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Bietar K, Chu S, Mandl G, Zhang E, Chabaytah N, Sabelli R, Capobianco JA, Stochaj U. Silica-coated LiYF 4:Yb 3+, Tm 3+ upconverting nanoparticles are non-toxic and activate minor stress responses in mammalian cells. RSC Adv 2024; 14:8695-8708. [PMID: 38495986 PMCID: PMC10938293 DOI: 10.1039/d3ra08869c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 03/05/2024] [Indexed: 03/19/2024] Open
Abstract
Lanthanide-doped upconverting nanoparticles (UCNPs) are ideal candidates for use in biomedicine. The interaction of nanomaterials with biological systems determines whether they are suitable for use in living cells. In-depth knowledge of the nano-bio interactions is therefore a pre-requisite for the development of biomedical applications. The current study evaluates fundamental aspects of the NP-cell interface for square bipyramidal UCNPs containing a LiYF4:Yb3+, Tm3+ core and two different silica surface coatings. Given their importance for mammalian physiology, fibroblast and renal proximal tubule epithelial cells were selected as cellular model systems. We have assessed the toxicity of the UCNPs and measured their impact on the homeostasis of living non-malignant cells. Rigorous analyses were conducted to identify possible toxic and sub-lethal effects of the UCNPs. To this end, we examined biomarkers that reveal if UCNPs induce cell killing or stress. Quantitative measurements demonstrate that short-term exposure to the UCNPs had no profound effects on cell viability, cell size or morphology. Indicators of oxidative, endoplasmic reticulum, or nucleolar stress, and the production of molecular chaperones varied with the surface modification of the UCNPs and the cell type analyzed. These differences emphasize the importance of evaluating cells of diverse origin that are relevant to the intended use of the nanomaterials. Taken together, we established that short-term, our square bipyramidal UCNPs are not toxic to non-malignant fibroblast and proximal renal epithelial cells. Compared with established inducers of cellular stress, these UCNPs have minor effects on cellular homeostasis. Our results build the foundation to explore square bipyramidal UCNPs for future in vivo applications.
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Affiliation(s)
- Kais Bietar
- Department of Physiology, McGill University Canada
| | - Siwei Chu
- Department of Physiology, McGill University Canada
| | - Gabrielle Mandl
- Department of Chemistry and Biochemistry, Centre for Nanoscience Research, Concordia University Canada
| | - Emma Zhang
- Department of Physiology, McGill University Canada
| | | | | | - John A Capobianco
- Department of Chemistry and Biochemistry, Centre for Nanoscience Research, Concordia University Canada
| | - Ursula Stochaj
- Department of Physiology, McGill University Canada
- Quantitative Life Sciences Program, McGill University Montreal Canada
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2
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Radhakrishnan S, Martin CA, Rammohan A, Vij M, Chandrasekar M, Rela M. Significance of nucleologenesis, ribogenesis, and nucleolar proteome in the pathogenesis and recurrence of hepatocellular carcinoma. Expert Rev Gastroenterol Hepatol 2023; 17:363-378. [PMID: 36919496 DOI: 10.1080/17474124.2023.2191189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
INTRODUCTION Emerging evidence suggests that enhanced ribosome biogenesis, increased size, and quantitative distribution of nucleoli are associated with dysregulated transcription, which in turn drives a cell into aberrant cellular proliferation and malignancy. Nucleolar alterations have been considered a prognostic histological marker for aggressive tumors. More recently, advancements in the understanding of chromatin network (nucleoplasm viscosity) regulated liquid-liquid phase separation mechanism of nucleolus formation and their multifunctional role shed light on other regulatory processes, apart from ribosomal biogenesis of the nucleolus. AREAS COVERED Using hepatocellular carcinoma as a model to study the role of nucleoli in tumor progression, we review the potential of nucleolus coalescence in the onset and development of tumors through non-ribosomal biogenesis pathways, thereby providing new avenues for early diagnosis and cancer therapy. EXPERT OPINION Molecular-based classifications have failed to identify the nucleolar-based molecular targets that facilitate cell-cycle progression. However, the algorithm-based tumor risk identification with high-resolution medical images suggests prominent nucleoli, karyotheca, and increased nucleus/cytoplasm ratio as largely associated with tumor recurrence. Nonetheless, the role of the non-ribosomal functions of nucleoli in tumorigenesis remains elusive. This clearly indicates the lacunae in the study of the nucleolar proteins pertaining to cancer. [Figure: see text].
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Affiliation(s)
| | | | - Ashwin Rammohan
- The Institute of Liver Disease & Transplantation, Dr. Rela Institute & Medical Centre, Chennai, India
| | - Mukul Vij
- Department of Pathology, Dr. Rela Institute & Medical Centre, Chennai, India
| | - Mani Chandrasekar
- Department of Oncology, Dr. Rela Institute & Medical Centre, Chennai, India
| | - Mohamed Rela
- Cell Laboratory, National Foundation for Liver Research, Chennai, India
- The Institute of Liver Disease & Transplantation, Dr. Rela Institute & Medical Centre, Chennai, India
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3
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Lavering ED, Petros IN, Weeks DL. Component analysis of nucleolar protein compartments using Xenopus laevis oocytes. Dev Growth Differ 2022; 64:306-317. [PMID: 35607824 PMCID: PMC9474603 DOI: 10.1111/dgd.12794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/12/2022] [Accepted: 05/17/2022] [Indexed: 12/19/2022]
Abstract
The nucleolus is a multi‐compartment, non‐membrane‐bound organelle within the nucleus. Nucleolar assembly is influenced by proteins capable of phase separation. Xenopus laevis oocytes contain hundreds of large nucleoli that provide experimental access for nucleoli that is unavailable in other systems. Here we detail methods to streamline the in vivo analysis of the compartmentalization of nucleolar proteins that are suspected of phase separation. The nucleolus is the main hub of ribosome biogenesis and here we present data supporting the division of proteins into nucleolar domains based on their function in ribosome biogenesis. We also describe the use of vital dyes such as Hoechst 33342 and Thioflavin T in nucleolar staining. Additionally, we quantify nucleolar morphology changes induced by heat shock and actinomycin D treatments. We suggest these approaches will be valuable in a variety of studies that seek to better understand the nucleolus, particularly those regarding phase separation. These approaches may also be instructive for other studies on phase separation, especially in the nucleus.
