during early embryonic neurodevelopment, especially during maternal exposure to alcohol and drugs that cause stress, glutamate neuroexcitotoxicity, and damage to the fetal brain, if prolonged. We have identified a novel protein, carboxypeptidase E-ΔN (CPE-ΔN), which is a splice variant of CPE that has neuroprotective effects on embryonic neurons. CPE-ΔN is transiently expressed in mouse embryos from embryonic day 5.5 to postnatal day 1. It is expressed in embryonic neurons, but not in 3 week or older mouse brains, suggesting a function primarily in utero. CPE-ΔN expression was up-regulated in embryonic hippocampal neurons in response to dexamethasone treatment. CPE-ΔN transduced into rat embryonic cortical and hippocampal neurons protected them from glutamate- and H2O2-induced cell death. When transduced into embryonic cortical neurons, CPE-ΔN was found in the nucleus and enhanced the transcription of FGF2 mRNA. Embryonic cortical neurons challenged with glutamate resulted in attenuated FGF2 levels and cell death, but CPE-ΔN transduced neurons treated in the same manner showed increased FGF2 expression and normal viability. This neuroprotective effect of CPE-ΔN was mediated by secreted FGF2. Through receptor signaling, FGF2 activated the AKT and ERK signaling pathways, which in turn increased BCL-2 expression. This led to inhibition of caspase-3 activity and cell survival.
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21
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Kararigas G, Fliegner D, Forler S, Klein O, Schubert C, Gustafsson JÅ, Klose J, Regitz-Zagrosek V. Comparative Proteomic Analysis Reveals Sex and Estrogen Receptor β Effects in the Pressure Overloaded Heart. J Proteome Res 2014; 13:5829-36. [DOI: 10.1021/pr500749j] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Georgios Kararigas
- Institute
of Gender in Medicine, Center for Cardiovascular Research, and DZHK (German Center for Cardiovascular Research), Berlin partner site, Charite University Hospital, 10117 Berlin, Germany
| | - Daniela Fliegner
- Institute
of Gender in Medicine, Center for Cardiovascular Research, and DZHK (German Center for Cardiovascular Research), Berlin partner site, Charite University Hospital, 10117 Berlin, Germany
| | - Stefanie Forler
- Institute
for Human Genetics, Charite University Hospital, 10117 Berlin, Germany
| | - Oliver Klein
- Institute
for Human Genetics, Charite University Hospital, 10117 Berlin, Germany
- Core
Unit Proteomics, Berlin-Brandenburg Center for Regenerative Therapies, Charite University Hospital, 10117 Berlin, Germany
| | - Carola Schubert
- Institute
of Gender in Medicine, Center for Cardiovascular Research, and DZHK (German Center for Cardiovascular Research), Berlin partner site, Charite University Hospital, 10117 Berlin, Germany
| | - Jan-Åke Gustafsson
- Center
for Nuclear Receptors and Cell Signaling, University of Houston, Houston, Texas 77004, United States
| | - Joachim Klose
- Institute
for Human Genetics, Charite University Hospital, 10117 Berlin, Germany
- Core
Unit Proteomics, Berlin-Brandenburg Center for Regenerative Therapies, Charite University Hospital, 10117 Berlin, Germany
| | - Vera Regitz-Zagrosek
- Institute
of Gender in Medicine, Center for Cardiovascular Research, and DZHK (German Center for Cardiovascular Research), Berlin partner site, Charite University Hospital, 10117 Berlin, Germany
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22
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Rehfeld F, Rohde AM, Nguyen DTT, Wulczyn FG. Lin28 and let-7: ancient milestones on the road from pluripotency to neurogenesis. Cell Tissue Res 2014; 359:145-60. [PMID: 24825413 DOI: 10.1007/s00441-014-1872-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/11/2014] [Indexed: 11/25/2022]
Abstract
Beginning with their discovery in the context of stem cell fate choice in Caenorhabditis elegans, the microRNA (miRNA) let-7 and the RNA-binding protein Lin28 have been recognized as a regulatory pair with far-reaching impact on stem cell behavior in a wide range of organisms and tissues, including the mammalian brain. In this review, we describe molecular interactions between Lin28 and let-7 and the biological role that each plays in implementing stem cell programs that either maintain stem cell self-renewal and plasticity or drive lineage commitment and differentiation. For Lin28, considerable progress has been made in defining let-7-dependent and let-7-independent functions in the maintenance of pluripotency, somatic cell reprogramming, tissue regeneration, and neural stem cell plasticity. For the pro-differentiation activity of let-7, we focus on emerging roles in mammalian neurogenesis and neuronal function. Specific targets and pathways for let-7 have been identified in embryonic and adult neurogenesis, including corticogenesis, retinal specification, and adult neurogenic niches. Special emphasis is given to examples of feedback and feedforward regulation, in particular within the miRNA biogenesis pathway.
