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Gupta P, Makkar TK, Goel L, Pahuja M. Role of inflammation and oxidative stress in chemotherapy-induced neurotoxicity. Immunol Res 2022; 70:725-741. [PMID: 35859244 DOI: 10.1007/s12026-022-09307-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022]
Abstract
Chemotherapeutic agents may adversely affect the nervous system, including the neural precursor cells as well as the white matter. Although the mechanisms are not completely understood, several hypotheses connecting inflammation and oxidative stress with neurotoxicity are now emerging. The proposed mechanisms differ depending on the class of drug. For example, toxicity due to cisplatin occurs due to activation of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), which alters hippocampal long-term potentiation. Free radical injury is also involved in the cisplatin-mediated neurotoxicity as dysregulation of nuclear factor erythroid 2-related factor 2 (Nrf2) has been seen which protects against the free radical injury by regulating glutathione S-transferases and hemeoxygenase-1 (HO-1). Thus, correcting the imbalance between NF-κB and Nrf2/HO-1 pathways may alleviate cisplatin-induced neurotoxicity. With newer agents like bortezomib, peripheral neuropathy occurs due to up-regulation of TNF-α and IL-6 in the sensory neurons. Superoxide dismutase dysregulation is also involved in bortezomib-induced neuropathy. This article reviews the available literature on inflammation and oxidative stress in neurotoxicity caused by various classes of chemotherapeutic agents. It covers the conventional medicines like platinum compounds, vinca alkaloids, and methotrexate, as well as the newer therapeutic agents like immunomodulators and immune checkpoint inhibitors. A better understanding of the pathophysiology will lead to further advancement in strategies for management of chemotherapy-induced neurotoxicity.
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Affiliation(s)
- Pooja Gupta
- Department of Pharmacology, All India Institute of Medical Sciences, New Delhi, 110029, India. .,Coordinator, AIIMS Adverse Drug Reaction Monitoring Centre, Pharmacovigilance Program of India, New Delhi, India.
| | - Tavneet Kaur Makkar
- Department of Pharmacology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Lavisha Goel
- Department of Pharmacology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Monika Pahuja
- Division of Basic Medical Sciences, Indian Council of Medical Research, New Delhi, India
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2
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Rehman AU, Rahman MU, Arshad T, Chen HF. Allosteric Modulation of Intrinsically Disordered Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:335-357. [PMID: 31707710 DOI: 10.1007/978-981-13-8719-7_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The allosteric property of globular proteins is applauded as their intrinsic ability to regulate distant sites, and this property further plays a critical role in a wide variety of cellular regulatory mechanisms. Recent advancements and studies have revealed the manifestation of allostery in intrinsically disordered proteins or regions as allosteric sites present within or mediated by IDP/IDRs facilitates the signaling interactions for various biological mechanisms which would otherwise be impossible for globular proteins to regulate. This thematic review has highlighted the biological outcomes that can be achieved by the mechanism of allosteric regulation of intrinsically disordered proteins or regions. The similar mechanism has been implemented on Adenovirus 5 early region 1A and tumor apoptosis protein p53 in correspondence with other partners in binary and ternary complexes, which are the subject of the current review. Both these proteins regulate once they bind to their partners, consequently, forming either a binary or a ternary complex. Allosteric regulation by IDPs is currently a subject undergoing intense study, and the ongoing research work will ensure a better understanding of precision and efficiency of cellular regulation by them. Allosteric regulation mechanism can also be researched by intrinsically disordered protein-specific force field.
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Affiliation(s)
- Ashfaq Ur Rehman
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Mueed Ur Rahman
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Taaha Arshad
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. .,Shanghai Center for Bioinformation Technology, Shanghai, China.
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3
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A comprehensive complex systems approach to the study and analysis of mammalian cell cycle control system in the presence of DNA damage stress. J Theor Biol 2017. [DOI: 10.1016/j.jtbi.2017.06.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Chakraborty P, Roy SS, Basu A, Bhattacharya S. Sensitization of cancer cells to cyclophosphamide therapy by an organoselenium compound through ROS-mediated apoptosis. Biomed Pharmacother 2016; 84:1992-1999. [DOI: 10.1016/j.biopha.2016.11.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/01/2016] [Accepted: 11/02/2016] [Indexed: 11/29/2022] Open
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5
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Song X, Shi Q, Liu Z, Wang Y, Wang Y, Song E, Song Y. Unpredicted Downregulation of RAD51 Suggests Genome Instability Induced by Tetrachlorobenzoquinone. Chem Res Toxicol 2016; 29:2184-2193. [DOI: 10.1021/acs.chemrestox.6b00369] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Xiufang Song
- Key Laboratory of Luminescence
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, People’s Republic of China
| | - Qiong Shi
- Key Laboratory of Luminescence
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, People’s Republic of China
| | - Zixuan Liu
- Key Laboratory of Luminescence
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, People’s Republic of China
| | - Yawen Wang
- Key Laboratory of Luminescence
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, People’s Republic of China
| | - Yuxin Wang
- Key Laboratory of Luminescence
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, People’s Republic of China
| | - Erqun Song
- Key Laboratory of Luminescence
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, People’s Republic of China
| | - Yang Song
- Key Laboratory of Luminescence
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, People’s Republic of China
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6
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Dias QC, Nunes IDS, Garcia PV, Favaro WJ. Potential therapeutic strategies for non - muscle invasive bladder cancer based on association of intravesical immunotherapy with p - mapa and systemic administration of cisplatin and doxorubicin. Int Braz J Urol 2016; 42:942-954. [PMID: 24893914 PMCID: PMC5066890 DOI: 10.1590/s1677-5538.ibju.2015.0381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 03/21/2016] [Indexed: 11/21/2022] Open
Abstract
The present study describes the histopathological and molecular effects of P-MAPA (Protein aggregate magnesium-ammonium phospholinoleate-palmitoleate anhydride) intravesical immunotherapy combined with systemic doxorubicin or cisplatin for treatment of non-muscle invasive bladder cancer (NMIBC) in an appropriate animal model. Our results showed an undifferentiated tumor, characterizing a tumor invading mucosa or submucosa of the bladder wall (pT1) and papillary carcinoma in situ (pTa) in the Cancer group. The histopathological changes were similar between the combined treatment with intravesical P-MAPA plus systemic Cisplatin and P-MAPA immunotherapy alone, showing decrease of urothelial neoplastic lesions progression and histopathological recovery in 80% of the animals. The animals treated systemically with cisplatin or doxorubicin singly, showed 100% of malignant lesions in the urinary bladder. Furthemore, the combined treatment with P-MAPA and Doxorubicin showed no decrease of urothelial neoplastic lesions progression and histopathological recovery. Furthermore, Akt, PI3K, NF-kB and VEGF protein levels were significantly lower in intravesical P-MAPA plus systemic cisplatin and in intravesical P-MAPA alone treatments than other groups. In contrast, PTEN protein levels were significantly higher in intravesical P-MAPA plus systemic cisplatin and in intravesical P-MAPA alone treatments. Thus, it could be concluded that combination of intravesical P-MAPA immunotherapy and systemic cisplatin in the NMIBC animal model was effective, well tolerated and showed no apparent signs of antagonism between the drugs. In addition, intravesical P-MAPA immunotherapy may be considered as a valuable option for treatment of BCG unresponsive patients that unmet the criteria for early cystectomy.
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Affiliation(s)
- Queila Cristina Dias
- Laboratório de Urogenital Carcinogênese e Imunoterapia do Departamento de Biologia Estrutural e Funcional da Universidade de Campinas (UNICAMP), Campinas, SP, Brasil
| | | | - Patrick Vianna Garcia
- Laboratório de Urogenital Carcinogênese e Imunoterapia do Departamento de Biologia Estrutural e Funcional da Universidade de Campinas (UNICAMP), Campinas, SP, Brasil
| | - Wagner Jose Favaro
- Laboratório de Urogenital Carcinogênese e Imunoterapia do Departamento de Biologia Estrutural e Funcional da Universidade de Campinas (UNICAMP), Campinas, SP, Brasil.,FarmaBrasilis R & D, Campinas, SP, Brasil
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7
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Fayzullina S, Martin LJ. DNA Damage Response and DNA Repair in Skeletal Myocytes From a Mouse Model of Spinal Muscular Atrophy. J Neuropathol Exp Neurol 2016; 75:889-902. [PMID: 27452406 DOI: 10.1093/jnen/nlw064] [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] [Indexed: 11/14/2022] Open
Abstract
We studied DNA damage response (DDR) and DNA repair capacities of skeletal muscle cells from a mouse model of infantile spinal muscular atrophy (SMA) caused by loss-of-function mutation of survival of motor neuron (Smn). Primary myocyte cultures derived from skeletal muscle satellite cells of neonatal control and mutant SMN mice had similar myotube length, myonuclei, satellite cell marker Pax7 and differentiated myotube marker myosin, and acetylcholine receptor clustering. DNA damage was induced in differentiated skeletal myotubes by γ-irradiation, etoposide, and methyl methanesulfonate (MMS). Unexposed control and SMA myotubes had stable genome integrity. After γ-irradiation and etoposide, myotubes repaired most DNA damage equally. Control and mutant myotubes exposed to MMS exhibited equivalent DNA damage without repair. Control and SMA myotube nuclei contained DDR proteins phospho-p53 and phospho-H2AX foci that, with DNA damage, dispersed and then re-formed similarly after recovery. We conclude that mouse primary satellite cell-derived myotubes effectively respond to and repair DNA strand-breaks, while DNA alkylation repair is underrepresented. Morphological differentiation, genome stability, genome sensor, and DNA strand-break repair potential are preserved in mouse SMA myocytes; thus, reduced SMN does not interfere with myocyte differentiation, genome integrity, and DNA repair, and faulty DNA repair is unlikely pathogenic in SMA.
