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Aydin O, Passaro AP, Raman R, Spellicy SE, Weinberg RP, Kamm RD, Sample M, Truskey GA, Zartman J, Dar RD, Palacios S, Wang J, Tordoff J, Montserrat N, Bashir R, Saif MTA, Weiss R. Principles for the design of multicellular engineered living systems. APL Bioeng 2022; 6:010903. [PMID: 35274072 PMCID: PMC8893975 DOI: 10.1063/5.0076635] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/02/2022] [Indexed: 12/14/2022] Open
Abstract
Remarkable progress in bioengineering over the past two decades has enabled the formulation of fundamental design principles for a variety of medical and non-medical applications. These advancements have laid the foundation for building multicellular engineered living systems (M-CELS) from biological parts, forming functional modules integrated into living machines. These cognizant design principles for living systems encompass novel genetic circuit manipulation, self-assembly, cell-cell/matrix communication, and artificial tissues/organs enabled through systems biology, bioinformatics, computational biology, genetic engineering, and microfluidics. Here, we introduce design principles and a blueprint for forward production of robust and standardized M-CELS, which may undergo variable reiterations through the classic design-build-test-debug cycle. This Review provides practical and theoretical frameworks to forward-design, control, and optimize novel M-CELS. Potential applications include biopharmaceuticals, bioreactor factories, biofuels, environmental bioremediation, cellular computing, biohybrid digital technology, and experimental investigations into mechanisms of multicellular organisms normally hidden inside the "black box" of living cells.
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Affiliation(s)
| | - Austin P. Passaro
- Regenerative Bioscience Center, University of Georgia, Athens, Georgia 30602, USA
| | - Ritu Raman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Robert P. Weinberg
- School of Pharmacy, Massachusetts College of Pharmacy and Health Sciences, Boston, Massachusetts 02115, USA
| | | | - Matthew Sample
- Center for Ethics and Law in the Life Sciences, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - George A. Truskey
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
| | - Jeremiah Zartman
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Roy D. Dar
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Sebastian Palacios
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - Jason Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jesse Tordoff
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Nuria Montserrat
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | | | - M. Taher A. Saif
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ron Weiss
- Author to whom correspondence should be addressed:
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Abstract
Several strands of evidence indicate the presence of marked similarities between human brain and testis. Understanding these similarities and their implications has become a topic of interest among the scientific community. Indeed, an association of intelligence with some semen quality parameters has been reported and a relation between dysfunctions of the human brain and testis has also been evident. Numerous common molecular features are evident when these tissues are compared, which is reflected in the huge number of common proteins. At the functional level, human neurons and sperm share a number of characteristics, including the importance of the exocytotic process and the presence of similar receptors and signalling pathways. The common proteins are mainly involved in exocytosis, tissue development and neuron/brain-associated biological processes. With this analysis, we conclude that human brain and testis share several biochemical characteristics which, in addition to their involvement in the speciation process, could, at least in part, be responsible for the expression of a huge number of common proteins. Nonetheless, this is an underexplored topic, and the connection between these tissues needs to be clarified, which could help to understand the dysfunctions affecting brain and testis, as well as to develop improved therapeutic strategies.
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Affiliation(s)
- Bárbara Matos
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Stephen J Publicover
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Luis Filipe C Castro
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.,Department of Biology, FCUP-Faculty of Sciences, University of Porto, Porto, Portugal
| | - Pedro J Esteves
- Department of Biology, FCUP-Faculty of Sciences, University of Porto, Porto, Portugal.,CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, Campus Agrico de Vairão, University of Porto, 4485-661 Vairão, Portugal
| | - Margarida Fardilha
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
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Kim YM, Kim HJ. Proteasome Inhibitor MG132 is Toxic and Inhibits the Proliferation of Rat Neural Stem Cells but Increases BDNF Expression to Protect Neurons. Biomolecules 2020; 10:biom10111507. [PMID: 33147870 PMCID: PMC7692322 DOI: 10.3390/biom10111507] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/21/2020] [Accepted: 10/27/2020] [Indexed: 12/31/2022] Open
Abstract
Regulation of protein expression is essential for maintaining normal cell function. Proteasomes play important roles in protein degradation and dysregulation of proteasomes is implicated in neurodegenerative disorders. In this study, using a proteasome inhibitor MG132, we showed that proteasome inhibition reduces neural stem cell (NSC) proliferation and is toxic to NSCs. Interestingly, MG132 treatment increased the percentage of neurons in both proliferation and differentiation culture conditions of NSCs. Proteasome inhibition reduced B-cell lymphoma 2 (Bcl-2)/Bcl-2 associated X protein ratio. In addition, MG132 treatment induced cAMP response element-binding protein phosphorylation and increased the expression of brain-derived neurotrophic factor transcripts and proteins. These data suggest that proteasome function is important for NSC survival and differentiation. Moreover, although MG132 is toxic to NSCs, it may increase neurogenesis. Therefore, by modifying MG132 chemical structure and developing none toxic proteasome inhibitors, neurogenic chemicals can be developed to control NSC cell fate.
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Affiliation(s)
| | - Hyun-Jung Kim
- Correspondence: ; Tel.: +82-2-820-5619; Fax: +82-2-816-7338
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Bunina D, Abazova N, Diaz N, Noh KM, Krijgsveld J, Zaugg JB. Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons. Cell Syst 2020; 10:480-494.e8. [PMID: 32553182 PMCID: PMC7322528 DOI: 10.1016/j.cels.2020.05.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 03/19/2020] [Accepted: 05/15/2020] [Indexed: 02/08/2023]
Abstract
Cellular differentiation requires dramatic changes in chromatin organization, transcriptional regulation, and protein production. To understand the regulatory connections between these processes, we generated proteomic, transcriptomic, and chromatin accessibility data during differentiation of mouse embryonic stem cells (ESCs) into postmitotic neurons and found extensive associations between different molecular layers within and across differentiation time points. We observed that SOX2, as a regulator of pluripotency and neuronal genes, redistributes from pluripotency enhancers to neuronal promoters during differentiation, likely driven by changes in its protein interaction network. We identified ATRX as a major SOX2 partner in neurons, whose co-localization correlated with an increase in active enhancer marks and increased expression of nearby genes, which we experimentally confirmed for three loci. Collectively, our data provide key insights into the regulatory transformation of SOX2 during neuronal differentiation, and we highlight the significance of multi-omic approaches in understanding gene regulation in complex systems. Complex interplay of RNA, protein, and chromatin during neuronal differentiation Multi-omic profiling reveals divergent roles of SOX2 in stem cells and neurons SOX2 on-chromatin interaction network changes from pluripotent to neuronal factors ATRX interacts with SOX2 in neurons and co-binds highly expressed neuronal genes
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Affiliation(s)
- Daria Bunina
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany; Genome Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany
| | - Nade Abazova
- Genome Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany; Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Collaboration for joint PhD degree between the European Molecular Biology Laboratory and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Nichole Diaz
- Genome Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany
| | - Kyung-Min Noh
- Genome Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany.
| | - Jeroen Krijgsveld
- Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Heidelberg University, Medical Faculty Heidelberg University, Faculty of Biosciences, Heidelberg, Germany.
| | - Judith B Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany.
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Loeliger BW, Hanu C, Panyutin IV, Maass-Moreno R, Wakim P, Pritchard WF, Neumann RD, Panyutin IG. Effect of Ionizing Radiation on Transcriptome during Neural Differentiation of Human Embryonic Stem Cells. Radiat Res 2020; 193:460-470. [PMID: 32216708 DOI: 10.1667/rr15535.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human embryonic brain development is highly sensitive to ionizing radiation. However, detailed information on the mechanisms of this sensitivity is not available due to limited experimental data. In this study, differentiation of human embryonic stem cells (hESCs) to neural lineages was used as a model for early embryonic brain development to assess the effect of exposure to low (17 mGy) and high (572 mGy) doses of radiation on gene expression. Transcriptomes were assessed using RNA sequencing during neural differentiation at three time points in control and irradiated samples. The first time point was when the cells were still pluripotent (day 0), the second time point was during the stage of embryoid body formation (day 6), and the third and final time point was during the stage of neural rosette formation (day 10). Analysis of the transcriptomes revealed neurodifferentiation in both the control and irradiated cells. Low-dose irradiation did not result in changes in gene expression at any of the time points, whereas high-dose irradiation resulted in downregulation of some major neurodifferentiation markers on days 6 and 10. Gene ontology analysis showed that pathways related to nervous system development, neurogenesis and generation of neurons were among the most affected. Expression of such key regulators of neuronal development as NEUROG1, ARX, ASCL1, RFX4 and INSM1 was reduced more than twofold. In conclusion, exposure to a 17 mGy low dose of radiation was well tolerated by hESCs while exposure to 572 mGy significantly affected their genetic reprogramming into neuronal lineages.
