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Serdyukova K, Swearingen AR, Coradin M, Nevo M, Tran H, Bajric E, Brumbaugh J. Leveraging dominant-negative histone H3 K-to-M mutations to study chromatin during differentiation and development. Development 2023; 150:dev202169. [PMID: 38771302 PMCID: PMC10617616 DOI: 10.1242/dev.202169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Histone modifications are associated with regulation of gene expression that controls a vast array of biological processes. Often, these associations are drawn by correlating the genomic location of a particular histone modification with gene expression or phenotype; however, establishing a causal relationship between histone marks and biological processes remains challenging. Consequently, there is a strong need for experimental approaches to directly manipulate histone modifications. A class of mutations on the N-terminal tail of histone H3, lysine-to-methionine (K-to-M) mutations, was identified as dominant-negative inhibitors of histone methylation at their respective and specific residues. The dominant-negative nature of K-to-M mutants makes them a valuable tool for studying the function of specific methylation marks on histone H3. Here, we review recent applications of K-to-M mutations to understand the role of histone methylation during development and homeostasis. We highlight important advantages and limitations that require consideration when using K-to-M mutants, particularly in a developmental context.
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Affiliation(s)
- Ksenia Serdyukova
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Alison R. Swearingen
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mariel Coradin
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mika Nevo
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Huong Tran
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Emir Bajric
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Justin Brumbaugh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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Kulus M, Sibiak R, Stefańska K, Zdun M, Wieczorkiewicz M, Piotrowska-Kempisty H, Jaśkowski JM, Bukowska D, Ratajczak K, Zabel M, Mozdziak P, Kempisty B. Mesenchymal Stem/Stromal Cells Derived from Human and Animal Perinatal Tissues-Origins, Characteristics, Signaling Pathways, and Clinical Trials. Cells 2021; 10:cells10123278. [PMID: 34943786 PMCID: PMC8699543 DOI: 10.3390/cells10123278] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/13/2021] [Accepted: 11/19/2021] [Indexed: 12/15/2022] Open
Abstract
Mesenchymal stem/stromal cells (MSCs) are currently one of the most extensively researched fields due to their promising opportunity for use in regenerative medicine. There are many sources of MSCs, of which cells of perinatal origin appear to be an invaluable pool. Compared to embryonic stem cells, they are devoid of ethical conflicts because they are derived from tissues surrounding the fetus and can be safely recovered from medical waste after delivery. Additionally, perinatal MSCs exhibit better self-renewal and differentiation properties than those derived from adult tissues. It is important to consider the anatomy of perinatal tissues and the general description of MSCs, including their isolation, differentiation, and characterization of different types of perinatal MSCs from both animals and humans (placenta, umbilical cord, amniotic fluid). Ultimately, signaling pathways are essential to consider regarding the clinical applications of MSCs. It is important to consider the origin of these cells, referring to the anatomical structure of the organs of origin, when describing the general and specific characteristics of the different types of MSCs as well as the pathways involved in differentiation.
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Affiliation(s)
- Magdalena Kulus
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (M.K.); (K.R.)
| | - Rafał Sibiak
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (R.S.); (K.S.)
- Division of Reproduction, Department of Obstetrics, Gynecology, and Gynecologic Oncology, Poznan University of Medical Sciences, 60-535 Poznan, Poland
| | - Katarzyna Stefańska
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (R.S.); (K.S.)
| | - Maciej Zdun
- Department of Basic and Preclinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (M.Z.); (M.W.); (H.P.-K.)
| | - Maria Wieczorkiewicz
- Department of Basic and Preclinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (M.Z.); (M.W.); (H.P.-K.)
| | - Hanna Piotrowska-Kempisty
- Department of Basic and Preclinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (M.Z.); (M.W.); (H.P.-K.)
