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Barravecchia I, De Cesari C, Forcato M, Scebba F, Pyankova OV, Bridger JM, Foster HA, Signore G, Borghini A, Andreassi M, Andreazzoli M, Bicciato S, Pè ME, Angeloni D. Microgravity and space radiation inhibit autophagy in human capillary endothelial cells, through either opposite or synergistic effects on specific molecular pathways. Cell Mol Life Sci 2021; 79:28. [PMID: 34936031 PMCID: PMC11072227 DOI: 10.1007/s00018-021-04025-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/12/2021] [Accepted: 11/05/2021] [Indexed: 12/13/2022]
Abstract
Microgravity and space radiation (SR) are two highly influential factors affecting humans in space flight (SF). Many health problems reported by astronauts derive from endothelial dysfunction and impaired homeostasis. Here, we describe the adaptive response of human, capillary endothelial cells to SF. Reference samples on the ground and at 1g onboard permitted discrimination between the contribution of microgravity and SR within the combined responses to SF. Cell softening and reduced motility occurred in SF cells, with a loss of actin stress fibers and a broader distribution of microtubules and intermediate filaments within the cytoplasm than in control cells. Furthermore, in space the number of primary cilia per cell increased and DNA repair mechanisms were found to be activated. Transcriptomics revealed the opposing effects of microgravity from SR for specific molecular pathways: SR, unlike microgravity, stimulated pathways for endothelial activation, such as hypoxia and inflammation, DNA repair and apoptosis, inhibiting autophagic flux and promoting an aged-like phenotype. Conversely, microgravity, unlike SR, activated pathways for metabolism and a pro-proliferative phenotype. Therefore, we suggest microgravity and SR should be considered separately to tailor effective countermeasures to protect astronauts' health.
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Affiliation(s)
- Ivana Barravecchia
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Via G. Moruzzi, 1, 56124, Pisa, Italy
- Department of Pharmacy, University of Pisa, 56126, Pisa, Italy
| | - Chiara De Cesari
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Via G. Moruzzi, 1, 56124, Pisa, Italy
- Department of Biology, University of Pisa, 56123, Pisa, Italy
| | - Mattia Forcato
- Center for Genome Research, Department of Life Science, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Francesca Scebba
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Via G. Moruzzi, 1, 56124, Pisa, Italy
| | - Olga V Pyankova
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Via G. Moruzzi, 1, 56124, Pisa, Italy
| | - Joanna M Bridger
- Laboratory of Nuclear and Genomic Health, Centre of Genome Engineering and Maintenance, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Helen A Foster
- Department of Biological and Environmental Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, UK
| | | | - Andrea Borghini
- Institute of Clinical Physiology, National Research Council, 56124, Pisa, Italy
| | | | | | - Silvio Bicciato
- Center for Genome Research, Department of Life Science, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Via G. Moruzzi, 1, 56124, Pisa, Italy
| | - Debora Angeloni
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Via G. Moruzzi, 1, 56124, Pisa, Italy.
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2
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Dent MAR, Aranda-Anzaldo A. Lessons we can learn from neurons to make cancer cells quiescent. J Neurosci Res 2019; 97:1141-1152. [PMID: 30985022 DOI: 10.1002/jnr.24428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 02/20/2019] [Accepted: 03/26/2019] [Indexed: 12/16/2022]
Abstract
Cancer is a major concern for contemporary societies. However, the incidence of cancer is unevenly distributed among tissues and cell types. In particular, the evidence indicates that neurons are absolutely resistant to cancer and this is commonly explained on the basis of the known postmitotic state of neurons. The dominant paradigm on cancer understands this problem as a disease caused by mutations in cellular genes that result in unrestrained cell proliferation and eventually in tissue invasion and metastasis. However, the evidence also shows that mutations and gross chromosomal anomalies are common in functional neurons that nevertheless do not become neoplastic. This fact suggests that in the real nonexperimental setting mutations per se are not enough for inducing carcinogenesis but also that the postmitotic state of neurons is not genetically controlled or determined, otherwise there should be reports of spontaneously transformed neurons. Here we discuss the evidence that the postmitotic state of neurons has a structural basis on the high stability of their nuclear higher order structure that performs like an absolute tumor suppressor. We also discuss evidence that it is possible to induce a similar structural postmitotic state in nonneural cell types as a practical strategy for stopping or reducing the progression of cancer.
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Affiliation(s)
- Myrna A R Dent
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Mexico
| | - Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Mexico
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3
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Bikkul MU, Clements CS, Godwin LS, Goldberg MW, Kill IR, Bridger JM. Farnesyltransferase inhibitor and rapamycin correct aberrant genome organisation and decrease DNA damage respectively, in Hutchinson-Gilford progeria syndrome fibroblasts. Biogerontology 2018; 19:579-602. [PMID: 29907918 PMCID: PMC6223735 DOI: 10.1007/s10522-018-9758-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/30/2018] [Indexed: 12/20/2022]
Abstract
Hutchinson–Gilford progeria syndrome (HGPS) is a rare and fatal premature ageing disease in children. HGPS is one of several progeroid syndromes caused by mutations in the LMNA gene encoding the nuclear structural proteins lamins A and C. In classic HGPS the mutation G608G leads to the formation of a toxic lamin A protein called progerin. During post-translational processing progerin remains farnesylated owing to the mutation interfering with a step whereby the farnesyl moiety is removed by the enzyme ZMPSTE24. Permanent farnesylation of progerin is thought to be responsible for the proteins toxicity. Farnesyl is generated through the mevalonate pathway and three drugs that interfere with this pathway and hence the farnesylation of proteins have been administered to HGPS children in clinical trials. These are a farnesyltransferase inhibitor (FTI), statin and a bisphosphonate. Further experimental studies have revealed that other drugs such as N-acetyl cysteine, rapamycin and IGF-1 may be of use in treating HGPS through other pathways. We have shown previously that FTIs restore chromosome positioning in interphase HGPS nuclei. Mis-localisation of chromosomes could affect the cells ability to regulate proper genome function. Using nine different drug treatments representing drug regimes in the clinic we have shown that combinatorial treatments containing FTIs are most effective in restoring specific chromosome positioning towards the nuclear periphery and in tethering telomeres to the nucleoskeleton. On the other hand, rapamycin was found to be detrimental to telomere tethering, it was, nonetheless, the most effective at inducing DNA damage repair, as revealed by COMET analyses.