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Affiliation(s)
- Saniya Fayzullina
- From the Department of Pathology, Division of Neuropathology, and the Pathobiology Graduate Training Program, Johns Hopkins School of Medicine, Baltimore, Maryland, USA (SF, LJM)
| | - Lee J Martin
- From the Department of Pathology, Division of Neuropathology, and the Pathobiology Graduate Training Program, Johns Hopkins School of Medicine, Baltimore, Maryland, USA (SF, LJM)
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8
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Jacovas VC, Rovaris DL, Peréz O, de Azevedo S, Macedo GS, Sandoval JR, Salazar-Granara A, Villena M, Dugoujon JM, Bisso-Machado R, Petzl-Erler ML, Salzano FM, Ashton-Prolla P, Ramallo V, Bortolini MC. Genetic Variations in the TP53 Pathway in Native Americans Strongly Suggest Adaptation to the High Altitudes of the Andes. PLoS One 2015; 10:e0137823. [PMID: 26382048 PMCID: PMC4575214 DOI: 10.1371/journal.pone.0137823] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/24/2015] [Indexed: 02/05/2023] Open
Abstract
The diversity of the five single nucleotide polymorphisms located in genes of the TP53 pathway (TP53, rs1042522; MDM2, rs2279744; MDM4, rs1563828; USP7, rs1529916; and LIF, rs929271) were studied in a total of 282 individuals belonging to Quechua, Aymara, Chivay, Cabanaconde, Yanke, Taquile, Amantani, Anapia, Uros, Guarani Ñandeva, and Guarani Kaiowá populations, characterized as Native American or as having a high level (> 90%) of Native American ancestry. In addition, published data pertaining to 100 persons from five other Native American populations (Surui, Karitiana, Maya, Pima, and Piapoco) were analyzed. The populations were classified as living in high altitude (≥ 2,500 m) or in lowlands (< 2,500 m). Our analyses revealed that alleles USP7-G, LIF-T, and MDM2-T showed significant evidence that they were selected for in relation to harsh environmental variables related to high altitudes. Our results show for the first time that alleles of classical TP53 network genes have been evolutionary co-opted for the successful human colonization of the Andes.
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Affiliation(s)
- Vanessa Cristina Jacovas
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Diego Luiz Rovaris
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Orlando Peréz
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Puerto Madryn, Argentina
| | - Soledad de Azevedo
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Puerto Madryn, Argentina
| | - Gabriel Souza Macedo
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - José Raul Sandoval
- Facultad de Medicina Humana, Universidad de San Martin de Porres (USMP), Lima, Peru
| | | | - Mercedes Villena
- Instituto Boliviano de Biología de Altura (IBBA), Universidad Mayor de San Andres, La Paz, Bolivia
| | - Jean-Michel Dugoujon
- Anthropologie Moléculaire et Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier Toulouse III, Toulouse, 31000, France
| | - Rafael Bisso-Machado
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Maria Luiza Petzl-Erler
- Laboratório de Genética Molecular, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - Francisco Mauro Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Patricia Ashton-Prolla
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
- Serviço de Genética Medica, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Virginia Ramallo
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Puerto Madryn, Argentina
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
- * E-mail:
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9
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Cuba CE, Valle AR, Ayala-Charca G, Villota ER, Coronado AM. Influence of parameter values on the oscillation sensitivities of two p53-Mdm2 models. SYSTEMS AND SYNTHETIC BIOLOGY 2015; 9:77-84. [PMID: 26279702 DOI: 10.1007/s11693-015-9173-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 05/16/2015] [Accepted: 05/30/2015] [Indexed: 10/23/2022]
Abstract
Biomolecular networks that present oscillatory behavior are ubiquitous in nature. While some design principles for robust oscillations have been identified, it is not well understood how these oscillations are affected when the kinetic parameters are constantly changing or are not precisely known, as often occurs in cellular environments. Many models of diverse complexity level, for systems such as circadian rhythms, cell cycle or the p53 network, have been proposed. Here we assess the influence of hundreds of different parameter sets on the sensitivities of two configurations of a well-known oscillatory system, the p53 core network. We show that, for both models and all parameter sets, the parameter related to the p53 positive feedback, i.e. self-promotion, is the only one that presents sizeable sensitivities on extrema, periods and delay. Moreover, varying the parameter set values to change the dynamical characteristics of the response is more restricted in the simple model, whereas the complex model shows greater tunability. These results highlight the importance of the presence of specific network patterns, in addition to the role of parameter values, when we want to characterize oscillatory biochemical systems.
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Affiliation(s)
- Christian E Cuba
- Faculty of Mechanical Engineering, Universidad Nacional de Ingeniería, Av. Túpac Amaru s/n - Puerta 3, Pabellón A, Lima 25, Peru
| | - Alexander R Valle
- Faculty of Mechanical Engineering, Universidad Nacional de Ingeniería, Av. Túpac Amaru s/n - Puerta 3, Pabellón A, Lima 25, Peru
| | - Giancarlo Ayala-Charca
- Faculty of Mechanical Engineering, Universidad Nacional de Ingeniería, Av. Túpac Amaru s/n - Puerta 3, Pabellón A, Lima 25, Peru
| | - Elizabeth R Villota
- Faculty of Mechanical Engineering, Universidad Nacional de Ingeniería, Av. Túpac Amaru s/n - Puerta 3, Pabellón A, Lima 25, Peru
| | - Alberto M Coronado
- Faculty of Mechanical Engineering, Universidad Nacional de Ingeniería, Av. Túpac Amaru s/n - Puerta 3, Pabellón A, Lima 25, Peru
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Fayzullina S, Martin LJ. Skeletal muscle DNA damage precedes spinal motor neuron DNA damage in a mouse model of Spinal Muscular Atrophy (SMA). PLoS One 2014; 9:e93329. [PMID: 24667816 PMCID: PMC3965546 DOI: 10.1371/journal.pone.0093329] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 03/03/2014] [Indexed: 12/27/2022] Open
Abstract
Spinal Muscular Atrophy (SMA) is a hereditary childhood disease that causes paralysis by progressive degeneration of skeletal muscles and spinal motor neurons. SMA is associated with reduced levels of full-length Survival of Motor Neuron (SMN) protein, due to mutations in the Survival of Motor Neuron 1 gene. The mechanisms by which lack of SMN causes SMA pathology are not known, making it very difficult to develop effective therapies. We investigated whether DNA damage is a perinatal pathological event in SMA, and whether DNA damage and cell death first occur in skeletal muscle or spinal cord of SMA mice. We used a mouse model of severe SMA to ascertain the extent of cell death and DNA damage throughout the body of prenatal and newborn mice. SMA mice at birth (postnatal day 0) exhibited internucleosomal fragmentation in genomic DNA from hindlimb skeletal muscle, but not in genomic DNA from spinal cord. SMA mice at postnatal day 5, compared with littermate controls, exhibited increased apoptotic cell death profiles in skeletal muscle, by hematoxylin and eosin, terminal deoxynucleotidyl transferase dUTP nick end labeling, and electron microscopy. SMA mice had no increased cell death, no loss of choline acetyl transferase (ChAT)-positive motor neurons, and no overt pathology in the ventral horn of the spinal cord. At embryonic days 13 and 15.5, SMA mice did not exhibit statistically significant increases in cell death profiles in spinal cord or skeletal muscle. Motor neuron numbers in the ventral horn, as identified by ChAT immunoreactivity, were comparable in SMA mice and control littermates at embryonic day 15.5 and postnatal day 5. These observations demonstrate that in SMA, disease in skeletal muscle emerges before pathology in spinal cord, including loss of motor neurons. Overall, this work identifies DNA damage and cell death in skeletal muscle as therapeutic targets for SMA.
