151
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Lee HJ, Gutierrez‐Garcia R, Vilchez D. Embryonic stem cells: a novel paradigm to study proteostasis? FEBS J 2016; 284:391-398. [DOI: 10.1111/febs.13810] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/22/2016] [Accepted: 07/08/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Hyun Ju Lee
- Cologne Excellence Cluster for Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Germany
| | - Ricardo Gutierrez‐Garcia
- Cologne Excellence Cluster for Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Germany
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152
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mRNA Cap Methylation in Pluripotency and Differentiation. Cell Rep 2016; 16:1352-1365. [PMID: 27452456 PMCID: PMC4977272 DOI: 10.1016/j.celrep.2016.06.089] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 05/24/2016] [Accepted: 06/24/2016] [Indexed: 11/26/2022] Open
Abstract
The mRNA cap recruits factors essential for transcript processing and translation initiation. We report that regulated mRNA cap methylation is a feature of embryonic stem cell (ESC) differentiation. Expression of the mRNA cap methyltransferase activating subunit RAM is elevated in ESCs, resulting in high levels of mRNA cap methylation and expression of a cohort of pluripotency-associated genes. During neural differentiation, RAM is suppressed, resulting in repression of pluripotency-associated factors and expression of a cohort of neural-associated genes. An established requirement of differentiation is increased ERK1/2 activity, which suppresses pluripotency-associated genes. During differentiation, ERK1/2 phosphorylates RAM serine-36, targeting it for ubiquitination and proteasomal degradation, ultimately resulting in changes in gene expression associated with loss of pluripotency. Elevated RAM expression also increases the efficiency of fibroblast reprogramming. Thus, the mRNA cap emerges as a dynamic mark that instructs change in gene expression profiles during differentiation and reprogramming. The mRNA cap methyltransferase RNMT-RAM is highly expressed in embryonic stem cells RNMT-RAM is important for the expression of pluripotency-associated genes During neural differentiation, the cap methyltransferase activator RAM is repressed Repression of RAM contributes to upregulation of neural genes and neural morphology
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153
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Chandrasekaran AP, Suresh B, Kim HH, Kim KS, Ramakrishna S. Concise Review: Fate Determination of Stem Cells by Deubiquitinating Enzymes. Stem Cells 2016; 35:9-16. [PMID: 27341175 DOI: 10.1002/stem.2446] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/05/2016] [Indexed: 12/22/2022]
Abstract
Post-translational modification by ubiquitin molecules is a key regulatory process for stem cell fate determination. Ubiquitination and deubiquitination are the major cellular processes used to balance the protein turnover of several transcription factors that regulate stem cell differentiation. Deubiquitinating enzymes (DUBs), which facilitate the processing of ubiquitin, significantly influence stem cell fate choices. Specifically, DUBs play a critical regulatory role during development by directing the production of new specialized cells. This review focuses on the regulatory role of DUBs in various cellular processes, including stem cell pluripotency and differentiation, adult stem cell signaling, cellular reprogramming, spermatogenesis, and oogenesis. Specifically, the identification of interactions of DUBs with core transcription factors has provided new insight into the role of DUBs in regulating stem cell fate determination. Thus, DUBs have emerged as key pharmacologic targets in the search to develop highly specific agents to treat various illnesses. Stem Cells 2017;35:9-16.
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Affiliation(s)
| | - Bharathi Suresh
- Department of Pharmacology and Brain Korea 21 plus Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Hyongbum Henry Kim
- Department of Pharmacology and Brain Korea 21 plus Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, Korea.,College of Medicine, Hanyang University, Seoul, South Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, Korea.,College of Medicine, Hanyang University, Seoul, South Korea
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154
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Suresh B, Lee J, Kim H, Ramakrishna S. Regulation of pluripotency and differentiation by deubiquitinating enzymes. Cell Death Differ 2016; 23:1257-64. [PMID: 27285106 DOI: 10.1038/cdd.2016.53] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 04/16/2016] [Accepted: 04/18/2016] [Indexed: 12/20/2022] Open
Abstract
Post-translational modifications (PTMs) of stemness-related proteins are essential for stem cell maintenance and differentiation. In stem cell self-renewal and differentiation, PTM of stemness-related proteins is tightly regulated because the modified proteins execute various stem cell fate choices. Ubiquitination and deubiquitination, which regulate protein turnover of several stemness-related proteins, must be carefully coordinated to ensure optimal embryonic stem cell maintenance and differentiation. Deubiquitinating enzymes (DUBs), which specifically disassemble ubiquitin chains, are a central component in the ubiquitin-proteasome pathway. These enzymes often control the balance between ubiquitination and deubiquitination. To maintain stemness and achieve efficient differentiation, the ubiquitination and deubiquitination molecular switches must operate in a balanced manner. Here we summarize the current information on DUBs, with a focus on their regulation of stem cell fate determination and deubiquitinase inhibition as a therapeutic strategy. Furthermore, we discuss the possibility of using DUBs with defined stem cell transcription factors to enhance cellular reprogramming efficiency and cell fate conversion. Our review provides new insight into DUB activity by emphasizing their cellular role in regulating stem cell fate. This role paves the way for future research focused on specific DUBs or deubiquitinated substrates as key regulators of pluripotency and stem cell differentiation.
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Affiliation(s)
- B Suresh
- Department of Pharmacology and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - J Lee
- Department of Physiology and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - H Kim
- Department of Pharmacology and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - S Ramakrishna
- Graduate School of Biomedical Science and Engineering, Department of Biomedical Science, Hanyang University, Seoul, South Korea.,College of Medicine, Department of Biomedical Science, Hanyang University, Seoul, South Korea
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155
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Gendron JM, Webb K, Yang B, Rising L, Zuzow N, Bennett EJ. Using the Ubiquitin-modified Proteome to Monitor Distinct and Spatially Restricted Protein Homeostasis Dysfunction. Mol Cell Proteomics 2016; 15:2576-93. [PMID: 27185884 DOI: 10.1074/mcp.m116.058420] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 01/01/2023] Open
Abstract
Protein homeostasis dysfunction has been implicated in the development and progression of aging related human pathologies. There is a need for the establishment of quantitative methods to evaluate global protein homoeostasis function. As the ubiquitin (ub) proteasome system plays a key role in regulating protein homeostasis, we applied quantitative proteomic methods to evaluate the sensitivity of site-specific ubiquitylation events as markers for protein homeostasis dysfunction. Here, we demonstrate that the ub-modified proteome can exceed the sensitivity of engineered fluorescent reporters as a marker for proteasome dysfunction and can provide unique signatures for distinct proteome challenges which is not possible with engineered reporters. We demonstrate that combining ub-proteomics with subcellular fractionation can effectively separate degradative and regulatory ubiquitylation events on distinct protein populations. Using a recently developed potent inhibitor of the critical protein homeostasis factor p97/VCP, we demonstrate that distinct insults to protein homeostasis function can elicit robust and largely unique alterations to the ub-modified proteome. Taken together, we demonstrate that proteomic approaches to monitor the ub-modified proteome can be used to evaluate global protein homeostasis and can be used to monitor distinct functional outcomes for spatially separated protein populations.
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Affiliation(s)
- Joshua M Gendron
- From the ‡Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California
| | - Kristofor Webb
- From the ‡Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California
| | - Bing Yang
- From the ‡Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California
| | - Lisa Rising
- From the ‡Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California
| | - Nathan Zuzow
- From the ‡Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California
| | - Eric J Bennett
- From the ‡Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California
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156
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Kos A, Olde Loohuis N, Meinhardt J, van Bokhoven H, Kaplan BB, Martens GJ, Aschrafi A. MicroRNA-181 promotes synaptogenesis and attenuates axonal outgrowth in cortical neurons. Cell Mol Life Sci 2016; 73:3555-67. [PMID: 27017280 DOI: 10.1007/s00018-016-2179-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 02/13/2016] [Accepted: 03/10/2016] [Indexed: 01/01/2023]
Abstract
MicroRNAs (miRs) are non-coding gene transcripts abundantly expressed in both the developing and adult mammalian brain. They act as important modulators of complex gene regulatory networks during neuronal development and plasticity. miR-181c is highly abundant in cerebellar cortex and its expression is increased in autism patients as well as in an animal model of autism. To systematically identify putative targets of miR-181c, we repressed this miR in growing cortical neurons and found over 70 differentially expressed target genes using transcriptome profiling. Pathway analysis showed that the miR-181c-modulated genes converge on signaling cascades relevant to neurite and synapse developmental processes. To experimentally examine the significance of these data, we inhibited miR-181c during rat cortical neuronal maturation in vitro; this loss-of miR-181c function resulted in enhanced neurite sprouting and reduced synaptogenesis. Collectively, our findings suggest that miR-181c is a modulator of gene networks associated with cortical neuronal maturation.
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Affiliation(s)
- Aron Kos
- Department of Cognitive Neuroscience, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, 6525 AJ, Nijmegen, The Netherlands
| | - Nikkie Olde Loohuis
- Department of Cognitive Neuroscience, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, 6525 AJ, Nijmegen, The Netherlands
| | - Julia Meinhardt
- Department of Cognitive Neuroscience, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, 6525 AJ, Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Department of Cognitive Neuroscience, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, 6525 AJ, Nijmegen, The Netherlands
| | - Barry B Kaplan
- Laboratory of Molecular Biology, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Gerard J Martens
- Department of Molecular Animal Physiology, Radboud University, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, 6525 AJ, Nijmegen, The Netherlands
| | - Armaz Aschrafi
- Department of Cognitive Neuroscience, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands.
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, 6525 AJ, Nijmegen, The Netherlands.
- Laboratory of Molecular Biology, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892, USA.
