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Meyfour A, Hosseini M, Sobhanian H, Pahlavan S. Iran's Contribution to Human Proteomic Research. CELL JOURNAL 2019; 21:229-235. [PMID: 31210427 PMCID: PMC6582420 DOI: 10.22074/cellj.2019.6303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/17/2018] [Indexed: 11/04/2022]
Abstract
Proteomics is a powerful approach to study the whole set of proteins expressed in an organism, organ, tissue or cell resulting in valuable information on physiological or pathological state of a biological system. High throughput proteomic data facilitated the understanding of various biological systems with respect to normal and pathological conditions particularly in the instances of human clinical manifestations. The important role of proteins as the functional gene products encouraged scientists to apply this technology to gain a better understanding of extremely complex biological systems. In last two decades, several proteomics teams have been gradually formed in Iran. In this review, we highlight the most important findings of proteomic research groups in Iran at various areas of stem cells, Y chromosome, infertility, infectious disease and biomarker discovery.
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Affiliation(s)
- Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mahya Hosseini
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | | | - Sara Pahlavan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.Electronic Address:
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Amjadi F, Mehdizadeh M, Ashrafi M, Nasrabadi D, Taleahmad S, Mirzaei M, Gupta V, Salekdeh GH, Aflatoonian R. Distinct changes in the proteome profile of endometrial tissues in polycystic ovary syndrome compared with healthy fertile women. Reprod Biomed Online 2018; 37:184-200. [PMID: 29729850 DOI: 10.1016/j.rbmo.2018.04.043] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 04/06/2018] [Accepted: 04/10/2018] [Indexed: 10/17/2022]
Abstract
RESEARCH QUESTION What is the molecular basis of infertility related to uterine dysfunction in women with polycystic ovary syndrome (PCOS)? DESIGN In this study, differences in protein expression between PCOS and normal endometrium were identified using a proteomic approach based on two-dimensional electrophoresis (2-DE) coupled with mass spectrometry (MS). The proteome of endometrium were analysed during the proliferative (on day 2 or 3 before ovulation, n = 6) and luteal phases (on day 3-5 after ovulation, n = 6) from healthy women and PCOS patients (12-14 days after spontaneous bleeding, n = 12). The differentially expressed proteins were categorized based on the biological process using the DAVID bioinformatics resources. RESULTS Over 803 reproducible protein spots were detected on gels, and 150 protein spots showed different intensities between PCOS and normal women during the proliferative and luteal phases. MS analysis detected 70 proteins out of 150 spots. For four of the 70 proteins, 14-3-3 protein, annexin A5, SERPINA1 and cathepsin D, 2-DE results were validated and localized by Western blot and immunohistochemistry, respectively, and their gene expression profiles were confirmed by real-time quantitative PCR. The obtained results corresponded to the proteomic analysis. The differentially expressed proteins identified are known to be involved in apoptosis, oxidative stress, inflammation and the cytoskeleton. CONCLUSIONS The processes related to the differentially expressed proteins play important roles in fecundity and fecundability. The present study may reveal the cause of various endometrial aberrations as a limiting factor for achieving pregnancy in PCOS women.
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Affiliation(s)
- Fatemehsadat Amjadi
- Department of Anatomy, School of Medicine, Iran University of Medical Science, Tehran, Iran
| | - Mehdi Mehdizadeh
- Cellular and Molecular Research Center, Faculty of Advanced Technologies, Department of Anatomical Sciences , Iran University of Medical Sciences, Tehran, Iran.