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Affiliation(s)
- Mehmet U Bikkul
- Progeria Research Team, Healthy Ageing Theme, Institute for Environment, Health and Societies, College of Health and Life Sciences, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK
| | - Craig S Clements
- Progeria Research Team, Healthy Ageing Theme, Institute for Environment, Health and Societies, College of Health and Life Sciences, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK
| | - Lauren S Godwin
- Progeria Research Team, Healthy Ageing Theme, Institute for Environment, Health and Societies, College of Health and Life Sciences, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK
| | - Martin W Goldberg
- Department of Biosciences, Durham University, Science Laboratories, South Road, Durham, DH1 3LE, UK
| | - Ian R Kill
- Progeria Research Team, Healthy Ageing Theme, Institute for Environment, Health and Societies, College of Health and Life Sciences, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK
| | - Joanna M Bridger
- Progeria Research Team, Healthy Ageing Theme, Institute for Environment, Health and Societies, College of Health and Life Sciences, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK.
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4
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Silva-Santiago E, Rivera-Mulia JC, Aranda-Anzaldo A. The Set of Structural DNA-Nuclear Matrix Interactions in Neurons Is Cell-Type Specific and Rather Independent of Functional Constraints. J Cell Biochem 2017; 118:2151-2160. [DOI: 10.1002/jcb.25852] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 12/19/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Evangelina Silva-Santiago
- Facultad de Medicina, Laboratorio de Biología Molecular y Neurociencias; Universidad Autónoma del Estado de México; Toluca 50180 Edo. Méx. Mexico
| | - Juan Carlos Rivera-Mulia
- Facultad de Medicina, Laboratorio de Biología Molecular y Neurociencias; Universidad Autónoma del Estado de México; Toluca 50180 Edo. Méx. Mexico
| | - Armando Aranda-Anzaldo
- Facultad de Medicina, Laboratorio de Biología Molecular y Neurociencias; Universidad Autónoma del Estado de México; Toluca 50180 Edo. Méx. Mexico
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5
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Silva-Santiago E, Pardo JP, Hernández-Muñoz R, Aranda-Anzaldo A. The nuclear higher-order structure defined by the set of topological relationships between DNA and the nuclear matrix is species-specific in hepatocytes. Gene 2017; 597:40-48. [PMID: 27771449 DOI: 10.1016/j.gene.2016.10.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/12/2016] [Accepted: 10/18/2016] [Indexed: 10/20/2022]
Abstract
During the interphase the nuclear DNA of metazoan cells is organized in supercoiled loops anchored to constituents of a nuclear substructure or compartment known as the nuclear matrix. The stable interactions between DNA and the nuclear matrix (NM) correspond to a set of topological relationships that define a nuclear higher-order structure (NHOS). Current evidence suggests that the NHOS is cell-type-specific. Biophysical evidence and theoretical models suggest that thermodynamic and structural constraints drive the actualization of DNA-NM interactions. However, if the topological relationships between DNA and the NM were the subject of any biological constraint with functional significance then they must be adaptive and thus be positively selected by natural selection and they should be reasonably conserved, at least within closely related species. We carried out a coarse-grained, comparative evaluation of the DNA-NM topological relationships in primary hepatocytes from two closely related mammals: rat and mouse, by determining the relative position to the NM of a limited set of target sequences corresponding to highly-conserved genomic regions that also represent a sample of distinct chromosome territories within the interphase nucleus. Our results indicate that the pattern of topological relationships between DNA and the NM is not conserved between the hepatocytes of the two closely related species, suggesting that the NHOS, like the karyotype, is species-specific.
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Affiliation(s)
- Evangelina Silva-Santiago
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, 50180, Edo. Méx., Mexico
| | - Juan Pablo Pardo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacan, 04510, Ciudad de México, Mexico
| | - Rolando Hernández-Muñoz
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacan, 04510, Ciudad de México, Mexico
| | - Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, 50180, Edo. Méx., Mexico.