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Affiliation(s)
- Emily D Lavering
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Irini N Petros
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Daniel L Weeks
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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4
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Wu T, Nance J, Chu F, Fazzio TG. Characterization of R-Loop-Interacting Proteins in Embryonic Stem Cells Reveals Roles in rRNA Processing and Gene Expression. Mol Cell Proteomics 2021; 20:100142. [PMID: 34478875 PMCID: PMC8461376 DOI: 10.1016/j.mcpro.2021.100142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 08/21/2021] [Accepted: 08/25/2021] [Indexed: 12/14/2022] Open
Abstract
Chromatin-associated RNAs have diverse roles in the nucleus. However, their mechanisms of action are poorly understood, in part because of the inability to identify proteins that specifically associate with chromatin-bound RNAs. Here, we address this problem for a subset of chromatin-associated RNAs that form R-loops-RNA-DNA hybrid structures that include a displaced strand of ssDNA. R-loops generally form cotranscriptionally and have important roles in regulation of gene expression, immunoglobulin class switching, and other processes. However, unresolved R-loops can lead to DNA damage and chromosome instability. To identify factors that may bind and regulate R-loop accumulation or mediate R-loop-dependent functions, we used a comparative immunoprecipitation/MS approach, with and without RNA-protein crosslinking, to identify a stringent set of R-loop-binding proteins in mouse embryonic stem cells. We identified 364 R-loop-interacting proteins, which were highly enriched for proteins with predicted RNA-binding functions. We characterized several R-loop-interacting proteins of the DEAD-box family of RNA helicases and found that these proteins localize to the nucleolus and, to a lesser degree, the nucleus. Consistent with their localization patterns, we found that these helicases are required for rRNA processing and regulation of gene expression. Surprisingly, depletion of these helicases resulted in misregulation of highly overlapping sets of protein-coding genes, including many genes that function in differentiation and development. We conclude that R-loop-interacting DEAD-box helicases have nonredundant roles that are critical for maintaining the normal embryonic stem cell transcriptome.
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Affiliation(s)
- Tong Wu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jennifer Nance
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Feixia Chu
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Thomas G Fazzio
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
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5
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Moujaber O, Fishbein F, Omran N, Liang Y, Colmegna I, Presley JF, Stochaj U. Cellular senescence is associated with reorganization of the microtubule cytoskeleton. Cell Mol Life Sci 2019; 76:1169-1183. [PMID: 30599068 PMCID: PMC11105446 DOI: 10.1007/s00018-018-2999-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 11/12/2018] [Accepted: 12/12/2018] [Indexed: 12/13/2022]
Abstract
Senescent cells undergo structural and functional changes that affect essentially every aspect of cell physiology. To date, the impact of senescence on the cytoskeleton is poorly understood. This study evaluated the cytoskeleton in two independent cellular models of kidney epithelium senescence. Our work identified multiple senescence-related alterations that impact microtubules and filamentous actin during interphase. Both filamentous systems reorganized profoundly when cells became senescent. As such, microtubule stability increased during senescence, making these filaments more resistant to disassembly in the cold or by nocodazole. Microtubule stabilization was accompanied by enhanced α-tubulin acetylation on lysine 40 and the depletion of HDAC6, the major deacetylase for α-tubulin lysine 40. Rho-associated kinase Rock1 is an upstream regulator that modulates key properties of the cytoplasmic cytoskeleton. Our research shows that Rock1 concentrations were reduced significantly in senescent cells, and we revealed a mechanistic link between microtubule stabilization and Rock1 depletion. Thus, Rock1 overexpression partially restored the cold sensitivity of microtubules in cells undergoing senescence. Additional components relevant to microtubules were affected by senescence. Specifically, we uncovered the senescence-related loss of the microtubule nucleating protein γ-tubulin and aberrant formation of γ-tubulin foci. Concomitant with the alterations of microtubule and actin filaments, senescent cells displayed functional changes. In particular, cell migration was impaired significantly in senescent cells. Taken together, our study identified new senescence-associated deficiencies of the microtubule and actin cytoskeleton, provided insights into the underlying molecular mechanisms and demonstrated functional consequences that are important to the physiology and function of renal epithelial cells.
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Affiliation(s)
- Ossama Moujaber
- Department of Physiology, McGill University, Montreal, Canada
| | | | - Nawal Omran
- Department of Physiology, McGill University, Montreal, Canada
| | - Yue Liang
- Department of Physiology, McGill University, Montreal, Canada
| | - Inés Colmegna
- Department of Rheumatology, McGill University, Montreal, Canada
| | - John F Presley
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada
| | - Ursula Stochaj
- Department of Physiology, McGill University, Montreal, Canada.