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Affiliation(s)
- Saniya Fayzullina
- Division of Neuropathology, Department of Pathology, and the Pathobiology Graduate Program, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
| | - Lee J. Martin
- Division of Neuropathology, Department of Pathology, and the Pathobiology Graduate Program, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
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de Oliveira DHIP, de Sousa Lopes MLD, de Santana Sarmento DJ, Queiroz LMG, da Costa Miguel MC, da Silveira EJD. Relationship between the epithelial expression of hMLH1, MDM2, and p63 and lower lip carcinogenesis. J Oral Pathol Med 2013; 43:357-63. [PMID: 24329813 DOI: 10.1111/jop.12144] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2013] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To evaluate the relationship between the epithelial expression of hMLH1, MDM2, and p63 in lower lip carcinogenesis, comparing the immunostaining of these proteins in cases of actinic cheilitis (AC) and lower lip squamous cell carcinoma (SCC). STUDY DESIGN Forty cases of AC and 40 cases of SCC were studied, both lesions were of lower lip. Histological sections of 3 μm were submitted to immunoperoxidase method, and 1000 cells were counted for immunohistochemical analysis of lesions. The results were analyzed quantitatively, and expression was compared by the Mann-Whitney, Student t-test, or one-way ANOVA, adopting a level of significance of 5%. RESULTS A higher percentage of epithelial cells expressing hMLH1 was observed in cases of AC without dysplasia or mild dysplasia (721.23 ± 88.116), whereas fewer positive cells were observed in lower lip SSCs (255.03 ± 199.47) when compared to the AC group (P < 0.001). Immunoexpression of MDM2 was higher in SCCs of the lower lip compared with AC (P = 0.019). For p63 protein, the expression was higher in AC than in SCC (P = 0.045). CONCLUSION The present results showed changes in the immunoexpression of hMLH1, MDM2, and p63 in epithelial cells from premalignant and malignant lip disease, supporting the hypothesis that these alterations are related to the process of lower lip carcinogenesis.
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Qi J, Ding Y, Zhu Y, Wu Y. Kinetic theory approach to modeling of cellular repair mechanisms under genome stress. PLoS One 2011; 6:e22228. [PMID: 21857915 PMCID: PMC3153456 DOI: 10.1371/journal.pone.0022228] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 06/17/2011] [Indexed: 01/08/2023] Open
Abstract
Under acute perturbations from outer environment, a normal cell can trigger cellular self-defense mechanism in response to genome stress. To investigate the kinetics of cellular self-repair process at single cell level further, a model of DNA damage generating and repair is proposed under acute Ion Radiation (IR) by using mathematical framework of kinetic theory of active particles (KTAP). Firstly, we focus on illustrating the profile of Cellular Repair System (CRS) instituted by two sub-populations, each of which is made up of the active particles with different discrete states. Then, we implement the mathematical framework of cellular self-repair mechanism, and illustrate the dynamic processes of Double Strand Breaks (DSBs) and Repair Protein (RP) generating, DSB-protein complexes (DSBCs) synthesizing, and toxins accumulating. Finally, we roughly analyze the capability of cellular self-repair mechanism, cellular activity of transferring DNA damage, and genome stability, especially the different fates of a certain cell before and after the time thresholds of IR perturbations that a cell can tolerate maximally under different IR perturbation circumstances.
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Affiliation(s)
- Jinpeng Qi
- College of Information Science and Technology, Donghua University, Shanghai, People's Republic of China.
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Luna A, Karac EI, Sunshine M, Chang L, Nussinov R, Aladjem MI, Kohn KW. A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method. BMC Bioinformatics 2011; 12:167. [PMID: 21586134 PMCID: PMC3118169 DOI: 10.1186/1471-2105-12-167] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 05/17/2011] [Indexed: 01/15/2023] Open
Abstract
Background The Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network diagrams. Such diagrams are essential for disseminating biological information in a concise manner. A lack of software tools for the notation restricts wider usage of the notation. Development of software is facilitated by a more detailed specification regarding software requirements than has previously existed for the MIM notation. Results A formal implementation of the MIM notation was developed based on a core set of previously defined glyphs. This implementation provides a detailed specification of the properties of the elements of the MIM notation. Building upon this specification, a machine-readable format is provided as a standardized mechanism for the storage and exchange of MIM diagrams. This new format is accompanied by a Java-based application programming interface to help software developers to integrate MIM support into software projects. A validation mechanism is also provided to determine whether MIM datasets are in accordance with syntax rules provided by the new specification. Conclusions The work presented here provides key foundational components to promote software development for the MIM notation. These components will speed up the development of interoperable tools supporting the MIM notation and will aid in the translation of data stored in MIM diagrams to other standardized formats. Several projects utilizing this implementation of the notation are outlined herein. The MIM specification is available as an additional file to this publication. Source code, libraries, documentation, and examples are available at http://discover.nci.nih.gov/mim.
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Affiliation(s)
- Augustin Luna
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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A Mathematical Framework for Cellular Repair Mechanisms under Genomic Stress Based on Kinetic Theory Approach. ACTA ACUST UNITED AC 2011. [DOI: 10.4028/www.scientific.net/amm.52-54.7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Generally, a cell can trigger its self-defense mechanism in response to genomic stress under acute perturbations from outer environment. To investigate the dynamic kinetics of cellular repair mechanisms in fighting against genomic stress, a mathematical model of representing and analyzing DNA damage generation and repair process is proposed under acute Ion Radiation (IR) by using the Kinetic Theory of Active Particles (KTAP). In this paper, we focus on describing a mathematical framework of Cellular Repair System (CRS). We also present the dynamic processes of Double Strand Breaks (DSBs) and Repair Protein (RP) generating, DSB-protein complexes (DSBCs) synthesizing, and toxins accumulating under continuous radiation time.
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15
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Scott BR. Modeling DNA double-strand break repair kinetics as an epiregulated cell-community-wide (epicellcom) response to radiation stress. Dose Response 2011; 9:579-601. [PMID: 22461762 DOI: 10.2203/dose-response.10-039.scott] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The multicellular signaling model (MULTISIG1) was recently introduced to simulate the kinetics of repair of DNA double-strand breaks (DSBs) that were induced in confluent (non-dividing) cultured cells by a very low radiation dose where at most a single induced DSB would be expected in a given cell nucleus. The repair kinetics was modeled as representing what is now called an epigenetically-regulated (epiregulated) cell-community-wide (epicellcom) response to radiation stress. DSB repair initiation is assumed to require a threshold number of cells with DSBs participating in intercellular stress-response signaling. The MULTISIG1 model is extended in this study to apply to moderate doses where several DSBs can occur on the same DNA molecule. The repair of multiple breaks on the same molecule is treated as sequential stochastic events. For cells of differing genetic characteristics and epigenetic statuses, relationships are provided for evaluating the relative susceptibility (RS) for DSB induction, relative repair capacity (RRC) for DSB repair, and relative epiapoptosis capacity (REC), for epigenetically regulated apoptosis. The modified MULTISIG1 model is used to characterize the expected repair kinetics for confluent, human lung fibroblasts (MRC-5 line) briefly exposed in vitro to 90-kV x-rays. Possible application of the model to biological dosimetry is also discussed.
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16
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Qi J, Ding Y, Shao S. Dynamic modeling of cellular response to DNA damage based on p53 stress response networks. PROGRESS IN NATURAL SCIENCE : COMMUNICATION OF STATE KEY LABORATORIES OF CHINA 2009; 19:1349-1356. [PMID: 32288404 PMCID: PMC7128557 DOI: 10.1016/j.pnsc.2009.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 03/10/2009] [Accepted: 03/17/2009] [Indexed: 06/11/2023]
Abstract
Under acute perturbations from the outside, cells can trigger self-defensive mechanisms to fight against genome stress. To investigate the cellular response to continuous ion radiation (IR), a dynamic model for p53 stress response networks at the cellular level is proposed. The model can successfully be used to simulate the dynamic processes of double-strand breaks (DSBs) generation and their repair, switch-like ataxia telangiectasia mutated (ATM) activation, oscillations occurring in the p53-MDM2 feedback loop, as well as toxins elimination triggered by p53 stress response networks. Especially, the model can predict the plausible outcomes of cellular response under different IR dose regimes.