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Affiliation(s)
| | | | | | | | - Paul Wakim
- Department of Biostatistics and Clinical Epidemiology Service, Clinical Center, National Institutes of Health, Bethesda, Maryland 20892
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Ding H, Yu J, Chang W, Liu F, He Z. Searching for differentially expressed proteins in spinal cord injury based on the proteomics analysis. Life Sci 2020; 242:117235. [DOI: 10.1016/j.lfs.2019.117235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 12/21/2019] [Accepted: 12/25/2019] [Indexed: 02/07/2023]
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Song Y, Subramanian K, Berberich MJ, Rodriguez S, Latorre IJ, Luria CM, Everley R, Albers MW, Mitchison TJ, Sorger PK. A dynamic view of the proteomic landscape during differentiation of ReNcell VM cells, an immortalized human neural progenitor line. Sci Data 2019; 6:190016. [PMID: 30778261 DOI: 10.1038/sdata.2019.16] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 12/21/2018] [Indexed: 01/25/2023] Open
Abstract
The immortalized human ReNcell VM cell line represents a reproducible and easy-to-propagate cell culture system for studying the differentiation of neural progenitors. To better characterize the starting line and its subsequent differentiation, we assessed protein and phospho-protein levels and cell morphology over a 15-day period during which ReNcell progenitors differentiated into neurons, astrocytes and oligodendrocytes. Five of the resulting datasets measured protein levels or states of phosphorylation based on tandem-mass-tag (TMT) mass spectrometry and four datasets characterized cellular phenotypes using high-content microscopy. Proteomic analysis revealed reproducible changes in pathways responsible for cytoskeletal rearrangement, cell phase transitions, neuronal migration, glial differentiation, neurotrophic signalling and extracellular matrix regulation. Proteomic and imaging data revealed accelerated differentiation in cells treated with the poly-selective CDK and GSK3 inhibitor kenpaullone or the HMG-CoA reductase inhibitor mevastatin, both of which have previously been reported to promote neural differentiation. These data provide in-depth information on the ReNcell progenitor state and on neural differentiation in the presence and absence of drugs, setting the stage for functional studies.
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Abstract
Heat shock proteins (Hsps) are a large family of molecular chaperones that are well-known for their roles in protein maturation, re-folding and degradation. While some Hsps are constitutively expressed in certain regions, others are rapidly upregulated in the presence of stressful stimuli. Numerous stressors, including hyperthermia and hypoxia, can induce the expression of Hsps, which, in turn, interact with client proteins and co-chaperones to regulate cell growth and survival. Such interactions must be tightly regulated, especially at critical points during embryonic and postnatal development. Hsps exhibit specific patterns of expression consistent with a spatio-temporally regulated role in neurodevelopment. There is also growing evidence that Hsps may promote or inhibit neurodevelopment through specific pathways regulating cell differentiation, neurite outgrowth, cell migration, or angiogenesis. This review will examine the regulatory role that these individual chaperones may play in neurodevelopment, and will focus specifically on the signaling pathways involved in the maturation of neuronal and glial cells as well as the underlying vascular network.
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Affiliation(s)
- David J Miller
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI, United States.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Patrice E Fort
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI, United States.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
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9
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Hosp F, Mann M. A Primer on Concepts and Applications of Proteomics in Neuroscience. Neuron 2017; 96:558-571. [DOI: 10.1016/j.neuron.2017.09.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/29/2017] [Accepted: 09/14/2017] [Indexed: 02/06/2023]
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10
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Govaert E, Van Steendam K, Willems S, Vossaert L, Dhaenens M, Deforce D. Comparison of fractionation proteomics for local SWATH library building. Proteomics 2017; 17:1700052. [PMID: 28664598 PMCID: PMC5601298 DOI: 10.1002/pmic.201700052] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/23/2017] [Accepted: 06/28/2017] [Indexed: 01/08/2023]
Abstract
For data-independent acquisition by means of sequential window acquisition of all theoretical fragment ion spectra (SWATH), a reference library of data-dependent acquisition (DDA) runs is typically used to correlate the quantitative data from the fragment ion spectra with peptide identifications. The quality and coverage of such a reference library is therefore essential when processing SWATH data. In general, library sizes can be increased by reducing the impact of DDA precursor selection with replicate runs or fractionation. However, these strategies can affect the match between the library and SWATH measurement, and thus larger library sizes do not necessarily correspond to improved SWATH quantification. Here, three fractionation strategies to increase local library size were compared to standard library building using replicate DDA injection: protein SDS-PAGE fractionation, peptide high-pH RP-HPLC fractionation and MS-acquisition gas phase fractionation. The impact of these libraries on SWATH performance was evaluated in terms of the number of extracted peptides and proteins, the match quality of the peptides and the extraction reproducibility of the transitions. These analyses were conducted using the hydrophilic proteome of differentiating human embryonic stem cells. Our results show that SWATH quantitative results and interpretations are affected by choice of fractionation technique. Data are available via ProteomeXchange with identifier PXD006190.
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Affiliation(s)
- Elisabeth Govaert
- Laboratory of Pharmaceutical BiotechnologyGhent UniversityGhentBelgium
| | | | - Sander Willems
- Laboratory of Pharmaceutical BiotechnologyGhent UniversityGhentBelgium
| | - Liesbeth Vossaert
- Laboratory of Pharmaceutical BiotechnologyGhent UniversityGhentBelgium
| | - Maarten Dhaenens
- Laboratory of Pharmaceutical BiotechnologyGhent UniversityGhentBelgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical BiotechnologyGhent UniversityGhentBelgium
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Sarkar P, Mischler A, Randall SM, Collier TS, Dorman KF, Boggess KA, Muddiman DC, Rao BM. Identification of Epigenetic Factor Proteins Expressed in Human Embryonic Stem Cell-Derived Trophoblasts and in Human Placental Trophoblasts. J Proteome Res 2016; 15:2433-44. [PMID: 27378238 DOI: 10.1021/acs.jproteome.5b01118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Human embryonic stem cells (hESCs) have been used to derive trophoblasts through differentiation in vitro. Intriguingly, mouse ESCs are prevented from differentiation to trophoblasts by certain epigenetic factor proteins such as Dnmt1, thus necessitating the study of epigenetic factor proteins during hESC differentiation to trophoblasts. We used stable isotope labeling by amino acids in cell culture and quantitative proteomics to study changes in the nuclear proteome during hESC differentiation to trophoblasts and identified changes in the expression of 30 epigenetic factor proteins. Importantly, the DNA methyltransferases DNMT1, DNMT3A, and DNMT3B were downregulated. Additionally, we hypothesized that nuclear proteomics of hESC-derived trophoblasts may be used for screening epigenetic factor proteins expressed by primary trophoblasts in human placental tissue. Accordingly, we conducted immunohistochemistry analysis of six epigenetic factor proteins identified from hESC-derived trophoblasts-DNMT1, DNMT3B, BAF155, BAF60A, BAF57, and ING5-in 6-9 week human placentas. Indeed, expression of these proteins was largely, though not fully, consistent with that observed in 6-9 week placental trophoblasts. Our results support the use of hESC-derived trophoblasts as a model for placental trophoblasts, which will enable further investigation of epigenetic factors involved in human trophoblast development.
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Affiliation(s)
| | | | | | | | - Karen F Dorman
- Department of Obstetrics and Gynecology, University of North Carolina-Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Kim A Boggess
- Department of Obstetrics and Gynecology, University of North Carolina-Chapel Hill , Chapel Hill, North Carolina 27599, United States
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Annese T, Corsi P, Ruggieri S, Tamma R, Marinaccio C, Picocci S, Errede M, Specchia G, De Luca A, Frassanito MA, Desantis V, Vacca A, Ribatti D, Nico B. Isolation and characterization of neural stem cells from dystrophic mdx mouse. Exp Cell Res 2016; 343:190-207. [DOI: 10.1016/j.yexcr.2016.03.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 03/17/2016] [Accepted: 03/19/2016] [Indexed: 10/22/2022]
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13
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Subbannayya T, Leal-Rojas P, Barbhuiya MA, Raja R, Renuse S, Sathe G, Pinto SM, Syed N, Nanjappa V, Patil AH, Garcia P, Sahasrabuddhe NA, Nair B, Guerrero-Preston R, Navani S, Tiwari PK, Santosh V, Sidransky D, Prasad TSK, Gowda H, Roa JC, Pandey A, Chatterjee A. Macrophage migration inhibitory factor - a therapeutic target in gallbladder cancer. BMC Cancer 2015; 15:843. [PMID: 26530123 PMCID: PMC4632274 DOI: 10.1186/s12885-015-1855-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 10/27/2015] [Indexed: 12/20/2022] Open
Abstract
Background Poor prognosis in gallbladder cancer is due to late presentation of the disease, lack of reliable biomarkers for early diagnosis and limited targeted therapies. Early diagnostic markers and novel therapeutic targets can significantly improve clinical management of gallbladder cancer. Methods Proteomic analysis of four gallbladder cancer cell lines based on the invasive property (non-invasive to highly invasive) was carried out using the isobaric tags for relative and absolute quantitation labeling-based quantitative proteomic approach. The expression of macrophage migration inhibitory factor was analysed in gallbladder adenocarcinoma tissues using immunohistochemistry. In vitro cellular assays were carried out in a panel of gallbladder cancer cell lines using MIF inhibitors, ISO-1 and 4-IPP or its specific siRNA. Results The quantitative proteomic experiment led to the identification of 3,653 proteins, among which 654 were found to be overexpressed and 387 were downregulated in the invasive cell lines (OCUG-1, NOZ and GB-d1) compared to the non-invasive cell line, TGBC24TKB. Among these, macrophage migration inhibitory factor (MIF) was observed to be highly overexpressed in two of the invasive cell lines. MIF is a pleiotropic proinflammatory cytokine that plays a causative role in multiple diseases, including cancer. MIF has been reported to play a central role in tumor cell proliferation and invasion in several cancers. Immunohistochemical labeling of tumor tissue microarrays for MIF expression revealed that it was overexpressed in 21 of 29 gallbladder adenocarcinoma cases. Silencing/inhibition of MIF using siRNA and/or MIF antagonists resulted in a significant decrease in cell viability, colony forming ability and invasive property of the gallbladder cancer cells. Conclusions Our findings support the role of MIF in tumor aggressiveness and suggest its potential application as a therapeutic target for gallbladder cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1855-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tejaswini Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,Amrita School of Biotechnology, Amrita University, Kollam, 690525, India.