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157
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Christoforou A, Mulvey CM, Breckels LM, Geladaki A, Hurrell T, Hayward PC, Naake T, Gatto L, Viner R, Martinez Arias A, Lilley KS. A draft map of the mouse pluripotent stem cell spatial proteome. Nat Commun 2016; 7:8992. [PMID: 26754106 PMCID: PMC4729960 DOI: 10.1038/ncomms9992] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 10/22/2015] [Indexed: 12/18/2022] Open
Abstract
Knowledge of the subcellular distribution of proteins is vital for understanding cellular mechanisms. Capturing the subcellular proteome in a single experiment has proven challenging, with studies focusing on specific compartments or assigning proteins to subcellular niches with low resolution and/or accuracy. Here we introduce hyperLOPIT, a method that couples extensive fractionation, quantitative high-resolution accurate mass spectrometry with multivariate data analysis. We apply hyperLOPIT to a pluripotent stem cell population whose subcellular proteome has not been extensively studied. We provide localization data on over 5,000 proteins with unprecedented spatial resolution to reveal the organization of organelles, sub-organellar compartments, protein complexes, functional networks and steady-state dynamics of proteins and unexpected subcellular locations. The method paves the way for characterizing the impact of post-transcriptional and post-translational modification on protein location and studies involving proteome-level locational changes on cellular perturbation. An interactive open-source resource is presented that enables exploration of these data.
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Affiliation(s)
- Andy Christoforou
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Claire M Mulvey
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Lisa M Breckels
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Aikaterini Geladaki
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Tracey Hurrell
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.,Department of Pharmacology, University of Pretoria, Arcadia 0007, Republic of South Africa
| | - Penelope C Hayward
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Thomas Naake
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Laurent Gatto
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Rosa Viner
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95314, USA
| | | | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
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158
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The Importance of Ubiquitination and Deubiquitination in Cellular Reprogramming. Stem Cells Int 2016; 2016:6705927. [PMID: 26880980 PMCID: PMC4736574 DOI: 10.1155/2016/6705927] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 11/04/2015] [Accepted: 11/12/2015] [Indexed: 01/09/2023] Open
Abstract
Ubiquitination of core stem cell transcription factors can directly affect stem cell maintenance and differentiation. Ubiquitination and deubiquitination must occur in a timely and well-coordinated manner to regulate the protein turnover of several stemness related proteins, resulting in optimal embryonic stem cell maintenance and differentiation. There are two switches: an E3 ubiquitin ligase enzyme that tags ubiquitin molecules to the target proteins for proteolysis and a second enzyme, the deubiquitinating enzyme (DUBs), that performs the opposite action, thereby preventing proteolysis. In order to maintain stemness and to allow for efficient differentiation, both ubiquitination and deubiquitination molecular switches must operate properly in a balanced manner. In this review, we have summarized the importance of the ubiquitination of core stem cell transcription factors, such as Oct3/4, c-Myc, Sox2, Klf4, Nanog, and LIN28, during cellular reprogramming. Furthermore, we emphasize the role of DUBs in regulating core stem cell transcriptional factors and their function in stem cell maintenance and differentiation. We also discuss the possibility of using DUBs, along with core transcription factors, to efficiently generate induced pluripotent stem cells. Our review provides a relatively new understanding regarding the importance of ubiquitination/deubiquitination of stem cell transcription factors for efficient cellular reprogramming.
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159
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Gao J, Buckley SM, Cimmino L, Guillamot M, Strikoudis A, Cang Y, Goff SP, Aifantis I. The CUL4-DDB1 ubiquitin ligase complex controls adult and embryonic stem cell differentiation and homeostasis. eLife 2015; 4. [PMID: 26613412 PMCID: PMC4721963 DOI: 10.7554/elife.07539] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 11/26/2015] [Indexed: 12/12/2022] Open
Abstract
Little is known on post-transcriptional regulation of adult and embryonic stem cell maintenance and differentiation. Here we characterize the role of Ddb1, a component of the CUL4-DDB1 ubiquitin ligase complex. Ddb1 is highly expressed in multipotent hematopoietic progenitors and its deletion leads to abrogation of both adult and fetal hematopoiesis, targeting specifically transiently amplifying progenitor subsets. However, Ddb1 deletion in non-dividing lymphocytes has no discernible phenotypes. Ddb1 silencing activates Trp53 pathway and leads to significant effects on cell cycle progression and rapid apoptosis. The abrogation of hematopoietic progenitor cells can be partially rescued by simultaneous deletion of Trp53. Conversely, depletion of DDB1 in embryonic stem cell (ESC) leads to differentiation albeit negative effects on cell cycle and apoptosis. Mass spectrometry reveals differing protein interactions between DDB1 and distinct DCAFs, the substrate recognizing components of the E3 complex, between cell types. Our studies identify CUL4-DDB1 complex as a novel post-translational regulator of stem and progenitor maintenance and differentiation. DOI:http://dx.doi.org/10.7554/eLife.07539.001 Stem cells can develop into other types of cells via a process called “differentiation”. When a stem cell divides in two, it typically produces another stem cell and a cell that goes on to differentiate. Hematopoietic stem cells (or HSCs) are found in the bone marrow and give rise to all blood cells throughout the life of an organism. It is therefore crucial that they divide correctly to maintain the balance between renewing their numbers and making new types of cells. Many studies have investigated how stem cells are maintained, but there are still major gaps in our knowledge. Recent research suggested that the cell’s “ubiquitin-proteasome system” might be important for regulating stem cell division. This system rapidly degrades proteins, thereby regulating protein abundance in cells. Enzymes known as E3 ligases form part of this system, and recognize proteins to be marked for destruction with a small protein tag. Gao et al. have now observed that a component of an E3 ligase called DDB1 is highly expressed in hematopoietic stem cells. Further experiments revealed that genetically engineered mice that lack DDB1 in their population of blood cells die soon after they are born and have fewer blood cells. Gao et al. next inhibited the production of DDB1 in adult mice. This stopped the adult mice’s hematopoietic stem cells from dividing, and the mice died because their bone marrow couldn’t produce new blood cells. These results show that DDB1 is necessary for stem cells to renew their numbers and differentiate into blood cells in both developing and adult animals. Next, Gao et al. investigated the how DDB1 regulates stem cell division, and discovered that a protein called p53, which is a key player in controlling cell division, is regulated by DDB1. Under normal conditions, p53 levels are kept low in cells. However, in the absence of DDB1, the levels of p53 rise, which triggers the death of the hematopoietic stem cells. Further experiments revealed that not all dividing cells undergo cell death with the loss of DDB1. Instead, Gao et al. found that rapidly dividing embryonic stem cells differentiate when DDB1 is lost but do not die. These findings suggest that specific components of the ubiquitin ligase complex play a key role in deciding a stem cell’s fate. In the future, identifying these components will further our understanding of the decision of stem cells to differentiate. DOI:http://dx.doi.org/10.7554/eLife.07539.002
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Affiliation(s)
- Jie Gao
- Department of Pathology, New York University School of Medicine, New York, United States.,Perlmutter Cancer Center, New York University School of Medicine, New York, United States
| | - Shannon M Buckley
- Department of Pathology, New York University School of Medicine, New York, United States.,Perlmutter Cancer Center, New York University School of Medicine, New York, United States.,Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, United States
| | - Luisa Cimmino
- Department of Pathology, New York University School of Medicine, New York, United States.,Perlmutter Cancer Center, New York University School of Medicine, New York, United States
| | - Maria Guillamot
- Department of Pathology, New York University School of Medicine, New York, United States.,Perlmutter Cancer Center, New York University School of Medicine, New York, United States
| | - Alexandros Strikoudis
- Department of Pathology, New York University School of Medicine, New York, United States.,Perlmutter Cancer Center, New York University School of Medicine, New York, United States
| | - Yong Cang
- Signal Transduction Program, Sanford-Burnham Medical Research Institute, La Jolla, United States
| | - Stephen P Goff
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, United States
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, United States.,Perlmutter Cancer Center, New York University School of Medicine, New York, United States
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160
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Lafon A, Taranum S, Pietrocola F, Dingli F, Loew D, Brahma S, Bartholomew B, Papamichos-Chronakis M. INO80 Chromatin Remodeler Facilitates Release of RNA Polymerase II from Chromatin for Ubiquitin-Mediated Proteasomal Degradation. Mol Cell 2015; 60:784-796. [PMID: 26656161 DOI: 10.1016/j.molcel.2015.10.028] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 08/17/2015] [Accepted: 10/14/2015] [Indexed: 12/13/2022]
Abstract
Stalling of RNA Polymerase II (RNAPII) on chromatin during transcriptional stress results in polyubiquitination and degradation of the largest subunit of RNAPII, Rpb1, by the ubiquitin proteasome system (UPS). Here, we report that the ATP-dependent chromatin remodeling complex INO80 is required for turnover of chromatin-bound RNAPII in yeast. INO80 interacts physically and functionally with Cdc48/p97/VCP, a component of UPS required for degradation of RNAPII. Cells lacking INO80 are defective in Rpb1 degradation and accumulate tightly bound ubiquitinated Rpb1 on chromatin. INO80 forms a ternary complex with RNAPII and Cdc48 and targets Rpb1 primed for degradation. The function of INO80 in RNAPII turnover is required for cell growth and survival during genotoxic stress. Our results identify INO80 as a bona fide component of the proteolytic pathway for RNAPII degradation and suggest that INO80 nucleosome remodeling activity promotes the dissociation of ubiquitinated Rpb1 from chromatin to protect the integrity of the genome.