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Aranda-Anzaldo A, Dent MAR. Why Cortical Neurons Cannot Divide, and Why Do They Usually Die in the Attempt? J Neurosci Res 2016; 95:921-929. [PMID: 27402311 DOI: 10.1002/jnr.23765] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/25/2016] [Accepted: 04/25/2016] [Indexed: 12/19/2022]
Abstract
Cortical neurons are prime examples of terminally differentiated, postmitotic cells. However, under experimental or pathological conditions, they can re-enter the cell cycle and replicate DNA but are unable to divide, dying by apoptosis or becoming either polyploid or aneuploid. Any cellular state that depends on the action of genes and their products can be reverted or bypassed by spontaneous or induced mutations, yet there are currently no reports of dividing cortical neurons. Thus, it seems unlikely that the remarkably stable postmitotic condition of cortical neurons depends on specific gene functions. This Review summarizes evidence that the postmitotic state of cortical neurons depends on the high stability of its underlying nuclear structure that results from an entropy-driven process aimed at dissipating the intrinsic structural stress present in chromosomal DNA in such a way that the structural stability of the neuronal nucleus becomes an insurmountable energy barrier for karyokinesis and mitosis. From this perspective, the integral properties of the nuclear higher order structure in neurons provide an explanation not only for why cortical neurons cannot divide but also for why they usually die if they happen to replicate their DNA. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Estado México, México
| | - Myrna A R Dent
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Estado México, México
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7
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Aranda-Anzaldo A. The interphase mammalian chromosome as a structural system based on tensegrity. J Theor Biol 2016; 393:51-9. [PMID: 26780650 DOI: 10.1016/j.jtbi.2016.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 12/11/2015] [Accepted: 01/04/2016] [Indexed: 10/22/2022]
Abstract
Each mammalian chromosome is constituted by a DNA fiber of macroscopic length that needs to be fitted in a microscopic nucleus. The DNA fiber is subjected at physiological temperature to random thermal bending and looping that must be constrained so as achieve structural stability thus avoiding spontaneous rupturing of the fiber. Standard textbooks assume that chromatin proteins are primarily responsible for the packaging of DNA and so of its protection against spontaneous breakage. Yet the dynamic nature of the interactions between chromatin proteins and DNA is unlikely to provide the necessary long-term structural stability for the chromosomal DNA. On the other hand, longstanding evidence indicates that stable interactions between DNA and constituents of a nuclear compartment commonly known as the nuclear matrix organize the chromosomal DNA as a series of topologically constrained, supercoiled loops during interphase. This results in a primary level of DNA condensation and packaging within the nucleus, as well as in protection against spontaneous DNA breakage, independently of chromatin proteins which nevertheless increase and dynamically modulate the degree of DNA packaging and its role in the regulation of DNA function. Thus current evidence, presented hereunder, supports a model for the organization of the interphase chromosome as resilient system that satisfies the principles of structural tensegrity.
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Affiliation(s)
- Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Paseo Tollocan y Jesús Carranza s/n, Toluca, 50180 Edo. Méx., México.
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8
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Clements CS, Bikkul U, Ahmed MH, Foster HA, Godwin LS, Bridger JM. Visualizing the Spatial Relationship of the Genome with the Nuclear Envelope Using Fluorescence In Situ Hybridization. Methods Mol Biol 2016; 1411:387-406. [PMID: 27147055 DOI: 10.1007/978-1-4939-3530-7_24] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The genome has a special relationship with the nuclear envelope in cells. Much of the genome is anchored at the nuclear periphery, tethered by chromatin binding proteins such nuclear lamins and other integral membrane proteins. Even though there are global assays such as DAM-ID or ChIP to assess what parts of the genome are associated with the nuclear envelope, it is also essential to be able to visualize regions of the genome in order to reveal their individual relationships with nuclear structures in single cells. This is executed by fluorescence in situ hybridization (FISH) in 2-dimensional flattened nuclei (2D-FISH) or 3-dimensionally preserved cells (3D-FISH) in combination with indirect immunofluorescence to reveal structural proteins. This chapter explains the protocols for 2D- and 3D-FISH in combination with indirect immunofluorescence and discusses options for image capture and analysis. Due to the nuclear envelope proteins being part of the non-extractable nucleoskeleton, we also describe how to prepare DNA halos through salt extraction and how they can be used to study genome behavior and association when combined with 2D-FISH.
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Affiliation(s)
- Craig S Clements
- Division of Biosciences, College of Life and Health Sciences, Brunel University London, Uxbridge, London, UB8 3PH, UK
| | - Ural Bikkul
- Division of Biosciences, College of Life and Health Sciences, Brunel University London, Uxbridge, London, UB8 3PH, UK
| | - Mai Hassan Ahmed
- Division of Biosciences, College of Life and Health Sciences, Brunel University London, Uxbridge, London, UB8 3PH, UK
| | - Helen A Foster
- Division of Biosciences, College of Life and Health Sciences, Brunel University London, Uxbridge, London, UB8 3PH, UK
| | - Lauren S Godwin
- Division of Biosciences, College of Life and Health Sciences, Brunel University London, Uxbridge, London, UB8 3PH, UK
| | - Joanna M Bridger
- Division of Biosciences, College of Life and Health Sciences, Brunel University London, Uxbridge, London, UB8 3PH, UK.