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Affiliation(s)
- Jinpeng Qi
- College of Information Sciences and Technology, Donghua University, Shanghai 201620, China
| | - Yongsheng Ding
- College of Information Sciences and Technology, Donghua University, Shanghai 201620, China
| | - Shihuang Shao
- College of Information Sciences and Technology, Donghua University, Shanghai 201620, China
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17
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Skladanowski A, Bozko P, Sabisz M. DNA structure and integrity checkpoints during the cell cycle and their role in drug targeting and sensitivity of tumor cells to anticancer treatment. Chem Rev 2009; 109:2951-73. [PMID: 19522503 DOI: 10.1021/cr900026u] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Andrzej Skladanowski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland.
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18
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Van Maerken T, Vandesompele J, Rihani A, De Paepe A, Speleman F. Escape from p53-mediated tumor surveillance in neuroblastoma: switching off the p14(ARF)-MDM2-p53 axis. Cell Death Differ 2009; 16:1563-72. [PMID: 19779493 DOI: 10.1038/cdd.2009.138] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A primary failsafe program against unrestrained proliferation and oncogenesis is provided by the p53 tumor suppressor protein, inactivation of which is considered as a hallmark of cancer. Intriguingly, mutations of the TP53 gene are rarely encountered in neuroblastoma tumors, suggesting that alternative p53-inactivating lesions account for escape from p53 control in this childhood malignancy. Several recent studies have shed light on the mechanisms by which neuroblastoma cells circumvent the p53-driven antitumor barrier. We review here these mechanisms for evasion of p53-mediated growth control and conclude that deregulation of the p14(ARF)-MDM2-p53 axis seems to be the principal mode of p53 inactivation in neuroblastoma, opening new perspectives for targeted therapeutic intervention.
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Affiliation(s)
- T Van Maerken
- Center for Medical Genetics, Ghent University Hospital, Ghent B-9000, Belgium.
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19
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Hamada H, Tashima Y, Kisaka Y, Iwamoto K, Hanai T, Eguchi Y, Okamoto M. Sophisticated framework between cell cycle arrest and apoptosis induction based on p53 dynamics. PLoS One 2009; 4:e4795. [PMID: 19274075 PMCID: PMC2650779 DOI: 10.1371/journal.pone.0004795] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Accepted: 02/11/2009] [Indexed: 01/08/2023] Open
Abstract
The tumor suppressor, p53, regulates several gene expressions that are related to the DNA repair protein, cell cycle arrest and apoptosis induction, which activates the implementation of both cell cycle arrest and induction of apoptosis. However, it is not clear how p53 specifically regulates the implementation of these functions. By applying several well-known kinetic mathematical models, we constructed a novel model that described the influence that DNA damage has on the implementation of both the G2/M phase cell cycle arrest and the intrinsic apoptosis induction via its activation of the p53 synthesis process. The model, which consisted of 32 dependent variables and 115 kinetic parameters, was used to examine interference by DNA damage in the implementation of both G2/M phase cell cycle arrest and intrinsic apoptosis induction. A low DNA damage promoted slightly the synthesis of p53, which showed a sigmoidal behavior with time. In contrast, in the case of a high DNA damage, the p53 showed an oscillation behavior with time. Regardless of the DNA damage level, there were delays in the G2/M progression. The intrinsic apoptosis was only induced in situations where grave DNA damage produced an oscillation of p53. In addition, to wreck the equilibrium between Bcl-2 and Bax the induction of apoptosis required an extreme activation of p53 produced by the oscillation dynamics, and was only implemented after the release of the G2/M phase arrest. When the p53 oscillation is observed, there is possibility that the cell implements the apoptosis induction. Moreover, in contrast to the cell cycle arrest system, the apoptosis induction system is responsible for safeguarding the system that suppresses malignant transformations. The results of these experiments will be useful in the future for elucidating of the dominant factors that determine the cell fate such as normal cell cycles, cell cycle arrest and apoptosis.
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Affiliation(s)
- Hiroyuki Hamada
- Laboratory for Bioinformatics, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshihiko Tashima
- Laboratory for Bioinformatics, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Yu Kisaka
- Laboratory for Bioinformatics, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Kazunari Iwamoto
- Laboratory for Bioinformatics, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Taizo Hanai
- Laboratory for Bioinformatics, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | | | - Masahiro Okamoto
- Laboratory for Bioinformatics, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
- * E-mail:
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20
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Lee JT, Lehmann BD, Terrian DM, Chappell WH, Stivala F, Libra M, Martelli AM, Steelman LS, McCubrey JA. Targeting prostate cancer based on signal transduction and cell cycle pathways. Cell Cycle 2008; 7:1745-62. [PMID: 18594202 DOI: 10.4161/cc.7.12.6166] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer remains a leading cause of death in men despite increased capacity to diagnose at earlier stages. After prostate cancer has become hormone independent, which often occurs after hormonal ablation therapies, it is difficult to effectively treat. Prostate cancer may arise from mutations and dysregulation of various genes involved in regulation signal transduction (e.g., PTEN, Akt, etc.,) and the cell cycle (e.g., p53, p21(Cip1), p27(Kip1), Rb, etc.,). This review focuses on the aberrant interactions of signal transduction and cell cycle genes products and how they can contribute to prostate cancer and alter therapeutic effectiveness.
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Affiliation(s)
- John T Lee
- Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, North Carolina 27858, USA
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21
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Puszyński K, Hat B, Lipniacki T. Oscillations and bistability in the stochastic model of p53 regulation. J Theor Biol 2008; 254:452-65. [PMID: 18577387 DOI: 10.1016/j.jtbi.2008.05.039] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2008] [Revised: 05/27/2008] [Accepted: 05/27/2008] [Indexed: 01/21/2023]
Abstract
The p53 regulatory pathway controls cell responses, which include cell cycle arrest, DNA repair, apoptosis and cellular senescence. We propose a stochastic model of p53 regulation, which is based on two feedback loops: the negative, coupling p53 with its immediate downregulator Mdm2, and the positive, which involves PTEN, PIP3 and Akt. Existence of the negative feedback assures homeostasis of healthy cells and oscillatory responses of DNA-damaged cells, which are persistent when DNA repair is inefficient and the positive feedback loop is broken. The positive feedback destroys the negative coupling between Mdm2 and p53 by sequestering most of Mdm2 in cytoplasm, so it may no longer prime the nuclear p53 for degradation. It works as a clock, giving the cell some time for DNA repair. However, when DNA repair is inefficient, the active p53 rises to a high level and triggers transcription of proapoptotic genes. As a result, small DNA damage may be repaired and the cell may return to its initial "healthy" state, while the extended damage results in apoptosis. The stochasticity of p53 regulation, introduced at the levels of gene expression, DNA damage and repair, leads to high heterogeneity of cell responses and causes cell population split after irradiation into subpopulations of apoptotic and surviving cells, with fraction of apoptotic cells growing with the irradiation dose.
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Affiliation(s)
- Krzysztof Puszyński
- Institute of Automatic Control, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
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22
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Schmid G, Kramer MP, Maurer M, Wandl S, Wesierska-Gadek J. Cellular and organismal ageing: Role of the p53 tumor suppressor protein in the induction of transient and terminal senescence. J Cell Biochem 2008; 101:1355-69. [PMID: 17471501 DOI: 10.1002/jcb.21383] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In recent years, an impact of the p53 tumor suppressor protein in the processes of cellular and organismal ageing became evident. First hints were found in model organisms like Saccharomyces cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster where a clear connection between ageing phenotypes and pathways that are regulated by p53, were found. Interestingly, pathways that are central to the ageing process are usually also involved in energy metabolism and are highly conserved throughout evolution. This also supports the long known empiric finding that caloric restriction has a positive impact on the life span of a wide variety of organisms. Within the last years, on the molecular level, an involvement of the insulin-like growth factor and of the histone deacetylase SRIT1 could be shown. Insight on the impact of p53 on ageing at the organismal level came from mice expressing aberrant forms of the p53 protein. Obviously, the balance of the full length p53 protein and of the shorter p44/DeltaNp53 isomer bear a strong impact on ageing. The shorter isoform regulates full length p53 and in cases where there is too much of the longer isoform, this leads to elevated apoptosis resulting in decreased tumor incidence but also in premature ageing due to exhaustion of the renewal potential. Therefore, modulating the expression of the truncated p53 isoform accordingly, might lead to increased health-span and elevated life-span.