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Affiliation(s)
- Frederick Rehfeld
- Institute for Cell and Neurobiology, Charité University Medicine Berlin, Berlin, Germany
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23
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Mußmann C, Hübner R, Trilck M, Rolfs A, Frech MJ. HES5 is a key mediator of Wnt-3a-induced neuronal differentiation. Stem Cells Dev 2014; 23:1328-39. [PMID: 24548083 DOI: 10.1089/scd.2013.0557] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Human neural stem/progenitor cell (hNPC)-derived neuronal progeny has been suggested as a promising cell source in a variety of neurodegenerative diseases. Understanding the underlying mechanisms that regulate neuronal differentiation is essential for efficient cell-based therapies. Wnt and Notch signaling has been shown to be crucial in this process. However, their interactions in the process of neuronal differentiation remain elusive. By using human fetal (ReNcell VM) and iPS-derived hNPCs we demonstrate that Wnt-3a immediately induced a transient HES1 upregulation and a sustained HES5 repression that was accompanied by upregulation of the proneural gene MASH1. Conversely, overexpression of HES5 resulted in reduced MASH1 expression. Remarkably, HES5 overexpression efficiently blocked Wnt-3a as well as γ-secretase inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT)-induced neuronal differentiation that was accompanied by a strong MASH1 downregulation thus directly linking HES5 repression/MASH1 induction to the proneurogenic effect of Wnt-3a. Stabilized β-catenin or treatment with the specific glycogen synthase kinase 3 beta (GSK3β) inhibitor SB-216763 failed to or only partially mimicked these effects, suggesting a GSK3β- and β-catenin-independent mechanism. Further, inhibition of Wnt-3a-LDL-receptor-related protein 5/6 (LRP5/6) interactions using Dickkopf-1 (Dkk-1) failed to inhibit the modulatory effect of Wnt-3a on HES1/5 and neuronal differentiation. Taken together, these data identify HES5 as a key mediator of the Wnt-3a proneurogenic effect occurring independently of the classical Wnt/β-catenin signaling cascade thus further deciphering crosstalk mechanisms of Wnt and Notch signaling pathways regulating cell fate of hNPCs.
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Affiliation(s)
- Carolin Mußmann
- Albrecht-Kossel-Institute for Neuroregeneration (AKos), University of Rostock , Rostock, Germany
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24
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Cheng G, Chen P, Wang ZG, Sui XJ, Zhang JL, Ni JZ. Immobilization of trypsin onto multifunctional meso-/macroporous core-shell microspheres: A new platform for rapid enzymatic digestion. Anal Chim Acta 2014; 812:65-73. [DOI: 10.1016/j.aca.2013.12.035] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 12/16/2013] [Accepted: 12/24/2013] [Indexed: 10/25/2022]
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25
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Lui JC, Chen W, Cheung CSF, Baron J. Broad shifts in gene expression during early postnatal life are associated with shifts in histone methylation patterns. PLoS One 2014; 9:e86957. [PMID: 24489814 PMCID: PMC3904965 DOI: 10.1371/journal.pone.0086957] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 12/19/2013] [Indexed: 01/08/2023] Open
Abstract
During early postnatal life, extensive changes in gene expression occur concomitantly in multiple major organs, indicating the existence of a common core developmental genetic program. This program includes hundreds of growth-promoting genes that are downregulated with age in liver, kidney, lung, and heart, and there is evidence that this component of the program drives the widespread decline in cell proliferation that occurs in juvenile life, as organs approach adult sizes. To investigate epigenetic changes that might orchestrate this program, we performed chromatin immunoprecipitation-promoter tiling array to assess temporal changes in histone H3K4 and H3K27 trimethylation (me3) at promoter regions throughout the genome in kidney and lung, comparing 1- to 4-wk-old mice. We found extensive genome-wide shifts in H3K4me3 and H3K27me3 occurring with age in both kidney and lung. The number of genes with concordant changes in the two organs was far greater than expected by chance. Temporal changes in H3K4me3 showed a strong, positive association with changes in gene expression, assessed by microarray, whereas changes in H3K27me3 showed a negative association. Gene ontology analysis indicated that shifts in specific histone methylation marks were associated with specific developmental functions. Of particular interest, genes with decreases in H3K4me3 with age in both organs were strongly implicated in cell cycle and cell proliferation functions. Taken together, the findings suggest that the common core developmental program of gene expression which occurs in multiple organs during juvenile life is associated with a common core developmental program of histone methylation. In particular, declining H3K4me3 is strongly associated with gene downregulation and occurs in the promoter regions of many growth-regulating genes, suggesting that this change in histone methylation may contribute to the component of the genetic program that drives juvenile body growth deceleration.
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Affiliation(s)
- Julian C. Lui
- Section on Growth and Development, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Weiping Chen
- Microarray Core Facility, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Crystal S. F. Cheung
- Section on Growth and Development, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jeffrey Baron
- Section on Growth and Development, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
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26
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Zabel C, Andreew A, Mao L, Hartl D. Protein expression overlap: more important than which proteins change in expression? Expert Rev Proteomics 2014; 5:187-205. [DOI: 10.1586/14789450.5.2.187] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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27
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Goggolidou P, Soneji S, Powles-Glover N, Williams D, Sethi S, Baban D, Simon MM, Ragoussis I, Norris DP. A chronological expression profile of gene activity during embryonic mouse brain development. Mamm Genome 2013; 24:459-72. [PMID: 24249052 PMCID: PMC3843766 DOI: 10.1007/s00335-013-9486-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 10/14/2013] [Indexed: 02/03/2023]
Abstract
The brain is a functionally complex organ, the patterning and development of which are key to adult health. To help elucidate the genetic networks underlying mammalian brain patterning, we conducted detailed transcriptional profiling during embryonic development of the mouse brain. A total of 2,400 genes were identified as showing differential expression between three developmental stages. Analysis of the data identified nine gene clusters to demonstrate analogous expression profiles. A significant group of novel genes of as yet undiscovered biological function were detected as being potentially relevant to brain development and function, in addition to genes that have previously identified roles in the brain. Furthermore, analysis for genes that display asymmetric expression between the left and right brain hemispheres during development revealed 35 genes as putatively asymmetric from a combined data set. Our data constitute a valuable new resource for neuroscience and neurodevelopment, exposing possible functional associations between genes, including novel loci, and encouraging their further investigation in human neurological and behavioural disorders.