| | - Mahnaz Ashrafi
- Obstetrics and Gynecology Department, School of Medicine, Iran University of Medical Science, Tehran, Iran
| | - Davood Nasrabadi
- Department of Molecular Systems Biology, Cell Science Research Centre, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sara Taleahmad
- Department of Molecular Systems Biology, Cell Science Research Centre, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Vivek Gupta
- Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Centre, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
| | - Reza Aflatoonian
- Department of Endocrinology and Female Infertility, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
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Uncovering stem cell differentiation factors for salivary gland regeneration by quantitative analysis of differential proteomes. PLoS One 2017; 12:e0169677. [PMID: 28158262 PMCID: PMC5291466 DOI: 10.1371/journal.pone.0169677] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 12/20/2016] [Indexed: 12/24/2022] Open
Abstract
Severe xerostomia (dry mouth) compromises the quality of life in patients with Sjögren's syndrome or radiation therapy for head and neck cancer. A clinical management of xerostomia is often unsatisfactory as most interventions are palliative with limited efficacy. Following up our previous study demonstrating that mouse BM-MSCs are capable of differentiating into salivary epithelial cells in a co-culture system, we further explored the molecular basis that governs the MSC reprogramming by utilizing high-throughput iTRAQ-2D-LC-MS/MS-based proteomics. Our data revealed the novel induction of pancreas-specific transcription factor 1a (PTF1α), muscle, intestine and stomach expression-1 (MIST-1), and achaete-scute complex homolog 3 (ASCL3) in 7 day co-cultured MSCs but not in control MSCs. More importantly, a common notion of pancreatic-specific expression of PTF1 α was challenged for the first time by our verification of PTF1 α expression in the mouse salivary glands. Furthermore, a molecular network simulation of our selected putative MSC reprogramming factors demonstrated evidence for their perspective roles in salivary gland development. In conclusion, quantitative proteomics with extensive data analyses narrowed down a set of MSC reprograming factors potentially contributing to salivary gland regeneration. Identification of their differential/synergistic impact on MSC conversion warrants further investigation.
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Mikhailova A, Jylhä A, Rieck J, Nättinen J, Ilmarinen T, Veréb Z, Aapola U, Beuerman R, Petrovski G, Uusitalo H, Skottman H. Comparative proteomics reveals human pluripotent stem cell-derived limbal epithelial stem cells are similar to native ocular surface epithelial cells. Sci Rep 2015; 5:14684. [PMID: 26423138 PMCID: PMC4589773 DOI: 10.1038/srep14684] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/08/2015] [Indexed: 12/13/2022] Open
Abstract
Limbal epithelial stem cells (LESCs) are tissue-specific stem cells responsible for renewing the corneal epithelium. Acute trauma or chronic disease affecting LESCs may disrupt corneal epithelial renewal, causing vision threatening and painful ocular surface disorders, collectively referred to as LESC deficiency (LESCD). These disorders cannot be treated with traditional corneal transplantation and therefore alternative cell sources for successful cell-based therapy are needed. LESCs derived from human pluripotent stem cells (hPSCs) are a prospective source for ocular surface reconstruction, yet critical evaluation of these cells is crucial before considering clinical applications. In order to quantitatively evaluate hPSC-derived LESCs, we compared protein expression in native human corneal cells to that in hPSC-derived LESCs using isobaric tag for relative and absolute quantitation (iTRAQ) technology. We identified 860 unique proteins present in all samples, including proteins involved in cell cycling, proliferation, differentiation and apoptosis, various LESC niche components, and limbal and corneal epithelial markers. Protein expression profiles were nearly identical in LESCs derived from two different hPSC lines, indicating that the differentiation protocol is reproducible, yielding homogeneous cell populations. Their protein expression profile suggests that hPSC-derived LESCs are similar to the human ocular surface epithelial cells, and possess LESC-like characteristics.