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Affiliation(s)
- Gerald Schmid
- Cell Cycle Regulation Group, Department of Medicine I, Division: Institute of Cancer Research, Medical University of Vienna, Vienna, Austria
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23
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Groskreutz DJ, Monick MM, Yarovinsky TO, Powers LS, Quelle DE, Varga SM, Look DC, Hunninghake GW. Respiratory syncytial virus decreases p53 protein to prolong survival of airway epithelial cells. THE JOURNAL OF IMMUNOLOGY 2007; 179:2741-7. [PMID: 17709487 DOI: 10.4049/jimmunol.179.5.2741] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Respiratory syncytial virus (RSV) is a clinically important pathogen. It preferentially infects airway epithelial cells causing bronchiolitis in infants, exacerbations in patients with obstructive lung disease, and life-threatening pneumonia in the immunosuppressed. The p53 protein is a tumor suppressor protein that promotes apoptosis and is tightly regulated for optimal cell growth and survival. A critical negative regulator of p53 is murine double minute 2 (Mdm2), an E3 ubiquitin ligase that targets p53 for proteasome degradation. Mdm2 is activated by phospho-Akt, and we previously showed that RSV activates Akt and delays apoptosis in primary human airway epithelial cells. In this study, we explore further the mechanism by which RSV regulates p53 to delay apoptosis but paradoxically enhance inflammation. We found that RSV activates Mdm2 1-6 h after infection resulting in a decrease in p53 6-24 h after infection. The p53 down-regulation correlates with increased airway epithelial cell longevity. Importantly, inhibition of the PI3K/Akt pathway blocks the activation of Mdm2 by RSV and preserves the p53 response. The effects of RSV infection are antagonized by Nutlin-3, a specific chemical inhibitor that prevents the Mdm2/p53 association. Nutlin-3 treatment increases endogenous p53 expression in RSV infected cells, causing earlier cell death. This same increase in p53 enhances viral replication and limits the inflammatory response as measured by IL-6 protein. These findings reveal that RSV decreases p53 by enhancing Akt/Mdm2-mediated p53 degradation, thereby delaying apoptosis and prolonging survival of airway epithelial cells.
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Affiliation(s)
- Dayna J Groskreutz
- Division of Pulmonary, Critical Care, and Occupational Medicine, Department of Pharmacology, University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, IA 52242, USA.
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24
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Van Maerken T, Speleman F, Vermeulen J, Lambertz I, De Clercq S, De Smet E, Yigit N, Coppens V, Philippé J, De Paepe A, Marine JC, Vandesompele J. Small-molecule MDM2 antagonists as a new therapy concept for neuroblastoma. Cancer Res 2007; 66:9646-55. [PMID: 17018622 DOI: 10.1158/0008-5472.can-06-0792] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Circumvention of the p53 tumor suppressor barrier in neuroblastoma is rarely caused by TP53 mutation but might arise from inappropriately increased activity of its principal negative regulator MDM2. We show here that targeted disruption of the p53-MDM2 interaction by the small-molecule MDM2 antagonist nutlin-3 stabilizes p53 and selectively activates the p53 pathway in neuroblastoma cells with wild-type p53, resulting in a pronounced antiproliferative and cytotoxic effect through induction of G(1) cell cycle arrest and apoptosis. A nutlin-3 response was observed regardless of MYCN amplification status. Remarkably, surviving SK-N-SH cells adopted a senescence-like phenotype, whereas CLB-GA and NGP cells underwent neuronal differentiation. p53 dependence of these alternative outcomes of nutlin-3 treatment was evidenced by abrogation of the effects when p53 was knocked down by lentiviral-mediated short hairpin RNA interference. The diversity of cellular responses reveals pleiotropic mechanisms of nutlins to disable neuroblastoma cells and exemplifies the feasibility of exploiting, by a single targeted intervention, the multiplicity of anticancer activities exerted by a key tumor suppressor as p53. The observed treatment effects without the need of imposing a genotoxic burden suggest that selective MDM2 antagonists might be beneficial for treatment of neuroblastoma patients with and without MYCN amplification.
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Affiliation(s)
- Tom Van Maerken
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
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25
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Brazhnik P, Kohn KW. HAUSP-regulated switch from auto- to p53 ubiquitination by Mdm2 (in silico discovery). Math Biosci 2007; 210:60-77. [PMID: 17585950 DOI: 10.1016/j.mbs.2007.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 12/19/2006] [Accepted: 05/15/2007] [Indexed: 11/17/2022]
Abstract
Stability of the 'guardian of the genome' tumor suppressor protein p53 is regulated predominantly through its ubiquitination. The ubiquitin-specific protease HAUSP plays an important role in this process. Recent experiments showed that p53 demonstrates a differential response to changes in HAUSP which nature and significance are not understood yet. Here a data-driven mathematical model of the Mdm2-mediated p53 ubiquitination network is presented which offers an explanation for the cause of such a response. The model predicts existence of the HAUSP-regulated switch from auto- to p53 ubiquitination by Mdm2. This switch suggests a potential role of HAUSP as a downstream target of stress signals in cells. The model accounts for a significant amount of experimental data, makes predictions for some rate constants, and can serve as a building block for the larger model describing a complex dynamic response of p53 to cellular stresses.
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Affiliation(s)
- Paul Brazhnik
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, United States.
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26
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Qi JP, Shao SH, Xie J, Zhu Y. A mathematical model of P53 gene regulatory networks under radiotherapy. Biosystems 2007; 90:698-706. [PMID: 17512110 PMCID: PMC7116929 DOI: 10.1016/j.biosystems.2007.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Accepted: 02/22/2007] [Indexed: 12/27/2022]
Abstract
P53, a vital anticancer gene, controls the transcription and translation of a series of genes, and implement the cell cycle arrest and cell apoptosis by regulating their complicated signal pathways. Under radiotherapy, cell can trigger internal self-defense mechanisms in fighting against genome stresses induced by acute ion radiation (IR). To simulate the investigating of cellular responding acute IR at single cell level further, we propose a model of P53 gene regulatory networks under radiotherapy. Our model can successfully implement the kinetics of double strand breaks (DSBs) generating and their repair, ataxia telangiectasia mutated (ATM) activation, as well as P53-MDM2 feedback regulating. By comparing simulations under different IR dose, we can try to find the optimal strategy in controlling of IR dose and therapy time, and provide some theoretical analysis to obtain much better outcome of radiotherapy further.
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Affiliation(s)
- J P Qi
- College of Information Sciences & Technology, Donghua University, Shanghai 201620, China.
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27
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Chandrakanthan V, Chami O, Stojanov T, O'Neill C. Variable expressivity of the tumour suppressor protein TRP53 in cryopreserved human blastocysts. Reprod Biol Endocrinol 2007; 5:39. [PMID: 17939878 PMCID: PMC2099431 DOI: 10.1186/1477-7827-5-39] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Accepted: 10/17/2007] [Indexed: 12/16/2022] Open
Abstract
In a mouse model, in vitro fertilization or extended embryo culture leads to the increased expression of TRP53 in susceptible embryos. Ablation of the TRP53 gene improved embryo viability indicating that increased expression of TRP53 is a cause of the reduction of embryo viability resulting from in vitro fertilization or embryo culture. This study investigates the status of TRP53 expression in human embryos produced by intracytoplasmic sperm injection. Following fertilization, embryos were cultured for 96 h and then cryopreserved. Immediately upon thawing they were fixed in formaldehyde and subjected to immunostaining for TRP53. Staining was visualized by confocal microscopy. Negative controls were incubated with isotype control immunoglobulin and showed negligible staining. All embryos showed TRP53 staining above negative controls. TRP53 staining was heterogenous within and between embryos. An embryo that showed retarded development showed high levels of TRP53 expression. A blastocyst that had a collapsed blastocoel also showed high levels of TRP53 compared to morphologically normal blastocysts. Most TRP53 staining was in the region of the nucleus. Morphologically normal blastocysts tended to show little nuclear accumulation of stain. However, some cells within these embryos had high levels of nuclear TRP53 expression. The results show that embryos have varying sensitivity to the stresses of production and culture in vitro, and this resulted in variable expressivity of TRP53.