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Affiliation(s)
- P Goggolidou
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK,
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Aprea J, Prenninger S, Dori M, Ghosh T, Monasor LS, Wessendorf E, Zocher S, Massalini S, Alexopoulou D, Lesche M, Dahl A, Groszer M, Hiller M, Calegari F. Transcriptome sequencing during mouse brain development identifies long non-coding RNAs functionally involved in neurogenic commitment. EMBO J 2013; 32:3145-60. [PMID: 24240175 DOI: 10.1038/emboj.2013.245] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 10/23/2013] [Indexed: 12/17/2022] Open
Abstract
Transcriptome analysis of somatic stem cells and their progeny is fundamental to identify new factors controlling proliferation versus differentiation during tissue formation. Here, we generated a combinatorial, fluorescent reporter mouse line to isolate proliferating neural stem cells, differentiating progenitors and newborn neurons that coexist as intermingled cell populations during brain development. Transcriptome sequencing revealed numerous novel long non-coding (lnc)RNAs and uncharacterized protein-coding transcripts identifying the signature of neurogenic commitment. Importantly, most lncRNAs overlapped neurogenic genes and shared with them a nearly identical expression pattern suggesting that lncRNAs control corticogenesis by tuning the expression of nearby cell fate determinants. We assessed the power of our approach by manipulating lncRNAs and protein-coding transcripts with no function in corticogenesis reported to date. This led to several evident phenotypes in neurogenic commitment and neuronal survival, indicating that our study provides a remarkably high number of uncharacterized transcripts with hitherto unsuspected roles in brain development. Finally, we focussed on one lncRNA, Miat, whose manipulation was found to trigger pleiotropic effects on brain development and aberrant splicing of Wnt7b. Hence, our study suggests that lncRNA-mediated alternative splicing of cell fate determinants controls stem-cell commitment during neurogenesis.
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Affiliation(s)
- Julieta Aprea
- DFG-Research Center and Cluster of Excellence for Regenerative Therapies, Dresden, Germany
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29
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Cain JT, Berosik MA, Snyder SD, Crawford NF, Nour SI, Schaubhut GJ, Darland DC. Shifts in the vascular endothelial growth factor isoforms result in transcriptome changes correlated with early neural stem cell proliferation and differentiation in mouse forebrain. Dev Neurobiol 2013; 74:63-81. [PMID: 24124161 DOI: 10.1002/dneu.22130] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 08/21/2013] [Accepted: 09/04/2013] [Indexed: 12/12/2022]
Abstract
Regulation of neural stem cell (NSC) fate decisions is critical during the transition from a multicellular mammalian forebrain neuroepithelium to the multilayered neocortex. Forebrain development requires coordinated vascular investment alongside NSC differentiation. Vascular endothelial growth factor A (Vegf) has proven to be a pleiotrophic gene whose multiple protein isoforms regulate a broad range of effects in neurovascular systems. To test the hypothesis that the Vegf isoforms (120, 164, and 188) are required for normal forebrain development, we analyzed the forebrain transcriptome of mice expressing specific Vegf isoforms, Vegf120, VegfF188, or a combination of Vegf120/188. Transcriptome analysis identified differentially expressed genes in embryonic day (E) 9.5 forebrain, a time point preceding dramatic neuroepithelial expansion and vascular investment in the telencephalon. Meta-analysis identified gene pathways linked to chromosome-level modifications, cell fate regulation, and neurogenesis that were altered in Vegf isoform mice. Based on these gene network shifts, we predicted that NSC populations would be affected in later stages of forebrain development. In the E11.5 telencephalon, we quantified mitotic cells [Phospho-Histone H3 (pHH3)-positive] and intermediate progenitor cells (Tbr2/Eomes-positive), observing quantitative and qualitative shifts in these populations. We observed qualitative shifts in cortical layering at P0, particularly with Ctip2-positive cells in layer V. The results identify a suite of genes and functional gene networks that can be used to further dissect the role of Vegf in regulating NSC differentiation and downstream consequences for NSC fate decisions.
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Affiliation(s)
- Jacob T Cain
- Department of Biology, University of North Dakota, Grand Forks, North Dakota
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30
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Emre Onat O, Gulsuner S, Bilguvar K, Nazli Basak A, Topaloglu H, Tan M, Tan U, Gunel M, Ozcelik T. Missense mutation in the ATPase, aminophospholipid transporter protein ATP8A2 is associated with cerebellar atrophy and quadrupedal locomotion. Eur J Hum Genet 2013; 21:281-5. [PMID: 22892528 PMCID: PMC3573203 DOI: 10.1038/ejhg.2012.170] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 07/03/2012] [Accepted: 07/06/2012] [Indexed: 02/02/2023] Open
Abstract
Cerebellar ataxia, mental retardation and dysequilibrium syndrome is a rare and heterogeneous condition. We investigated a consanguineous family from Turkey with four affected individuals exhibiting the condition. Homozygosity mapping revealed that several shared homozygous regions, including chromosome 13q12. Targeted next-generation sequencing of an affected individual followed by segregation analysis, population screening and prediction approaches revealed a novel missense variant, p.I376M, in ATP8A2. The mutation lies in a highly conserved C-terminal transmembrane region of E1 E2 ATPase domain. The ATP8A2 gene is mainly expressed in brain and development, in particular cerebellum. Interestingly, an unrelated individual has been identified, in whom mental retardation and severe hypotonia is associated with a de novo t(10;13) balanced translocation resulting with the disruption of ATP8A2. These findings suggest that ATP8A2 is involved in the development of the cerebro-cerebellar structures required for posture and gait in humans.