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Affiliation(s)
| | - Antti Jylhä
- Department of Ophthalmology, School of Medicine, University of Tampere, Finland
| | | | - Janika Nättinen
- Department of Ophthalmology, School of Medicine, University of Tampere, Finland
| | | | - Zoltán Veréb
- Stem Cells and Eye Research Laboratory, Department of Ophthalmology, Faculty of Medicine, University of Szeged, Hungary
| | - Ulla Aapola
- Department of Ophthalmology, School of Medicine, University of Tampere, Finland
| | - Roger Beuerman
- Department of Ophthalmology, School of Medicine, University of Tampere, Finland.,Singapore Eye Research Institute and School of Medicine, Singapore
| | - Goran Petrovski
- Stem Cells and Eye Research Laboratory, Department of Ophthalmology, Faculty of Medicine, University of Szeged, Hungary
| | - Hannu Uusitalo
- Department of Ophthalmology, School of Medicine, University of Tampere, Finland.,Tampere University Hospital Eye Center, University of Tampere, Finland
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Lee JG, McKinney KQ, Lee YY, Chung HN, Pavlopoulos AJ, Jung KY, Kim WK, Kuroda MJ, Han DK, Hwang S. A draft map of rhesus monkey tissue proteome for biomedical research. PLoS One 2015; 10:e0126243. [PMID: 25974132 PMCID: PMC4431823 DOI: 10.1371/journal.pone.0126243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 03/28/2015] [Indexed: 01/14/2023] Open
Abstract
Though the rhesus monkey is one of the most valuable non-human primate animal models for various human diseases because of its manageable size and genetic and proteomic similarities with humans, proteomic research using rhesus monkeys still remains challenging due to the lack of a complete protein sequence database and effective strategy. To investigate the most effective and high-throughput proteomic strategy, comparative data analysis was performed employing various protein databases and search engines. The UniProt databases of monkey, human, bovine, rat and mouse were used for the comparative analysis and also a universal database with all protein sequences from all available species was tested. At the same time, de novo sequencing was compared to the SEQUEST search algorithm to identify an optimal work flow for monkey proteomics. Employing the most effective strategy, proteomic profiling of monkey organs identified 3,481 proteins at 0.5% FDR from 9 male and 10 female tissues in an automated, high-throughput manner. Data are available via ProteomeXchange with identifier PXD001972. Based on the success of this alternative interpretation of MS data, the list of proteins identified from 12 organs of male and female subjects will benefit future rhesus monkey proteome research.
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Affiliation(s)
- Jin-Gyun Lee
- Proteomics Laboratory for Clinical and Translational Research, Carolinas HealthCare System, Charlotte, North Carolina, United States of America
| | - Kimberly Q. McKinney
- Proteomics Laboratory for Clinical and Translational Research, Carolinas HealthCare System, Charlotte, North Carolina, United States of America
| | - Yong-Yook Lee
- Proteomics Laboratory for Clinical and Translational Research, Carolinas HealthCare System, Charlotte, North Carolina, United States of America
| | - Hae-Na Chung
- Proteomics Laboratory for Clinical and Translational Research, Carolinas HealthCare System, Charlotte, North Carolina, United States of America
| | - Antonis J. Pavlopoulos
- Proteomics Laboratory for Clinical and Translational Research, Carolinas HealthCare System, Charlotte, North Carolina, United States of America
| | - Kook Y. Jung
- Proteomics Laboratory for Clinical and Translational Research, Carolinas HealthCare System, Charlotte, North Carolina, United States of America
| | - Woong-Ki Kim
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia, United States of America
| | - Marcelo J. Kuroda
- Tulane National Primate Research Center, Tulane University, Covington, Louisiana, United States of America
| | - David K. Han
- Department of Cell Biology and Center for Vascular Biology, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Sunil Hwang
- Proteomics Laboratory for Clinical and Translational Research, Carolinas HealthCare System, Charlotte, North Carolina, United States of America
- * E-mail:
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Wang H, Zhang Q, Fang X. Transcriptomics and proteomics in stem cell research. Front Med 2014; 8:433-44. [PMID: 24972645 DOI: 10.1007/s11684-014-0336-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 03/14/2014] [Indexed: 12/20/2022]
Abstract
Stem cells are capable of self-renewal and differentiation, and the processes regulating these events are among the most comprehensively investigated topics in life sciences. In particular, the molecular mechanisms of the self-renewal, proliferation, and differentiation of stem cells have been extensively examined. Multi-omics integrative analysis, such as transcriptomics combined with proteomics, is one of the most promising approaches to the systemic investigation of stem cell biology. We reviewed the available information on stem cells by examining published results using transcriptomic and proteomic characterization of the different stem cell processes. Comprehensive understanding of these important processes can only be achieved using a systemic methodology, and employing such method will strengthen the study on stem cell biology and promote the clinical applications of stem cells.