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Affiliation(s)
- Vashe Chandrakanthan
- Human Reproduction Unit, Royal North Shore Hospital, St Leonards, NSW, 2065, Australia and the Discipline of Physiology, University of Sydney, Sydney, NSW, Australia
| | - Omar Chami
- Sydney IVF, 321 Kent St. Sydney, NSW, Australia
| | | | - Chris O'Neill
- Human Reproduction Unit, Royal North Shore Hospital, St Leonards, NSW, 2065, Australia and the Discipline of Physiology, University of Sydney, Sydney, NSW, Australia
- Discipline of Medicine, University of Sydney, Sydney, NSW, Australia
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28
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Kurata H, Inoue K, Maeda K, Masaki K, Shimokawa Y, Zhao Q. Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis. Nucleic Acids Res 2007; 35:e134. [PMID: 17940089 PMCID: PMC2175333 DOI: 10.1093/nar/gkm769] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Biochemical network maps are helpful for understanding the mechanism of how a collection of biochemical reactions generate particular functions within a cell. We developed a new and computationally feasible notation that enables drawing a wide resolution map from the domain-level reactions to phenomenological events and implemented it as the extended GUI network constructor of CADLIVE (Computer-Aided Design of LIVing systEms). The new notation presents ‘Domain expansion’ for proteins and RNAs, ‘Virtual reaction and nodes’ that are responsible for illustrating domain-based interaction and ‘InnerLink’ that links real complex nodes to virtual nodes to illustrate the exact components of the real complex. A modular box is also presented that packs related reactions as a module or a subnetwork, which gives CADLIVE a capability to draw biochemical maps in a hierarchical modular architecture. Furthermore, we developed a pathway search module for virtual knockout mutants as a built-in application of CADLIVE. This module analyzes gene function in the same way as molecular genetics, which simulates a change in mutant phenotypes or confirms the validity of the network map. The extended CADLIVE with the newly proposed notation is demonstrated to be feasible for computational simulation and analysis.
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Affiliation(s)
- Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, 820-8502, Fukuoka, Japan.
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29
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Lehmann BD, McCubrey JA, Terrian DM. Radiosensitization of prostate cancer by priming the wild-type p53-dependent cellular senescence pathway. Cancer Biol Ther 2007; 6:1165-70. [PMID: 18059157 DOI: 10.4161/cbt.6.8.4544] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A dramatic stage-migration in diagnosis of prostate cancer has led to earlier detection of clinically localized carcinoma and an increased use of radiation therapy. The p53 protein responds to irradiation-induced DNA damage by removing critically damaged cells from the proliferative pool. This review will focus on the dominant role that p53-dependent cellular senescence, rather than cell death, plays in determining the radiosensitivity of human prostate cancer cells in vitro. The finding that senescence is a primary mechanism of tumor regression indicates that p53 activators or downstream effectors may prove effective in radiosensitizing some carcinoma of the prostate.
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Affiliation(s)
- Brian D Lehmann
- Departments of Anatomy and Cell Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
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30
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Voutsadakis IA. Pathogenesis of colorectal carcinoma and therapeutic implications: the roles of the ubiquitin-proteasome system and Cox-2. J Cell Mol Med 2007; 11:252-85. [PMID: 17488476 PMCID: PMC3822826 DOI: 10.1111/j.1582-4934.2007.00032.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Pathways of the molecular pathogenesis of colorectal carcinoma have been extensively studied and molecular lesions during the development of the disease have been revealed. High up in the list of colorectal cancer lesions are APC (adenomatous polyposis coli), K-ras, Smad4 (or DPC4-deleted in pancreatic cancer 4) and p53 genes. All these molecules are part of important pathways for the regulation of cell proliferation and apoptosis and as a result perturbation of these processes lead to carcinogenesis. The ubiquitin-proteasome system (UPS) is comprised of a multi-unit cellular protease system that regulates several dozens of cell proteins after their ligation with the protein ubiquitin. Given that among these proteins are regulators of the cell cycle, apoptosis, angiogenesis, adhesion and cell signalling, this system plays a significant role in cell fate and carcinogenesis. UPS inhibition has been found to be a pre-requisite for apoptosis and is already clinically exploited with the proteasome inhibitor bortezomib in multiple myeloma. Cyclooxygenase-2 (Cox-2) is the inducible form of the enzyme that metabolizes the lipid arachidonic acid to prostaglandin H2, the first step of prostaglandins production. This enzyme is up-regulated in colorectal cancer and in several other cancers. Inhibition of Cox-2 by aspirin and other non-steroidal anti-inflammatory drugs (NSAIDs) has been found to inhibit proliferation of colorectal cancer cells and in epidemiologic studies has been shown to reduce colon polyp formation in genetically predisposed populations and in the general population. NSAIDs have also Cox-independent anti-proliferative effects. Targeted therapies, the result of increasingly understanding carcinogenesis in the molecular level, have entered the field of anti-neoplastic treatment and are used by themselves and in combination with chemotherapy drugs. Combinations of targeted drugs have started also to be investigated. This article reviews the molecular pathogenesis of colorectal cancer, the roles of UPS and Cox-2 in it and puts forward a rational for their combined inhibition in colorectal cancer treatment.
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Affiliation(s)
- Ioannis A Voutsadakis
- Division of Medical Oncology, University Hospital of Larissa, Larissa 41110, Greece.
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31
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Qi JP, Shao SH, Li DD, Zhou GP. A dynamic model for the p53 stress response networks under ion radiation. Amino Acids 2007; 33:75-83. [PMID: 17072789 PMCID: PMC7088058 DOI: 10.1007/s00726-006-0454-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Accepted: 09/29/2006] [Indexed: 12/27/2022]
Abstract
P53 controls the cell cycle arrest and cell apoptosis through interaction with the downstream genes and their signal pathways. To stimulate the investigation into the complicated responses of p53 under the circumstance of ion radiation (IR) in the cellular level, a dynamic model for the p53 stress response networks is proposed. The model can be successfully used to simulate the dynamic processes of generating the double-strand breaks (DSBs) and their repairing, ataxia telangiectasia mutated (ATM) activation, as well as the oscillations occurring in the p53-MDM2 feedback loop.
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Affiliation(s)
- J-P Qi
- Bio-Informatics Research Center, Donghua University, Shanghai, China.
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32
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Meng LH, Kohn KW, Pommier Y. Dose-response transition from cell cycle arrest to apoptosis with selective degradation of Mdm2 and p21WAF1/CIP1 in response to the novel anticancer agent, aminoflavone (NSC 686,288). Oncogene 2007; 26:4806-16. [PMID: 17297446 DOI: 10.1038/sj.onc.1210283] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Aminoflavone (AF, NSC 686,288) is beginning clinical trials. It induces replication-mediated histone H2AX phosphorylation, DNA-protein crosslinks and activates p53. Here, we studied p21(CIP1/WAF1) and Mdm2 responses to AF. Although p53 stabilization and phosphorylation at serine 15 increased with dose and time of exposure, Mdm2 and p21(CIP1/WAF1) protein levels displayed a biphasic response, as they accumulated at submicromolar doses and then decreased with increasing AF. As both Mdm2 and p21(CIP1/WAF1) mRNA levels increased with AF concentration without reduction at higher concentrations, we measured the half-lives of Mdm2 and p21(CIP1/WAF1) proteins. Mdm2 and p21(CIP1/WAF1) half-lives were shortened with increasing AF concentrations. Proteasomal degradation appears responsible for the decrease of both Mdm2 and p21(CIP1/WAF1), as MG-132 prevented their degradation and revealed AF-induced Mdm2 polyubiquitylation. AF also induced protein kinase B (Akt) activation, which was reduced with increasing AF concentrations. Suppression of Akt by small interfering RNA was associated with downregulation of Mdm2 and p21(CIP1/WAF1) and with enhanced apoptosis. These results suggest that the cellular responses to AF are determined at least in part by Mdm2 and p21(CIP1/WAF1) protein levels, as well as by Akt activity, leading either to cell cycle arrest when Mdm2 and p21(CIP1/WAF1) are elevated, or to apoptosis when Mdm2 and p21(CIP1/WAF1) are degraded by the proteasome and Akt insufficiently activated to protect against apoptosis.
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Affiliation(s)
- L-H Meng
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4255, USA
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33
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Garza R, Hudson RA, McMahan CA, Walter CA, Vogel KS. A mild mutator phenotype arises in a mouse model for malignancies associated with neurofibromatosis type 1. Mutat Res 2007; 615:98-110. [PMID: 17208258 DOI: 10.1016/j.mrfmmm.2006.11.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Revised: 10/25/2006] [Accepted: 11/10/2006] [Indexed: 05/13/2023]
Abstract
Defects in genes that control DNA repair, proliferation, and apoptosis can increase genomic instability, and thus promote malignant progression. Although most tumors that arise in humans with neurofibromatosis type 1 (NF1) are benign, these individuals are at increased risk for malignant peripheral nerve sheath tumors (MPNST). To characterize additional mutations required for the development of MPNST from benign plexiform neurofibromas, we generated a mouse model for these tumors by combining targeted null mutations in Nf1 and p53, in cis. CisNf1+/-; p53+/- mice spontaneously develop PNST, and these tumors exhibit loss-of-heterozygosity at both the Nf1 and p53 loci. Because p53 has well-characterized roles in the DNA damage response, DNA repair, and apoptosis, and because DNA repair genes have been proposed to act as modifiers in NF1, we used the cisNf1+/-; p53+/- mice to determine whether a mutator phenotype arises in NF1-associated malignancies. To quantitate spontaneous mutant frequencies (MF), we crossed the Big Blue mouse, which harbors a lacI transgene, to the cisNf1+/-; p53+/- mice, and isolated genomic DNA from both tumor and normal tissues in compound heterozygotes and wild-type siblings. Many of the PNST exhibited increased mutant frequencies (MF=4.70) when compared to normal peripheral nerve and brain (MF=2.09); mutations occurred throughout the entire lacI gene, and included base substitutions, insertions, and deletions. Moreover, the brains, spleens, and livers of these cisNf1+/-; p53+/- animals exhibited increased mutant frequencies when compared to tissues from wild-type littermates. We conclude that a mild mutator phenotype arises in the tumors and tissues of cisNf1+/-; p53+/- mice, and propose that genomic instability influences NF1 tumor progression and disease severity.