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Affiliation(s)
- Onur Emre Onat
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey
| | - Suleyman Gulsuner
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey
| | - Kaya Bilguvar
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Center for Human Genetics and Genomics and Program on Neurogenetics, Yale University School of Medicine, New Haven, CT, USA
| | - Ayse Nazli Basak
- Department of Molecular Biology and Genetics, NDAL Laboratory, School of Arts and Sciences, Bogazici University, Istanbul, Turkey
| | - Haluk Topaloglu
- Department of Pediatric Neurology, Ihsan Dogramaci Children's Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Meliha Tan
- Department of Neurology, Baskent University Faculty of Medicine, Ankara, Turkey
| | - Uner Tan
- Department of Physiology, Cukurova University Faculty of Medicine, Adana, Turkey
| | - Murat Gunel
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Center for Human Genetics and Genomics and Program on Neurogenetics, Yale University School of Medicine, New Haven, CT, USA
| | - Tayfun Ozcelik
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey
- Institute of Materials Science and Nanotechnology (UNAM), Bilkent University, Ankara, Turkey
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31
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Qiu X, Ding S, Shi T. From understanding the development landscape of the canonical fate-switch pair to constructing a dynamic landscape for two-step neural differentiation. PLoS One 2012; 7:e49271. [PMID: 23300518 PMCID: PMC3530918 DOI: 10.1371/journal.pone.0049271] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 10/05/2012] [Indexed: 01/08/2023] Open
Abstract
Recent progress in stem cell biology, notably cell fate conversion, calls for novel theoretical understanding for cell differentiation. The existing qualitative concept of Waddington’s “epigenetic landscape” has attracted particular attention because it captures subsequent fate decision points, thus manifesting the hierarchical (“tree-like”) nature of cell fate diversification. Here, we generalized a recent work and explored such a developmental landscape for a two-gene fate decision circuit by integrating the underlying probability landscapes with different parameters (corresponding to distinct developmental stages). The change of entropy production rate along the parameter changes indicates which parameter changes can represent a normal developmental process while other parameters’ change can not. The transdifferentiation paths over the landscape under certain conditions reveal the possibility of a direct and reversible phenotypic conversion. As the intensity of noise increases, we found that the landscape becomes flatter and the dominant paths more straight, implying the importance of biological noise processing mechanism in development and reprogramming. We further extended the landscape of the one-step fate decision to that for two-step decisions in central nervous system (CNS) differentiation. A minimal network and dynamic model for CNS differentiation was firstly constructed where two three-gene motifs are coupled. We then implemented the SDEs (Stochastic Differentiation Equations) simulation for the validity of the network and model. By integrating the two landscapes for the two switch gene pairs, we constructed the two-step development landscape for CNS differentiation. Our work provides new insights into cellular differentiation and important clues for better reprogramming strategies.
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Affiliation(s)
- Xiaojie Qiu
- Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Shanshan Ding
- Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
- * E-mail:
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Choi YS, Karelina K, Alzate-Correa D, Hoyt KR, Impey S, Arthur JS, Obrietan K. Mitogen- and stress-activated kinases regulate progenitor cell proliferation and neuron development in the adult dentate gyrus. J Neurochem 2012; 123:676-88. [PMID: 23020821 PMCID: PMC3575744 DOI: 10.1111/jnc.12035] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 08/21/2012] [Accepted: 09/25/2012] [Indexed: 01/19/2023]
Abstract
The neurogenic niche within the subgranular zone (SGZ) of the dentate gyrus is a source of new neurons throughout life. Interestingly, SGZ proliferative capacity is regulated by both physiological and pathophysiological conditions. One outstanding question involves the molecular mechanisms that regulate both basal and inducible adult neurogenesis. Here, we examined the role of the MAPK-regulated kinases, mitogen- and stress-activated kinase (MSK)1 and MSK2. as regulators of dentate gyrus SGZ progenitor cell proliferation and neurogenesis. Under basal conditions, MSK1/2 null mice exhibited significantly reduced progenitor cell proliferation capacity and a corollary reduction in the number of doublecortin (DCX)-positive immature neurons. Strikingly, seizure-induced progenitor proliferation was totally blocked in MSK1/2 null mice. This blunting of cell proliferation in MSK1/2 null mice was partially reversed by forskolin infusion, indicating that the inducible proliferative capacity of the progenitor cell population was intact. Furthermore, in MSK1/2 null mice, DCX-positive immature neurons exhibited reduced neurite arborization. Together, these data reveal a critical role for MSK1/2 as regulators of both basal and activity-dependent progenitor cell proliferation and morphological maturation in the SGZ.