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9
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Makkonen H, Palvimo JJ. Androgen receptor: acting in the three-dimensional chromatin landscape of prostate cancer cells. Horm Mol Biol Clin Investig 2015; 5:17-26. [PMID: 25961240 DOI: 10.1515/hmbci.2010.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 10/05/2010] [Indexed: 01/08/2023]
Abstract
Androgen receptor (AR) acts as a hormone-controlled transcription factor that conveys the messages of both natural and synthetic androgens to the level of genes and gene programs. Defective AR signaling leads to a wide array of androgen insensitivity disorders, and deregulated AR function, in particular overexpression of AR, is involved in the growth and progression of prostate cancer. Classic models of AR action view AR-binding sites as upstream regulatory elements in gene promoters or their proximity. However, recent wider genomic screens indicate that AR target genes are commonly activated through very distal chromatin-binding sites. This highlights the importance of long-range chromatin regulation of transcription by the AR, shifting the focus from the linear gene models to three-dimensional models of AR target genes and gene programs. The capability of AR to regulate promoters from long distances in the chromatin is particularly important when evaluating the role of AR in the regulation of genes in malignant prostate cells that frequently show striking genomic aberrations, especially gene fusions. Therefore, in addition to the mechanisms of DNA loop formation between the enhancer bound ARs and the transcription apparatus at the target core promoter, the mechanisms insulating distally bound ARs from promiscuously making contacts and activating other than their normal target gene promoters are critical for proper physiological regulation and thus currently under intense investigation. This review discusses the current knowledge about the AR action in the context of gene aberrations and the three-dimensional chromatin landscape of prostate cancer cells.
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Barboro P, Ferrari N, Capaia M, Petretto A, Salvi S, Boccardo S, Balbi C. Expression of nuclear matrix proteins binding matrix attachment regions in prostate cancer. PARP-1: New player in tumor progression. Int J Cancer 2015; 137:1574-86. [DOI: 10.1002/ijc.29531] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/11/2015] [Accepted: 03/17/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Paola Barboro
- IRCCS AOU San Martino IST-Istituto Nazionale per la Ricerca sul Cancro, Dipartimento Diagnostica della Patologia e delle Cure ad Alta Complessità Tecnologica; Genoa Italy
| | - Nicoletta Ferrari
- IRCCs AOU San Martino IST-Istituto Nazionale per la Ricerca sul Cancro, Dipartimento Terapie Oncologiche Integrate; Genoa Italy
| | - Matteo Capaia
- IRCCS AOU San Martino IST-Istituto Nazionale per la Ricerca sul Cancro, Dipartimento Diagnostica della Patologia e delle Cure ad Alta Complessità Tecnologica; Genoa Italy
| | - Andrea Petretto
- Laboratorio di Spettrometria di Massa, Core Facility, Istituto Giannina Gaslini; Genoa Italy
| | - Sandra Salvi
- IRCCS AOU San Martino IST-Istituto Nazionale per la Ricerca sul Cancro, Dipartimento Diagnostica della Patologia e delle Cure ad Alta Complessità Tecnologica; Genoa Italy
| | - Simona Boccardo
- IRCCS AOU San Martino IST-Istituto Nazionale per la Ricerca sul Cancro, Dipartimento Diagnostica della Patologia e delle Cure ad Alta Complessità Tecnologica; Genoa Italy
| | - Cecilia Balbi
- IRCCS AOU San Martino IST-Istituto Nazionale per la Ricerca sul Cancro, Dipartimento Diagnostica della Patologia e delle Cure ad Alta Complessità Tecnologica; Genoa Italy
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11
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The higher-order structure in the cells nucleus as the structural basis of the post-mitotic state. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:137-45. [DOI: 10.1016/j.pbiomolbio.2014.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 02/09/2014] [Indexed: 11/19/2022]
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Nuclear morphometry, epigenetic changes, and clinical relevance in prostate cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 773:77-99. [PMID: 24563344 PMCID: PMC7123969 DOI: 10.1007/978-1-4899-8032-8_4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nuclear structure alterations in cancer involve global genetic (mutations, amplifications, copy number variations, translocations, etc.) and epigenetic (DNA methylation and histone modifications) events that dramatically and dynamically spatially change chromatin, nuclear body, and chromosome organization. In prostate cancer (CaP) there appears to be early (<50 years) versus late (>60 years) onset clinically significant cancers, and we have yet to clearly understand the hereditary and somatic-based molecular pathways involved. We do know that once cancer is initiated, dedifferentiation of the prostate gland occurs with significant changes in nuclear structure driven by numerous genetic and epigenetic processes. This review focuses upon the nuclear architecture and epigenetic dynamics with potential translational clinically relevant applications to CaP. Further, the review correlates changes in the cancer-driven epigenetic process at the molecular level and correlates these alterations to nuclear morphological quantitative measurements. Finally, we address how we can best utilize this knowledge to improve the efficacy of personalized treatment of cancer.
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Sethman CR, Hawiger J. The innate immunity adaptor SARM translocates to the nucleus to stabilize lamins and prevent DNA fragmentation in response to pro-apoptotic signaling. PLoS One 2013; 8:e70994. [PMID: 23923041 PMCID: PMC3726548 DOI: 10.1371/journal.pone.0070994] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 07/02/2013] [Indexed: 02/06/2023] Open
Abstract
Sterile alpha and armadillo-motif containing protein (SARM), a highly conserved and structurally unique member of the MyD88 family of Toll-like receptor adaptors, plays an important role in innate immunity signaling and apoptosis. Its exact mechanism of intracellular action remains unclear. Apoptosis is an ancient and ubiquitous process of programmed cell death that results in disruption of the nuclear lamina and, ultimately, dismantling of the nucleus. In addition to supporting the nuclear membrane, lamins serve important roles in chromatin organization, epigenetic regulation, transcription, nuclear transport, and mitosis. Mutations and other damage that destabilize nuclear lamins (laminopathies) underlie a number of intractable human diseases. Here, we report that SARM translocates to the nucleus of human embryonic kidney cells by using its amino-terminal Armadillo repeat region. Within the nucleus, SARM forms a previously unreported lattice akin to the nuclear lamina scaffold. Moreover, we show that SARM protects lamins from apoptotic degradation and reduces internucleosomal DNA fragmentation in response to signaling induced by the proinflammatory cytokine Tumor Necrosis Factor alpha. These findings indicate an important link between the innate immunity adaptor SARM and stabilization of nuclear lamins during inflammation-driven apoptosis in human cells.