| | - Pamela Leal-Rojas
- Department of Pathology, Center of Genetic and Immunological Studies (CEGIN) and Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile. .,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Mustafa A Barbhuiya
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,Adrienne Helis Malvin Research Foundation, New Orleans, LA, 70130, USA.
| | - Remya Raja
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.
| | - Santosh Renuse
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,Amrita School of Biotechnology, Amrita University, Kollam, 690525, India.
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,Manipal University, Madhav Nagar, Manipal, 576104, India.
| | - Sneha M Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018, India.
| | - Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India.
| | - Vishalakshi Nanjappa
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,Amrita School of Biotechnology, Amrita University, Kollam, 690525, India.
| | - Arun H Patil
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India.
| | - Patricia Garcia
- Department of Pathology, Advanced Center for Chronic Diseases (ACCDiS), CITO, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | | | - Bipin Nair
- Amrita School of Biotechnology, Amrita University, Kollam, 690525, India.
| | - Rafael Guerrero-Preston
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA.
| | | | - Pramod K Tiwari
- Centre for Genomics, Molecular and Human Genetics, Jiwaji University, Gwalior, 474011, India. .,School of Studies in Zoology, Jiwaji University, Gwalior, India.
| | - Vani Santosh
- Department of Pathology, National Institute of Mental Health and Neurosciences, Bangalore, 560029, India.
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA.
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,Amrita School of Biotechnology, Amrita University, Kollam, 690525, India. .,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018, India. .,NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, 560029, India.
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018, India.
| | - Juan Carlos Roa
- Department of Pathology, Advanced Center for Chronic Diseases (ACCDiS), CITO, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,Departments of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,Manipal University, Madhav Nagar, Manipal, 576104, India. .,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018, India.
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Abstract
Neural stem cells (NSCs) can self-renew and give rise to the major cell types of the CNS. Studies of NSCs include the investigation of primary, CNS-derived cells as well as animal and human embryonic stem cell (ESC)-derived and induced pluripotent stem cell (iPSC)-derived sources. NSCs provide a means with which to study normal neural development, neurodegeneration, and neurological disease and are clinically relevant sources for cellular repair to the damaged and diseased CNS. Proteomics studies of NSCs have the potential to delineate molecules and pathways critical for NSC biology and the means by which NSCs can participate in neural repair. In this review, we provide a background to NSC biology, including the means to obtain them and the caveats to these processes. We then focus on advances in the proteomic interrogation of NSCs. This includes the analysis of posttranslational modifications (PTMs); approaches to analyzing different proteomic compartments, such the secretome; as well as approaches to analyzing temporal differences in the proteome to elucidate mechanisms of differentiation. We also discuss some of the methods that will undoubtedly be useful in the investigation of NSCs but which have not yet been applied to the field. While many proteomics studies of NSCs have largely catalogued the proteome or posttranslational modifications of specific cellular states, without delving into specific functions, some have led to understandings of functional processes or identified markers that could not have been identified via other means. Many challenges remain in the field, including the precise identification and standardization of NSCs used for proteomic analyses, as well as how to translate fundamental proteomics studies to functional biology. The next level of investigation will require interdisciplinary approaches, combining the skills of those interested in the biochemistry of proteomics with those interested in modulating NSC function.
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Affiliation(s)
- Lorelei D Shoemaker
- From the ‡Department of Neurosurgery, Stanford Neuromolecular Innovation Program, Stanford University, 300 Pasteur Drive, Stanford, CA 94305
| | - Harley I Kornblum
- §NPI-Semel Institute for Neuroscience & Human Behavior, Departments of Psychiatry and Biobehavioral Sciences, and of Molecular and Medical Pharmacology, The Molecular Biology Institute, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, and The Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los, Angeles, CA 90095
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Melo-Braga MN, Meyer M, Zeng X, Larsen MR. Characterization of human neural differentiation from pluripotent stem cells using proteomics/PTMomics-Current state-of-the-art and challenges. Proteomics 2015; 15:656-74. [DOI: 10.1002/pmic.201400388] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 11/11/2014] [Accepted: 11/19/2014] [Indexed: 01/18/2023]
Affiliation(s)
- Marcella Nunes Melo-Braga
- Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense Denmark
- Center for Clinical Proteomics; University of Southern Denmark; Odense Denmark
| | - Morten Meyer
- Department of Neurobiology Research; Institute of Molecular Medicine; University of Southern Denmark; Odense Denmark
| | | | - Martin Røssel Larsen
- Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense Denmark
- Center for Clinical Proteomics; University of Southern Denmark; Odense Denmark
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Ambekar AS, Kelkar DS, Pinto SM, Sharma R, Hinduja I, Zaveri K, Pandey A, Prasad TSK, Gowda H, Mukherjee S. Proteomics of follicular fluid from women with polycystic ovary syndrome suggests molecular defects in follicular development. J Clin Endocrinol Metab 2015; 100:744-53. [PMID: 25393639 PMCID: PMC5393508 DOI: 10.1210/jc.2014-2086] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
CONTEXT Polycystic ovary syndrome (PCOS), a major cause of anovulatory infertility, is characterized by arrested follicular growth. Altered protein levels in the follicular fluid surrounding the ovum may reflect the molecular defects of folliculogenesis in these women. OBJECTIVE To identify differentially regulated proteins in PCOS by comparing the follicular fluid protein repertoire of PCOS with healthy women. METHODS The follicular fluid samples were collected from PCOS and normo-ovulatory women undergoing in vitro fertilization. Follicular fluid proteins were subjected to digestion using trypsin, and resultant peptides were labeled with isobaric tags for relative and absolute quantification reagents and analyzed by liquid chromatography tandem mass spectrometry. Differential abundance of selected proteins was confirmed by ELISA. RESULTS A total of 770 proteins were identified, of which 186 showed differential abundance between controls and women with PCOS. Proteins involved in various processes of follicular development including amphiregulin; heparan sulfate proteoglycan 2; tumor necrosis factor, α-induced protein 6; plasminogen; and lymphatic vessel endothelial hyaluronan receptor 1 were found to be deregulated in PCOS. We also identified a number of new proteins from follicular fluid, whose function in the ovary is not yet clearly established. These include suprabasin; S100 calcium binding protein A7; and helicase with zinc finger 2, transcriptional coactivator. CONCLUSIONS Proteins indispensable for follicular growth were found to be differentially expressed in follicular fluid of women with PCOS, which may in part explain the aberrant folliculogenesis observed in these women.