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Affiliation(s)
- Anne Lafon
- Institut Curie, PSL Research University, CNRS, UMR3664, 26 rue d'Ulm, 75248 Paris, France
| | - Surayya Taranum
- Institut Curie, PSL Research University, CNRS, UMR3664, 26 rue d'Ulm, 75248 Paris, France
| | - Federico Pietrocola
- Institut Curie, PSL Research University, CNRS, UMR3664, 26 rue d'Ulm, 75248 Paris, France
| | - Florent Dingli
- Institut Curie, PSL Research University, Laboratory of Proteomics and Mass Spectrometry, 26 rue d'Ulm, 75248 Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Laboratory of Proteomics and Mass Spectrometry, 26 rue d'Ulm, 75248 Paris, France
| | - Sandipan Brahma
- UT MD Anderson Cancer Center, Science Park, 1808 Park Road 1C, Smithville, TX 78957, USA
| | - Blaine Bartholomew
- UT MD Anderson Cancer Center, Science Park, 1808 Park Road 1C, Smithville, TX 78957, USA
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161
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Gonzales KAU, Ng HH. Biological Networks Governing the Acquisition, Maintenance, and Dissolution of Pluripotency: Insights from Functional Genomics Approaches. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2015; 80:189-98. [PMID: 26582790 DOI: 10.1101/sqb.2015.80.027326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The repertoire of transcripts encoded by the genome contributes to the diversity of cellular states. Functional genomics aims to comprehensively uncover the roles of these transcripts to reconstruct biological networks and transform this information into useful knowledge. High-throughput functional screening has served as a powerful genetic discovery tool by enabling massively parallel implementation of biological assays. In recent years, high-throughput screening has unearthed crucial players in the regulation of different aspects of pluripotency, which is a unique property that enables a cell to differentiate into multiple cell types of the three major lineages. Pluripotency thus represents an interesting biological paradigm for studying the acquisition, maintenance, and dissolution of cellular states. In this review, we highlight the major findings of high-throughput studies to dissect these three aspects of pluripotency for the mouse and human systems. Collectively, they provide new insights into cell fate maintenance and transition. In addition, we also discuss the opportunities and challenges awaiting high-throughput screening in the future.
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Affiliation(s)
| | - Huck-Hui Ng
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore 138672, Singapore Department of Biochemistry, National University of Singapore, Singapore 117597, Singapore Department of Biological Sciences, National University of Singapore, Singapore 117597, Singapore School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore
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162
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Ebrahimi B. Reprogramming barriers and enhancers: strategies to enhance the efficiency and kinetics of induced pluripotency. CELL REGENERATION (LONDON, ENGLAND) 2015; 4:10. [PMID: 26566431 PMCID: PMC4642739 DOI: 10.1186/s13619-015-0024-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 09/19/2015] [Indexed: 12/13/2022]
Abstract
Induced pluripotent stem cells are powerful tools for disease modeling, drug screening, and cell transplantation therapies. These cells can be generated directly from somatic cells by ectopic expression of defined factors through a reprogramming process. However, pluripotent reprogramming is an inefficient process because of various defined and unidentified barriers. Recent studies dissecting the molecular mechanisms of reprogramming have methodically improved the quality, ease, and efficiency of reprogramming. Different strategies have been applied for enhancing reprogramming efficiency, including depletion/inhibition of barriers (p53, p21, p57, p16(Ink4a)/p19(Arf), Mbd3, etc.), overexpression of enhancing genes (e.g., FOXH1, C/EBP alpha, UTF1, and GLIS1), and administration of certain cytokines and small molecules. The current review provides an in-depth overview of the cutting-edge findings regarding distinct barriers of reprogramming to pluripotency and strategies to enhance reprogramming efficiency. By incorporating the mechanistic insights from these recent findings, a combined method of inhibition of roadblocks and application of enhancing factors may yield the most reliable and effective approach in pluripotent reprogramming.
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Affiliation(s)
- Behnam Ebrahimi
- Yazd Cardiovascular Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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163
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Wang B, Ma A, Zhang L, Jin WL, Qian Y, Xu G, Qiu B, Yang Z, Liu Y, Xia Q, Liu Y. POH1 deubiquitylates and stabilizes E2F1 to promote tumour formation. Nat Commun 2015; 6:8704. [PMID: 26510456 PMCID: PMC4846323 DOI: 10.1038/ncomms9704] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 09/23/2015] [Indexed: 12/29/2022] Open
Abstract
Hyperactivation of the transcriptional factor E2F1 occurs frequently in human cancers and contributes to malignant progression. E2F1 activity is regulated by proteolysis mediated by the ubiquitin–proteasome system. However, the deubiquitylase that controls E2F1 ubiquitylation and stability remains undefined. Here we demonstrate that the deubiquitylase POH1 stabilizes E2F1 protein through binding to and deubiquitylating E2F1. Conditional knockout of Poh1 alleles results in reduced E2F1 expression in primary mouse liver cells. The POH1-mediated regulation of E2F1 expression strengthens E2F1-downstream prosurvival signals, including upregulation of Survivin and FOXM1 protein levels, and efficiently facilitates tumour growth of liver cancer cells in nude mice. Importantly, human hepatocellular carcinomas (HCCs) recapitulate POH1 regulation of E2F1 expression, as nuclear abundance of POH1 is increased in HCCs and correlates with E2F1 overexpression and tumour growth. Thus, our study suggests that the hyperactivated POH1–E2F1 regulation may contribute to the development of liver cancer. The transcription factor E2F1 controls the expression of multiple genes and is frequently overactivated in cancer. Here, the authors show that E2F1 is deubiquitinated by POH1 and that this enhances the role of E2F1 in cell survival, and contributes to the pathogenesis of liver cancer.
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Affiliation(s)
- Boshi Wang
- State Key laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200032, China
| | - Aihui Ma
- State Key laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200032, China
| | - Li Zhang
- State Key laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200032, China
| | - Wei-Lin Jin
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, Key Laboratory for Thin Film and Microfabrication Technology of Ministry of Education, School of Electronic Information and Electronic Engineering, Shanghai Jiaotong University, Shanghai 200240, China
| | - Yu Qian
- State Key laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200032, China
| | - Guiqin Xu
- State Key laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200032, China
| | - Bijun Qiu
- Department of Liver Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200217, China
| | - Zhaojuan Yang
- State Key laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200032, China
| | - Yun Liu
- State Key laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200032, China
| | - Qiang Xia
- Department of Liver Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200217, China
| | - Yongzhong Liu
- State Key laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200032, China
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164
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Shoemaker LD, Kornblum HI. Neural Stem Cells (NSCs) and Proteomics. Mol Cell Proteomics 2015; 15:344-54. [PMID: 26494823 PMCID: PMC4739658 DOI: 10.1074/mcp.o115.052704] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Indexed: 01/09/2023] Open
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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165
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Shearer RF, Iconomou M, Watts CKW, Saunders DN. Functional Roles of the E3 Ubiquitin Ligase UBR5 in Cancer. Mol Cancer Res 2015; 13:1523-32. [PMID: 26464214 DOI: 10.1158/1541-7786.mcr-15-0383] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/06/2015] [Indexed: 11/16/2022]
Abstract
The Ubiquitin-Proteasome System (UPS) is an important regulator of cell signaling and proteostasis, which are essential to a variety of cellular processes. The UPS is disrupted in many diseases including cancer, and targeting the UPS for cancer therapy is gaining wide interest. E3 ubiquitin ligases occupy a key position in the hierarchical UPS enzymatic cascade, largely responsible for determining substrate specificity and ubiquitin (Ub) chain topology. The E3 ligase UBR5 (aka EDD1) is emerging as a key regulator of the UPS in cancer and development. UBR5 expression is deregulated in many cancer types and UBR5 is frequently mutated in mantle cell lymphoma. UBR5 is highly conserved in metazoans, has unique structural features, and has been implicated in regulation of DNA damage response, metabolism, transcription, and apoptosis. Hence, UBR5 is a key regulator of cell signaling relevant to broad areas of cancer biology. However, the mechanism by which UBR5 may contribute to tumor initiation and progression remains poorly defined. This review synthesizes emerging insights from genetics, biochemistry, and cell biology to inform our understanding of UBR5 in cancer. These molecular insights indicate a role for UBR5 in integrating/coordinating various cellular signaling pathways. Finally, we discuss outstanding questions in UBR5 biology and highlight the need to systematically characterize substrates, and address limitations in current animal models, to better define the role of UBR5 in cancer.
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Affiliation(s)
- Robert F Shearer
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, Australia. St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Mary Iconomou
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, Australia. St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Colin K W Watts
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Darren N Saunders
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, Australia. School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia.
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166
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Kourtis N, Strikoudis A, Aifantis I. Emerging roles for the FBXW7 ubiquitin ligase in leukemia and beyond. Curr Opin Cell Biol 2015; 37:28-34. [PMID: 26426760 DOI: 10.1016/j.ceb.2015.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/16/2015] [Accepted: 09/16/2015] [Indexed: 01/03/2023]
Abstract
Protein degradation plays key roles in diverse pathways in cell division, growth and differentiation. Aberrant stabilization of crucial proteins participating in oncogenic pathways is often observed in cancer. The importance of proper protein turnover is exemplified by the SCF(Fbxw7) ubiquitin ligase, which is frequently mutated in human cancer, including T cell acute lymphoblastic leukemia. Recent studies have revealed novel substrates of Fbxw7 and shed light on its role on differentiation of stem cells and expansion of stem-cell-like cells driving tumorigenesis. Detailed understanding of the contribution of the Fbxw7-regulated network of proteins in initiation and progression of cancer will facilitate the identification of candidate intervention targets in human cancer.
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Affiliation(s)
- Nikos Kourtis
- Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; NYU Cancer Institute and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Alexandros Strikoudis
- Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; NYU Cancer Institute and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Iannis Aifantis
- Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; NYU Cancer Institute and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016, USA.