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Affiliation(s)
- Chad R. Sethman
- Department of Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Jacek Hawiger
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- * E-mail:
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14
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Castillo-Mora RC, Aranda-Anzaldo A. Reorganization of the DNA-nuclear matrix interactions in a 210 kb genomic region centered on c-myc after DNA replication in vivo. J Cell Biochem 2012; 113:2451-63. [PMID: 22396210 DOI: 10.1002/jcb.24123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In the interphase nucleus of metazoan cells DNA is organized in supercoiled loops anchored to a nuclear matrix (NM). DNA loops are operationally classified in structural and facultative. Varied evidence indicates that DNA replication occurs in replication foci organized upon the NM and that structural DNA loops may correspond to the replicons in vivo. In normal rat liver the hepatocytes are arrested in G0 but synchronously re-enter the cell cycle after partial-hepatectomy leading to liver regeneration. Using this model we have previously determined that the DNA loops corresponding to a gene-rich genomic region move in a sequential fashion towards the NM during replication and then return to their original configuration in newly quiescent cells, once liver regeneration has been achieved. In the present work we determined the organization into structural DNA loops of a gene-poor region centered on c-myc and tracked-down its movement at the peak of S phase and after the return to cellular quiescence during and after liver regeneration. The results confirmed that looped DNA moves towards the NM during replication but in this case the configuration of the gene-poor region into DNA loops becomes reorganized and after replication only the loop containing c-myc resembles the original in the control G0 hepatocytes. Our results suggest that the local chromatin configuration around potentially active genes constraints the formation of specific structural DNA loops after DNA replication, while in non-coding regions the structural DNA loops are only loosely determined after DNA replication by structural constraints that modulate the DNA-NM interactions.
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Affiliation(s)
- Rebeca C Castillo-Mora
- Facultad de Medicina, Universidad Autónoma del Estado de México, Paseo Tollocan y Jesús Carranza s/n, Toluca, Edo. México, Mexico
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15
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Dynamic changes in nuclear localization of a DNA-binding protein tyrosine phosphatase TCPTP in response to DNA damage and replication arrest. Cell Biol Toxicol 2012; 28:409-19. [DOI: 10.1007/s10565-012-9232-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 08/28/2012] [Indexed: 01/07/2023]
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Veltri RW, Christudass CS, Isharwal S. Nuclear morphometry, nucleomics and prostate cancer progression. Asian J Androl 2012; 14:375-84. [PMID: 22504875 DOI: 10.1038/aja.2011.148] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Prostate cancer (PCa) results from a multistep process. This process includes initiation, which occurs through various aging events and multiple insults (such as chronic infection, inflammation and genetic instability through reactive oxygen species causing DNA double-strand breaks), followed by a multistep process of progression. These steps include several genetic and epigenetic alterations, as well as alterations to the chromatin structure, which occur in response to the carcinogenic stress-related events that sustain proliferative signaling. Events such as evading growth suppressors, resisting cell death, enabling replicative immortality, inducing angiogenesis, and activating invasion and metastasis are readily observed. In addition, in conjunction with these critical drivers of carcinogenesis, other factors related to the etiopathogenesis of PCa, involving energy metabolism and evasion of the immune surveillance system, appear to be involved. In addition, when cancer spread and metastasis occur, the 'tumor microenvironment' in the bone of PCa patients may provide a way to sustain dormancy or senescence and eventually establish a 'seed and soil' site where PCa proliferation and growth may occur over time. When PCa is initiated and progression ensues, significant alterations in nuclear size, shape and heterochromatin (DNA transcription) organization are found, and key nuclear transcriptional and structural proteins, as well as multiple nuclear bodies can lead to precancerous and malignant changes. These series of cellular and tissue-related malignancy-associated events can be quantified to assess disease progression and management.
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Affiliation(s)
- Robert W Veltri
- Fisher Biomarker & Biorepository Laboratory, The Brady Urological Research Institute, Baltimore, MD 21287, USA.
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17
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Aranda-Anzaldo A. The post-mitotic state in neurons correlates with a stable nuclear higher-order structure. Commun Integr Biol 2012; 5:134-9. [PMID: 22808316 PMCID: PMC3376047 DOI: 10.4161/cib.18761] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Neurons become terminally differentiated (TD) post-mitotic cells very early during development yet they may remain alive and functional for decades. TD neurons preserve the molecular machinery necessary for DNA synthesis that may be reactivated by different stimuli but they never complete a successful mitosis. The non-reversible nature of the post-mitotic state in neurons suggests a non-genetic basis for it since no set of mutations has been able to revert it. Comparative studies of the nuclear higher-order structure in neurons and cells with proliferating potential suggest that the non-reversible nature of the post-mitotic state in neurons has a structural basis in the stability of the nuclear higher-order structure.