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Affiliation(s)
- Rene Garza
- Department of Cellular and Structural Biology, The University of Texas, Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
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34
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Quevedo C, Kaplan DR, Derry WB. AKT-1 Regulates DNA-Damage-Induced Germline Apoptosis in C. elegans. Curr Biol 2007; 17:286-92. [PMID: 17276923 DOI: 10.1016/j.cub.2006.12.038] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Revised: 12/12/2006] [Accepted: 12/18/2006] [Indexed: 01/22/2023]
Abstract
The cellular response to genotoxic stress involves the integration of multiple prosurvival and proapoptotic signals that dictate whether a cell lives or dies. In mammals, AKT/PKB regulates cell survival by modulating the activity of several apoptotic proteins, including p53. In Caenorhabditis elegans, akt-1 and akt-2 regulate development in response to environmental cues by controlling the FOXO transcription factor daf-16, but the role of these genes in regulating p53-dependent apoptosis is not known. In this study, we show that akt-1 and akt-2 negatively regulate DNA-damage-induced apoptosis in the C. elegans germline. The antiapoptotic activity of akt-1 is independent of its target gene daf-16 but dependent on cep-1/p53. Although only akt-1 regulates the apoptotic activity of cep-1, both akt-1 and akt-2 modulate the intensity of the apoptotic response independently of the transcriptional activity of CEP-1. Finally, we show that AKT-1 regulates apoptosis but not cell-cycle progression downstream of the HUS-1/MRT-2 branch of the DNA damage checkpoint.
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Affiliation(s)
- Celia Quevedo
- Cancer Research Program, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
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35
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Minsavage GD, Dillman JF. Bifunctional Alkylating Agent-Induced p53 and Nonclassical Nuclear Factor κB Responses and Cell Death Are Altered by Caffeic Acid Phenethyl Ester: A Potential Role for Antioxidant/Electrophilic Response-Element Signaling. J Pharmacol Exp Ther 2007; 321:202-12. [PMID: 17204746 DOI: 10.1124/jpet.106.116145] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Bifunctional alkylating agents (BFA) such as mechlorethamine (nitrogen mustard) and bis-(2-chloroethyl) sulfide (sulfur mustard; SM) covalently modify DNA and protein. The roles of nuclear factor kappaB (NF-kappaB) and p53, transcription factors involved in inflammatory and cell death signaling, were examined in normal human epidermal keratinocytes (NHEK) and immortalized HaCaT keratinocytes, a p53-mutated cell line, to delineate molecular mechanisms of action of BFA. NHEK and HaCaT cells exhibited classical NF-kappaB signaling as degradation of inhibitor protein of NF-kappaBalpha (IkappaBalpha) occurred within 5 min after exposure to tumor necrosis factor-alpha. However, exposure to BFA induced nonclassical NF-kappaB signaling as loss of IkappaBalpha was not observed until 2 or 6 h in NHEK or HaCaT cells, respectively. Exposure of an NF-kappaB reporter gene-expressing HaCaT cell line to 12.5, 50, or 100 muM SM activated the reporter gene within 9 h. Pretreatment with caffeic acid phenethyl ester (CAPE), a known inhibitor of NF-kappaB signaling, significantly decreased BFA-induced reporter gene activity. A 1.5-h pretreatment or 30-min postexposure treatment with CAPE prevented BFA-induced loss of membrane integrity by 24 h in HaCaT cells but not in NHEK. CAPE disrupted BFA-induced phosphorylation of p53 and p90 ribosomal S6 kinase (p90RSK) in both cell lines. CAPE also increased nuclear factor E2-related factor 2 and decreased aryl hydrocarbon receptor protein expression, both of which are involved in antioxidant/electrophilic response element (ARE/EpRE) signaling. Thus, disruption of p53/p90RSK-mediated NF-kappaB signaling and activation of ARE/EpRE pathways may be effective strategies to delineate mechanisms of action of BFA-induced inflammation and cell death signaling in immortalized versus normal skin systems.
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Affiliation(s)
- Gary D Minsavage
- Cell and Molecular Biology Branch, U.S. Army Medical Research Institute of Chemical Defense, 3100 Ricketts Point Road, Aberdeen Proving Ground, MD 21010-5400, USA
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36
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Chandrakanthan V, Li A, Chami O, O'Neill C. Effects of in vitro fertilization and embryo culture on TRP53 and Bax expression in B6 mouse embryos. Reprod Biol Endocrinol 2006; 4:61. [PMID: 17118206 PMCID: PMC1687191 DOI: 10.1186/1477-7827-4-61] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Accepted: 11/21/2006] [Indexed: 11/10/2022] Open
Abstract
In the mouse, embryo culture results in a characteristic phenotype of retarded embryo preimplantation development and reduced numbers of cells within embryos. The expression of TRP53 is central to the regulation of the cell's capacity to proliferate and survive. In this study we found that Trp53 mRNA is expressed throughout the preimplantation stage of development. Levels of TRP53 protein expression were low during the cleavage stages and increased at the morula and blastocyst stages in B6 embryos collected from the reproductive tract. Embryos collected at the zygote stage and cultured for 96 h also showed low levels of TRP53 expression at precompaction stages. There were higher levels of TRP53 in cultured morula and the level in cultured blastocysts was clearly increased above blastocysts collected directly from the uterus. Immunolocalization of TRP53 showed that its increased expression in cultured blastocysts corresponded with a marked accumulation of TRP53 within the nuclei of embryonic cells. This pattern of expression was enhanced in embryos produced by in vitro fertilization and subjected to culture. The TRP53 was transcriptionally active since culture also induced increased expression of Bax, yet this did not occur in embryos lacking Trp53 (Trp53-/-). The rate of development of Trp53-/- zygotes to the blastocyst stage was not different to wildtype controls when embryos were cultured in groups of ten but was significantly faster when cultured individually. The results show that zygote culture resulted in the accumulation of transcription activity of TRP53 in the resulting blastocysts. This accounts for the adverse effects of culture of embryos individually, but does not appear to be the sole cause of the retarded preimplantation stage growth phenotype associated with culture in vitro.
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Affiliation(s)
- Vashe Chandrakanthan
- Discipline of Physiology, University of Sydney, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
| | - Aiqing Li
- Discipline of Physiology, University of Sydney, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
| | - Omar Chami
- Discipline of Physiology, University of Sydney, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
| | - Christopher O'Neill
- Discipline of Physiology, University of Sydney, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
- Discipline of Medicine, University of Sydney, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
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37
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Kohn KW, Aladjem MI, Kim S, Weinstein JN, Pommier Y. Depicting combinatorial complexity with the molecular interaction map notation. Mol Syst Biol 2006; 2:51. [PMID: 17016517 PMCID: PMC1681518 DOI: 10.1038/msb4100088] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2006] [Accepted: 07/02/2006] [Indexed: 12/26/2022] Open
Abstract
To help us understand how bioregulatory networks operate, we need a standard notation for diagrams analogous to electronic circuit diagrams. Such diagrams must surmount the difficulties posed by complex patterns of protein modifications and multiprotein complexes. To meet that challenge, we have designed the molecular interaction map (MIM) notation (http://discover.nci.nih.gov/mim/). Here we show the advantages of the MIM notation for three important types of diagrams: (1) explicit diagrams that define specific pathway models for computer simulation; (2) heuristic maps that organize the available information about molecular interactions and encompass the possible processes or pathways; and (3) diagrams of combinatorially complex models. We focus on signaling from the epidermal growth factor receptor family (EGFR, ErbB), a network that reflects the major challenges of representing in a compact manner the combinatorial complexity of multimolecular complexes. By comparing MIMs with other diagrams of this network that have recently been published, we show the utility of the MIM notation. These comparisons may help cell and systems biologists adopt a graphical language that is unambiguous and generally understood.