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Affiliation(s)
- Yun-Sik Choi
- Department of Pharmaceutical Science & Technology, Catholic University of Daegu, Gyeongbuk, Rep. of Korea
| | - Kate Karelina
- Department of Neuroscience, Ohio State University, Columbus, OH 43210
| | | | - Kari R. Hoyt
- Division of Pharmacology, Ohio State University, Columbus, OH 43210
| | - Soren Impey
- Department of Cell and Developmental Biology, Oregon Health & Sciences University, Portland, OR 97239
| | - J. Simon Arthur
- MRC Protein Phosphorylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, U.K
| | - Karl Obrietan
- Department of Neuroscience, Ohio State University, Columbus, OH 43210
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33
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Kaltwaßer B, Schulenborg T, Beck F, Klotz M, Schäfer KH, Schmitt M, Sickmann A, Friauf E. Developmental changes of the protein repertoire in the rat auditory brainstem: a comparative proteomics approach in the superior olivary complex and the inferior colliculus with DIGE and iTRAQ. J Proteomics 2012. [PMID: 23201114 DOI: 10.1016/j.jprot.2012.11.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Protein profiles of developing neural circuits undergo manifold changes. The aim of this proteomic analysis was to quantify postnatal changes in two auditory brainstem areas in a comparative approach. Protein samples from the inferior colliculus (IC) and the superior olivary complex (SOC) were obtained from neonatal (P4) and young adult (P60) rats. The cytosolic fractions of both areas were examined by 2-D DIGE, and the plasma membrane-enriched fraction of the IC was analyzed via iTRAQ. iTRAQ showed a regulation in 34% of the quantified proteins. DIGE revealed 12% regulated spots in both the SOC and IC and, thus, numeric congruency. Although regulation in KEGG pathways displayed a similar pattern in both areas, only 13 of 71 regulated DIGE proteins were regulated in common, implying major area-specific differences. 89% of regulated glycolysis/gluconeogenesis and citrate cycle proteins were up-regulated in the SOC or IC, suggesting a higher energy demand in adulthood. Seventeen cytoskeleton proteins were regulated, consistent with complex morphological reorganization between P4 and P60. Fourteen were uniquely regulated in the SOC, providing further evidence for area-specific differences. Altogether, we provide the first elaborate catalog of proteins involved in auditory brainstem development, several of them possibly of particular developmental relevance.
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Affiliation(s)
- Bernd Kaltwaßer
- Animal Physiology Group, Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
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34
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Diz AP, Páez de la Cadena M, Rolán-Alvarez E. Proteomic evidence of a paedomorphic evolutionary process within a marine snail species: a strategy for adapting to extreme ecological conditions? J Evol Biol 2012; 25:2569-81. [PMID: 23020901 DOI: 10.1111/jeb.12001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 08/28/2012] [Accepted: 08/30/2012] [Indexed: 11/28/2022]
Abstract
The exposed and sheltered ecotypes of the marine snail Littorina saxatilis from European rocky shores are considered a key model system to study adaptation and ecological speciation. Previous studies showed that two ecotypes (RB and SU) of this species in NW Spain have adapted differently to different shore levels and microhabitats. In order to understand how this divergent adaptive process has been accomplished, we followed a quantitative proteomic approach to investigate the proteome variation in a number of different biological factors, that is, ecotype, ontogeny and their interactions. This approach allowed testing the hypothesis that one of the ecotypes has evolved by paedomorphosis, and also whether or not the molecular mechanisms related to ecotype differentiation are set up in early developmental stages. Additionally, the identification of some candidate proteins using mass spectrometry provides some functional insights into these evolutionary processes. Results from this study provided evidence of higher ontogenetic differentiation at proteome level in the RB (metamorphic) than in SU (paedomorphic) ecotype that point to the possibility of juvenile stage retention in this latter ecotype. The level of protein expression (proteome) differences between ecotypes maintained nearly constant from late embryonic stages to adulthood, although some proteins involved in these changes considerably differed in embryonic compared to other ontogenetic stages. Paedomorphosis may be the evolutionary response of the SU ecotype of solving the trade-off during sexually immaturity that is caused by the evolution of small size arising from adaptation to the wave-exposed habitat. Some potential candidate genes of adaptation related to energetic metabolism have been identified, providing a promising baseline for future functional analyses.
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Affiliation(s)
- A P Diz
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, Spain.
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35
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Hartl D, Schuldt V, Forler S, Zabel C, Klose J, Rohe M. Presymptomatic alterations in energy metabolism and oxidative stress in the APP23 mouse model of Alzheimer disease. J Proteome Res 2012; 11:3295-304. [PMID: 22568827 DOI: 10.1021/pr300021e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glucose hypometabolism is the earliest symptom observed in the brains of Alzheimer disease (AD) patients. In a former study, we analyzed the cortical proteome of the APP23 mouse model of AD at presymptomatic age (1 month) using a 2-D electrophoresis-based approach. Interestingly, long before amyloidosis can be observed in APP23 mice, proteins associated with energy metabolism were predominantly altered in transgenic as compared to wild-type mice indicating presymptomatic changes in energy metabolism. In the study presented here, we analyzed whether the observed changes were associated with oxidative stress and confirmed our previous findings in primary cortical neurons, which exhibited altered ADP/ATP levels if transgenic APP was expressed. Reactive oxygen species produced during energy metabolism have important roles in cell signaling and homeostasis as they modify proteins. We observed an overall up-regulation of protein oxidation status as shown by increased protein carbonylation in the cortex of presymptomatic APP23 mice. Interestingly, many carbonylated proteins, such as Vilip1 and Syntaxin were associated to synaptic plasticity. This demonstrates an important link between energy metabolism and synaptic function, which is altered in AD. In summary, we demonstrate that changes in cortical energy metabolism and increased protein oxidation precede the amyloidogenic phenotype in a mouse model for AD. These changes might contribute to synaptic failure observed in later disease stages, as synaptic transmission is particularly dependent on energy metabolism.