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Affiliation(s)
- Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular; Facultad de Medicina; Universidad Autónoma del Estado de México; Toluca, México
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18
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The organization of a large transcriptional unit (Fyn) into structural DNA loops is cell-type specific and independent of transcription. Gene 2012; 493:1-8. [DOI: 10.1016/j.gene.2011.11.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 10/21/2011] [Accepted: 11/14/2011] [Indexed: 11/19/2022]
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19
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Mehta IS, Eskiw CH, Arican HD, Kill IR, Bridger JM. Farnesyltransferase inhibitor treatment restores chromosome territory positions and active chromosome dynamics in Hutchinson-Gilford progeria syndrome cells. Genome Biol 2011; 12:R74. [PMID: 21838864 PMCID: PMC3245614 DOI: 10.1186/gb-2011-12-8-r74] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 07/20/2011] [Accepted: 08/12/2011] [Indexed: 12/18/2022] Open
Abstract
Background Hutchinson-Gilford progeria syndrome (HGPS) is a premature ageing syndrome that affects children leading to premature death, usually from heart infarction or strokes, making this syndrome similar to normative ageing. HGPS is commonly caused by a mutation in the A-type lamin gene, LMNA (G608G). This leads to the expression of an aberrant truncated lamin A protein, progerin. Progerin cannot be processed as wild-type pre-lamin A and remains farnesylated, leading to its aberrant behavior during interphase and mitosis. Farnesyltransferase inhibitors prevent the accumulation of farnesylated progerin, producing a less toxic protein. Results We have found that in proliferating fibroblasts derived from HGPS patients the nuclear location of interphase chromosomes differs from control proliferating cells and mimics that of control quiescent fibroblasts, with smaller chromosomes toward the nuclear interior and larger chromosomes toward the nuclear periphery. For this study we have treated HGPS fibroblasts with farnesyltransferase inhibitors and analyzed the nuclear location of individual chromosome territories. We have found that after exposure to farnesyltransferase inhibitors mis-localized chromosome territories were restored to a nuclear position akin to chromosomes in proliferating control cells. Furthermore, not only has this treatment afforded chromosomes to be repositioned but has also restored the machinery that controls their rapid movement upon serum removal. This machinery contains nuclear myosin 1β, whose distribution is also restored after farnesyltransferase inhibitor treatment of HGPS cells. Conclusions This study not only progresses the understanding of genome behavior in HGPS cells but demonstrates that interphase chromosome movement requires processed lamin A.
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Affiliation(s)
- Ishita S Mehta
- Progeria Research Team, Centre for Cell and Chromosome Biology, Biosciences, School of Health Sciences and Social Care, Brunel University, West London, UB8 3PH, UK
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20
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Trembley JH, Unger GM, Tobolt DK, Korman VL, Wang G, Ahmad KA, Slaton JW, Kren BT, Ahmed K. Systemic administration of antisense oligonucleotides simultaneously targeting CK2α and α' subunits reduces orthotopic xenograft prostate tumors in mice. Mol Cell Biochem 2011; 356:21-35. [PMID: 21761204 DOI: 10.1007/s11010-011-0943-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 06/24/2011] [Indexed: 01/03/2023]
Abstract
CK2 is a highly conserved, ubiquitous, signal responsive protein serine/threonine kinase. CK2 promotes cell proliferation and suppresses apoptosis, and increased CK2 expression is observed in all cancers examined. We previously reported that direct injection of antisense (AS) CK2α phosphorothioate oligonucleotides (PTO) into xenograft prostate tumors in mice significantly reduced tumor size. Downregulation of CK2α in tumor cells in vivo appeared to result in overexpression of CK2α' protein. This suggested that in cancer cells downregulation of CK2α might be compensated by CK2α' in vivo, prompting us to design a bispecific (bs) AS PTO (bs-AS-CK2) targeting both catalytic subunits. bs-AS-CK2 reduced CK2α and α' protein expression, decreased cell proliferation, and induced apoptosis in cultured cells. Biodistribution studies of administered bs-AS-CK2 oligonucleotide demonstrated its presence in orthotopic prostate xenograft tumors. High dose injections of bs-AS-CK2 resulted in no damage to normal liver or prostate, but induced extensive cell death in tumor tissue. Intraperitoneal treatment with bs-AS-CK2 PTO decreased orthotopic tumor size and downregulated both CK2 mRNA and protein expression. Tumor reduction was accomplished using remarkably low doses and was improved by dividing the dose using a multi-day schedule. Decreased expression of the key signaling pathway proteins NF-κB p65 and AKT was also observed. We propose that the molecular downregulation of CK2 through bispecific targeting of the two catalytic subunits may be uniquely useful for therapeutic elimination of tumors.