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6
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Hayes MH, Peuchen EH, Dovichi NJ, Weeks DL. Dual roles for ATP in the regulation of phase separated protein aggregates in Xenopus oocyte nucleoli. eLife 2018; 7:35224. [PMID: 30015615 PMCID: PMC6050040 DOI: 10.7554/elife.35224] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 07/01/2018] [Indexed: 12/25/2022] Open
Abstract
For many proteins, aggregation is one part of a structural equilibrium that can occur. Balancing productive aggregation versus pathogenic aggregation that leads to toxicity is critical and known to involve adenosine triphosphate (ATP) dependent action of chaperones and disaggregases. Recently a second activity of ATP was identified, that of a hydrotrope which, independent of hydrolysis, was sufficient to solubilize aggregated proteins in vitro. This novel function of ATP was postulated to help regulate proteostasis in vivo. We tested this hypothesis on aggregates found in Xenopus oocyte nucleoli. Our results indicate that ATP has dual roles in the maintenance of protein solubility. We provide evidence of endogenous hydrotropic action of ATP but show that hydrotropic solubilization of nucleolar aggregates is preceded by a destabilizing event. Destabilization is accomplished through an energy dependent process, reliant upon ATP and one or more soluble nuclear factors, or by disruption of a co-aggregate like RNA.
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Affiliation(s)
- Michael H Hayes
- Molecular Medicine Doctoral Program, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Elizabeth H Peuchen
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, United States
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, United States
| | - Daniel L Weeks
- Molecular Medicine Doctoral Program, University of Iowa Carver College of Medicine, Iowa City, United States.,Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, United States
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7
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Abstract
The nucleolus is a prominent subnuclear compartment, where ribosome biosynthesis takes place. Recently, the nucleolus has gained attention for its novel role in the regulation of cellular stress. Nucleolar stress is emerging as a new concept, which is characterized by diverse cellular insult-induced abnormalities in nucleolar structure and function, ultimately leading to activation of p53 or other stress signaling pathways and alterations in cell behavior. Despite a number of comprehensive reviews on this concept, straightforward and clear-cut way criteria for a nucleolar stress state, regarding the factors that elicit this state, the morphological and functional alterations as well as the rationale for p53 activation are still missing. Based on literature of the past two decades, we herein summarize the evolution of the concept and provide hallmarks of nucleolar stress. Along with updated information and thorough discussion of existing confusions in the field, we pay particular attention to the current understanding of the sensing mechanisms, i.e., how stress is integrated by p53. In addition, we propose our own emphasis regarding the role of nucleolar protein NPM1 in the hallmarks of nucleolar stress and sensing mechanisms. Finally, the links of nucleolar stress to human diseases are briefly and selectively introduced.
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Affiliation(s)
- Kai Yang
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China.,Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases with Integrated Chinese-Western Medicine, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai, 200025, China
| | - Jie Yang
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Jing Yi
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
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8
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Neben CL, Tuzon CT, Mao X, Lay FD, Merrill AE. FGFR2 mutations in bent bone dysplasia syndrome activate nucleolar stress and perturb cell fate determination. Hum Mol Genet 2018; 26:3253-3270. [PMID: 28595297 DOI: 10.1093/hmg/ddx209] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/31/2017] [Indexed: 12/21/2022] Open
Abstract
Fibroblast Growth Factor (FGF) signaling promotes self-renewal in progenitor cells by encouraging proliferation and inhibiting cellular senescence. Yet, these beneficial effects can be hijacked by disease-causing mutations in FGF receptor (FGFR) during embryogenesis. By studying dominant FGFR2 mutations that are germline in bent bone dysplasia syndrome (BBDS), we reveal a mechanistic connection between FGFR2, ribosome biogenesis, and cellular stress that links cell fate determination to disease pathology. We previously showed that FGFR2 mutations in BBDS, which amplify nucleolar targeting of FGFR2, activate ribosomal DNA (rDNA) transcription and delay differentiation in osteoprogenitor cells and patient-derived bone. Here we find that the BBDS mutations augment the ability of FGFR2 to recruit histone-remodeling factors that epigenetically activate transcriptionally silent rDNA. Nucleolar morphology is controlled by chromatin structure, and the high levels of euchromatic rDNA induced by the BBDS mutations direct nucleolar disorganization, alter ribosome biogenesis, and activate the Rpl11-Mdm2-p53 nucleolar stress response pathway. Inhibition of p53 in cells expressing the FGFR2 mutations in BBDS rescues delayed osteoblast differentiation, suggesting that p53 activation is an essential pathogenic factor in, and potential therapeutic target for, BBDS. This work establishes rDNA as developmentally regulated loci that receive direct input from FGF signaling to balance self-renewal and cell fate determination.