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Affiliation(s)
- Daniela Hartl
- Institute for Medical Genetics and Human Genetics, Charité-University Medicine , Berlin, Germany
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36
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Xu Y, Qian H, Feng X, Xiong Y, Lei M, Ren Z, Zuo B, Xu D, Ma Y, Yuan H. Differential proteome and transcriptome analysis of porcine skeletal muscle during development. J Proteomics 2012; 75:2093-108. [DOI: 10.1016/j.jprot.2012.01.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2011] [Revised: 01/04/2012] [Accepted: 01/08/2012] [Indexed: 11/26/2022]
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37
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Robinson JF, Verhoef A, Piersma AH. Transcriptomic analysis of neurulation and early organogenesis in rat embryos: an in vivo and ex vivo comparison. Toxicol Sci 2012; 126:255-66. [PMID: 22262562 DOI: 10.1093/toxsci/kfr343] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cultured embryos mimic the morphological developmental progression of embryos (in vivo) undergoing neurulation and early organogenesis. Using available genomics technologies, comparative molecular-based assessments between cultured embryos and in vivo models may further clarify commonalities and dissimilarities, which contribute to differences between systems. Therefore, in this study, using a transcriptomic approach, we compared cultured whole rat embryos and embryos in vivo at comparable time points in development (gestational day (GD) 10 + 2-48 h, GD 0 = copulatory plug) to assess for commonalities and differences in gene expression in relation to morphology. We reveal strong parallels in time-dependent expression of genes in terms of magnitude, directionality, and functionality between whole embryo culture (WEC) and in vivo (rat). Genes changing in expression over time resemble previously hypothesized mechanisms underlying early development in mammalian systems. Furthermore, at the gene and functional level, we identify genes, which differ in expression between models, including genes related to development, oxygen transport, and metabolism. In summary, our results support the use of WEC for toxicological studies aimed at representing in vivo development during this time window at the molecular level. Additionally, we indicate genes, which differ in expression between models, providing possible insights for improvement of culture conditions.
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Affiliation(s)
- Joshua F Robinson
- Laboratory for Health Protection Research, National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, the Netherlands
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38
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Zheng G, Wang H, Wei C, Li Y. iGepros: an integrated gene and protein annotation server for biological nature exploration. BMC Bioinformatics 2011; 12 Suppl 14:S6. [PMID: 22373022 PMCID: PMC3287471 DOI: 10.1186/1471-2105-12-s14-s6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background In the post-genomic era, transcriptomics and proteomics provide important information to understand the genomes. With fast development of high-throughput technology, more and more transcriptomics and proteomics data are generated at an unprecedented rate. Therefore, requirement of software to annotate those omics data and explore their biological nature arises. In the past decade, some pioneer works were presented to address this issue, but limitations still exist. Fox example, some of these tools offer command line only, which is not suitable for those users with little or no experience in programming. Besides, some tools don’t support large scale gene and protein analysis. Results To overcome these limitations, an integrated gene and protein annotation server named iGepros has been developed. The server provides user-friendly interfaces and detailed on-line examples, so most researchers even those with little or no programming experience can use it smoothly. Moreover, the server provides many functionalities to compare transcriptomics and proteomics data. Especially, the server is constructed under a model-view-control framework, which makes it easy to incorporate more functions to the server in the future. Conclusions In this paper, we present a server with powerful capability not only for gene and protein functional annotation, but also for transcriptomics and proteomics data comparison. Researchers can survey biological characters behind gene and protein datasets and accelerate their investigation of transcriptome and proteome by applying the server. The server is publicly available at http://www.biosino.org/iGepros/.
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Affiliation(s)
- Guangyong Zheng
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
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39
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Gulsuner S, Tekinay AB, Doerschner K, Boyaci H, Bilguvar K, Unal H, Ors A, Onat OE, Atalar E, Basak AN, Topaloglu H, Kansu T, Tan M, Tan U, Gunel M, Ozcelik T. Homozygosity mapping and targeted genomic sequencing reveal the gene responsible for cerebellar hypoplasia and quadrupedal locomotion in a consanguineous kindred. Genome Res 2011; 21:1995-2003. [PMID: 21885617 DOI: 10.1101/gr.126110.111] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The biological basis for the development of the cerebro-cerebellar structures required for posture and gait in humans is poorly understood. We investigated a large consanguineous family from Turkey exhibiting an extremely rare phenotype associated with quadrupedal locomotion, mental retardation, and cerebro-cerebellar hypoplasia, linked to a 7.1-Mb region of homozygosity on chromosome 17p13.1-13.3. Diffusion weighted imaging and fiber tractography of the patients' brains revealed morphological abnormalities in the cerebellum and corpus callosum, in particular atrophy of superior, middle, and inferior peduncles of the cerebellum. Structural magnetic resonance imaging showed additional morphometric abnormalities in several cortical areas, including the corpus callosum, precentral gyrus, and Brodmann areas BA6, BA44, and BA45. Targeted sequencing of the entire homozygous region in three affected individuals and two obligate carriers uncovered a private missense mutation, WDR81 p.P856L, which cosegregated with the condition in the extended family. The mutation lies in a highly conserved region of WDR81, flanked by an N-terminal BEACH domain and C-terminal WD40 beta-propeller domains. WDR81 is predicted to be a transmembrane protein. It is highly expressed in the cerebellum and corpus callosum, in particular in the Purkinje cell layer of the cerebellum. WDR81 represents the third gene, after VLDLR and CA8, implicated in quadrupedal locomotion in humans.