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Affiliation(s)
- Aditi S Ambekar
- Department of Molecular Endocrinology (A.S.A., S.M.), National Institute for Research in Reproductive Health, Indian Council of Medical Research, Mumbai 400012, India; Institute of Bioinformatics (D.S.K., S.M.P., A.P., T.S.K.P., H.G.), International Technology Park, Bangalore 560066, India; Manipal University (S.M.P.), Madhav Nagar, Manipal 576104, Karnataka, India; Department of Neurochemistry (R.S.), National Institute of Mental Health and Neuro Sciences, Bangalore 560066, India; INKUS IVF Clinic (I.H., K.Z.), Mumbai 400004, India; and McKusick-Nathans Institute of Genetic Medicine and Departments of Biological Chemistry, Pathology and Oncology (A.P.), Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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All AH, Gharibani P, Gupta S, Bazley FA, Pashai N, Chou BK, Shah S, Resar LM, Cheng L, Gearhart JD, Kerr CL. Early intervention for spinal cord injury with human induced pluripotent stem cells oligodendrocyte progenitors. PLoS One 2015; 10:e0116933. [PMID: 25635918 PMCID: PMC4311989 DOI: 10.1371/journal.pone.0116933] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 12/16/2014] [Indexed: 12/16/2022] Open
Abstract
Induced pluripotent stem (iPS) cells are at the forefront of research in regenerative medicine and are envisaged as a source for personalized tissue repair and cell replacement therapy. Here, we demonstrate for the first time that oligodendrocyte progenitors (OPs) can be derived from iPS cells generated using either an episomal, non-integrating plasmid approach or standard integrating retroviruses that survive and differentiate into mature oligodendrocytes after early transplantation into the injured spinal cord. The efficiency of OP differentiation in all 3 lines tested ranged from 40% to 60% of total cells, comparable to those derived from human embryonic stem cells. iPS cell lines derived using episomal vectors or retroviruses generated a similar number of early neural progenitors and glial progenitors while the episomal plasmid-derived iPS line generated more OPs expressing late markers O1 and RIP. Moreover, we discovered that iPS-derived OPs (iPS-OPs) engrafted 24 hours following a moderate contusive spinal cord injury (SCI) in rats survived for approximately two months and that more than 70% of the transplanted cells differentiated into mature oligodendrocytes that expressed myelin associated proteins. Transplanted OPs resulted in a significant increase in the number of myelinated axons in animals that received a transplantation 24 h after injury. In addition, nearly a 5-fold reduction in cavity size and reduced glial scarring was seen in iPS-treated groups compared to the control group, which was injected with heat-killed iPS-OPs. Although further investigation is needed to understand the mechanisms involved, these results provide evidence that patient-specific, iPS-derived OPs can survive for three months and improve behavioral assessment (BBB) after acute transplantation into SCI. This is significant as determining the time in which stem cells are injected after SCI may influence their survival and differentiation capacity.
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Affiliation(s)
- Angelo H. All
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Singapore Institute for Neurotechnology, National University of Singapore, Singapore, Singapore
- Departments of Orthopedic Surgery, Biomedical Engineering and Medicine, Division of Neurology, National University of Singapore, Singapore, Singapore
| | - Payam Gharibani
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Siddharth Gupta
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Faith A. Bazley
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Singapore Institute for Neurotechnology, National University of Singapore, Singapore, Singapore
| | - Nikta Pashai
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Bin-Kuan Chou
- Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sandeep Shah
- Division of Hematology in Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Linda M. Resar
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Division of Hematology in Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Linzhao Cheng
- Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Division of Hematology in Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - John D. Gearhart
- Department of Cell and Developmental Biology in the School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Animal Biology in the School of Veterinary Medicine; University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Candace L. Kerr
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Obstetrics and Gynecology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Biochemistry and Molecular Biology, Unversity of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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Zizkova M, Sucha R, Tyleckova J, Jarkovska K, Mairychova K, Kotrcova E, Marsala M, Gadher SJ, Kovarova H. Proteome-wide analysis of neural stem cell differentiation to facilitate transition to cell replacement therapies. Expert Rev Proteomics 2014; 12:83-95. [PMID: 25363140 DOI: 10.1586/14789450.2015.977381] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Neurodegenerative diseases are devastating disorders and the demands on their treatment are set to rise in connection with higher disease incidence. Knowledge of the spatiotemporal profile of cellular protein expression during neural differentiation and definition of a set of markers highly specific for targeted neural populations is a key challenge. Intracellular proteins may be utilized as a readout for follow-up transplantation and cell surface proteins may facilitate isolation of the cell subpopulations, while secreted proteins could help unravel intercellular communication and immunomodulation. This review summarizes the potential of proteomics in revealing molecular mechanisms underlying neural differentiation of stem cells and presents novel candidate proteins of neural subpopulations, where understanding of their functionality may accelerate transition to cell replacement therapies.
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Affiliation(s)
- Martina Zizkova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics, AS CR, v.v.i., Libechov, Czech Republic
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Fathi A, Hatami M, Vakilian H, Han CL, Chen YJ, Baharvand H, Salekdeh GH. Quantitative proteomics analysis highlights the role of redox hemostasis and energy metabolism in human embryonic stem cell differentiation to neural cells. J Proteomics 2014; 101:1-16. [PMID: 24530625 DOI: 10.1016/j.jprot.2014.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/16/2014] [Accepted: 02/01/2014] [Indexed: 01/15/2023]
Abstract
UNLABELLED Neural differentiation of human embryonic stem cells (hESCs) is a unique opportunity for in vitro analyses of neurogenesis in humans. Extrinsic cues through neural plate formation are well described in the hESCs although intracellular mechanisms underlying neural development are largely unknown. Proteome analysis of hESC differentiation to neural cells will help to further define molecular mechanisms involved in neurogenesis in humans. Using a two-dimensional differential gel electrophoresis (2D-DIGE) system, we analyzed the proteome of hESC differentiation to neurons at three stages, early neural differentiation, neural ectoderm and mature neurons. Out of 137 differentially accumulated protein spots, 118 spots were identified using MALDI-TOF/TOF and LC MS/MS. We observed that proteins involved in redox hemostasis, vitamin and energy metabolism and ubiquitin dependent proteolysis were more abundant in differentiated cells, whereas the abundance of proteins associated with RNA processing and protein folding was higher in hESCs. Higher abundance of proteins involved in maintaining cellular redox state suggests the importance of redox hemostasis in neural differentiation. Furthermore, our results support the concept of a coupling mechanism between neuronal activity and glucose utilization. The protein network analysis showed that the majority of the interacting proteins were associated with the cell cycle and cellular proliferation. These results enhanced our understanding of the molecular dynamics that underlie neural commitment and differentiation. BIOLOGICAL SIGNIFICANCE In highlighting the role of redox and unique metabolic properties of neuronal cells, the present findings add insight to our understanding of hESC differentiation to neurons. The abundance of fourteen proteins involved in maintaining cellular redox state, including 10 members of peroxiredoxin (Prdx) family, mainly increased during differentiation, thus highlighting a link of neural differentiation to redox. Our results revealed markedly higher expression of genes encoding enzymes involved in the glycolysis and amino acid synthesis during differentiation. Protein network analysis predicted a number of critical mediators in hESC differentiation. These proteins included TP53, CTNNB1, SMARCA4, TNF, TERT, E2F1, MYC, RB1, and AR.
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Honecker F, Rohlfing T, Harder S, Braig M, Gillis AJ, Glaesener S, Barett C, Bokemeyer C, Buck F, Brümmendorf TH, Looijenga LH, Balabanov S. Proteome analysis of the effects of all-trans retinoic acid on human germ cell tumor cell lines. J Proteomics 2014; 96:300-13. [DOI: 10.1016/j.jprot.2013.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 10/29/2013] [Accepted: 11/12/2013] [Indexed: 01/16/2023]
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Melo-Braga MN, Schulz M, Liu Q, Swistowski A, Palmisano G, Engholm-Keller K, Jakobsen L, Zeng X, Larsen MR. Comprehensive quantitative comparison of the membrane proteome, phosphoproteome, and sialiome of human embryonic and neural stem cells. Mol Cell Proteomics 2013; 13:311-28. [PMID: 24173317 DOI: 10.1074/mcp.m112.026898] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Human embryonic stem cells (hESCs) can differentiate into neural stem cells (NSCs), which can further be differentiated into neurons and glia cells. Therefore, these cells have huge potential as source for treatment of neurological diseases. Membrane-associated proteins are very important in cellular signaling and recognition, and their function and activity are frequently regulated by post-translational modifications such as phosphorylation and glycosylation. To obtain information about membrane-associated proteins and their modified amino acids potentially involved in changes of hESCs and NSCs as well as to investigate potential new markers for these two cell stages, we performed large-scale quantitative membrane-proteomic of hESCs and NSCs. This approach employed membrane purification followed by peptide dimethyl labeling and peptide enrichment to study the membrane subproteome as well as changes in phosphorylation and sialylation between hESCs and NSCs. Combining proteomics and modification specific proteomics we identified a total of 5105 proteins whereof 57% contained transmembrane domains or signal peptides. The enrichment strategy yielded a total of 10,087 phosphorylated peptides in which 78% of phosphopeptides were identified with ≥99% confidence in site assignment and 1810 unique formerly sialylated N-linked glycopeptides. Several proteins were identified as significantly regulated in hESCs and NSC, including proteins involved in the early embryonic and neural development. In the latter group of proteins, we could identify potential NSC markers as Crumbs 2 and several novel proteins. A motif analysis of the altered phosphosites showed a sequence consensus motif (R-X-XpS/T) significantly up-regulated in NSC. This motif is among other kinases recognized by the calmodulin-dependent protein kinase-2, emphasizing a possible importance of this kinase for this cell stage. Collectively, this data represent the most diverse set of post-translational modifications reported for hESCs and NSCs. This study revealed potential markers to distinguish NSCs from hESCs and will contribute to improve our understanding on the differentiation process.