- Department of Toxicology, Poznan University of Medical Sciences, 60-631 Poznan, Poland
| | - Jędrzej M. Jaśkowski
- Department of Diagnostics and Clinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (J.M.J.); (D.B.)
| | - Dorota Bukowska
- Department of Diagnostics and Clinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (J.M.J.); (D.B.)
| | - Kornel Ratajczak
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (M.K.); (K.R.)
| | - Maciej Zabel
- Division of Anatomy and Histology, University of Zielona Gora, 65-046 Zielona Gora, Poland;
| | - Paul Mozdziak
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA;
| | - Bartosz Kempisty
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (M.K.); (K.R.)
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (R.S.); (K.S.)
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA;
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland
- Correspondence:
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3
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Dolgalev G, Poverennaya E. Applications of CRISPR-Cas Technologies to Proteomics. Genes (Basel) 2021; 12:1790. [PMID: 34828396 PMCID: PMC8625504 DOI: 10.3390/genes12111790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/12/2022] Open
Abstract
CRISPR-Cas-based genome editing is a revolutionary approach that has provided an unprecedented investigational power for the life sciences. Rapid and efficient, CRISPR-Cas technologies facilitate the generation of complex biological models and at the same time provide the necessary methods required to study these models in depth. The field of proteomics has already significantly benefited from leveraging the power of CRISPR-Cas technologies, however, many potential applications of these technologies in the context of proteomics remain unexplored. In this review, we intend to provide an introduction to the CRISPR-Cas technologies and demonstrate how they can be applied to solving proteome-centric questions. To achieve this goal, we begin with the description of the modern suite of CRISPR-Cas-based tools, focusing on the more mature CRISPR-Cas9 system. In the second part of this review, we highlight both established and potential applications of the CRISPR-Cas technologies to proteomics.
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4
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Sun B. Proteomics and glycoproteomics of pluripotent stem-cell surface proteins. Proteomics 2014; 15:1152-63. [DOI: 10.1002/pmic.201400300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/07/2014] [Accepted: 09/08/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Bingyun Sun
- Department of Chemistry and Department of Molecular Biology and Biochemistry, Simon Fraser University; Burnaby British Columbia Canada
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Artemenko K, Horáková J, Steinberger B, Besenfelder U, Brem G, Bergquist J, Mayrhofer C. A proteomic approach to monitor the dynamic response of the female oviductal epithelial cell surface to male gametes. J Proteomics 2014; 113:1-14. [PMID: 25281772 DOI: 10.1016/j.jprot.2014.09.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/18/2014] [Accepted: 09/22/2014] [Indexed: 12/11/2022]
Abstract
UNLABELLED Sophisticated strategies to analyze cell surface proteins are indispensable to study fundamental biological processes, such as the response of cells to environmental changes or cell-cell communication. Herein, we describe a refined mass spectrometry-based approach for the specific characterization and quantitation of cell surface proteins expressed in the female reproductive tract. The strategy is based on in situ biotinylation of rabbit oviducts, affinity enrichment of surface exposed biotin tagged proteins and dimethyl labeling of the obtained tryptic peptides followed by LC-MS/MS analysis. This approach proved to be sensitive enough to analyze small sample amounts (<1μg) and allowed further to trace the dynamic composition of the surface proteome of the oviductal epithelium in response to male gametes. The relative protein expression ratios of 175 proteins were quantified. Thirty-one of them were found to be altered over time, namely immediately, 1h and 2h after insemination compared to the time-matched control groups. Functional analysis demonstrated that structural reorganization of the oviductal epithelial cell surface was involved in the early response of the female organ to semen. In summary, this study outlines a workflow that is capable to monitor alterations in the female oviduct that are related to key reproductive processes in vivo. BIOLOGICAL SIGNIFICANCE The proper interaction between the female reproductive tract, in particular, the oviduct and the male gametes, is fundamental to fertilization and embryonic development under physiological conditions. Thereby the oviductal epithelial cell surface proteins play an important role. Besides their direct interaction with male gametes, these molecules participate in signal transduction and, thus, are involved in the mandatory cellular response of the oviductal epithelium. In this study we present a refined LC-MS/MS based workflow that is capable to quantitatively analyze the expression of oviductal epithelial cell surface proteins in response to insemination in vivo. A special focus was on the very early interaction between the female organ and the male gametes. At first, this study clearly revealed an immediate response of the surface proteome to semen, which was modulated over time. The described methodology can be applied for studies of further distinct biological events in the oviduct and therefore contribute to a deeper insight into the formation of new life.