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Affiliation(s)
- Suleyman Gulsuner
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
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40
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Parisi C, Giorgi C, Batassa EM, Braccini L, Maresca G, D'agnano I, Caputo V, Salvatore A, Pietrolati F, Cogoni C, Catalanotto C. Ago1 and Ago2 differentially affect cell proliferation, motility and apoptosis when overexpressed in SH-SY5Y neuroblastoma cells. FEBS Lett 2011; 585:2965-71. [PMID: 21846468 DOI: 10.1016/j.febslet.2011.08.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 08/01/2011] [Accepted: 08/01/2011] [Indexed: 01/20/2023]
Abstract
Argonaute are a conserved class of proteins central to the microRNA pathway. We have highlighted a novel and non-redundant function of Ago1 versus Ago2; the two core factors of the miRNA-associated RISC complex. Stable overexpression of Ago1 in neuroblastoma cells causes the cell cycle to slow down, a decrease in cellular motility and a stronger apoptotic response upon UV irradiation. These effects, together with a significant increase in p53 levels, suggest that Ago1 may act as a tumor-suppressor factor, a function also supported by GEO Profiles microarrays that inversely correlate Ago1 expression levels with cell proliferation rates.
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Affiliation(s)
- Chiara Parisi
- Department of Cellular Biotechnology and Hematology, Sapienza University, Rome, Italy
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41
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Yun SJ, Byun K, Bhin J, Oh JH, Nhung LTH, Hwang D, Lee B. Transcriptional regulatory networks associated with self-renewal and differentiation of neural stem cells. J Cell Physiol 2010; 225:337-47. [PMID: 20607797 DOI: 10.1002/jcp.22294] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Neural stem cells (NSCs) are self-renewing, multipotent cells that can generate neurons, astrocytes, and oligodendrocytes of the nervous system. NSCs have been extensively studied because they can be used to treat impaired cells and tissues or improve regenerative power of degenerating cells in neurodegenerative diseases or spinal cord injuries. For successful clinical applications of NSCs, it is essential to understand the mechanisms underlying self-renewal and differentiation of NSCs, which involve complex interplays among key factors including transcription factors, epigenetic control, microRNAs, and signaling pathways. Despite numerous studies on such factors, a holistic view of their interplays during neural development still remains elusive. In this review, we present recently identified potential regulatory factors and their targets by genomics and proteomics technologies and then integrate them into regulatory networks that describe their complex interplays to achieve self-renewal and differentiation of NSCs.
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Affiliation(s)
- So Jeong Yun
- School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea
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Proteasome and oxidative phoshorylation changes may explain why aging is a risk factor for neurodegenerative disorders. J Proteomics 2010; 73:2230-8. [DOI: 10.1016/j.jprot.2010.08.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 08/24/2010] [Accepted: 08/25/2010] [Indexed: 01/17/2023]
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Bilgüvar K, Oztürk AK, Louvi A, Kwan KY, Choi M, Tatli B, Yalnizoğlu D, Tüysüz B, Cağlayan AO, Gökben S, Kaymakçalan H, Barak T, Bakircioğlu M, Yasuno K, Ho W, Sanders S, Zhu Y, Yilmaz S, Dinçer A, Johnson MH, Bronen RA, Koçer N, Per H, Mane S, Pamir MN, Yalçinkaya C, Kumandaş S, Topçu M, Ozmen M, Sestan N, Lifton RP, State MW, Günel M. Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations. Nature 2010; 467:207-10. [PMID: 20729831 PMCID: PMC3129007 DOI: 10.1038/nature09327] [Citation(s) in RCA: 373] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Accepted: 06/30/2010] [Indexed: 11/12/2022]
Abstract
The development of the human cerebral cortex is an orchestrated process involving the birth of neural progenitors in the peri-ventricular germinal zones, cell proliferation characterized by both symmetric and asymmetric mitoses, followed by migration of post-mitotic neurons to their final destinations in 6 highly ordered, functionally-specialized layers1,2. An understanding of the molecular mechanisms guiding these intricate processes is in its infancy, substantially driven by the discovery of rare mutations that cause malformations of cortical development (MCD)3-6. Mapping of disease loci in putative Mendelian forms of MCD has been hindered by marked locus heterogeneity, small kindred sizes and diagnostic classifications that may not reflect molecular pathogenesis. Here we demonstrate the use of whole-exome sequencing to overcome these obstacles by identifying recessive mutations in WDR62 as the cause of a wide spectrum of severe cerebral cortical malformations including microcephaly, pachygria with cortical thickening as well as hypoplasia of the corpus callosum. Some patients with WDR62 mutations had evidence of additional abnormalities including lissencephaly, schizencephaly, polymicrogyria and, in one instance, cerebellar hypoplasia, all traits traditionally regarded as distinct entities. In mouse and humans, WDR62 transcripts and protein are enriched in neural progenitors within the ventricular and subventricular zones. WDR62 expression in the neocortex is transient, spanning the period of embryonic neurogenesis. Unlike other known microcephaly genes, WDR62 does not apparently associate with centrosomes and is predominantly nuclear in localization. These findings unify previously disparate aspects of cerebral cortical development and highlight the utility of whole-exome sequencing to identify disease loci in settings in which traditional methods have proved challenging.