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Hansson J, Krijgsveld J. Proteomic analysis of cell fate decision. Curr Opin Genet Dev 2013; 23:540-7. [DOI: 10.1016/j.gde.2013.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 06/05/2013] [Accepted: 06/23/2013] [Indexed: 02/08/2023]
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Li Q, Jain MR, Chen W, Li H. A multidimensional approach to an in-depth proteomics analysis of transcriptional regulators in neuroblastoma cells. J Neurosci Methods 2013; 216:118-27. [PMID: 23558336 DOI: 10.1016/j.jneumeth.2013.03.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/21/2013] [Accepted: 03/24/2013] [Indexed: 12/13/2022]
Abstract
The dynamic regulation of transcriptional events is fundamental to many aspects of neuronal cell functions. However, proteomics methods have not been routinely used in global neuroproteomics analyses of transcriptional regulators because they are much less abundant than the "house-keeping" proteins in cells and tissues. Recent improvements in both biochemical preparations of nuclear proteins and detection sensitivities of proteomics technologies have made the global analysis of nuclear transcriptional regulators possible. We report here an optimised neuroproteomic method for the analysis of transcriptional regulators in the nuclear extracts of SHSY-5Y neuroblastoma cells by combining an improved nuclear protein extraction procedure with multidimensional peptide separation approaches. We found that rigorous removal of cytoplasmic proteins and solubilisation of DNA-associated proteins improved the number of nuclear proteins identified. Furthermore, we discovered that multidimensional peptide separations by either strong cation exchange (SCX) chromatography or electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) analysis detected more than 1800 nuclear proteins, which constitutes one of the largest datasets of nuclear proteins reported for a neuronal cell. Thus, in-depth analysis of transcriptional regulators for studying neurological diseases are increasingly feasible.
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Affiliation(s)
- Qing Li
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School Cancer Center, 205 S. Orange Avenue, F-1226, Newark, NJ 07103, USA
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Raad M, El Tal T, Gul R, Mondello S, Zhang Z, Boustany RM, Guingab J, Wang KK, Kobeissy F. Neuroproteomics approach and neurosystems biology analysis: ROCK inhibitors as promising therapeutic targets in neurodegeneration and neurotrauma. Electrophoresis 2012; 33:3659-68. [DOI: 10.1002/elps.201200470] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 10/07/2012] [Accepted: 10/08/2012] [Indexed: 12/14/2022]
Affiliation(s)
- Mohamad Raad
- Department of Biochemistry and Molecular Genetics; Faculty of Medicine; American University of Beirut; Beirut; Lebanon
| | - Tala El Tal
- Faculty of Medicine; American University of Beirut; Beirut; Lebanon
| | - Rukhsana Gul
- Department of Internal Medicine; Harry S. Truman Veterans Affairs Medical Center; University of Missouri; Columbia; MO; USA
| | - Stefania Mondello
- Center of Innovative Research Banyan Biomarkers Inc.; Alachua; FL; USA
| | - Zhiqun Zhang
- Department of Psychiatry; University of Florida; Gainesville; FL; USA
| | | | - Joy Guingab
- Center of Innovative Research Banyan Biomarkers Inc.; Alachua; FL; USA
| | - Kevin K. Wang
- Department of Psychiatry; University of Florida; Gainesville; FL; USA
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Kanakasabai S, Pestereva E, Chearwae W, Gupta SK, Ansari S, Bright JJ. PPARγ agonists promote oligodendrocyte differentiation of neural stem cells by modulating stemness and differentiation genes. PLoS One 2012. [PMID: 23185633 PMCID: PMC3503969 DOI: 10.1371/journal.pone.0050500] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Neural stem cells (NSCs) are a small population of resident cells that can grow, migrate and differentiate into neuro-glial cells in the central nervous system (CNS). Peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor transcription factor that regulates cell growth and differentiation. In this study we analyzed the influence of PPARγ agonists on neural stem cell growth and differentiation in culture. We found that in vitro culture of mouse NSCs in neurobasal medium with B27 in the presence of epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF) induced their growth and expansion as neurospheres. Addition of all-trans retinoic acid (ATRA) and PPARγ agonist ciglitazone or 15-Deoxy-Δ12,14-Prostaglandin J2 (15d-PGJ2) resulted in a dose-dependent inhibition of cell viability and proliferation of NSCs in culture. Interestingly, NSCs cultured with PPARγ agonists, but not ATRA, showed significant increase in oligodendrocyte precursor-specific O4 and NG2 reactivity with a reduction in NSC marker nestin, in 3–7 days. In vitro treatment with PPARγ agonists and ATRA also induced modest increase in the expression of neuronal β-III tubulin and astrocyte-specific GFAP in NSCs in 3–7 days. Further analyses showed that PPARγ agonists and ATRA induced significant alterations in the expression of many stemness and differentiation genes associated with neuro-glial differentiation in NSCs. These findings highlight the influence of PPARγ agonists in promoting neuro-glial differentiation of NSCs and its significance in the treatment of neurodegenerative diseases.
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Affiliation(s)
- Saravanan Kanakasabai
- Neuroscience Research Laboratory, Methodist Research Institute, Indiana University Health, Indianapolis, Indiana, United States of America
| | - Ecaterina Pestereva
- Neuroscience Research Laboratory, Methodist Research Institute, Indiana University Health, Indianapolis, Indiana, United States of America
| | - Wanida Chearwae
- Neuroscience Research Laboratory, Methodist Research Institute, Indiana University Health, Indianapolis, Indiana, United States of America
| | - Sushil K. Gupta
- Neuroscience Research Laboratory, Methodist Research Institute, Indiana University Health, Indianapolis, Indiana, United States of America
| | - Saif Ansari
- Neuroscience Research Laboratory, Methodist Research Institute, Indiana University Health, Indianapolis, Indiana, United States of America
| | - John J. Bright
- Neuroscience Research Laboratory, Methodist Research Institute, Indiana University Health, Indianapolis, Indiana, United States of America
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
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Shah SN, Kerr C, Cope L, Zambidis E, Liu C, Hillion J, Belton A, Huso DL, Resar LMS. HMGA1 reprograms somatic cells into pluripotent stem cells by inducing stem cell transcriptional networks. PLoS One 2012; 7:e48533. [PMID: 23166588 PMCID: PMC3499526 DOI: 10.1371/journal.pone.0048533] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 09/26/2012] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Although recent studies have identified genes expressed in human embryonic stem cells (hESCs) that induce pluripotency, the molecular underpinnings of normal stem cell function remain poorly understood. The high mobility group A1 (HMGA1) gene is highly expressed in hESCs and poorly differentiated, stem-like cancers; however, its role in these settings has been unclear. METHODS/PRINCIPAL FINDINGS We show that HMGA1 is highly expressed in fully reprogrammed iPSCs and hESCs, with intermediate levels in ECCs and low levels in fibroblasts. When hESCs are induced to differentiate, HMGA1 decreases and parallels that of other pluripotency factors. Conversely, forced expression of HMGA1 blocks differentiation of hESCs. We also discovered that HMGA1 enhances cellular reprogramming of somatic cells to iPSCs together with the Yamanaka factors (OCT4, SOX2, KLF4, cMYC - OSKM). HMGA1 increases the number and size of iPSC colonies compared to OSKM controls. Surprisingly, there was normal differentiation in vitro and benign teratoma formation in vivo of the HMGA1-derived iPSCs. During the reprogramming process, HMGA1 induces the expression of pluripotency genes, including SOX2, LIN28, and cMYC, while knockdown of HMGA1 in hESCs results in the repression of these genes. Chromatin immunoprecipitation shows that HMGA1 binds to the promoters of these pluripotency genes in vivo. In addition, interfering with HMGA1 function using a short hairpin RNA or a dominant-negative construct blocks cellular reprogramming to a pluripotent state. CONCLUSIONS Our findings demonstrate for the first time that HMGA1 enhances cellular reprogramming from a somatic cell to a fully pluripotent stem cell. These findings identify a novel role for HMGA1 as a key regulator of the stem cell state by inducing transcriptional networks that drive pluripotency. Although further studies are needed, these HMGA1 pathways could be exploited in regenerative medicine or as novel therapeutic targets for poorly differentiated, stem-like cancers.