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Affiliation(s)
- Hai Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
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Proteomic profiling of rabbit embryonic stem cells derived from parthenotes and fertilized embryos. PLoS One 2013; 8:e67772. [PMID: 23861804 PMCID: PMC3701598 DOI: 10.1371/journal.pone.0067772] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 05/22/2013] [Indexed: 11/19/2022] Open
Abstract
Rabbit embryonic stem (rES) cells can be derived from various sources of embryos. However, understanding of the gene expression profile, which distincts embryonic stem (ES) cells from other cell types, is still extremely limited. In this study, we compared the protein profiles of three independent lines of rabbit cells, i.e., fibroblasts, fertilized embryo-derived stem (f-rES) cells, and parthenote-derived ES (p-rES) cells. Proteomic analyses were performed using two-dimensional gel electrophoresis (2-DE) and mass spectrometry. Collectively, the expression levels of 100 out of 284 protein spots differed significantly among these three cell types (p<0.05). Of those differentially expressed spots, 91% were identified in the protein database and represented 63 distinct proteins. Proteins with known identities are mainly localized in the cytoplasmic compartments (48%), nucleus (14%), and cytoskeletal machineries (13%). These proteins were majorly involved in biological functions of energy and metabolic pathways (25%), cell growth and maintenance (25%), signal transduction (14%), and protein metabolisms (10%). When protein expression levels among cell types were compared, six proteins associated with a variety of cellular activities, including structural constituents of the cytoskeleton (tubulins), structural molecule (KRT8), catalytic molecules (α-enolase), receptor complex scaffold (14-3-3 protein sigma), microfilament motor proteins (Myosin-9), and heat shock protein (HSP60), were found highly expressed in p-rES cells. Two proteins related to HSP activity and structural constituent of cytoskeleton in f-rES cells, and one structural molecule activity protein in fibroblasts showed significantly higher expression levels (p<0.05). Marker protein expressions in f-rES and p-rES cells were further confirmed by Western blotting and immunocytochemical staining. This study demonstrated unique proteomic profiles of the three rabbit cell types and revealed some novel proteins differentially expressed between f-rES and p-rES cells. These analyses provide insights into rES cell biology and would invite more in-depth studies toward rES cell applications.
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Embryonic Stem Cell Interactomics: The Beginning of a Long Road to Biological Function. Stem Cell Rev Rep 2012; 8:1138-54. [DOI: 10.1007/s12015-012-9400-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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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] [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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NIRF/UHRF2 occupies a central position in the cell cycle network and allows coupling with the epigenetic landscape. FEBS Lett 2012; 586:1570-83. [DOI: 10.1016/j.febslet.2012.04.038] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 04/18/2012] [Accepted: 04/18/2012] [Indexed: 11/23/2022]
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Reiland S, Salekdeh GH, Krijgsveld J. Defining pluripotent stem cells through quantitative proteomic analysis. Expert Rev Proteomics 2011; 8:29-42. [PMID: 21329426 DOI: 10.1586/epr.10.100] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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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Shekari F, Taei A, Pan TL, Wang PW, Baharvand H, Salekdeh GH. Identification of cytoplasmic and membrane-associated complexes in human embryonic stem cells using blue native PAGE. MOLECULAR BIOSYSTEMS 2011; 7:2688-701. [DOI: 10.1039/c1mb05135k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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He