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Affiliation(s)
- Konstantin Artemenko
- Institute of Analytical Chemistry, Department of Chemistry - Biomedical Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Jana Horáková
- Institute of Analytical Chemistry, Department of Chemistry - Biomedical Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Birgit Steinberger
- Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria; Institute of Biotechnology in Animal Production, Department for Agrobiotechnology (IFA Tulln), University of Natural Resources and Applied Life Sciences, Vienna, Tulln, Austria
| | - Urban Besenfelder
- Institute of Biotechnology in Animal Production, Department for Agrobiotechnology (IFA Tulln), University of Natural Resources and Applied Life Sciences, Vienna, Tulln, Austria
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria
| | - Jonas Bergquist
- Institute of Analytical Chemistry, Department of Chemistry - Biomedical Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Corina Mayrhofer
- Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria; Institute of Biotechnology in Animal Production, Department for Agrobiotechnology (IFA Tulln), University of Natural Resources and Applied Life Sciences, Vienna, Tulln, Austria
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6
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Sui P, Watanabe H, Ossipov MH, Bakalkin G, Artemenko K, Bergquist J. Proteomics of Neuropathic Pain: Proteins and Signaling Pathways Affected in a Rat Model. J Proteome Res 2014; 13:3957-65. [DOI: 10.1021/pr500241q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | | | - Michael H. Ossipov
- Department
of Pharmacology, University of Arizona Health Sciences Center, 1501
North Campbell Avenue, Tucson, Arizona 85724, United States
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Brumbaugh J, Russell JD, Yu P, Westphall MS, Coon JJ, Thomson JA. NANOG is multiply phosphorylated and directly modified by ERK2 and CDK1 in vitro. Stem Cell Reports 2014; 2:18-25. [PMID: 24678451 PMCID: PMC3966117 DOI: 10.1016/j.stemcr.2013.12.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 12/04/2013] [Accepted: 12/05/2013] [Indexed: 11/28/2022] Open
Abstract
NANOG is a divergent homeobox protein and a core component of the transcriptional circuitry that sustains pluripotency and self-renewal. Although NANOG has been extensively studied on the transcriptional level, little is known regarding its posttranslational regulation, likely due to its low abundance and challenging physical properties. Here, we identify eleven phosphorylation sites on endogenous human NANOG, nine of which mapped to single amino acids. To screen for the signaling molecules that impart these modifications, we developed the multiplexed assay for kinase specificity (MAKS). MAKS simultaneously tests activity for up to ten kinases while directly identifying the substrate and exact site of phosphorylation. Using MAKS, we discovered site-specific phosphorylation by ERK2 and CDK1/CyclinA2, providing a putative link between key signaling pathways and NANOG.