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Affiliation(s)
- Sandeep N. Shah
- Hematology Division, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Medicine, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Candace Kerr
- Obstetrics & Gynecology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Leslie Cope
- Oncology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Biostatistics, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Elias Zambidis
- Oncology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Comparative Molecular & Pathobiology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Cyndi Liu
- Obstetrics & Gynecology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Joelle Hillion
- Hematology Division, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Amy Belton
- Hematology Division, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Medicine, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - David L. Huso
- Oncology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Comparative Molecular & Pathobiology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Pathology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Linda M. S. Resar
- Hematology Division, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Medicine, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Oncology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Pediatrics, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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Thirant C, Galan-Moya EM, Dubois LG, Pinte S, Chafey P, Broussard C, Varlet P, Devaux B, Soncin F, Gavard J, Junier MP, Chneiweiss H. Differential proteomic analysis of human glioblastoma and neural stem cells reveals HDGF as a novel angiogenic secreted factor. Stem Cells 2012; 30:845-53. [PMID: 22331796 DOI: 10.1002/stem.1062] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Presence in glioblastomas of cancer cells with normal neural stem cell (NSC) properties, tumor initiating capacity, and resistance to current therapies suggests that glioblastoma stem-like cells (GSCs) play central roles in glioblastoma development. We cultured human GSCs endowed with all features of tumor stem cells, including tumor initiation after xenograft and radio-chemoresistance. We established proteomes from four GSC cultures and their corresponding whole tumor tissues (TTs) and from human NSCs. Two-dimensional difference gel electrophoresis and tandem mass spectrometry revealed a twofold increase of hepatoma-derived growth factor (HDGF) in GSCs as compared to TTs and NSCs. Western blot analysis confirmed HDGF overexpression in GSCs as well as its presence in GSC-conditioned medium, while, in contrast, no HDGF was detected in NSC secretome. At the functional level, GSC-conditioned medium induced migration of human cerebral endothelial cells that can be blocked by anti-HDGF antibodies. In vivo, GSC-conditioned medium induced neoangiogenesis, whereas HDGF-targeting siRNAs abrogated this effect. Altogether, our results identify a novel candidate, by which GSCs can support neoangiogenesis, a high-grade glioma hallmark. Our strategy illustrates the usefulness of comparative proteomic analysis to decipher molecular pathways, which underlie GSC properties.
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Affiliation(s)
- Cécile Thirant
- INSERM U894, Psychiatry and Neuroscience Center, Glial Plasticity Team, Cochin Institute, Paris Descartes University, Paris, France
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29
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Jadaliha M, Lee HJ, Pakzad M, Fathi A, Jeong SK, Cho SY, Baharvand H, Paik YK, Salekdeh GH. Quantitative proteomic analysis of human embryonic stem cell differentiation by 8-plex iTRAQ labelling. PLoS One 2012; 7:e38532. [PMID: 22723866 PMCID: PMC3377673 DOI: 10.1371/journal.pone.0038532] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 05/07/2012] [Indexed: 12/24/2022] Open
Abstract
Analysis of gene expression to define molecular mechanisms and pathways involved in human embryonic stem cells (hESCs) proliferation and differentiations has allowed for further deciphering of the self-renewal and pluripotency characteristics of hESC. Proteins associated with hESCs were discovered through isobaric tags for relative and absolute quantification (iTRAQ). Undifferentiated hESCs and hESCs in different stages of spontaneous differentiation by embryoid body (EB) formation were analyzed. Using the iTRAQ approach, we identified 156 differentially expressed proteins involved in cell proliferation, apoptosis, transcription, translation, mRNA processing, and protein synthesis. Proteins involved in nucleic acid binding, protein synthesis, and integrin signaling were downregulated during differentiation, whereas cytoskeleton proteins were upregulated. The present findings added insight to our understanding of the mechanisms involved in hESC proliferation and differentiation.
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Affiliation(s)
- Mahdieh Jadaliha
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Hyoung-Joo Lee
- Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Yonsei University, Sudaemoon-Ku, Seoul, Korea
| | - Mohammad Pakzad
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Ali Fathi
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Seul-Ki Jeong
- Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Yonsei University, Sudaemoon-Ku, Seoul, Korea
| | - Sang-Yun Cho
- Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Yonsei University, Sudaemoon-Ku, Seoul, Korea
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, ACECR, Tehran, Iran
| | - Young-Ki Paik
- Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Yonsei University, Sudaemoon-Ku, Seoul, Korea
- * E-mail: (GSH); (Y-KP)
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
- * E-mail: (GSH); (Y-KP)
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Abstract
Genomics methodologies have advanced to the extent that it is now possible to interrogate the gene expression in a single cell but proteomics has traditionally lagged behind and required much greater cellular input and was not quantitative. Coupling protein with gene expression data is essential for understanding how cell behavior is regulated. Advances primarily in mass spectrometry have, however, greatly improved the sensitivity of proteomics methods over the last decade and the outcome of proteomic analyses can now also be quantified. Nevertheless, it is still difficult to obtain sufficient tissue from staged mammalian embryos to combine proteomic and genomic analyses. Recent developments in pluripotent stem cell biology have in part addressed this issue by providing surrogate scalable cell systems in which early developmental events can be modeled. Here we present an overview of current proteomics methodologies and the kind of information this can provide on the biology of human and mouse pluripotent stem cells.
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Affiliation(s)
- Dennis van Hoof
- Department of Anatomy and Embryology, Leiden University Medical Center, ZC Leiden
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31
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Cao R, Chen K, Song Q, Zang Y, Li J, Wang X, Chen P, Liang S. Quantitative proteomic analysis of membrane proteins involved in astroglial differentiation of neural stem cells by SILAC labeling coupled with LC-MS/MS. J Proteome Res 2012; 11:829-38. [PMID: 22149100 DOI: 10.1021/pr200677z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Membrane proteins play a critical role in the process of neural stem cell self-renewal and differentiation. Here, we apply the SILAC (stable isotope labeling by amino acids in cell culture) approach to quantitatively compare the membrane proteome of the self-renewing and the astroglial differentiating cells. High-resolution analysis on a linear ion trap-Orbitrap instrument (LTQ-Orbitrap) at sub-ppm mass accuracy resulted in confident identification and quantitation of more than 700 distinct membrane proteins during the astroglial differentiation. Of the 735 quantified proteins, seven cell surface proteins display significantly higher expression levels in the undifferentiated state membrane compared to astroglial differentiating membrane. One cell surface protein transferrin receptor protein 1 may serve as a new candidate for NSCs surface markers. Functional clustering of differentially expressed proteins by Ingenuity Pathway Analysis revealed that most of overexpressed membrane proteins in the astroglial differentiation neural stem cells are involved in cellular growth, nervous system development, and energy metabolic pathway. Taken together, this study increases our understanding of the underlying mechanisms that modulate complex biological processes of neural stem cell proliferation and differentiation.
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Affiliation(s)
- Rui Cao
- Key Laboratory of Protein Chemistry and Developmental Biology of Education Committee, College of Life Sciences, Hunan Normal University , Changsha 410081, PR China.
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32
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Chaerkady R, Letzen B, Renuse S, Sahasrabuddhe NA, Kumar P, All AH, Thakor NV, Delanghe B, Gearhart JD, Pandey A, Kerr CL. Quantitative temporal proteomic analysis of human embryonic stem cell differentiation into oligodendrocyte progenitor cells. Proteomics 2011; 11:4007-20. [PMID: 21770034 DOI: 10.1002/pmic.201100107] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 06/19/2011] [Accepted: 07/01/2011] [Indexed: 11/11/2022]
Abstract
Oligodendrocytes (OLs) are glial cells of the central nervous system, which produce myelin. Cultured OLs provide immense therapeutic opportunities for treating a variety of neurological conditions. One of the most promising sources for such therapies is human embryonic stem cells (ESCs) as well as providing a model to study human OL development. For these purposes, an investigation of proteome level changes is critical for understanding the process of OL differentiation. In this report, an iTRAQ-based quantitative proteomic approach was used to study multiple steps during OL differentiation including neural progenitor cells, glial progenitor cells and oligodendrocyte progenitor cells (OPCs) compared to undifferentiated ESCs. Using a 1% false discovery rate cutoff, ∼3145 proteins were quantitated and several demonstrated progressive stage-specific expression. Proteins such as transferrin, neural cell adhesion molecule 1, apolipoprotein E and wingless-related MMTV integration site 5A showed increased expression from the neural progenitor cell to the OPC stage. Several proteins that have demonstrated evidence or been suspected in OL maturation were also found upregulated in OPCs including fatty acid-binding protein 4, THBS1, bone morphogenetic protein 1, CRYAB, transferrin, tenascin C, COL3A1, TGFBI and EPB41L3. Thus, by providing the first extensive proteomic profiling of human ESC differentiation into OPCs, this study provides many novel proteins that are potentially involved in OL development.