J, Liu Y, Zhu TS, Xie X, Costello MA, Talsma CE, Flack CG, Crowley JG, Dimeco F, Vescovi AL, Fan X, Lubman DM. Glycoproteomic analysis of glioblastoma stem cell differentiation. J Proteome Res 2010; 10:330-8. [PMID: 21110520 DOI: 10.1021/pr101158p] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cancer stem cells are responsible for tumor formation through self-renewal and differentiation into multiple cell types and thus represent a new therapeutic target for tumors. Glycoproteins play a critical role in determining the fates of stem cells such as self-renewal, proliferation, and differentiation. Here we applied a multilectin affinity chromatography and quantitative glycoproteomics approach to analyze alterations of glycoproteins relevant to the differentiation of a glioblastoma-derived stem cell line HSR-GBM1. Three lectins including concanavalin A (Con A), wheat germ agglutinin (WGA), and peanut agglutinin (PNA) were used to capture glycoproteins, followed by LC-MS/MS analysis. A total of 73 and 79 high-confidence (FDR < 0.01) glycoproteins were identified from the undifferentiated and differentiated cells, respectively. Label-free quantitation resulted in the discovery of 18 differentially expressed glycoproteins, wherein 9 proteins are localized in the lysosome. All of these lysosomal glycoproteins were up-regulated after differentiation, where their principal function was hydrolysis of glycosyl residues. Protein-protein interaction and functional analyses revealed the active involvement of lysosomes during the process of glioblastoma stem cell differentiation. This work provides glycoprotein markers to characterize differentiation status of glioblastoma stem cells that may be useful in stem-cell therapy of glioblastoma.
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Affiliation(s)
- Jintang He
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
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Hatami-Baroogh L, Razavi S, Zarkesh-Esfahani H, Tavalaee M, Tanhaei S, Ghaedi K, Deemeh MR, Rabiee F, Nasr-Esfahani MH. Evaluation of the leptin receptor in human spermatozoa. Reprod Biol Endocrinol 2010; 8:17. [PMID: 20178606 PMCID: PMC2841190 DOI: 10.1186/1477-7827-8-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2009] [Accepted: 02/23/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Leptin, a 167 amino acid peptide hormone, profoundly effects reproduction exerting its biological effects via interaction with the leptin receptor (ObR) which is widely expressed on peripheral tissues. In this study, we have attempted to assess leptin receptor expression in the spermatozoa of fertile males and those diagnosed with male factor infertility; both at the mRNA or protein levels. METHODS Semen samples were collected from fertile males and individuals with male factor infertility. In order to evaluate leptin receptor expression several techniques were utilized, including: reverse transcriptase-polymerase chain reaction (RT-PCR), immunostaining, flow cytometry, and western blotting. Mononuclear cells isolated from volunteers' peripheral blood were used as positive controls for leptin receptor expression. RESULTS leptin receptor was noted on mononuclear cells but we were unable to detect this receptor on spermatozoa at the protein level. Leptin receptor expression was detected on peripheral blood mononuclear cells (PBMCs) as positive controls; however it was not detectable on the spermatozoa of both groups by immunofluorescence microscopy or flow cytometry. Furthermore, positive expression of the ObR long isoform as assessed by RT-PCR was observed in the sperm of only four cases, whereas expression of beta-Actin, a house keeping gene, and HspA2, a testis specific gene, was present in all cases. CONCLUSION The long isoform of leptin receptor may not be present on human sperm. Species difference may be accounted for diverse reproductive physiology which depends on metabolic requirement. Leptin receptor expression at the mRNA level in some individuals may be related to contamination by other cells in semen.