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Affiliation(s)
- Kaya Bilgüvar
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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Zhang C. Proteomic Studies on the Development of the Central Nervous System and Beyond. Neurochem Res 2010; 35:1487-500. [DOI: 10.1007/s11064-010-0218-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2010] [Indexed: 11/27/2022]
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Mao L, Römer I, Nebrich G, Klein O, Koppelstätter A, Hin SC, Hartl D, Zabel C. Aging in Mouse Brain Is a Cell/Tissue-Level Phenomenon Exacerbated by Proteasome Loss. J Proteome Res 2010; 9:3551-60. [DOI: 10.1021/pr100059j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lei Mao
- Institute for Human Genetics, Charité - University Medicine Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Irmgard Römer
- Institute for Human Genetics, Charité - University Medicine Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Grit Nebrich
- Institute for Human Genetics, Charité - University Medicine Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Oliver Klein
- Institute for Human Genetics, Charité - University Medicine Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Andrea Koppelstätter
- Institute for Human Genetics, Charité - University Medicine Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Sascha C. Hin
- Institute for Human Genetics, Charité - University Medicine Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Daniela Hartl
- Institute for Human Genetics, Charité - University Medicine Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Claus Zabel
- Institute for Human Genetics, Charité - University Medicine Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
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Nebrich G, Herrmann M, Hartl D, Diedrich M, Kreitler T, Wierling C, Klose J, Giavalisco P, Zabel C, Mao L. PROTEOMER: A workflow-optimized laboratory information management system for 2-D electrophoresis-centered proteomics. Proteomics 2009; 9:1795-808. [DOI: 10.1002/pmic.200800522] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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47
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Myung JK, Shim KS, Li L, Höger H, Lubec G. Developmental Brain Protein Level Changes in the C57BL/6J Mouse. J Proteome Res 2009; 8:1207-19. [DOI: 10.1021/pr800990x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jae-Kyung Myung
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria, and Institute for Animal Genetics, Medical University of Vienna, Himberg, Austria
| | - Ki Shuk Shim
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria, and Institute for Animal Genetics, Medical University of Vienna, Himberg, Austria
| | - Lin Li
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria, and Institute for Animal Genetics, Medical University of Vienna, Himberg, Austria
| | - Harald Höger
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria, and Institute for Animal Genetics, Medical University of Vienna, Himberg, Austria
| | - Gert Lubec
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria, and Institute for Animal Genetics, Medical University of Vienna, Himberg, Austria
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Zabel C, Mao L, Woodman B, Rohe M, Wacker MA, Kläre Y, Koppelstätter A, Nebrich G, Klein O, Grams S, Strand A, Luthi-Carter R, Hartl D, Klose J, Bates GP. A large number of protein expression changes occur early in life and precede phenotype onset in a mouse model for huntington disease. Mol Cell Proteomics 2008; 8:720-34. [PMID: 19043139 DOI: 10.1074/mcp.m800277-mcp200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Huntington disease (HD) is fatal in humans within 15-20 years of symptomatic disease. Although late stage HD has been studied extensively, protein expression changes that occur at the early stages of disease and during disease progression have not been reported. In this study, we used a large two-dimensional gel/mass spectrometry-based proteomics approach to investigate HD-induced protein expression alterations and their kinetics at very early stages and during the course of disease. The murine HD model R6/2 was investigated at 2, 4, 6, 8, and 12 weeks of age, corresponding to absence of disease and early, intermediate, and late stage HD. Unexpectedly the most HD stage-specific protein changes (71-100%) as well as a drastic alteration (almost 6% of the proteome) in protein expression occurred already as early as 2 weeks of age. Early changes included mainly the up-regulation of proteins involved in glycolysis/gluconeogenesis and the down-regulation of the actin cytoskeleton. This suggests a period of highly variable protein expression that precedes the onset of HD phenotypes. Although an up-regulation of glycolysis/gluconeogenesis-related protein alterations remained dominant during HD progression, late stage alterations at 12 weeks showed an up-regulation of proteins involved in proteasomal function. The early changes in HD coincide with a peak in protein alteration during normal mouse development at 2 weeks of age that may be responsible for these massive changes. Protein and mRNA data sets showed a large overlap on the level of affected pathways but not single proteins/mRNAs. Our observations suggest that HD is characterized by a highly dynamic disease pathology not represented by linear protein concentration alterations over the course of disease.
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Affiliation(s)
- Claus Zabel
- Institute for Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
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Yamanaka factors critically regulate the developmental signaling network in mouse embryonic stem cells. Cell Res 2008; 18:1177-89. [DOI: 10.1038/cr.2008.309] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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50
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Reintsch WE, Mandato CA. Deciphering animal development through proteomics: requirements and prospects. Proteome Sci 2008; 6:21. [PMID: 18652672 PMCID: PMC2516511 DOI: 10.1186/1477-5956-6-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 07/24/2008] [Indexed: 12/28/2022] Open
Abstract
In recent years proteomic techniques have started to become very useful tools in a variety of model systems of developmental biology. Applications cover many different aspects of development, including the characterization of changes in the proteome during early embryonic stages. During early animal development the embryo becomes patterned through the temporally and spatially controlled activation of distinct sets of genes. Patterning information is then translated, from gastrulation onwards, into regional specific morphogenetic cell and tissue movements that give the embryo its characteristic shape. On the molecular level, patterning is the outcome of intercellular communication via signaling molecules and the local activation or repression of transcription factors. Genetic approaches have been used very successfully to elucidate the processes behind these events. Morphogenetic movements, on the other hand, have to be orchestrated through regional changes in the mechanical properties of cells. The molecular mechanisms that govern these changes have remained much more elusive, at least in part due to the fact that they are more under translational/posttranslational control than patterning events. However, recent studies indicate that proteomic approaches can provide the means to finally unravel the mechanisms that link patterning to the generation of embryonic form. To intensify research in this direction will require close collaboration between proteome scientists and developmental researchers. It is with this aim in mind that we first give an outline of the classical questions of patterning and morphogenesis. We then summarize the proteomic approaches that have been applied in developmental model systems and describe the pioneering studies that have been done to study morphogenesis. Finally we discuss current and future strategies that will allow characterizing the changes in the embryonic proteome and ultimately lead to a deeper understanding of the cellular mechanisms that govern the generation of embryonic form.
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Affiliation(s)
- Wolfgang E Reintsch
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec, H3A 2B2, Canada
| | - Craig A Mandato
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec, H3A 2B2, Canada
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