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Affiliation(s)
- Justin Brumbaugh
- Stem Cells and Regenerative Medicine, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Jason D Russell
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Pengzhi Yu
- Stem Cells and Regenerative Medicine, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Michael S Westphall
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA ; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA ; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - James A Thomson
- Stem Cells and Regenerative Medicine, Morgridge Institute for Research, Madison, WI 53715, USA ; Department of Cell & Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA ; Department of Molecular, Cellular & Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
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8
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Benevento M, Munoz J. Role of mass spectrometry-based proteomics in the study of cellular reprogramming and induced pluripotent stem cells. Expert Rev Proteomics 2014; 9:379-99. [DOI: 10.1586/epr.12.30] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Sudhir PR, Kumari MP, Hsu WT, Massiot J, Chen CH, Kuo HC, Chen CH. Quantitative proteomics of protein complexes and their implications for cell reprograming and pluripotency. J Proteome Res 2013; 12:5878-90. [PMID: 24256468 DOI: 10.1021/pr4008877] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pluripotency of embryonic stem cells (ESCs)/induced pluripotent stem cells (iPSCs) and reprograming of somatic cells (SCs) to pluripotency are governed by known and unknown factors. These factors, including protein complexes, are poorly described at the proteome level. Here, we established the quantitative proteomic profiles across three types of cells (iPSCs, ESCs, and SCs) using OFFGEL fractionation coupled with LTQ-Orbitrp analysis. Additionally, we utilized the previously published proteomic profiles of iPSCs, ESCs, and SCs. By integrating these proteomic profiles with protein-protein interaction resources, we identified numerous protein complexes in iPSCs and/or ESCs, which include known and novel chromatin remodeling complexes that facilitate cell reprograming. The identified protein complexes also include the previously unreported ones that are associated with the imperfect aspects of iPSCs or cell reprograming process. Further, we performed a comparison between our study and previously published studies and highlighted a partial conservation of the identified protein complexes across the iPSCs generated by different laboratories and iPS cell-type specific protein complexes. The identified protein complexes were validated by integrated in silico analysis of microarray repository data related to ESCs differentiation into embryoid bodies. A majority of the protein complexes exhibited significant (p < 0.005) co-regulation of their components upon ESC differentiation, suggesting their role in the maintenance of the pluripotent state. Finally, we showed a link between the components of the protein complexes and embryonic development using the existing loss-of-function phenotype data. Together, our integrated approach provides the first comprehensive view of the protein complexes that may have implications for cell reprograming and pluripotency.
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Affiliation(s)
- Putty-Reddy Sudhir
- Genomics Research Center and ‡Institute of Cellular and Organismic Biology, Academia Sinica , Taipei 11529, Taiwan
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Wierstra I. The transcription factor FOXM1 (Forkhead box M1): proliferation-specific expression, transcription factor function, target genes, mouse models, and normal biological roles. Adv Cancer Res 2013; 118:97-398. [PMID: 23768511 DOI: 10.1016/b978-0-12-407173-5.00004-2] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
FOXM1 (Forkhead box M1) is a typical proliferation-associated transcription factor, which stimulates cell proliferation and exhibits a proliferation-specific expression pattern. Accordingly, both the expression and the transcriptional activity of FOXM1 are increased by proliferation signals, but decreased by antiproliferation signals, including the positive and negative regulation by protooncoproteins or tumor suppressors, respectively. FOXM1 stimulates cell cycle progression by promoting the entry into S-phase and M-phase. Moreover, FOXM1 is required for proper execution of mitosis. Accordingly, FOXM1 regulates the expression of genes, whose products control G1/S-transition, S-phase progression, G2/M-transition, and M-phase progression. Additionally, FOXM1 target genes encode proteins with functions in the execution of DNA replication and mitosis. FOXM1 is a transcriptional activator with a forkhead domain as DNA binding domain and with a very strong acidic transactivation domain. However, wild-type FOXM1 is (almost) inactive because the transactivation domain is repressed by three inhibitory domains. Inactive FOXM1 can be converted into a very potent transactivator by activating signals, which release the transactivation domain from its inhibition by the inhibitory domains. FOXM1 is essential for embryonic development and the foxm1 knockout is embryonically lethal. In adults, FOXM1 is important for tissue repair after injury. FOXM1 prevents premature senescence and interferes with contact inhibition. FOXM1 plays a role for maintenance of stem cell pluripotency and for self-renewal capacity of stem cells. The functions of FOXM1 in prevention of polyploidy and aneuploidy and in homologous recombination repair of DNA-double-strand breaks suggest an importance of FOXM1 for the maintenance of genomic stability and chromosomal integrity.