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Affiliation(s)
- Leila Hatami-Baroogh
- Department of Biology, Science and Culture University, Tehran, Iran
- Department of Reproduction and Development, Royan Institute for Animal Biotechnology, ACER, Isfahan, Iran
| | - Shahnaz Razavi
- Department of Anatomy, Isfahan Medical University, Isfahan, Iran
| | | | - Marziyeh Tavalaee
- Department of Reproduction and Development, Royan Institute for Animal Biotechnology, ACER, Isfahan, Iran
| | - Somayeh Tanhaei
- Department of Cell and Molecular Biology, Royan Institute for Animal Biotechnology, ACECR, Isfahan, Iran
| | - Kamran Ghaedi
- Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
- Department of Cell and Molecular Biology, Royan Institute for Animal Biotechnology, ACECR, Isfahan, Iran
| | | | - Farzaneh Rabiee
- Department of Cell and Molecular Biology, Royan Institute for Animal Biotechnology, ACECR, Isfahan, Iran
| | - Mohammad Hossein Nasr-Esfahani
- Department of Reproduction and Development, Royan Institute for Animal Biotechnology, ACER, Isfahan, Iran
- Department of Cell and Molecular Biology, Royan Institute for Animal Biotechnology, ACECR, Isfahan, Iran
- Isfahan Fertility and Infertility Center, Isfahan, Iran
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Nasrabadi D, Larijani MR, Fathi A, Gourabi H, Dizaj AV, Baharvand H, Salekdeh GH. Nuclear proteome analysis of monkey embryonic stem cells during differentiation. Stem Cell Rev Rep 2010; 6:50-61. [PMID: 20091144 DOI: 10.1007/s12015-009-9109-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 12/02/2009] [Indexed: 12/18/2022]
Abstract
The nuclear proteome enables, manages, and regulates the genome by the collective actions and interactions of proteins found in the nucleus. We applied a proteomic approach to analyze a nuclear proteome during embryonic stem cell (ESC) proliferation, and 3 and 9 days after initiation of differentiation. The nuclei were isolated from cells and their proteins were separated using 2-DE. Out of about 560 protein spots reproducible detected on any give gel, 49 differentially expressed proteins were identified by Matrix Assisted Laser Desorption Ionization-Time of Flight (MALDI TOF/TOF) mass spectrometry. Of them, several nuclear located proteins involved in chromatin remodeling, transcription regulation, apoptosis, cell proliferation, and differentiation were identified including CTBP1, MM-1, RUVBL1, HCC-1, SGTA, SUMO2, and Galectin-1. Functional interaction analysis of differentially expressed proteins revealed that most of nuclear proteins had a direct interaction with c-Myc and p53.
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Affiliation(s)
- Davood Nasrabadi
- Department of Molecular Systems Biology, Royan Institute for Stem Cell Biology and Technology, ACECR, P.O. Box: 19395-4644, Karaj, Iran
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Fathi A, Pakzad M, Taei A, Brink TC, Pirhaji L, Ruiz G, Sharif Tabe Bordbar M, Gourabi H, Adjaye J, Baharvand H, Salekdeh GH. Comparative proteome and transcriptome analyses of embryonic stem cells during embryoid body-based differentiation. Proteomics 2009; 9:4859-70. [PMID: 19862760 DOI: 10.1002/pmic.200900003] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Gene expression analyses of embryonic stem cells (ESCs) will help to uncover or further define signaling pathways and molecular mechanisms involved in the maintenance of self-renewal and pluripotency. We employed a 2-DE-based proteomics approach to analyze human ESC line, Royan H5, in undifferentiated cells and different stages of spontaneous differentiation (days 3, 6, 12, and 20) by embryoid body formation. Out of 945 proteins reproducibly detected on gels, the expression of 96 spots changed during differentiation. Using MS, 87 ESC-associated proteins were identified including several proteins involved in cell proliferation, cell apoptosis, transcription, translation, mRNA processing, and protein folding. Transcriptional changes accompanying differentiation of Royan H5 were also analyzed using microarrays. We developed a comprehensive data set that shows the use of human ESC lines in vitro to mimic gastrulation and organogenesis. Our results showed that proteomics and transcriptomics data are complementary rather than duplicative. Although regulation of many genes during differentiation were observed only at transcript level, modulation of several proteins was revealed only by proteome analysis.
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Affiliation(s)
- Ali Fathi
- Department of Molecular Systems Biology, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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