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167
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Ube2s regulates Sox2 stability and mouse ES cell maintenance. Cell Death Differ 2015; 23:393-404. [PMID: 26292759 DOI: 10.1038/cdd.2015.106] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 06/21/2015] [Accepted: 07/01/2015] [Indexed: 11/09/2022] Open
Abstract
Sox2 has a critical role in embryonic stem (ES) cell maintenance and differentiation. Interestingly, its activity is highly dosage-dependent. Although transcriptional regulation of Sox2 has been extensively studied, the mechanisms orchestrating its degradation remain unclear. In this study, we identified ubiquitin-conjugating enzyme E2S (Ube2s) as a novel effector for Sox2 protein degradation. Ube2s mediates K11-linked polyubiquitin chain formation at the Sox2-K123 residue, thus marking it for proteasome-mediated degradation. Besides its role in fine-tuning the precise level of Sox2, Ube2s reinforces the self-renewing and pluripotent state of ES cells. Importantly, it also represses Sox2-mediated ES cell differentiation toward the neural ectodermal lineage.
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168
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Abstract
Ubiquitin (UB)-driven signaling systems permeate biology, and are often integrated with other types of post-translational modifications (PTMs), including phosphorylation. Flux through such pathways is dictated by the fractional stoichiometry of distinct modifications and protein assemblies as well as the spatial organization of pathway components. Yet, we rarely understand the dynamics and stoichiometry of rate-limiting intermediates along a reaction trajectory. Here, we review how quantitative proteomic tools and enrichment strategies are being used to quantify UB-dependent signaling systems, and to integrate UB signaling with regulatory phosphorylation events, illustrated with the PINK1/PARKIN pathway. A key feature of ubiquitylation is that the identity of UB chain linkage types can control downstream processes. We also describe how proteomic and enzymological tools can be used to identify and quantify UB chain synthesis and linkage preferences. The emergence of sophisticated quantitative proteomic approaches will set a new standard for elucidating biochemical mechanisms of UB-driven signaling systems.
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Affiliation(s)
- Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Christian Münch
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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169
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Gingold JA, Coakley ES, Su J, Lee DF, Lau Z, Zhou H, Felsenfeld DP, Schaniel C, Lemischka IR. Distribution Analyzer, a methodology for identifying and clustering outlier conditions from single-cell distributions, and its application to a Nanog reporter RNAi screen. BMC Bioinformatics 2015. [PMID: 26198214 PMCID: PMC4511455 DOI: 10.1186/s12859-015-0636-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Chemical or small interfering (si) RNA screens measure the effects of many independent experimental conditions, each applied to a population of cells (e.g., all of the cells in a well). High-content screens permit a readout (e.g., fluorescence, luminescence, cell morphology) from each cell in the population. Most analysis approaches compare the average effect on each population, precluding identification of outliers that affect the distribution of the reporter in the population but not its average. Other approaches only measure changes to the distribution with a single parameter, precluding accurate distinction and clustering of interesting outlier distributions. Results We describe a methodology to identify outlier conditions by considering the cell-level measurements from each condition as a sample of an underlying distribution. With appropriate selection of a distance metric, all effects can be embedded in a fixed-dimensionality Euclidean basis, facilitating identification and clustering of biologically interesting outliers. We demonstrate that measurement of distances with the Hellinger distance metric offers substantial computational efficiencies over alternative metrics. We validate this methodology using an RNA interference (RNAi) screen in mouse embryonic stem cells (ESC) with a Nanog reporter. The methodology clusters effects of multiple control siRNAs into their true identities better than conventional approaches describing the median cell fluorescence or the commonly used Kolmogorov-Smirnov distance between the observed fluorescence distribution and the null distribution. It identifies outlier genes with effects on the reporter distribution that would have been missed by other methods. Among them, siRNA targeting Chek1 leads to a wider Nanog reporter fluorescence distribution. Similarly, siRNA targeting Med14 or Med27 leads to a narrower Nanog reporter fluorescence distribution. We confirm the roles of these three genes in regulating pluripotency by mRNA expression and alkaline phosphatase staining using independent short hairpin (sh) RNAs. Conclusions Using our methodology, we describe each experimental condition by a probability distribution. Measuring distances between probability distributions permits a multivariate rather than univariate readout. Clustering points derived from these distances allows us to obtain greater biological insight than methods based solely on single parameters. We find several outliers from a mouse ESC RNAi screen that we confirm to be pluripotency regulators. Many of these outliers would have been missed by other analysis methods. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0636-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julian A Gingold
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Ed S Coakley
- Program in Applied Mathematics, Yale University, New Haven, CT, 06511, USA.
| | - Jie Su
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Dung-Fang Lee
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Zerlina Lau
- Integrated Screening Core, Experimental Therapeutics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Hongwei Zhou
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Dan P Felsenfeld
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Integrated Screening Core, Experimental Therapeutics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Christoph Schaniel
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Ihor R Lemischka
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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170
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Nishiyama M, Nita A, Yumimoto K, Nakayama KI. FBXL12-Mediated Degradation of ALDH3 is Essential for Trophoblast Differentiation During Placental Development. Stem Cells 2015; 33:3327-40. [DOI: 10.1002/stem.2088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 06/20/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Masaaki Nishiyama
- Department of Molecular and Cellular Biology; Medical Institute of Bioregulation, Kyushu University; Higashi-ku Fukuoka, Fukuoka Japan
| | - Akihiro Nita
- Department of Molecular and Cellular Biology; Medical Institute of Bioregulation, Kyushu University; Higashi-ku Fukuoka, Fukuoka Japan
| | - Kanae Yumimoto
- Department of Molecular and Cellular Biology; Medical Institute of Bioregulation, Kyushu University; Higashi-ku Fukuoka, Fukuoka Japan
| | - Keiichi I. Nakayama
- Department of Molecular and Cellular Biology; Medical Institute of Bioregulation, Kyushu University; Higashi-ku Fukuoka, Fukuoka Japan
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171
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Loss of microRNA-27b contributes to breast cancer stem cell generation by activating ENPP1. Nat Commun 2015; 6:7318. [PMID: 26065921 PMCID: PMC4490376 DOI: 10.1038/ncomms8318] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/28/2015] [Indexed: 02/06/2023] Open
Abstract
Cancer stem cells (CSCs) have been identified in various types of cancer; however, the mechanisms by which cells acquire CSC properties such as drug resistance and tumour seeding ability are not fully understood. Here, we identified microRNA-27b (miR-27b) as a key regulator for the generation of a side-population in breast cancer cells that showed CSC properties, and also found that the anti-type II diabetes (T2D) drug metformin reduced this side-population via miR-27b-mediated repression of ectonucleotide pyrophosphatase/phosphodiesterase family member 1 (ENPP1), which is involved in T2D development. ENPP1 induced the generation of the side-population via upregulation of the ABCG2 transporter. ENPP1 was also identified as a substrate of the 26S proteasome, the activity of which is downregulated in CSCs. Overall, these results demonstrate that a T2D-associated gene plays an important role in tumour development and that its expression is strictly controlled at the mRNA and protein levels. MicroRNAs have a role in the acquisition of stem cell-like properties of cancer cells. Here the authors show that microRNA-27b mediates generation of a side-population of breast cancer stem cells, in part by regulating the protein ENPP1, which has been previously linked to the development of diabetes.
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172
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Jang J, Wang Y, Kim HS, Lalli MA, Kosik KS. Nrf2, a regulator of the proteasome, controls self-renewal and pluripotency in human embryonic stem cells. Stem Cells 2015; 32:2616-25. [PMID: 24895273 DOI: 10.1002/stem.1764] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 03/18/2014] [Accepted: 04/25/2014] [Indexed: 12/30/2022]
Abstract
Nuclear factor, erythroid 2-like 2 (Nrf2) is a master transcription factor for cellular defense against endogenous and exogenous stresses by regulating expression of many antioxidant and detoxification genes. Here, we show that Nrf2 acts as a key pluripotency gene and a regulator of proteasome activity in human embryonic stem cells (hESCs). Nrf2 expression is highly enriched in hESCs and dramatically decreases upon differentiation. Nrf2 inhibition impairs both the self-renewal ability of hESCs and re-establishment of pluripotency during cellular reprogramming. Nrf2 activation can delay differentiation. During early hESC differentiation, Nrf2 closely colocalizes with OCT4 and NANOG. As an underlying mechanism, our data show that Nrf2 regulates proteasome activity in hESCs partially through proteasome maturation protein (POMP), a proteasome chaperone, which in turn controls the proliferation of self-renewing hESCs, three germ layer differentiation and cellular reprogramming. Even modest proteasome inhibition skews the balance of early differentiation toward mesendoderm at the expense of an ectodermal fate by decreasing the protein level of cyclin D1 and delaying the degradation of OCT4 and NANOG proteins. Taken together, our findings suggest a new potential link between environmental stress and stemness with Nrf2 and the proteasome coordinately positioned as key mediators.
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Affiliation(s)
- Jiwon Jang
- Neuroscience Research Institute, Department of Molecular Cellular Developmental Biology, University of California, Santa Barbara, California, USA
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173
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Wang S, Xia P, Rehm M, Fan Z. Autophagy and cell reprogramming. Cell Mol Life Sci 2015; 72:1699-713. [PMID: 25572296 PMCID: PMC11113636 DOI: 10.1007/s00018-014-1829-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 12/23/2014] [Accepted: 12/30/2014] [Indexed: 12/17/2022]
Abstract
Autophagy is an evolutionarily conserved process that degrades cytoplasmic components, thus contributing to cell survival and tissue homeostasis. Recent studies have demonstrated that autophagy maintains stem cells in relatively undifferentiated states (stemness) and also contributes to differentiation processes. Autophagy likewise plays a crucial role in somatic cell reprogramming, a finely regulated process that resets differentiated cells to a pluripotent state and that requires comprehensive alterations in transcriptional activities and epigenetic signatures. Autophagy assists in manifesting the functional consequences that arise from these alterations by modifying cellular protein expression profiles. The role of autophagy appears to be particularly relevant for early phases of cell reprogramming during the generation of induced pluripotent stems cells (iPSCs). In this review, we provide an overview of the core molecular machinery that constitutes the autophagic degradation system, describe the roles of autophagy in maintenance, self-renewal, and differentiation of stem cells, and discuss the autophagic process and its regulation during cell reprogramming.