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Affiliation(s)
- Raghothama Chaerkady
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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33
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Abstract
Embryonic stem cells (ESCs) are at the center stage of intense research, inspired by their potential to give rise to all cell types of the adult individual. This property makes ESCs suitable candidates for generating specialized cells to replace damaged tissue lost after injury or disease. However, such clinical applications require a detailed insight of the molecular mechanisms underlying the self-renewal, expansion and differentiation of stem cells. This has gained further relevance since the introduction of induced pluripotent stem cells (iPSCs), which are functionally very similar to ESCs. The key property that iPSCs can be derived from somatic cells lifts some of the major ethical issues related to the need for embryos to generate ESCs. Yet, this has only increased the need to define the similarity of iPSCs and ESCs at the molecular level, both before and after they are induced to differentiate. In this article, we describe the proteomic approaches that have been used to characterize ESCs with regard to self-renewal and differentiation, with an emphasis on signaling cascades and histone modifications. We take this as a lead to discuss how quantitative proteomics can be deployed to study reprogramming and iPSC identity. In addition, we discuss how emerging proteomic technologies can become a useful tool to monitor the (de)differentiation status of ESCs and iPSCs.
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Affiliation(s)
- Sonja Reiland
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
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34
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Hughes CS, Nuhn AA, Postovit LM, Lajoie GA. Proteomics of human embryonic stem cells. Proteomics 2011; 11:675-90. [DOI: 10.1002/pmic.201000407] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 09/13/2010] [Accepted: 10/14/2010] [Indexed: 01/01/2023]
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35
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Abstract
Heat shock factors form a family of transcription factors (four in mammals), which were named according to the first discovery of their activation by heat shock. As a result of the universality and robustness of their response to heat shock, the stress-dependent activation of heat shock factor became a ‘paradigm’: by binding to conserved DNA sequences (heat shock elements), heat shock factors trigger the expression of genes encoding heat shock proteins that function as molecular chaperones, contributing to establish a cytoprotective state to various proteotoxic stress and in several pathological conditions. Besides their roles in the stress response, heat shock factors perform crucial roles during gametogenesis and development in physiological conditions. First, during these process, in stress conditions, they are either proactive for survival or, conversely, for apoptotic process, allowing elimination or, inversely, protection of certain cell populations in a way that prevents the formation of damaged gametes and secure future reproductive success. Second, heat shock factors display subtle interplay in a tissue- and stage-specific manner, in regulating very specific sets of heat shock genes, but also many other genes encoding growth factors or involved in cytoskeletal dynamics. Third, they act not only by their classical transcription factor activities, but are necessary for the establishment of chromatin structure and, likely, genome stability. Finally, in contrast to the heat shock gene paradigm, heat shock elements bound by heat shock factors in developmental process turn out to be extremely dispersed in the genome, which is susceptible to lead to the future definition of ‘developmental heat shock element’.
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Affiliation(s)
- Ryma Abane
- CNRS, UMR7216 Epigenetics and Cell Fate, Paris, France
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36
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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37
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Chaerkady R, Kerr CL, Kandasamy K, Marimuthu A, Gearhart JD, Pandey A. Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells. Proteomics 2010; 10:1359-73. [PMID: 20104618 DOI: 10.1002/pmic.200900483] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Pluripotent human embryonic stem cells (ESCs) can be differentiated in vitro into a variety of cells which hold promise for transplantation therapy. Human embryonal carcinoma cells (ECCs), stem cells of human teratocarcinomas, are considered a close but malignant counterpart to human ESCs. In this study, a comprehensive quantitative proteomic analysis of ESCs and ECCs was carried out using the iTRAQ method. Using two-dimensional LC and MS/MS analyses, we identified and quantitated approximately 1800 proteins. Among these are proteins associated with pluripotency and development as well as tight junction signaling and TGFbeta receptor pathway. Nearly approximately 200 proteins exhibit more than twofold difference in abundance between ESCs and ECCs. Examples of early developmental markers high in ESCs include beta-galactoside-binding lectin, undifferentiated embryonic cell transcription factor-1, DNA cytosine methyltransferase 3beta isoform-B, melanoma antigen family-A4, and interferon-induced transmembrane protein-1. In contrast, CD99-antigen (CD99), growth differentiation factor-3, cellular retinoic acid binding protein-2, and developmental pluripotency associated-4 were among the highly expressed proteins in ECCs. Several proteins that were highly expressed in ECCs such as heat shock 27 kDa protein-1, mitogen-activated protein kinase kinase-1, nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor like-2, and S100 calcium-binding protein-A4 have also been attributed to malignancy in other systems. Importantly, immunocytochemistry was used to validate the proteomic analyses for a subset of the proteins. In summary, this is the first large-scale quantitative proteomic study of human ESCs and ECCs, which provides critical information about the regulators of these two closely related, but developmentally distinct, stem cells.
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38
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Yang Y, Chaerkady R, Kandasamy K, Huang TC, Selvan LDN, Dwivedi SB, Kent OA, Mendell JT, Pandey A. Identifying targets of miR-143 using a SILAC-based proteomic approach. Mol Biosyst 2010. [PMID: 20544124 DOI: 10.1039/c00401f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Although the targets of most miRNAs have not been experimentally identified, microRNAs (miRNAs) have begun to be extensively characterized in physiological, developmental and disease-related contexts in recent years. Thus far, mainly computational approaches have been employed to predict potential targets for the large majority of miRNAs. Although miRNAs exert a major influence on the efficiency of translation of their targets in animals, most studies describing experimental identification of miRNA target genes are based on detection of altered mRNA levels. miR-143 is a miRNA involved in tumorigenesis in multiple types of cancer, smooth muscle cell fate and adipocyte differentiation. Only a few miR-143 targets are experimentally verified, so we employed a SILAC-based quantitative proteomic strategy to systematically identify potential targets of miR-143. In total, we identified >1200 proteins from MiaPaCa2 pancreatic cancer cells, of which 93 proteins were downregulated >2-fold in miR-143 mimic transfected cells as compared to controls. Validation of 34 of these candidate targets in luciferase assays showed that 10 of them were likely direct targets of miR-143. Importantly, we also carried out gene expression profiling of the same cells and observed that the majority of the candidate targets identified by proteomics did not show a concomitant decrease in mRNA levels confirming that miRNAs affect the expression of most targets through translational inhibition. Our study clearly demonstrates that quantitative proteomic approaches are important and necessary for identifying miRNA targets.
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Affiliation(s)
- Yi Yang
- McKusick-Nathans Institute of Genetic Medicine, Baltimore, Maryland 21205, USA
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39
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Yang Y, Chaerkady R, Kandasamy K, Huang TC, Selvan LDN, Dwivedi SB, Kent OA, Mendell JT, Pandey A. Identifying targets of miR-143 using a SILAC-based proteomic approach. Mol Biosyst 2010; 6:1873-82. [PMID: 20544124 DOI: 10.1039/c004401f] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Although the targets of most miRNAs have not been experimentally identified, microRNAs (miRNAs) have begun to be extensively characterized in physiological, developmental and disease-related contexts in recent years. Thus far, mainly computational approaches have been employed to predict potential targets for the large majority of miRNAs. Although miRNAs exert a major influence on the efficiency of translation of their targets in animals, most studies describing experimental identification of miRNA target genes are based on detection of altered mRNA levels. miR-143 is a miRNA involved in tumorigenesis in multiple types of cancer, smooth muscle cell fate and adipocyte differentiation. Only a few miR-143 targets are experimentally verified, so we employed a SILAC-based quantitative proteomic strategy to systematically identify potential targets of miR-143. In total, we identified >1200 proteins from MiaPaCa2 pancreatic cancer cells, of which 93 proteins were downregulated >2-fold in miR-143 mimic transfected cells as compared to controls. Validation of 34 of these candidate targets in luciferase assays showed that 10 of them were likely direct targets of miR-143. Importantly, we also carried out gene expression profiling of the same cells and observed that the majority of the candidate targets identified by proteomics did not show a concomitant decrease in mRNA levels confirming that miRNAs affect the expression of most targets through translational inhibition. Our study clearly demonstrates that quantitative proteomic approaches are important and necessary for identifying miRNA targets.