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Affiliation(s)
- Cynthia L Neben
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry.,Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Creighton T Tuzon
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry.,Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xiaojing Mao
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry.,Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Fides D Lay
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Amy E Merrill
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry.,Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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9
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Schosserer M, Grillari J, Breitenbach M. The Dual Role of Cellular Senescence in Developing Tumors and Their Response to Cancer Therapy. Front Oncol 2017; 7:278. [PMID: 29218300 PMCID: PMC5703792 DOI: 10.3389/fonc.2017.00278] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/06/2017] [Indexed: 12/11/2022] Open
Abstract
Cellular senescence describes an irreversible growth arrest characterized by distinct morphology, gene expression pattern, and secretory phenotype. The final or intermediate stages of senescence can be reached by different genetic mechanisms and in answer to different external and internal stresses. It has been maintained in the literature but never proven by clearcut experiments that the induction of senescence serves the evolutionary purpose of protecting the individual from development and growth of cancers. This hypothesis was recently scrutinized by new experiments and found to be partly true, but part of the gene activities now known to happen in senescence are also needed for cancer growth, leading to the view that senescence is a double-edged sword in cancer development. In current cancer therapy, cellular senescence is, on the one hand, intended to occur in tumor cells, as thereby the therapeutic outcome is improved, but might, on the other hand, also be induced unintentionally in non-tumor cells, causing inflammation, secondary tumors, and cancer relapse. Importantly, organismic aging leads to accumulation of senescent cells in tissues and organs of aged individuals. Senescent cells can occur transiently, e.g., during embryogenesis or during wound healing, with beneficial effects on tissue homeostasis and regeneration or accumulate chronically in tissues, which detrimentally affects the microenvironment by de- or transdifferentiation of senescent cells and their neighboring stromal cells, loss of tissue specific functionality, and induction of the senescence-associated secretory phenotype, an increased secretory profile consisting of pro-inflammatory and tissue remodeling factors. These factors shape their surroundings toward a pro-carcinogenic microenvironment, which fuels the development of aging-associated cancers together with the accumulation of mutations over time. We are presenting an overview of well-documented stress situations and signals, which induce senescence. Among them, oncogene-induced senescence and stress-induced premature senescence are prominent. New findings about the role of senescence in tumor biology are critically reviewed with respect to new suggestions for cancer therapy leveraging genetic and pharmacological methods to prevent senescence or to selectively kill senescent cells in tumors.
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Affiliation(s)
- Markus Schosserer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Johannes Grillari
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Austrian Cluster for Tissue Regeneration, Vienna, Austria.,Christian Doppler Laboratory for Biotechnology of Skin Aging, Vienna, Austria.,Evercyte GmbH, Vienna, Austria
| | - Michael Breitenbach
- Department of Cell Biology, Division of Genetics, University of Salzburg, Salzburg, Austria
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10
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Dissecting the molecular mechanisms that impair stress granule formation in aging cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:475-486. [DOI: 10.1016/j.bbamcr.2016.12.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 11/21/2016] [Accepted: 12/09/2016] [Indexed: 01/20/2023]
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11
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The Chromatin-Associated Phf12 Protein Maintains Nucleolar Integrity and Prevents Premature Cellular Senescence. Mol Cell Biol 2017; 37:MCB.00522-16. [PMID: 27956701 DOI: 10.1128/mcb.00522-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/04/2016] [Indexed: 12/17/2022] Open
Abstract
Pf1, also known as Phf12 (plant homeodomain [PHD] zinc finger protein 12), is a member of the PHD zinc finger family of proteins. Pf1 associates with a chromatin-interacting protein complex comprised of MRG15, Sin3B, and histone deacetylase 1 (HDAC1) that functions as a transcriptional modulator. The biological function of Pf1 remains largely elusive. We undertook the generation of Pf1 knockout mice to elucidate its physiological role. We demonstrate that Pf1 is required for mid- to late gestation viability. Pf1 inactivation impairs the proliferative potential of mouse embryonic fibroblasts (MEFs) and is associated with a significant decrease in bromodeoxyuridine incorporation; an increase in senescence-associated β-galactosidase (SA-β-Gal) activity, a marker of cellular senescence; and elevated levels of phosphorylated H2AX (γ-H2A.X), a marker associated with DNA double-strand breaks. Analysis of transcripts differentially expressed in wild-type and Pf1-deficient cells revealed the impact of Pf1 in multiple regulatory arms of the ribosome biogenesis pathways. Strikingly, assessment of the morphology of the nucleoli exposed an abnormal nucleolar structure in Pf1-deficient cells. Finally, proteomic analysis of the Pf1-interacting complexes highlighted proteins involved in ribosome biogenesis. Taken together, our data reveal an unsuspected function for the Pf1-associated chromatin complex in the ribosomal biogenesis and senescence pathways.
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12
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Yang K, Wang M, Zhao Y, Sun X, Yang Y, Li X, Zhou A, Chu H, Zhou H, Xu J, Wu M, Yang J, Yi J. A redox mechanism underlying nucleolar stress sensing by nucleophosmin. Nat Commun 2016; 7:13599. [PMID: 27886181 PMCID: PMC5133708 DOI: 10.1038/ncomms13599] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 10/18/2016] [Indexed: 12/24/2022] Open
Abstract
The nucleolus has been recently described as a stress sensor. The nucleoplasmic translocation of nucleolar protein nucleophosmin (NPM1) is a hallmark of nucleolar stress; however, the causes of this translocation and its connection to p53 activation are unclear. Using single live-cell imaging and the redox biosensors, we demonstrate that nucleolar oxidation is a general response to various cellular stresses. During nucleolar oxidation, NPM1 undergoes S-glutathionylation on cysteine 275, which triggers the dissociation of NPM1 from nucleolar nucleic acids. The C275S mutant NPM1, unable to be glutathionylated, remains in the nucleolus under nucleolar stress. Compared with wild-type NPM1 that can disrupt the p53–HDM2 interaction, the C275S mutant greatly compromises the activation of p53, highlighting that nucleoplasmic translocation of NPM1 is a prerequisite for stress-induced activation of p53. This study elucidates a redox mechanism for the nucleolar stress sensing and may help the development of therapeutic strategies. Nucleoplasmic translocation of NPM1 is integral to nucleolar stress sensing. Here, the authors show that nucleolar oxidation is a general cellular stress response, and that oxidation-related glutathionylation of NPM1 triggers its translocation and facilitates p53 activation.