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MESH Headings
- Animals
- Base Sequence
- Casein Kinase II/antagonists & inhibitors
- Casein Kinase II/genetics
- Casein Kinase II/metabolism
- Cell Line, Tumor
- Dose-Response Relationship, Drug
- Down-Regulation/drug effects
- Drug Administration Schedule
- Fluorescein-5-isothiocyanate/metabolism
- Gene Expression Regulation, Neoplastic/drug effects
- Gene Knockdown Techniques
- Humans
- Injections, Intraperitoneal
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Oligonucleotides, Antisense/administration & dosage
- Oligonucleotides, Antisense/pharmacokinetics
- Oligonucleotides, Antisense/pharmacology
- Prostatic Neoplasms/enzymology
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/pathology
- Protein Subunits/antagonists & inhibitors
- Protein Subunits/genetics
- Protein Subunits/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Tissue Distribution/drug effects
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Janeen H Trembley
- Research Service, Minneapolis VA Health Care System, University of Minnesota, Minneapolis, MN 55417, USA
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21
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Rivera-Mulia JC, Hernández-Muñoz R, Martínez F, Aranda-Anzaldo A. DNA moves sequentially towards the nuclear matrix during DNA replication in vivo. BMC Cell Biol 2011; 12:3. [PMID: 21244708 PMCID: PMC3037911 DOI: 10.1186/1471-2121-12-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 01/19/2011] [Indexed: 11/21/2022] Open
Abstract
Background In the interphase nucleus of metazoan cells DNA is organized in supercoiled loops anchored to a nuclear matrix (NM). There is varied evidence indicating that DNA replication occurs in replication factories organized upon the NM and that DNA loops may correspond to the actual replicons in vivo. In normal rat liver the hepatocytes are arrested in G0 but they synchronously re-enter the cell cycle after partial-hepatectomy leading to liver regeneration in vivo. We have previously determined in quiescent rat hepatocytes that a 162 kbp genomic region containing members of the albumin gene family is organized into five structural DNA loops. Results In the present work we tracked down the movement relative to the NM of DNA sequences located at different points within such five structural DNA loops during the S phase and after the return to cellular quiescence during liver regeneration. Our results indicate that looped DNA moves sequentially towards the NM during replication and then returns to its original position in newly quiescent cells, once the liver regeneration has been achieved. Conclusions Looped DNA moves in a sequential fashion, as if reeled in, towards the NM during DNA replication in vivo thus supporting the notion that the DNA template is pulled progressively towards the replication factories on the NM so as to be replicated. These results provide further evidence that the structural DNA loops correspond to the actual replicons in vivo.
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Affiliation(s)
- Juan Carlos Rivera-Mulia
- Laboratorio de Biología Molecular, Facultad de Medicina, Universidad Autónoma del Estado de México, Apartado Postal 428, CP 50000 Toluca, Edo Méx, México
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22
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Guillou E, Ibarra A, Coulon V, Casado-Vela J, Rico D, Casal I, Schwob E, Losada A, Méndez J. Cohesin organizes chromatin loops at DNA replication factories. Genes Dev 2010; 24:2812-22. [PMID: 21159821 PMCID: PMC3003199 DOI: 10.1101/gad.608210] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 10/22/2010] [Indexed: 12/23/2022]
Abstract
Genomic DNA is packed in chromatin fibers organized in higher-order structures within the interphase nucleus. One level of organization involves the formation of chromatin loops that may provide a favorable environment to processes such as DNA replication, transcription, and repair. However, little is known about the mechanistic basis of this structuration. Here we demonstrate that cohesin participates in the spatial organization of DNA replication factories in human cells. Cohesin is enriched at replication origins and interacts with prereplication complex proteins. Down-regulation of cohesin slows down S-phase progression by limiting the number of active origins and increasing the length of chromatin loops that correspond with replicon units. These results give a new dimension to the role of cohesin in the architectural organization of interphase chromatin, by showing its participation in DNA replication.
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Affiliation(s)
- Emmanuelle Guillou
- DNA Replication Group, Spanish National Cancer Research Centre (CNIO), E-28029 Madrid, Spain
| | - Arkaitz Ibarra
- DNA Replication Group, Spanish National Cancer Research Centre (CNIO), E-28029 Madrid, Spain
| | - Vincent Coulon
- Institut de Génétique Moléculaire de Montpellier, CNRS-Université Montpellier 1 et 2, 34293 Montpellier, Cedex 5, France
| | - Juan Casado-Vela
- Protein Technology Unit, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), E-28029 Madrid, Spain
| | - Daniel Rico
- Structural Computational Biology Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), E-28029 Madrid, Spain
| | - Ignacio Casal
- Protein Technology Unit, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), E-28029 Madrid, Spain
| | - Etienne Schwob
- Institut de Génétique Moléculaire de Montpellier, CNRS-Université Montpellier 1 et 2, 34293 Montpellier, Cedex 5, France
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), E-28029 Madrid, Spain
| | - Juan Méndez
- DNA Replication Group, Spanish National Cancer Research Centre (CNIO), E-28029 Madrid, Spain
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Malonia SK, Sinha S, Lakshminarasimhan P, Singh K, Jalota-Badhwar A, Rampalli S, Kaul-Ghanekar R, Chattopadhyay S. Gene regulation by SMAR1: Role in cellular homeostasis and cancer. Biochim Biophys Acta Rev Cancer 2010; 1815:1-12. [PMID: 20709157 DOI: 10.1016/j.bbcan.2010.08.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Revised: 08/04/2010] [Accepted: 08/06/2010] [Indexed: 12/22/2022]
Abstract
Changes in the composition of nuclear matrix associated proteins contribute to alterations in nuclear structure, one of the major phenotypes of malignant cancer cells. The malignancy-induced changes in this structure lead to alterations in chromatin folding, the fidelity of genome replication and gene expression programs. The nuclear matrix forms a scaffold upon which the chromatin is organized into periodic loop domains called matrix attachment regions (MAR) by binding to various MAR binding proteins (MARBPs). Aberrant expression of MARBPs modulates the chromatin organization and disrupt transcriptional network that leads to oncogenesis. Dysregulation of nuclear matrix associated MARBPs has been reported in different types of cancers. Some of these proteins have tumor specific expression and are therefore considered as promising diagnostic or prognostic markers in few cancers. SMAR1 (scaffold/matrix attachment region binding protein 1), is one such nuclear matrix associated protein whose expression is drastically reduced in higher grades of breast cancer. SMAR1 gene is located on human chromosome 16q24.3 locus, the loss of heterozygosity (LOH) of which has been reported in several types of cancers. This review elaborates on the multiple roles of nuclear matrix associated protein SMAR1 in regulating various cellular target genes involved in cell growth, apoptosis and tumorigenesis.