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Affiliation(s)
- Yi Yang
- McKusick-Nathans Institute of Genetic Medicine, Baltimore, Maryland 21205, USA
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40
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Pewsey E, Bruce C, Tonge P, Evans C, Ow SY, Georgiou AS, Wright PC, Andrews PW, Fazeli A. Nuclear Proteome Dynamics in Differentiating Embryonic Carcinoma (NTERA-2) Cells. J Proteome Res 2010; 9:3412-26. [DOI: 10.1021/pr901069d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emma Pewsey
- Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Level 4, The Jessop Wing, S10 2SF Sheffield, United Kingdom, The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom, Department of Chemical and Process Engineering, ChELSI Institute, Mappin Street, Sheffield, S1 3JD, United Kingdom, and Centre for Developmental Genetics, School of Medicine and Biomedical Science, University of Sheffield,
| | - Christine Bruce
- Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Level 4, The Jessop Wing, S10 2SF Sheffield, United Kingdom, The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom, Department of Chemical and Process Engineering, ChELSI Institute, Mappin Street, Sheffield, S1 3JD, United Kingdom, and Centre for Developmental Genetics, School of Medicine and Biomedical Science, University of Sheffield,
| | - Peter Tonge
- Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Level 4, The Jessop Wing, S10 2SF Sheffield, United Kingdom, The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom, Department of Chemical and Process Engineering, ChELSI Institute, Mappin Street, Sheffield, S1 3JD, United Kingdom, and Centre for Developmental Genetics, School of Medicine and Biomedical Science, University of Sheffield,
| | - Caroline Evans
- Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Level 4, The Jessop Wing, S10 2SF Sheffield, United Kingdom, The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom, Department of Chemical and Process Engineering, ChELSI Institute, Mappin Street, Sheffield, S1 3JD, United Kingdom, and Centre for Developmental Genetics, School of Medicine and Biomedical Science, University of Sheffield,
| | - Saw Yen Ow
- Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Level 4, The Jessop Wing, S10 2SF Sheffield, United Kingdom, The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom, Department of Chemical and Process Engineering, ChELSI Institute, Mappin Street, Sheffield, S1 3JD, United Kingdom, and Centre for Developmental Genetics, School of Medicine and Biomedical Science, University of Sheffield,
| | - A. Stephen Georgiou
- Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Level 4, The Jessop Wing, S10 2SF Sheffield, United Kingdom, The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom, Department of Chemical and Process Engineering, ChELSI Institute, Mappin Street, Sheffield, S1 3JD, United Kingdom, and Centre for Developmental Genetics, School of Medicine and Biomedical Science, University of Sheffield,
| | - Phillip C. Wright
- Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Level 4, The Jessop Wing, S10 2SF Sheffield, United Kingdom, The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom, Department of Chemical and Process Engineering, ChELSI Institute, Mappin Street, Sheffield, S1 3JD, United Kingdom, and Centre for Developmental Genetics, School of Medicine and Biomedical Science, University of Sheffield,
| | - Peter W. Andrews
- Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Level 4, The Jessop Wing, S10 2SF Sheffield, United Kingdom, The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom, Department of Chemical and Process Engineering, ChELSI Institute, Mappin Street, Sheffield, S1 3JD, United Kingdom, and Centre for Developmental Genetics, School of Medicine and Biomedical Science, University of Sheffield,
| | - Alireza Fazeli
- Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Level 4, The Jessop Wing, S10 2SF Sheffield, United Kingdom, The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom, Department of Chemical and Process Engineering, ChELSI Institute, Mappin Street, Sheffield, S1 3JD, United Kingdom, and Centre for Developmental Genetics, School of Medicine and Biomedical Science, University of Sheffield,
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41
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Swelstad BB, Kerr CL. Current protocols in the generation of pluripotent stem cells: theoretical, methodological and clinical considerations. Stem Cells Cloning 2009; 3:13-27. [PMID: 24198508 PMCID: PMC3781729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Pluripotent stem cells have been derived from various embryonic, fetal and adult sources. Embryonic stem cells (ESCs) and parthenogenic ESCs (pESCs) are derived from the embryo proper while embryonic germ cells (EGCs), embryonal carcinoma cells (ECCs), and germ-line stem cells (GSC) are produced from germ cells. ECCs were the first pluripotent stem cell lines established from adult testicular tumors while EGCs are generated in vitro from primordial germ cells (PGCs) isolated in late embryonic development. More recently, studies have also demonstrated the ability to produce GSCs from adult germ cells, known as spermatogonial stem cells. Unlike ECCs, the source of GSCs are normal, non-cancerous adult tissue. The study of these unique cell lines has provided information that has led to the ability to reprogram somatic cells into an ESC-like state. These cells, called induced pluripotent stem cells (iPSCs), have been derived from a number of human fetal and adult origins. With the promises pluripotent stem cells bring to cell-based therapies there remain several considerations that need to be carefully studied prior to their clinical use. Many of these issues involve understanding key factors regulating their generation, including those which define pluripotency. In this regard, the following article discusses critical aspects of pluripotent stem cell derivation and current issues about their therapeutic potential.
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Affiliation(s)
- Brad B Swelstad
- Institute for Cell Engineering, Department of Obstetrics and Gynecology, Johns Hopkins University, Baltimore, MA, USA
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42
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Reimer MM, Kuscha V, Wyatt C, Sörensen I, Frank RE, Knüwer M, Becker T, Becker CG. Sonic hedgehog is a polarized signal for motor neuron regeneration in adult zebrafish. J Neurosci 2009; 29:15073-82. [PMID: 19955358 DOI: 10.1523/JNEUROSCI.4748-09.2009] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In contrast to mammals, the spinal cord of adult zebrafish has the capacity to reinitiate generation of motor neurons after a lesion. Here we show that genes involved in motor neuron development, i.e., the ventral morphogen sonic hedgehog a (shha), as well as the transcription factors nkx6.1 and pax6, together with a Tg(olig2:egfp) transgene, are expressed in the unlesioned spinal cord of adult zebrafish. Expression is found in ependymoradial glial cells lining the central canal in ventrodorsal positions that match expression domains of these genes in the developing neural tube. Specifically, Tg(olig2:egfp)(+) ependymoradial glial cells, the adult motor neuron progenitors (pMNs), coexpress Nkx6.1 and Pax6, thus defining an adult pMN-like zone. shha is expressed in distinct ventral ependymoradial glial cells. After a lesion, expression of all these genes is strongly increased, while relative spatial expression domains are maintained. In addition, expression of the hedgehog (hh) receptors patched1 and smoothened becomes detectable in ependymoradial glial cells including those of the pMN-like zone. Cyclopamine-induced knock down of hh signaling significantly reduces ventricular proliferation and motor neuron regeneration. Expression of indicator genes for the FGF and retinoic acid signaling pathways was also increased in the lesioned spinal cord. This suggests that a subclass of ependymoradial glial cells retain their identity as motor neuron progenitors into adulthood and are capable of reacting to a sonic hedgehog signal and potentially other developmental signals with motor neuron regeneration after a spinal lesion.
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43
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Chen WQ, Siegel N, Li L, Pollak A, Hengstschläger M, Lubec G. Variations of Protein Levels in Human Amniotic Fluid Stem Cells CD117/2 Over Passages 5−25. J Proteome Res 2009; 8:5285-95. [DOI: 10.1021/pr900630s] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Wei-Qiang Chen
- Department of Pediatrics, Medical University of Vienna, Währinger Gürtel 18, 1090 Vienna, Austria, and Department of Medical Genetics, Medical University of Vienna, Währinger Gürtel 18, 1090 Vienna, Austria
| | - Nicol Siegel
- Department of Pediatrics, Medical University of Vienna, Währinger Gürtel 18, 1090 Vienna, Austria, and Department of Medical Genetics, Medical University of Vienna, Währinger Gürtel 18, 1090 Vienna, Austria
| | - Lin Li
- Department of Pediatrics, Medical University of Vienna, Währinger Gürtel 18, 1090 Vienna, Austria, and Department of Medical Genetics, Medical University of Vienna, Währinger Gürtel 18, 1090 Vienna, Austria
| | - Arnold Pollak
- Department of Pediatrics, Medical University of Vienna, Währinger Gürtel 18, 1090 Vienna, Austria, and Department of Medical Genetics, Medical University of Vienna, Währinger Gürtel 18, 1090 Vienna, Austria
| | - Markus Hengstschläger
- Department of Pediatrics, Medical University of Vienna, Währinger Gürtel 18, 1090 Vienna, Austria, and Department of Medical Genetics, Medical University of Vienna, Währinger Gürtel 18, 1090 Vienna, Austria
| | - Gert Lubec
- Department of Pediatrics, Medical University of Vienna, Währinger Gürtel 18, 1090 Vienna, Austria, and Department of Medical Genetics, Medical University of Vienna, Währinger Gürtel 18, 1090 Vienna, Austria
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Perry RBT, Fainzilber M. Nuclear transport factors in neuronal function. Semin Cell Dev Biol 2009; 20:600-6. [PMID: 19409503 DOI: 10.1016/j.semcdb.2009.04.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2009] [Revised: 04/22/2009] [Accepted: 04/24/2009] [Indexed: 12/31/2022]
Abstract
Active nucleocytoplasmic transport of macromolecules requires soluble transport carriers of the importin/karyopherin superfamily. Although the nuclear transport machinery is essential in all eukaryotic cells, neurons must also mobilise importins and associated proteins to overcome unique spatiotemporal challenges. These include switches in importin alpha subtype expression during neuronal differentiation, localized axonal synthesis of importin beta1 to coordinate a retrograde injury signaling complex on axonal dynein, and trafficking of regulatory and signaling molecules from synaptic terminals to cell bodies. Targeting of RNAs encoding critical components of the importins complex and the Ran system to axons allows sophisticated local regulation of the system for mobilization upon need. Finally, a number of importin family members have been associated with mental or neurodegenerative diseases. The extended roles recently discovered for importins in the nervous system might also be relevant in non-neuronal cells, and the localized modes of importin regulation in neurons offer new avenues to interrogate their cytoplasmic functions.
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Affiliation(s)
- Rotem Ben-Tov Perry
- Dept. of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
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