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Affiliation(s)
- Kai Yang
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Ming Wang
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Yuzheng Zhao
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Xuxu Sun
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Yi Yang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Xie Li
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Aiwu Zhou
- Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Huilin Chu
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Hu Zhou
- Shanghai Institute of Materia Medica, 555 Zu Chong Zhi Road, Zhang Jiang Hi-Tech Park, Shanghai 201203, China
| | - Jianrong Xu
- Department of Pharmacology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Mian Wu
- School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230022, China
| | - Jie Yang
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Jing Yi
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
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13
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Abstract
The nucleolus is the largest nuclear organelle and is the primary site of ribosome subunit biogenesis in eukaryotic cells. It is assembled around arrays of ribosomal DNA genes, forming specific chromosomal features known as nucleolar organizing regions (NORs) which are the sites of ribosomal DNA transcription. While the nucleolus main activity involve different steps of ribosome biogenesis, the presence of proteins with no obvious relationship with ribosome subunit production suggests additional functions for the nucleolus, such as regulation of mitosis, cell cycle progression, stress response and biogenesis of multiple ribonucleoprotein complexes. The many novel factors and separate classes of proteins identified within the nucleolus support this view that the nucleolus may perform additional functions beyond its known role in ribosome subunit biogenesis. Here we review our knowledge of the nucleolar functions and will provide a detailed picture of how the nucleolus is involved in many cellular pathways.
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Affiliation(s)
- David P. Bazett-Jones
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario Canada
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14
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The relationship between the nucleolus and cancer: Current evidence and emerging paradigms. Semin Cancer Biol 2015; 37-38:36-50. [PMID: 26721423 DOI: 10.1016/j.semcancer.2015.12.004] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/15/2015] [Accepted: 12/19/2015] [Indexed: 12/13/2022]
Abstract
The nucleolus is the most prominent nuclear substructure assigned to produce ribosomes; molecular machines that are responsible for carrying out protein synthesis. To meet the increased demand for proteins during cell growth and proliferation the cell must increase protein synthetic capacity by upregulating ribosome biogenesis. While larger nucleolar size and number have been recognized as hallmark features of many tumor types, recent evidence has suggested that, in addition to overproduction of ribosomes, decreased ribosome biogenesis as well as qualitative changes in this process could also contribute to tumor initiation and cancer progression. Furthermore, the nucleolus has become the focus of intense attention for its involvement in processes that are clearly unrelated to ribosome biogenesis such as sensing and responding to endogenous and exogenous stressors, maintenance of genome stability, regulation of cell-cycle progression, cellular senescence, telomere function, chromatin structure, establishment of nuclear architecture, global regulation of gene expression and biogenesis of multiple ribonucleoprotein particles. The fact that dysregulation of many of these fundamental cellular processes may contribute to the malignant phenotype suggests that normal functioning of the nucleolus safeguards against the development of cancer and indicates its potential as a therapeutic approach. Here we review the recent advances made toward understanding these newly-recognized nucleolar functions and their roles in normal and cancer cells, and discuss possible future research directions.
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15
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Quantitative and integrated proteome and microRNA analysis of endothelial replicative senescence. J Proteomics 2015; 126:12-23. [DOI: 10.1016/j.jprot.2015.05.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/05/2015] [Accepted: 05/20/2015] [Indexed: 12/31/2022]
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16
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Val MM, Mendes LA, Alarcão A, Carvalho L, Carreira I, Rodrigues CFD, Alpoim MC. Senescent bronchial fibroblasts induced to senescence by Cr(VI) promote epithelial-mesenchymal transition when co-cultured with bronchial epithelial cells in the presence of Cr(VI). Mutagenesis 2014; 30:277-86. [PMID: 25406472 DOI: 10.1093/mutage/geu070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Cellular senescence is a physiological process that serves as a powerful barrier for tumorigenesis. However, senescent cells can be deleterious for the tissue microenvironment. Such is the case of senescent fibroblasts that release several pro-tumorigenic factors that promote malignant transformation in the nearby epithelial cells. Occupational exposure to hexavalent chromium [Cr(VI)] compounds is a cause of respiratory cancers. Although Cr(VI) is known to induce senescence in human foreskin fibroblasts, the role of senescent fibroblasts in the Cr(VI)-induced malignant transformation of human bronchial epithelial cells was never assessed. Thus, to study the evolutionary dynamics generated by the interaction between human bronchial epithelial cells and senescent bronchial fibroblasts, the non-tumorigenic human bronchial epithelial BEAS-2B cells were co-cultured with Cr(VI)-induced senescent human bronchial fibroblasts for 4 weeks. Under the pressure of 0.5 µM Cr(VI), senescent fibroblasts promoted the acquisition of mesenchymal features on BEAS-2B cells, e.g. the fusiform shape and increased Vimentin expression, consistent with the occurrence of an epithelial-mesenchymal transition-like process. Features of transformed cells including larger nuclei, as well as nuclei with heterogeneous size, were also observed. Altogether the results obtained demonstrate that besides acting over the epithelium, Cr(VI) also affects bronchial fibroblasts driving them senescent. As a consequence, a paracrine communication loop is established with the above-placed epithelium prompting the epithelial cells for malignant transformation and thus facilitating the initial steps of tumorigenesis.