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Affiliation(s)
- Shuo Wang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Pengyan Xia
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Markus Rehm
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Zusen Fan
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
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174
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Abstract
The post-translational modification of proteins with ubiquitin represents a complex signalling system that co-ordinates essential cellular functions, including proteolysis, DNA repair, receptor signalling and cell communication. DUBs (deubiquitinases), the enzymes that disassemble ubiquitin chains and remove ubiquitin from proteins, are central to this system. Reflecting the complexity and versatility of ubiquitin signalling, DUB activity is controlled in multiple ways. Although several lines of evidence indicate that aberrant DUB function may promote human disease, the underlying molecular mechanisms are often unclear. Notwithstanding, considerable interest in DUBs as potential drug targets has emerged over the past years. The future success of DUB-based therapy development will require connecting the basic science of DUB function and enzymology with drug discovery. In the present review, we discuss new insights into DUB activity regulation and their links to disease, focusing on the role of DUBs as regulators of cell identity and differentiation, and discuss their potential as emerging drug targets.
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175
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Floyd ZE, Floyd EZ, Staszkiewicz J, Power RA, Kilroy G, Kirk-Ballard H, Barnes CW, Strickler KL, Rim JS, Harkins LL, Gao R, Kim J, Eilertsen KJ. Prolonged proteasome inhibition cyclically upregulates Oct3/4 and Nanog gene expression, but reduces induced pluripotent stem cell colony formation. Cell Reprogram 2015; 17:95-105. [PMID: 25826722 DOI: 10.1089/cell.2014.0030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
There is ample evidence that the ubiquitin-proteasome system is an important regulator of transcription and its activity is necessary for maintaining pluripotency and promoting cellular reprogramming. Moreover, proteasome activity contributes to maintaining the open chromatin structure found in pluripotent stem cells, acting as a transcriptional inhibitor at specific gene loci generally associated with differentiation. The current study was designed to understand further the role of proteasome inhibition in reprogramming and its ability to modulate endogenous expression of pluripotency-related genes and induced pluripotent stem cells (iPSCs) colony formation. Herein, we demonstrate that acute combinatorial treatment with the proteasome inhibitors MG101 or MG132 and the histone deacetylase (HDAC) inhibitor valproic acid (VPA) increases gene expression of the pluripotency marker Oct3/4, and that MG101 alone is as effective as VPA in the induction of Oct3/4 mRNA expression in fibroblasts. Prolonged proteasome inhibition cyclically upregulates gene expression of Oct3/4 and Nanog, but reduces colony formation in the presence of the iPSC induction cocktail. In conclusion, our results demonstrate that the 26S proteasome is an essential modulator in the reprogramming process. Its inhibition enhances expression of pluripotency-related genes; however, efficient colony formation requires proteasome activity. Therefore, discovery of small molecules that increase proteasome activity might lead to more efficient cell reprogramming and generation of pluripotent cells.
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Affiliation(s)
| | - Elizabeth Z Floyd
- 1 Ubiquitin Lab, Pennington Biomedical Research Center, Louisiana State University System , Baton Rouge, LA, 70803
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176
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Sheshadri P, Ashwini A, Jahnavi S, Bhonde R, Prasanna J, Kumar A. Novel role of mitochondrial manganese superoxide dismutase in STAT3 dependent pluripotency of mouse embryonic stem cells. Sci Rep 2015; 5:9516. [PMID: 25822711 PMCID: PMC5380158 DOI: 10.1038/srep09516] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 03/06/2015] [Indexed: 02/06/2023] Open
Abstract
Leukemia Inhibitory Factor (LIF)/Signal transducer and activator of transcription 3 (STAT3) signaling pathway maintains the stemness and pluripotency of mouse embryonic stem cells (mESCs). Detailed knowledge on key intermediates in this pathway as well as any parallel pathways is largely missing. We initiated our study by investigating the effect of small molecule Curcumin on various signalling pathways essential for self-renewal. Curcumin sustained the LIF independent self-renewal of mESCs and induced pluripotent stem cells (miPSCs) in a STAT3 activity dependent manner. Gene expression analysis showed LIF/STAT3 and redox signaling components to be majorly modulated. Amongst ROS genes, expression of Manganese Superoxide Dismutase (MnSOD) specifically relied on STAT3 signaling as evidenced by STAT3 inhibition and reporter assay. The silencing of MnSOD, but not Cu-ZnSOD expression, resulted in the loss of mESC pluripotency in presence of LIF, and the overexpression of MnSOD is sufficient for maintaining the expression of pluripotent genes in the absence of STAT3 signaling. Finally, we demonstrate MnSOD to stabilize the turnover of pluripotent proteins at the post-translational level by modulating proteasomal activity. In conclusion, our findings unravel a novel role of STAT3 mediated MnSOD in the self-renewal of mESCs.
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Affiliation(s)
- Preethi Sheshadri
- School of Regenerative Medicine, Manipal University, Bangalore-560065
| | | | - Sowmya Jahnavi
- School of Regenerative Medicine, Manipal University, Bangalore-560065
| | - Ramesh Bhonde
- School of Regenerative Medicine, Manipal University, Bangalore-560065
| | - Jyothi Prasanna
- School of Regenerative Medicine, Manipal University, Bangalore-560065
| | - Anujith Kumar
- School of Regenerative Medicine, Manipal University, Bangalore-560065
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177
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Gupta P, Leahul L, Wang X, Wang C, Bakos B, Jasper K, Hansen D. Proteasome regulation of the chromodomain protein MRG-1 controls the balance between proliferative fate and differentiation in the C. elegans germ line. Development 2015; 142:291-302. [PMID: 25564623 DOI: 10.1242/dev.115147] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The level of stem cell proliferation must be tightly controlled for proper development and tissue homeostasis. Multiple levels of gene regulation are often employed to regulate stem cell proliferation to ensure that the amount of proliferation is aligned with the needs of the tissue. Here we focus on proteasome-mediated protein degradation as a means of regulating the activities of proteins involved in controlling the stem cell proliferative fate in the C. elegans germ line. We identify five potential E3 ubiquitin ligases, including the RFP-1 RING finger protein, as being involved in regulating proliferative fate. RFP-1 binds to MRG-1, a homologue of the mammalian chromodomain-containing protein MRG15 (MORF4L1), which has been implicated in promoting the proliferation of neural precursor cells. We find that C. elegans with reduced proteasome activity, or that lack RFP-1 expression, have increased levels of MRG-1 and a shift towards increased proliferation in sensitized genetic backgrounds. Likewise, reduction of MRG-1 partially suppresses stem cell overproliferation. MRG-1 levels are controlled independently of the spatially regulated GLP-1/Notch signalling pathway, which is the primary signal controlling the extent of stem cell proliferation in the C. elegans germ line. We propose a model in which MRG-1 levels are controlled, at least in part, by the proteasome, and that the levels of MRG-1 set a threshold upon which other spatially regulated factors act in order to control the balance between the proliferative fate and differentiation in the C. elegans germ line.
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Affiliation(s)
- Pratyush Gupta
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Lindsay Leahul
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Xin Wang
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Chris Wang
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Brendan Bakos
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Katie Jasper
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Dave Hansen
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
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178
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The L1TD1 protein interactome reveals the importance of post-transcriptional regulation in human pluripotency. Stem Cell Reports 2015; 4:519-28. [PMID: 25702638 PMCID: PMC4376047 DOI: 10.1016/j.stemcr.2015.01.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 01/16/2015] [Accepted: 01/16/2015] [Indexed: 11/24/2022] Open
Abstract
The RNA-binding protein L1TD1 is one of the most specific and abundant proteins in pluripotent stem cells and is essential for the maintenance of pluripotency in human cells. Here, we identify the protein interaction network of L1TD1 in human embryonic stem cells (hESCs) and provide insights into the interactome network constructed in human pluripotent cells. Our data reveal that L1TD1 has an important role in RNA splicing, translation, protein traffic, and degradation. L1TD1 interacts with multiple stem-cell-specific proteins, many of which are still uncharacterized in the context of development. Further, we show that L1TD1 is a part of the pluripotency interactome network of OCT4, SOX2, and NANOG, bridging nuclear and cytoplasmic regulation and highlighting the importance of RNA biology in pluripotency. A protein interactome is constructed in human embryonic stem cells L1TD1 interacts with U2af1 and Srsf3, which are vital for somatic cell reprogramming L1TD1 is involved in the high proteasome activity of pluripotent cells L1TD1 connects uncharacterized factors to the OCT4, SOX2, and NANOG network
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179
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Khodakarami A, Saez I, Mels J, Vilchez D. Mediation of organismal aging and somatic proteostasis by the germline. Front Mol Biosci 2015; 2:3. [PMID: 25988171 PMCID: PMC4428440 DOI: 10.3389/fmolb.2015.00003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/07/2015] [Indexed: 12/22/2022] Open
Abstract
Experimental interventions that reduce reproduction cause an extension in lifespan. In invertebrates, such as Caenorhabditis elegans, the aging of the soma is regulated by signals from the germline. Indeed, ablation of germ cells significantly extends lifespan. Notably, germline-deficient animals exhibit heightened resistance to proteotoxic stress. This phenotype correlates with increased potential of intracellular clearance mechanisms such as the proteasome and autophagy in somatic tissues. Here we review the molecular mechanisms by which signals from the germline regulate lifespan in C. elegans with special emphasis on clearance mechanisms.