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24
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Gavrilov AA, Zukher IS, Philonenko ES, Razin SV, Iarovaia OV. Mapping of the nuclear matrix-bound chromatin hubs by a new M3C experimental procedure. Nucleic Acids Res 2010; 38:8051-60. [PMID: 20705651 PMCID: PMC3001081 DOI: 10.1093/nar/gkq712] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have developed an experimental procedure to analyze the spatial proximity of nuclear matrix-bound DNA fragments. This protocol, referred to as Matrix 3C (M3C), includes a high salt extraction of nuclei, the removal of distal parts of unfolded DNA loops using restriction enzyme treatment, ligation of the nuclear matrix-bound DNA fragments and a subsequent analysis of ligation frequencies. Using the M3C procedure, we have demonstrated that CpG islands of at least three housekeeping genes that surround the chicken α-globin gene domain are assembled into a complex (presumably, a transcription factory) that is stabilized by the nuclear matrix in both erythroid and non-erythroid cells. In erythroid cells, the regulatory elements of the α-globin genes are attracted to this complex to form a new assembly: an active chromatin hub that is linked to the pre-existing transcription factory. The erythroid-specific part of the assembly is removed by high salt extraction. Based on these observations, we propose that mixed transcription factories that mediate the transcription of both housekeeping and tissue-specific genes are composed of a permanent compartment containing integrated into the nuclear matrix promoters of housekeeping genes and a ‘guest’ compartment where promoters and regulatory elements of tissue-specific genes can be temporarily recruited.
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Affiliation(s)
- Alexey A Gavrilov
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology of the Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia
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25
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Rouquette J, Cremer C, Cremer T, Fakan S. Functional nuclear architecture studied by microscopy: present and future. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2010; 282:1-90. [PMID: 20630466 DOI: 10.1016/s1937-6448(10)82001-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this review we describe major contributions of light and electron microscopic approaches to the present understanding of functional nuclear architecture. The large gap of knowledge, which must still be bridged from the molecular level to the level of higher order structure, is emphasized by differences of currently discussed models of nuclear architecture. Molecular biological tools represent new means for the multicolor visualization of various nuclear components in living cells. New achievements offer the possibility to surpass the resolution limit of conventional light microscopy down to the nanometer scale and require improved bioinformatics tools able to handle the analysis of large amounts of data. In combination with the much higher resolution of electron microscopic methods, including ultrastructural cytochemistry, correlative microscopy of the same cells in their living and fixed state is the approach of choice to combine the advantages of different techniques. This will make possible future analyses of cell type- and species-specific differences of nuclear architecture in more detail and to put different models to critical tests.
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Affiliation(s)
- Jacques Rouquette
- Biocenter, Ludwig Maximilians University (LMU), Martinsried, Germany
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26
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Exploring the relationship between interphase gene positioning, transcriptional regulation and the nuclear matrix. Biochem Soc Trans 2010; 38:263-7. [DOI: 10.1042/bst0380263] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Since the advent of FISH (fluorescence in situ hybridization), there have been major advances in our understanding of how the genome is organized in interphase nuclei. Indeed, this organization is found to be non-random and individual chromosomes occupy discrete regions known as territories. Determining the factors that drive the spatial positioning of these territories within nuclei has caused much debate; however, in proliferating cells, there is evidently a correlation between radial positioning and gene density. Indeed, gene-poor chromosomes tend to be located towards the nuclear edge, while those that are more gene-rich are positioned more internally. These observations pose a number of questions: first, what is the function of this global organization and, secondly, is it representative of that occurring at a more local scale? During the course of this review, these questions will be considered, in light of the current literature regarding the role of transcription factories and the nuclear matrix in interphase genome organization.
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27
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Fluorescence in situ hybridization on DNA halo preparations and extended chromatin fibres. Methods Mol Biol 2010; 659:21-31. [PMID: 20809301 DOI: 10.1007/978-1-60761-789-1_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although many fluorescence in situ hybridisation (FISH) protocols involve the use of intact, fixed nuclei, the resolution achieved is not always sufficient, especially for physical mapping. In light of this, several techniques are commonly used to create extended chromatin fibres or extruded loops of DNA. As a result, it is possible to visualise and distinguish regions of the genome at a resolution higher than that attained with conventional preparations for FISH. Such methodologies include fibre-FISH and the DNA halo preparation. While fibre-FISH involves the stretching of chromatin fibres across a glass slide, the DNA halo preparation is somewhat more complex; whereby DNA loops instead of chromatin fibres are generated from interphase nuclei. Furthermore, the DNA halo preparation coupled with FISH is a useful tool for examining interactions between the inextractable nuclear matrix and the cell's genome.In this chapter, we describe how to successfully generate extended chromatin fibres and extruded DNA loops. We will also provide detailed methodologies for coupling either procedure with two distinct FISH procedures; 2D-FISH, which allows for the visualisation of specific chromosomal regions, while telomere peptide nucleic acid (PNA) FISH, enables the detection of all telomeres present within human nuclei.
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