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Affiliation(s)
- Mariana Monteiro Val
- Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal, Center of Investigation in Environment, Genetics and Oncobiology, University of Coimbra, Coimbra, Portugal, Center for Neuroscience and Cell Biology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal and
| | - Luís André Mendes
- Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal, Center of Investigation in Environment, Genetics and Oncobiology, University of Coimbra, Coimbra, Portugal, Center for Neuroscience and Cell Biology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal and
| | - Ana Alarcão
- Center of Investigation in Environment, Genetics and Oncobiology, University of Coimbra, Coimbra, Portugal, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Lina Carvalho
- Center of Investigation in Environment, Genetics and Oncobiology, University of Coimbra, Coimbra, Portugal, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Isabel Carreira
- Center of Investigation in Environment, Genetics and Oncobiology, University of Coimbra, Coimbra, Portugal, Center for Neuroscience and Cell Biology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal and Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Carlos Fernando D Rodrigues
- Center of Investigation in Environment, Genetics and Oncobiology, University of Coimbra, Coimbra, Portugal, Center for Neuroscience and Cell Biology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal and Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Maria Carmen Alpoim
- Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal, Center of Investigation in Environment, Genetics and Oncobiology, University of Coimbra, Coimbra, Portugal, Center for Neuroscience and Cell Biology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal and
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Diesch J, Hannan RD, Sanij E. Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease. Cell Biosci 2014; 4:43. [PMID: 25949792 PMCID: PMC4422213 DOI: 10.1186/2045-3701-4-43] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 07/27/2014] [Indexed: 01/05/2023] Open
Abstract
Ribosomal RNA (rRNA) gene (rDNA) transcription by RNA Polymerase I (Pol I) drives cell growth and underlies nucleolar structure and function, indirectly coordinating many fundamental cellular processes. The importance of keeping rDNA transcription under tight control is reflected by the fact that deranged Pol I transcription is a feature of cancer and other human disorders. In this review, we discuss multiple aspects of rDNA function including the relationship between Pol I transcription and proliferative capacity, the role of Pol I transcription in mediating nucleolar structure and integrity, and rDNA/nucleolar interactions with the genome and their influence on heterochromatin and global genome stability. Furthermore, we discuss how perturbations in the structure of the rDNA loci might contribute to human disease, in some cases independent of effects on ribosome biogenesis.
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Affiliation(s)
- Jeannine Diesch
- Growth Control Laboratory, Research Division, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, Victoria 3002, Australia ; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ross D Hannan
- Growth Control Laboratory, Research Division, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, Victoria 3002, Australia ; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia ; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia ; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia ; Division of Cancer Medicine, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, Victoria 3002, Australia ; School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Elaine Sanij
- Growth Control Laboratory, Research Division, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, Victoria 3002, Australia ; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia ; Department of Pathology, University of Melbourne, Parkville, Victoria 3010, Australia
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18
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Mahboubi H, Stochaj U. Nucleoli and Stress Granules: Connecting Distant Relatives. Traffic 2014; 15:1179-93. [DOI: 10.1111/tra.12191] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 06/30/2014] [Accepted: 06/30/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Hicham Mahboubi
- Department of Physiology; McGill University; 3655 Promenade Sir William Osler Montreal Quebec H3G 1Y6 Canada
| | - Ursula Stochaj
- Department of Physiology; McGill University; 3655 Promenade Sir William Osler Montreal Quebec H3G 1Y6 Canada
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19
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Lee N, Kim DK, Kim ES, Park SJ, Kwon JH, Shin J, Park SM, Moon YH, Wang HJ, Gho YS, Choi KY. Comparative interactomes of SIRT6 and SIRT7: Implication of functional links to aging. Proteomics 2014; 14:1610-22. [PMID: 24782448 DOI: 10.1002/pmic.201400001] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 04/01/2014] [Accepted: 04/25/2014] [Indexed: 12/21/2022]
Abstract
Sirtuins are NAD(+) -dependent deacetylases that regulate a range of cellular processes. Although diverse functions of sirtuins have been proposed, those functions of SIRT6 and SIRT7 that are mediated by their interacting proteins remain elusive. In the present study, we identified SIRT6- and SIRT7-interacting proteins, and compared their interactomes to investigate functional links. Our interactomes revealed 136 interacting proteins for SIRT6 and 233 for SIRT7 while confirming seven and 111 proteins identified previously for SIRT6 and SIRT7, respectively. Comparison of SIRT6 and SIRT7 interactomes under the same experimental conditions disclosed 111 shared proteins, implying related functional links. The interaction networks of interactomes indicated biological processes associated with DNA repair, chromatin assembly, and aging. Interactions of two highly acetylated proteins, nucleophosmin (NPM1) and nucleolin, with SIRT6 and SIRT7 were confirmed by co-immunoprecipitation. NPM1 was found to be deacetylated by both SIRT6 and SIRT7. In senescent cells, the acetylation level of NPM1 was increased in conjunction with decreased levels of SIRT6 and SIRT7, suggesting that the acetylation of NPM1 could be regulated by SIRT6 and SIRT7 in the aging process. Our comparative interactomic study of SIRT6 and SIRT7 implies important functional links to aging by their associations with interacting proteins. All MS data have been deposited in the ProteomeXchange with identifiers PXD000159 and PXD000850 (http://proteomecentral.proteomexchange.org/dataset/PXD000159, http://proteomecentral.proteomexchange.org/dataset/PXD000850).