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Affiliation(s)
- Amirabbas Khodakarami
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne Cologne, Germany
| | - Isabel Saez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne Cologne, Germany
| | - Johanna Mels
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne Cologne, Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne Cologne, Germany
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180
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Saez I, Vilchez D. Protein clearance mechanisms and their demise in age-related neurodegenerative diseases. AIMS MOLECULAR SCIENCE 2015. [DOI: 10.3934/molsci.2015.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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181
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The role of protein clearance mechanisms in organismal ageing and age-related diseases. Nat Commun 2014; 5:5659. [DOI: 10.1038/ncomms6659] [Citation(s) in RCA: 442] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 10/24/2014] [Indexed: 12/27/2022] Open
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182
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Demasi M, Simões V, Bonatto D. Cross-talk between redox regulation and the ubiquitin-proteasome system in mammalian cell differentiation. Biochim Biophys Acta Gen Subj 2014; 1850:1594-606. [PMID: 25450485 DOI: 10.1016/j.bbagen.2014.10.031] [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: 08/25/2014] [Revised: 10/24/2014] [Accepted: 10/28/2014] [Indexed: 12/15/2022]
Abstract
BACKGROUND Embryogenesis and stem cell differentiation are complex and orchestrated signaling processes. Reactive oxygen species (ROS) act as essential signal transducers in cellular differentiation, as has been shown through recent discoveries. On the other hand, the ubiquitin-proteasome system (UPS) has long been known to play an important role in all cellular regulated processes, including differentiation. SCOPE OF REVIEW In the present review, we focus on findings that highlight the interplay between redox signaling and the UPS regarding cell differentiation. Through systems biology analyses, we highlight major routes during cardiomyocyte differentiation based on redox signaling and UPS modulation. MAJOR CONCLUSION Oxygen availability and redox signaling are fundamental regulators of cell fate upon differentiation. The UPS plays an important role in the maintenance of pluripotency and the triggering of differentiation. GENERAL SIGNIFICANCE Cellular differentiation has been a matter of intense investigation mainly because of its potential therapeutic applications. Understanding regulatory mechanisms underlying cell differentiation is an important issue. Correspondingly, the role of UPS and regulation of redox processes have been emerged as essential factors to control the fate of cells upon differentiation. This article is part of a Special Issue entitled Redox regulation of differentiation and de-differentiation.
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Affiliation(s)
- Marilene Demasi
- Laboratory of Biochemistry and Biophysics, Instituto Butantan, São Paulo, SP, Brazil.
| | - Vanessa Simões
- Department of Genetics and Evolutive Biology, IB, Universidade de São Paulo, São Paulo, Brazil
| | - Diego Bonatto
- Center of Biotechnology, Universidade Federal do Rio Grande do Sul., Porto Alegre, RS, Brazil.
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183
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Qin H, Diaz A, Blouin L, Lebbink RJ, Patena W, Tanbun P, LeProust EM, McManus MT, Song JS, Ramalho-Santos M. Systematic identification of barriers to human iPSC generation. Cell 2014; 158:449-461. [PMID: 25036638 DOI: 10.1016/j.cell.2014.05.040] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 03/05/2014] [Accepted: 05/27/2014] [Indexed: 12/13/2022]
Abstract
Reprogramming of somatic cells to induced pluripotent stem cells (iPSCs) holds enormous promise for regenerative medicine. To elucidate endogenous barriers limiting this process, we systematically dissected human cellular reprogramming by combining a genome-wide RNAi screen, innovative computational methods, extensive single-hit validation, and mechanistic investigation of relevant pathways and networks. We identify reprogramming barriers, including genes involved in transcription, chromatin regulation, ubiquitination, dephosphorylation, vesicular transport, and cell adhesion. Specific a disintegrin and metalloproteinase (ADAM) proteins inhibit reprogramming, and the disintegrin domain of ADAM29 is necessary and sufficient for this function. Clathrin-mediated endocytosis can be targeted with small molecules and opposes reprogramming by positively regulating TGF-β signaling. Genetic interaction studies of endocytosis or ubiquitination reveal that barrier pathways can act in linear, parallel, or feedforward loop architectures to antagonize reprogramming. These results provide a global view of barriers to human cellular reprogramming.
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Affiliation(s)
- Han Qin
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Departments of Ob/Gyn and Pathology, Center for Reproductive Sciences, and Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aaron Diaz
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laure Blouin
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Departments of Ob/Gyn and Pathology, Center for Reproductive Sciences, and Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robert Jan Lebbink
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, Diabetes Center, and the WM Keck Center for Noncoding RNAs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Weronika Patena
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, Diabetes Center, and the WM Keck Center for Noncoding RNAs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Priscilia Tanbun
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Departments of Ob/Gyn and Pathology, Center for Reproductive Sciences, and Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emily M LeProust
- Genomics Solution Unit, Agilent Technologies Inc., Santa Clara, CA 95051, USA
| | - Michael T McManus
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, Diabetes Center, and the WM Keck Center for Noncoding RNAs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jun S Song
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Epidemiology and Biostatistics and Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Departments of Ob/Gyn and Pathology, Center for Reproductive Sciences, and Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA.
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184
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Gingold JA, Fidalgo M, Guallar D, Lau Z, Sun Z, Zhou H, Faiola F, Huang X, Lee DF, Waghray A, Schaniel C, Felsenfeld DP, Lemischka IR, Wang J. A genome-wide RNAi screen identifies opposing functions of Snai1 and Snai2 on the Nanog dependency in reprogramming. Mol Cell 2014; 56:140-52. [PMID: 25240402 PMCID: PMC4184964 DOI: 10.1016/j.molcel.2014.08.014] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/21/2014] [Accepted: 08/08/2014] [Indexed: 12/30/2022]
Abstract
Nanog facilitates embryonic stem cell self-renewal and induced pluripotent stem cell generation during the final stage of reprogramming. From a genome-wide small interfering RNA screen using a Nanog-GFP reporter line, we discovered opposing effects of Snai1 and Snai2 depletion on Nanog promoter activity. We further discovered mutually repressive expression profiles and opposing functions of Snai1 and Snai2 during Nanog-driven reprogramming. We found that Snai1, but not Snai2, is both a transcriptional target and protein partner of Nanog in reprogramming. Ectopic expression of Snai1 or depletion of Snai2 greatly facilitates Nanog-driven reprogramming. Snai1 (but not Snai2) and Nanog cobind to and transcriptionally activate pluripotency-associated genes including Lin28 and miR-290-295. Ectopic expression of miR-290-295 cluster genes partially rescues reprogramming inefficiency caused by Snai1 depletion. Our study thus uncovers the interplay between Nanog and mesenchymal factors Snai1 and Snai2 in the transcriptional regulation of pluripotency-associated genes and miRNAs during the Nanog-driven reprogramming process.
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Affiliation(s)
- Julian A Gingold
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miguel Fidalgo
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Diana Guallar
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zerlina Lau
- Integrated Screening Core, Experimental Therapeutics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhen Sun
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hongwei Zhou
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Francesco Faiola
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xin Huang
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dung-Fang Lee
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Avinash Waghray
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christoph Schaniel
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dan P Felsenfeld
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Integrated Screening Core, Experimental Therapeutics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ihor R Lemischka
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Jianlong Wang
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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185
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Hede SM, Savov V, Weishaupt H, Sangfelt O, Swartling FJ. Oncoprotein stabilization in brain tumors. Oncogene 2014; 33:4709-21. [PMID: 24166497 DOI: 10.1038/onc.2013.445] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 09/11/2013] [Accepted: 09/12/2013] [Indexed: 12/12/2022]
Abstract
Proteins involved in promoting cell proliferation and viability need to be timely expressed and carefully controlled for the proper development of the brain but also efficiently degraded in order to prevent cells from becoming brain cancer cells. A major pathway for targeted protein degradation in cells is the ubiquitin-proteasome system (UPS). Oncoproteins that drive tumor development and tumor maintenance are often deregulated and stabilized in malignant cells. This can occur when oncoproteins escape degradation by the UPS because of mutations in either the oncoprotein itself or in the UPS components responsible for recognition and ubiquitylation of the oncoprotein. As the pathogenic accumulation of an oncoprotein can lead to effectively sustained cell growth, viability and tumor progression, it is an indisputable target for cancer treatment. The most common types of malignant brain tumors in children and adults are medulloblastoma and glioma, respectively. Here, we review different ways of how deregulated proteolysis of oncoproteins involved in major signaling cancer pathways contributes to medulloblastoma and glioma development. We also describe means of targeting relevant oncoproteins in brain tumors with treatments affecting their stability or therapeutic strategies directed against the UPS itself.
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Affiliation(s)
- S-M Hede
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - V Savov
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - H Weishaupt
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - O Sangfelt
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - F J Swartling
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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186
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Cho YH, Han KM, Kim D, Lee J, Lee SH, Choi KW, Kim J, Han YM. Autophagy regulates homeostasis of pluripotency-associated proteins in hESCs. Stem Cells 2014; 32:424-35. [PMID: 24170349 DOI: 10.1002/stem.1589] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 08/26/2013] [Accepted: 09/05/2013] [Indexed: 01/01/2023]
Abstract
The pluripotency of embryonic stem cells (ESCs) is maintained by intracellular networks of many pluripotency-associated (PA) proteins such as OCT4, SOX2, and NANOG. However, the mechanisms underlying the regulation of protein homeostasis for pluripotency remain elusive. Here, we first demonstrate that autophagy acts together with the ubiquitin-proteasome system (UPS) to modulate the levels of PA proteins in human ESCs (hESCs). Autophagy inhibition impaired the pluripotency despite increment of PA proteins in hESCs. Immunogold-electron microscopy confirmed localization of OCT4 molecules within autophagosomes. Also, knockdown of LC3 expression led to accumulation of PA proteins and reduction of pluripotency in hESCs. Interestingly, autophagy and the UPS showed differential kinetics in the degradation of PA proteins. Autophagy inhibition caused enhanced accumulation of both cytoplasmic and nuclear PA proteins, whereas the UPS inhibition led to preferentially degrade nuclear PA proteins. Our findings suggest that autophagy modulates homeostasis of PA proteins, providing a new insight in the regulation of pluripotency in hESCs.