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Sui P, Watanabe H, Ossipov MH, Porreca F, Bakalkin G, Bergquist J, Artemenko K. Dimethyl-Labeling-Based Protein Quantification and Pathway Search: A Novel Method of Spinal Cord Analysis Applicable for Neurological Studies. J Proteome Res 2013; 12:2245-52. [DOI: 10.1021/pr4001064] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | | | - Michael H. Ossipov
- Department of Pharmacology, University of Arizona Health Sciences Center, Tucson,
Arizona 85724, United States
| | - Frank Porreca
- Department of Pharmacology, University of Arizona Health Sciences Center, Tucson,
Arizona 85724, United States
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12
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Wierstra I. FOXM1 (Forkhead box M1) in tumorigenesis: overexpression in human cancer, implication in tumorigenesis, oncogenic functions, tumor-suppressive properties, and target of anticancer therapy. Adv Cancer Res 2013; 119:191-419. [PMID: 23870513 DOI: 10.1016/b978-0-12-407190-2.00016-2] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
FOXM1 (Forkhead box M1) is a typical proliferation-associated transcription factor and is also intimately involved in tumorigenesis. FOXM1 stimulates cell proliferation and cell cycle progression by promoting the entry into S-phase and M-phase. Additionally, FOXM1 is required for proper execution of mitosis. In accordance with its role in stimulation of cell proliferation, FOXM1 exhibits a proliferation-specific expression pattern and its expression is regulated by proliferation and anti-proliferation signals as well as by proto-oncoproteins and tumor suppressors. Since these factors are often mutated, overexpressed, or lost in human cancer, the normal control of the foxm1 expression by them provides the basis for deregulated FOXM1 expression in tumors. Accordingly, FOXM1 is overexpressed in many types of human cancer. FOXM1 is intimately involved in tumorigenesis, because it contributes to oncogenic transformation and participates in tumor initiation, growth, and progression, including positive effects on angiogenesis, migration, invasion, epithelial-mesenchymal transition, metastasis, recruitment of tumor-associated macrophages, tumor-associated lung inflammation, self-renewal capacity of cancer cells, prevention of premature cellular senescence, and chemotherapeutic drug resistance. However, in the context of urethane-induced lung tumorigenesis, FOXM1 has an unexpected tumor suppressor role in endothelial cells because it limits pulmonary inflammation and canonical Wnt signaling in epithelial lung cells, thereby restricting carcinogenesis. Accordingly, FOXM1 plays a role in homologous recombination repair of DNA double-strand breaks and maintenance of genomic stability, that is, prevention of polyploidy and aneuploidy. The implication of FOXM1 in tumorigenesis makes it an attractive target for anticancer therapy, and several antitumor drugs have been reported to decrease FOXM1 expression.
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Rigbolt KTG, Blagoev B. Quantitative phosphoproteomics to characterize signaling networks. Semin Cell Dev Biol 2012; 23:863-71. [PMID: 22677334 DOI: 10.1016/j.semcdb.2012.05.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 05/29/2012] [Indexed: 11/20/2022]
Abstract
Reversible protein phosphorylation is involved in the regulation of most, if not all, major cellular processes via dynamic signal transduction pathways. During the last decade quantitative phosphoproteomics have evolved from a highly specialized area to a powerful and versatile platform for analyzing protein phosphorylation at a system-wide scale and has become the intuitive strategy for comprehensive characterization of signaling networks. Contemporary phosphoproteomics use highly optimized procedures for sample preparation, mass spectrometry and data analysis algorithms to identify and quantify thousands of phosphorylations, thus providing extensive overviews of the cellular signaling networks. As a result of these developments quantitative phosphoproteomics have been applied to study processes as diverse as immunology, stem cell biology and DNA damage. Here we review the developments in phosphoproteomics technology that have facilitated the application of phosphoproteomics to signaling networks and introduce examples of recent system-wide applications of quantitative phosphoproteomics. Despite the great advances in phosphoproteomics technology there are still several outstanding issues and we provide here our outlook on the current limitations and challenges in the field.
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Affiliation(s)
- Kristoffer T G Rigbolt
- Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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