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Affiliation(s)
- Namgyu Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
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20
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The nucleolus—guardian of cellular homeostasis and genome integrity. Chromosoma 2014; 122:487-97. [PMID: 24022641 DOI: 10.1007/s00412-013-0430-0] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/05/2013] [Indexed: 01/25/2023]
Abstract
All organisms sense and respond to conditions that stress their homeostasis by downregulating the synthesis of rRNA and ribosome biogenesis, thus designating the nucleolus as the central hub in coordinating the cellular stress response. One of the most intriguing roles of the nucleolus, long regarded as a mere ribosome-producing factory, is its participation in monitoring cellular stress signals and transmitting them to the RNA polymerase I (Pol I) transcription machinery. As rRNA synthesis is a most energy-consuming process, switching off transcription of rRNA genes is an effective way of saving the energy required to maintain cellular homeostasis during acute stress. The Pol I transcription machinery is the key convergence point that collects and integrates a vast array of information from cellular signaling cascades to regulate ribosome production which, in turn, guides cell growth and proliferation. This review focuses on the mechanisms that link cell physiology to rDNA silencing, a prerequisite for nucleolar integrity and cell survival.
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21
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Quin JE, Devlin JR, Cameron D, Hannan KM, Pearson RB, Hannan RD. Targeting the nucleolus for cancer intervention. Biochim Biophys Acta Mol Basis Dis 2014; 1842:802-16. [PMID: 24389329 DOI: 10.1016/j.bbadis.2013.12.009] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 12/17/2013] [Indexed: 12/17/2022]
Abstract
The contribution of the nucleolus to cancer is well established with respect to its traditional role in facilitating ribosome biogenesis and proliferative capacity. More contemporary studies however, infer that nucleoli contribute a much broader role in malignant transformation. Specifically, extra-ribosomal functions of the nucleolus position it as a central integrator of cellular proliferation and stress signaling, and are emerging as important mechanisms for modulating how oncogenes and tumor suppressors operate in normal and malignant cells. The dependence of certain tumor cells to co-opt nucleolar processes to maintain their cancer phenotypes has now clearly been demonstrated by the application of small molecule inhibitors of RNA Polymerase I to block ribosomal DNA transcription and disrupt nucleolar function (Bywater et al., 2012 [1]). These drugs, which selectively kill tumor cells in vivo while sparing normal cells, have now progressed to clinical trials. It is likely that we have only just begun to scratch the surface of the potential of the nucleolus as a new target for cancer therapy, with "suppression of nucleolar stress" representing an emerging "hallmark" of cancer. This article is part of a Special Issue entitled: Role of the Nucleolus in Human Disease.
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Affiliation(s)
- Jaclyn E Quin
- Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Jennifer R Devlin
- Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Donald Cameron
- Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Kate M Hannan
- Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Richard B Pearson
- Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Ross D Hannan
- Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia; Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia; School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland, Australia.
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22
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Su H, Kodiha M, Lee S, Stochaj U. Identification of novel markers that demarcate the nucleolus during severe stress and chemotherapeutic treatment. PLoS One 2013; 8:e80237. [PMID: 24223222 PMCID: PMC3819286 DOI: 10.1371/journal.pone.0080237] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 10/01/2013] [Indexed: 01/08/2023] Open
Abstract
The nucleolus, the ribosomal factory of the cell, has emerged as a key player that regulates many aspects of cell biology. Several thousand proteins associate at least transiently with nucleoli, thereby generating a highly dynamic compartment with a protein profile which is sensitive to changes in cell physiology and pharmacological agents. Powerful tools that reliably demarcate the nucleoli are a prerequisite to measure their composition and activities. Previously, we developed quantitative methods to measure fluorescently labeled molecules in nucleoli. While these tools identify nucleoli under control and mild stress conditions, the accurate detection of nucleolar boundaries under harsh experimental conditions is complicated by the lack of appropriate markers for the nucleolar compartment. Using fluorescence microscopy we have now identified new marker proteins to detect nucleoli upon (a) severe stress and (b) drug treatments that trigger a pronounced reorganization of nucleoli. Our results demonstrate that nucleolin is an ideal marker to delimit nucleoli when cells are exposed to heat or oxidative stress. Furthermore, we show for the first time that cellular apoptosis susceptibility protein (CAS) and human antigen R protein (HuR) are excluded from nucleoli and can be employed to delimit these compartments under severe conditions that redistribute major nucleolar proteins. As proof-of-principle, we used these markers to demarcate nucleoli in cells treated with pharmacological compounds that disrupt the nucleolar organization. Furthermore, to gain new insights into the biology of the nucleolus, we applied our protocols and quantified stress- and drug-induced changes in nucleolar organization and function. Finally, we show that CAS, HuR and nucleolin not only identify nucleoli in optical sections, but are also suitable to demarcate the nucleolar border following 3D reconstruction. Taken together, our studies present novel marker proteins that delimit nucleoli with high confidence under a variety of experimental settings.