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Affiliation(s)
- Yun-Hee Cho
- Department of Biological Sciences and Center for Stem Cell Differentiation, Daejeon, Republic of Korea
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187
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Wang L, Miao YL, Zheng X, Lackford B, Zhou B, Han L, Yao C, Ward JM, Burkholder A, Lipchina I, Fargo DC, Hochedlinger K, Shi Y, Williams CJ, Hu G. The THO complex regulates pluripotency gene mRNA export and controls embryonic stem cell self-renewal and somatic cell reprogramming. Cell Stem Cell 2014; 13:676-90. [PMID: 24315442 DOI: 10.1016/j.stem.2013.10.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/14/2013] [Accepted: 10/16/2013] [Indexed: 12/20/2022]
Abstract
Embryonic stem cell (ESC) self-renewal and differentiation are governed by a broad-ranging regulatory network. Although the transcriptional regulatory mechanisms involved have been investigated extensively, posttranscriptional regulation is still poorly understood. Here we describe a critical role of the THO complex in ESC self-renewal and differentiation. We show that THO preferentially interacts with pluripotency gene transcripts through Thoc5 and is required for self-renewal at least in part by regulating their export and expression. During differentiation, THO loses its interaction with those transcripts due to reduced Thoc5 expression, leading to decreased expression of pluripotency proteins that facilitates exit from self-renewal. THO is also important for the establishment of pluripotency, because its depletion inhibits somatic cell reprogramming and blastocyst development. Together, our data indicate that THO regulates pluripotency gene mRNA export to control ESC self-renewal and differentiation, and therefore uncover a role for this aspect of posttranscriptional regulation in stem cell fate specification.
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Affiliation(s)
- Li Wang
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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188
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Re A, Workman CT, Waldron L, Quattrone A, Brunak S. Lineage-specific interface proteins match up the cell cycle and differentiation in embryo stem cells. Stem Cell Res 2014; 13:316-28. [PMID: 25173649 DOI: 10.1016/j.scr.2014.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/25/2014] [Accepted: 07/26/2014] [Indexed: 11/25/2022] Open
Abstract
The shortage of molecular information on cell cycle changes along embryonic stem cell (ESC) differentiation prompts an in silico approach, which may provide a novel way to identify candidate genes or mechanisms acting in coordinating the two programs. We analyzed germ layer specific gene expression changes during the cell cycle and ESC differentiation by combining four human cell cycle transcriptome profiles with thirteen in vitro human ESC differentiation studies. To detect cross-talk mechanisms we then integrated the transcriptome data that displayed differential regulation with protein interaction data. A new class of non-transcriptionally regulated genes was identified, encoding proteins which interact systematically with proteins corresponding to genes regulated during the cell cycle or cell differentiation, and which therefore can be seen as interface proteins coordinating the two programs. Functional analysis gathered insights in fate-specific candidates of interface functionalities. The non-transcriptionally regulated interface proteins were found to be highly regulated by post-translational ubiquitylation modification, which may synchronize the transition between cell proliferation and differentiation in ESCs.
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Affiliation(s)
- Angela Re
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Via delle Regole 101, I38123 Trento, Italy; Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, DK2800 Lyngby, Denmark
| | - Christopher T Workman
- Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, DK2800 Lyngby, Denmark
| | - Levi Waldron
- City University of New York School of Public Health, Hunter College, 2180 3rd Avenue, NY 10035, USA
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Via delle Regole 101, I38123 Trento, Italy.
| | - Søren Brunak
- Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, DK2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK2200 Copenhagen, Denmark.
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189
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Gouti M, Tsakiridis A, Wymeersch FJ, Huang Y, Kleinjung J, Wilson V, Briscoe J. In vitro generation of neuromesodermal progenitors reveals distinct roles for wnt signalling in the specification of spinal cord and paraxial mesoderm identity. PLoS Biol 2014; 12:e1001937. [PMID: 25157815 PMCID: PMC4144800 DOI: 10.1371/journal.pbio.1001937] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/21/2014] [Indexed: 12/21/2022] Open
Abstract
Cells of the spinal cord and somites arise from shared, dual-fated precursors, located towards the posterior of the elongating embryo. Here we show that these neuromesodermal progenitors (NMPs) can readily be generated in vitro from mouse and human pluripotent stem cells by activating Wnt and Fgf signalling, timed to emulate in vivo development. Similar to NMPs in vivo, these cells co-express the neural factor Sox2 and the mesodermal factor Brachyury and differentiate into neural and paraxial mesoderm in vitro and in vivo. The neural cells produced by NMPs have spinal cord but not anterior neural identity and can differentiate into spinal cord motor neurons. This is consistent with the shared origin of spinal cord and somites and the distinct ontogeny of the anterior and posterior nervous system. Systematic analysis of the transcriptome during differentiation identifies the molecular correlates of each of the cell identities and the routes by which they are obtained. Moreover, we take advantage of the system to provide evidence that Brachyury represses neural differentiation and that signals from mesoderm are not necessary to induce the posterior identity of spinal cord cells. This indicates that the mesoderm inducing and posteriorising functions of Wnt signalling represent two molecularly separate activities. Together the data illustrate how reverse engineering normal developmental mechanisms allows the differentiation of specific cell types in vitro and the analysis of previous difficult to access aspects of embryo development.
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Affiliation(s)
- Mina Gouti
- MRC-National Institute for Medical Research, London, United Kingdom
| | - Anestis Tsakiridis
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Filip J. Wymeersch
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Yali Huang
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jens Kleinjung
- MRC-National Institute for Medical Research, London, United Kingdom
| | - Valerie Wilson
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - James Briscoe
- MRC-National Institute for Medical Research, London, United Kingdom
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190
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Wolff S, Weissman JS, Dillin A. Differential scales of protein quality control. Cell 2014; 157:52-64. [PMID: 24679526 DOI: 10.1016/j.cell.2014.03.007] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 03/06/2014] [Accepted: 03/07/2014] [Indexed: 02/06/2023]
Abstract
Proteins are notorious for their unpleasant behavior-continually at risk of misfolding, collecting damage, aggregating, and causing toxicity and disease. To counter these challenges, cells have evolved elaborate chaperone and quality control networks that can resolve damage at the level of the protein, organelle, cell, or tissue. On the smallest scale, the integrity of individual proteins is monitored during their synthesis. On a larger scale, cells use compartmentalized defenses and networks of communication, capable sometimes of signaling between cells, to respond to changes in the proteome's health. Together, these layered defenses help protect cells from damaged proteins.
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Affiliation(s)
- Suzanne Wolff
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, California Institute of Quantitative Biology, Center for RNA Systems Biology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Andrew Dillin
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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191
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Role of Fbxw7 in the maintenance of normal stem cells and cancer-initiating cells. Br J Cancer 2014; 111:1054-9. [PMID: 24853181 PMCID: PMC4453837 DOI: 10.1038/bjc.2014.259] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 03/12/2014] [Accepted: 04/15/2014] [Indexed: 01/15/2023] Open
Abstract
In addition to the properties of self-renewal and multipotency, stem cells are characterised by their distinct cell cycle status. Somatic stem cells are maintained in a quiescent state but switch reversibly from quiescence to proliferation as needed. On the other hand, embryonic stem cells and induced pluripotent stem cells proliferate rapidly until the induction of differentiation results in inhibition of cell cycle progression. Uncovering the mechanisms underlying cell cycle control in stem cells should thus provide insight into regulation of the balance between self-renewal and differentiation, a key goal of stem cell biology. Recent research has shown that cancer-initiating cells (CICs), a cell population with stem cell-like properties in cancer, are also quiescent, with this characteristic conferring resistance to anticancer therapies that target dividing cells. Elucidation of the mechanisms of CIC quiescence might therefore be expected to provide a basis for the eradication of cancer. This review summarises our current understanding of the role of F-box and WD40 repeat domain-containing 7 (Fbxw7), a key regulator of the cell cycle, in the maintenance of normal stem cells and CICs, as well as attempts to define future challenges in this field.
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192
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Saunders A, Faiola F, Wang J. Concise review: pursuing self-renewal and pluripotency with the stem cell factor Nanog. Stem Cells 2014; 31:1227-36. [PMID: 23653415 DOI: 10.1002/stem.1384] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 03/04/2013] [Indexed: 01/06/2023]
Abstract
Pluripotent embryonic stem cells and induced pluripotent stem cells hold great promise for future use in tissue replacement therapies due to their ability to self-renew indefinitely and to differentiate into all adult cell types. Harnessing this therapeutic potential efficiently requires a much deeper understanding of the molecular processes at work within the pluripotency network. The transcription factors Nanog, Oct4, and Sox2 reside at the core of this network, where they interact and regulate their own expression as well as that of numerous other pluripotency factors. Of these core factors, Nanog is critical for blocking the differentiation of pluripotent cells, and more importantly, for establishing the pluripotent ground state during somatic cell reprogramming. Both mouse and human Nanog are able to form dimers in vivo, allowing them to preferentially interact with certain factors and perform unique functions. Recent studies have identified an evolutionary functional conservation among vertebrate Nanog orthologs from chick, zebrafish, and the axolotl salamander, adding an additional layer of complexity to Nanog function. Here, we present a detailed overview of published work focusing on Nanog structure, function, dimerization, and regulation at the genetic and post-translational levels with regard to the establishment and maintenance of pluripotency. The full spectrum of Nanog function in pluripotent stem cells and in cancer is only beginning to be revealed. We therefore use this evidence to advocate for more comprehensive analysis of Nanog in the context of disease, development, and regeneration.
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Affiliation(s)
- Arven Saunders
- Department of Developmental and Regenerative Biology, Black Family Stem Cell Institute, New York, NY, USA
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193
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Sui D, Sun Z, Xu C, Wu Y, Capecchi MR, Wu S, Li N. Fine-tuning of iPSC derivation by an inducible reprogramming system at the protein level. Stem Cell Reports 2014; 2:721-33. [PMID: 24936457 PMCID: PMC4050490 DOI: 10.1016/j.stemcr.2014.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 03/25/2014] [Accepted: 03/27/2014] [Indexed: 12/29/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) generated from somatic cells by ectopic expression of reprogramming factors, e.g., POU5F1 (OCT4), KLF4, and SOX2, have great potential for regenerative medicine. However, before they can be used in a clinical setting, the mechanism of reprogramming needs to be better understood. Here, by engineering reprogramming factors to a destabilizing protein domain, we achieved inducible generation of mouse and pig iPSCs. Stability of the fusion protein was precisely regulated by the addition of the cell-permeable small molecule trimethoprim (TMP) in a dose-dependent manner. With these tools, we found that during the early and middle stages of reprogramming, exogenous OCT4 or KLF4 could be omitted, whereas exogenous SOX2 expression at early and middle stages was required for successful reprogramming. Our TMP reprogramming system is useful for defining the stoichiometry and temporal requirements of transcription factors for reprogramming. TMP reprogramming system can be used for inducible generation of iPSCs Stability of reprogramming factors is precisely regulated by TMP During early/middle stages of reprogramming, exogenous OCT4 or KLF4 can be omitted During early/middle stages of reprogramming, exogenous SOX2 expression is required
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Affiliation(s)
- Dandan Sui
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Zhaolin Sun
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Chunlong Xu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Yuanyuan Wu
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Mario R Capecchi
- Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT 84112, USA ; Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Sen Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Ning Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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194
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Cinghu S, Yellaboina S, Freudenberg JM, Ghosh S, Zheng X, Oldfield AJ, Lackford BL, Zaykin DV, Hu G, Jothi R. Integrative framework for identification of key cell identity genes uncovers determinants of ES cell identity and homeostasis. Proc Natl Acad Sci U S A 2014; 111:E1581-90. [PMID: 24711389 PMCID: PMC4000800 DOI: 10.1073/pnas.1318598111] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Identification of genes associated with specific biological phenotypes is a fundamental step toward understanding the molecular basis underlying development and pathogenesis. Although RNAi-based high-throughput screens are routinely used for this task, false discovery and sensitivity remain a challenge. Here we describe a computational framework for systematic integration of published gene expression data to identify genes defining a phenotype of interest. We applied our approach to rank-order all genes based on their likelihood of determining ES cell (ESC) identity. RNAi-mediated loss-of-function experiments on top-ranked genes unearthed many novel determinants of ESC identity, thus validating the derived gene ranks to serve as a rich and valuable resource for those working to uncover novel ESC regulators. Underscoring the value of our gene ranks, functional studies of our top-hit Nucleolin (Ncl), abundant in stem and cancer cells, revealed Ncl's essential role in the maintenance of ESC homeostasis by shielding against differentiation-inducing redox imbalance-induced oxidative stress. Notably, we report a conceptually novel mechanism involving a Nucleolin-dependent Nanog-p53 bistable switch regulating the homeostatic balance between self-renewal and differentiation in ESCs. Our findings connect the dots on a previously unknown regulatory circuitry involving genes associated with traits in both ESCs and cancer and might have profound implications for understanding cell fate decisions in cancer stem cells. The proposed computational framework, by helping to prioritize and preselect candidate genes for tests using complex and expensive genetic screens, provides a powerful yet inexpensive means for identification of key cell identity genes.
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Affiliation(s)
| | - Sailu Yellaboina
- Systems Biology Section and
- Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; and
- CR Rao Advanced Institute of Mathematics, Statistics, and Computer Science, Hyderabad, Andhra Pradesh 500 046, India
| | - Johannes M. Freudenberg
- Systems Biology Section and
- Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; and
| | | | - Xiaofeng Zheng
- Stem Cell Biology Section, Laboratory of Molecular Carcinogenesis, and
| | | | - Brad L. Lackford
- Stem Cell Biology Section, Laboratory of Molecular Carcinogenesis, and
| | - Dmitri V. Zaykin
- Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; and
| | - Guang Hu
- Stem Cell Biology Section, Laboratory of Molecular Carcinogenesis, and
| | - Raja Jothi
- Systems Biology Section and
- Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; and
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195
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Affiliation(s)
- Siem Van der Laan
- Genome Surveillance and Stability Laboratory; Department Molecular Bases of Human Diseases; CNRS-UPR1142; Institute of Human Genetics; Montpellier, France
| | - Domenico Maiorano
- Genome Surveillance and Stability Laboratory; Department Molecular Bases of Human Diseases; CNRS-UPR1142; Institute of Human Genetics; Montpellier, France
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196
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David L, Polo JM. Phases of reprogramming. Stem Cell Res 2014; 12:754-61. [PMID: 24735951 DOI: 10.1016/j.scr.2014.03.007] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 03/21/2014] [Accepted: 03/23/2014] [Indexed: 12/16/2022] Open
Abstract
Despite advances in the field of somatic cell reprogramming, an understanding and exploration of the underlying mechanisms governing this process are only recently emerging. It is now increasingly apparent that key sequential events correlate with the reprogramming process; a process previously thought to be random and unpredictable is now looking, to a greater extent, defined and controlled. Herein, we will review the key cellular and molecular events associated with the reprogramming process, giving an integrative and conciliatory view of the different studies addressing the mechanism of nuclear reprogramming.
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Affiliation(s)
- Laurent David
- INSERM, UMR 1064, Nantes, France; Faculté de Médecine, Université de Nantes, France; iPSC Facility, SFR F. Bonamy, Université de Nantes, France.
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Australia; Australian Regenerative Medicine Institute, Monash University, Australia.
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197
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Saez I, Vilchez D. The Mechanistic Links Between Proteasome Activity, Aging and Age-related Diseases. Curr Genomics 2014; 15:38-51. [PMID: 24653662 PMCID: PMC3958958 DOI: 10.2174/138920291501140306113344] [Citation(s) in RCA: 219] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 01/13/2014] [Accepted: 01/15/2014] [Indexed: 01/17/2023] Open
Abstract
Damaged and misfolded proteins accumulate during the aging process, impairing cell function and tissue homeostasis. These perturbations to protein homeostasis (proteostasis) are hallmarks of age-related neurodegenerative disorders such as Alzheimer’s, Parkinson’s or Huntington’s disease. Damaged proteins are degraded by cellular clearance mechanisms such as the proteasome, a key component of the proteostasis network. Proteasome activity declines during aging, and proteasomal dysfunction is associated with late-onset disorders. Modulation of proteasome activity extends lifespan and protects organisms from symptoms associated with proteostasis disorders. Here we review the links between proteasome activity, aging and neurodegeneration. Additionally, strategies to modulate proteasome activity and delay the onset of diseases associated to proteasomal dysfunction are discussed herein.
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Affiliation(s)
- Isabel Saez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Co-logne, Joseph Stelzmann Strasse 26, 50931 Cologne, Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Co-logne, Joseph Stelzmann Strasse 26, 50931 Cologne, Germany
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198
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Strikoudis A, Guillamot M, Aifantis I. Regulation of stem cell function by protein ubiquitylation. EMBO Rep 2014; 15:365-82. [PMID: 24652853 DOI: 10.1002/embr.201338373] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Tissue homeostasis depends largely on the ability to replenish impaired or aged cells. Thus, tissue-resident stem cells need to provide functional progeny throughout the lifetime of an organism. Significant work in the past years has characterized how stem cells integrate signals from their environment to shape regulatory transcriptional networks and chromatin-regulating factors that control stem cell differentiation or maintenance. There is increasing interest in how post-translational modifications, and specifically ubiquitylation, control these crucial decisions. Ubiquitylation modulates the stability and function of important factors that regulate key processes in stem cell behavior. In this review, we analyze the role of ubiquitylation in embryonic stem cells and different adult multipotent stem cell systems and discuss the underlying mechanisms that control the balance between quiescence, self-renewal, and differentiation. We also discuss deregulated processes of ubiquitin-mediated protein degradation that lead to the development of tumor-initiating cells.
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Affiliation(s)
- Alexandros Strikoudis
- Howard Hughes Medical Institute New York University School of Medicine, New York, NY, USA
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199
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Proteostasis and aging of stem cells. Trends Cell Biol 2014; 24:161-70. [DOI: 10.1016/j.tcb.2013.09.002] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/04/2013] [Accepted: 09/04/2013] [Indexed: 12/13/2022]
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200
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Schröter F, Adjaye J. The proteasome complex and the maintenance of pluripotency: sustain the fate by mopping up? Stem Cell Res Ther 2014; 5:24. [PMID: 25127410 PMCID: PMC4035846 DOI: 10.1186/scrt413] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The proteasome is a multi-enzyme complex responsible for orchestrating protein quality control by degrading misfolded, damaged, abnormal and foreign proteins. Studies related to the association of the proteasomal system in the preservation of self-renewal in both human and mouse pluripotent cells are sparse, and therefore a clear indication of the emergence of a new and important field of research. Under specific conditions the standard proteasome switches to the newly synthesized immunoproteasome, a catalytically active protein chamber also involved in the regulation of protein homeostasis, cell signaling and gene expression. Herein we review recent data to help elucidate and highlight the pivotal role of the proteasome complex, constitutive as well as inducible, in the regulation of self-renewal, pluripotency and differentiation of both embryonic and induced pluripotent stem cells. The proteasome that is endowed with enhanced proteolytic activity maintains self-renewal by regulating gene expression. In addition to protein degradation, the proteasome activator PA28, compartments of the 19S regulatory particle and key members of the ubiquitin pathway dictate the fate of a pluripotent stem cell. We anticipate that our observations will stimulate active research in this new and emerging theme related to stem cell biology, disease and regenerative medicine.
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