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Affiliation(s)
- Haitong Su
- McGill University, Department of Physiology, Montreal, Quebec, Canada
| | - Mohamed Kodiha
- McGill University, Department of Physiology, Montreal, Quebec, Canada
| | - Sunghoon Lee
- McGill University, Department of Physiology, Montreal, Quebec, Canada
| | - Ursula Stochaj
- McGill University, Department of Physiology, Montreal, Quebec, Canada
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Liang YM, Wang X, Ramalingam R, So KY, Lam YW, Li ZF. Novel nucleolar isolation method reveals rapid response of human nucleolar proteomes to serum stimulation. J Proteomics 2012; 77:521-30. [DOI: 10.1016/j.jprot.2012.09.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 09/23/2012] [Accepted: 09/24/2012] [Indexed: 12/31/2022]
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24
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Jarboui MA, Bidoia C, Woods E, Roe B, Wynne K, Elia G, Hall WW, Gautier VW. Nucleolar protein trafficking in response to HIV-1 Tat: rewiring the nucleolus. PLoS One 2012; 7:e48702. [PMID: 23166591 PMCID: PMC3499507 DOI: 10.1371/journal.pone.0048702] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 10/03/2012] [Indexed: 12/20/2022] Open
Abstract
The trans-activator Tat protein is a viral regulatory protein essential for HIV-1 replication. Tat trafficks to the nucleoplasm and the nucleolus. The nucleolus, a highly dynamic and structured membrane-less sub-nuclear compartment, is the site of rRNA and ribosome biogenesis and is involved in numerous cellular functions including transcriptional regulation, cell cycle control and viral infection. Importantly, transient nucleolar trafficking of both Tat and HIV-1 viral transcripts are critical in HIV-1 replication, however, the role(s) of the nucleolus in HIV-1 replication remains unclear. To better understand how the interaction of Tat with the nucleolar machinery contributes to HIV-1 pathogenesis, we investigated the quantitative changes in the composition of the nucleolar proteome of Jurkat T-cells stably expressing HIV-1 Tat fused to a TAP tag. Using an organellar proteomic approach based on mass spectrometry, coupled with Stable Isotope Labelling in Cell culture (SILAC), we quantified 520 proteins, including 49 proteins showing significant changes in abundance in Jurkat T-cell nucleolus upon Tat expression. Numerous proteins exhibiting a fold change were well characterised Tat interactors and/or known to be critical for HIV-1 replication. This suggests that the spatial control and subcellular compartimentaliation of these cellular cofactors by Tat provide an additional layer of control for regulating cellular machinery involved in HIV-1 pathogenesis. Pathway analysis and network reconstruction revealed that Tat expression specifically resulted in the nucleolar enrichment of proteins collectively participating in ribosomal biogenesis, protein homeostasis, metabolic pathways including glycolytic, pentose phosphate, nucleotides and amino acids biosynthetic pathways, stress response, T-cell signaling pathways and genome integrity. We present here the first differential profiling of the nucleolar proteome of T-cells expressing HIV-1 Tat. We discuss how these proteins collectively participate in interconnected networks converging to adapt the nucleolus dynamic activities, which favor host biosynthetic activities and may contribute to create a cellular environment supporting robust HIV-1 production.
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Affiliation(s)
- Mohamed Ali Jarboui
- Centre for Research in Infectious Diseases (CRID), School of Medicine and Medical Science (SMMS), University College Dublin (UCD), Dublin, Ireland
| | - Carlo Bidoia
- Centre for Research in Infectious Diseases (CRID), School of Medicine and Medical Science (SMMS), University College Dublin (UCD), Dublin, Ireland
| | - Elena Woods
- Centre for Research in Infectious Diseases (CRID), School of Medicine and Medical Science (SMMS), University College Dublin (UCD), Dublin, Ireland
| | - Barbara Roe
- Centre for Research in Infectious Diseases (CRID), School of Medicine and Medical Science (SMMS), University College Dublin (UCD), Dublin, Ireland
| | - Kieran Wynne
- Mass Spectrometry Resource (MSR), Conway Institute for Biomolecular and Biomedical Research, University College Dublin (UCD), Dublin, Ireland
| | - Giuliano Elia
- Mass Spectrometry Resource (MSR), Conway Institute for Biomolecular and Biomedical Research, University College Dublin (UCD), Dublin, Ireland
| | - William W. Hall
- Centre for Research in Infectious Diseases (CRID), School of Medicine and Medical Science (SMMS), University College Dublin (UCD), Dublin, Ireland
| | - Virginie W. Gautier
- Centre for Research in Infectious Diseases (CRID), School of Medicine and Medical Science (SMMS), University College Dublin (UCD), Dublin, Ireland
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Abstract
The nucleolus is a distinct subnuclear compartment known as the site for ribosome biogenesis in eukaryotes. Consequently, the nucleolus is also proposed to function in cell-cycle control, stress sensing and senescence, as well as in viral infection. An increasing number of viral proteins have been found to localize to the nucleolus. In this article, we review the current understanding of the functions of the nucleolus, the molecular mechanism of cellular and viral protein targeting to the nucleolus and the functional roles of the nucleolus during viral infection with a specific focus on the herpesvirus family.
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Affiliation(s)
- Liwen Ni
- Molecular Virology and Viral Immunology Research Group, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Shuai Wang
- Molecular Virology and Viral Immunology Research Group, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Chunfu Zheng
- Molecular Virology and Viral Immunology Research Group, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
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