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Affiliation(s)
- Kurt W Kohn
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
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38
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Kostic M, Matt T, Martinez-Yamout MA, Dyson HJ, Wright PE. Solution Structure of the Hdm2 C2H2C4 RING, a Domain Critical for Ubiquitination of p53. J Mol Biol 2006; 363:433-50. [PMID: 16965791 DOI: 10.1016/j.jmb.2006.08.027] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Revised: 08/09/2006] [Accepted: 08/10/2006] [Indexed: 11/16/2022]
Abstract
Regulation of the transcriptional response to the tumor suppressor p53 occurs at many levels, including control of its transcriptional activity, and of its stability and concentration within the cell. p53 stability is regulated by the protein Hdm2, an E3 ubiquitin ligase that binds to p53 and promotes its ubiquitination and degradation. The C-terminal domain of Hdm2, which is critical for this activity, has been classified as a RING domain on the basis of sequence homology, although it lacks the canonical set of zinc ligands (RING domains typically have C3HC4 or C4C4 zinc coordination). Here, we report the solution structure of the C2H2C4 RING domain of Hdm2(429-491), which reveals a symmetrical dimer with a unique cross-brace zinc-binding scheme. Each subunit has one Cys4 Zn site and one His2Cys2 Zn site. The global fold of each subunit is similar to those reported for other RING domains, with a compact betabetaalphabeta fold, a small hydrophobic core, and two Zn ions, which are essential for maintaining the domain structure. The dimer structure is maintained by an extensive interface that buries a large hydrophobic area on each subunit. It has been proposed that Hdm2 and its homologue HdmX form a stable heterodimer through their RING domains, resulting in a synergistic increase in observed E3 activity. To test this proposal, we prepared an HdmX RING construct and showed by NMR titration that it forms a tight 1:1 complex with the Hdm2 RING. The resonances most perturbed by heterodimer formation are located within the subunit interface of the homodimer, far removed from the surface expected to form the docking site of the E2 ubiquitin-conjugating enzyme, providing a structure-based rationale for the function of the RING domains in p53 ubiquitination.
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Affiliation(s)
- Milka Kostic
- Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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39
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Kulikov R, Winter M, Blattner C. Binding of p53 to the Central Domain of Mdm2 Is Regulated by Phosphorylation. J Biol Chem 2006; 281:28575-83. [PMID: 16870621 DOI: 10.1074/jbc.m513311200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Mdm2 protein is the major regulator of the tumor suppressor protein p53. We show that the p53 protein associates both with the N-terminal and with the central domain of Mdm2. The central p53-binding site of Mdm2 encompasses amino acids 235-300. Binding of p53 to the central domain is significantly enhanced after phosphorylation of the central domain of Mdm2. The N-terminal and central domains of Mdm2 act synergistically in binding to p53. p53 mutants that have mutations in the tetramerization domain and that fail to oligomerize do not show such an enhancement of binding in the presence of the other binding site.
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Affiliation(s)
- Roman Kulikov
- Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, 76021 Karlsruhe, Germany
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40
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Pommier Y, Weinstein JN, Aladjem MI, Kohn KW. Chk2 molecular interaction map and rationale for Chk2 inhibitors. Clin Cancer Res 2006; 12:2657-61. [PMID: 16675556 DOI: 10.1158/1078-0432.ccr-06-0743] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
To organize the rapidly accumulating information on bioregulatory networks related to the histone gamma-H2AX-ATM-Chk2-p53-Mdm2 pathways in concise and unambiguous diagrams, we used the molecular interaction map notation (http://discover.nci.nih.gov/min). Molecular interaction maps are particularly useful for networks that include protein-protein binding and posttranslational modifications (e.g., phosphorylation). Both are important for nearly all of the proteins involved in DNA double-strand break signaling. Visualizing the regulatory circuits underlying cellular signaling may help identify key regulatory reactions and defects that can serve as targets for anticancer drugs.
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Affiliation(s)
- Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892-4255, USA.
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41
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Hopkins-Donaldson S, Belyanskaya LL, Simões-Wüst AP, Sigrist B, Kurtz S, Zangemeister-Wittke U, Stahel R. p53-induced apoptosis occurs in the absence of p14(ARF) in malignant pleural mesothelioma. Neoplasia 2006; 8:551-9. [PMID: 16867217 PMCID: PMC1601933 DOI: 10.1593/neo.06148] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Malignant pleural mesotheliomas (MPMs) are usually wild type for the p53 gene but contain homozygous deletions in the INK4A locus that encodes p14(ARF), an inhibitor of p53-MDM2 interaction. Previous findings suggest that lack of p14(ARF) expression and the presence of SV40 large T antigen (L-Tag) result in p53 inactivation in MPM. We did not detect SV40 L-Tag mRNA in either MPM cell lines or primary cultures, and treatment of p14(ARF)-deficient cells with cisplatin (CDDP) increased both total and phosphorylated p53 and enhanced p53 DNA-binding activity. On incubation with CDDP, levels of positively regulated p53 transcriptional targets p21(WAF), PIG3, MDM2, Bax, and PUMA increased in p14(ARF)-deficient cells, whereas negatively regulated survivin decreased. Significantly, p53-induced apoptosis was activated by CDDP in p14(ARF)-deficient cells, and treatment with p53-specific siRNA rendered them more CDDP-resistant. p53 was also activated by: 1) inhibition of MDM2 (using nutlin-3); 2) transient overexpression of p14(ARF); and 3) targeting of survivin using antisense oligonucleotides. However, it is noteworthy that only survivin downregulation sensitized cells to CDDP-induced apoptosis. These results suggest that p53 is functional in the absence of p14(ARF) in MPM and that targeting of the downstream apoptosis inhibitor survivin can sensitize to CDDP-induced apoptosis.
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Affiliation(s)
- Sally Hopkins-Donaldson
- Laboratory for Molecular Oncology, University Hospital Zurich, Haeldeliweg 4, CH-8044 Zurich, Switzerland.
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42
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Abstract
Systems theory has been applied to process analysis in a variety of scientific disciplines from engineering to evolutionary biology. In the recent postgenomic era, the accumulation of an enormous amount of data gained from a variety of technologies has led to a revisiting of systems theory concepts. This systems biology approach has been integral in understanding a variety of processes in a number of model organisms. This review gives an overview of systems biology approaches, from component identification to modeling of networks. Various features of the root, including its development and the availability of high resolution gene expression data sets that describe root development, make the root amenable to a systems approach. The current status of systems approaches to understanding root development is reviewed.
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43
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Yang YC, Hsu YT, Wu CC, Chen HT, Chang MS. Silencing of astrin induces the p53-dependent apoptosis by suppression of HPV18 E6 expression and sensitizes cells to paclitaxel treatment in HeLa cells. Biochem Biophys Res Commun 2006; 343:428-34. [PMID: 16546135 DOI: 10.1016/j.bbrc.2006.02.166] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Accepted: 02/25/2006] [Indexed: 10/24/2022]
Abstract
Astrin is a microtubule-associated protein and localizes with mitotic spindles in the M-phase. We silenced the expression of astrin protein and tested the cell viability in response to paclitaxel treatment in paclitaxel-sensitive and paclitaxel-resistant cells. We found that the absence of astrin by siRNA resulted in the activation of a p53-dependent apoptosis, which elevated pro-apoptotic Bax expression and increased the activity of caspase-3 in astrin-depleted cells. The HPV18 E6 transcription was found to be inhibited along with the increase expression of p53. Intriguingly, the expression of astrin decreased in paclitaxel-sensitive HeLa cells but remained steady in paclitaxel-resistant cells in response to paclitaxel treatment. Furthermore, we identified that the depletion of astrin caused more cell death both in paclitaxel-sensitive and -resistant cells in combination with paclitaxel treatment. These findings suggest that the silencing of astrin induce a p53-dependent apoptosis and has an additive effect on paclitaxel treatment.
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Affiliation(s)
- Yuh-Cheng Yang
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
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44
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Wyttenbach A, Tolkovsky AM. The BH3-only protein Puma is both necessary and sufficient for neuronal apoptosis induced by DNA damage in sympathetic neurons. J Neurochem 2006; 96:1213-26. [PMID: 16478523 DOI: 10.1111/j.1471-4159.2005.03676.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA damage activates apoptosis in several neuronal populations and is an important component of neuropathological conditions. While it is well established that neuronal apoptosis, induced by DNA damage, is dependent on the key cell death regulators p53 and Bax, it is unknown which proteins link the p53 signal to Bax. Using rat sympathetic neurons as an in vitro model of neuronal apoptosis, we show that cytosine arabinoside is a DNA damaging drug that induces the expression of the BH3-only pro-apoptotic genes Noxa, Puma and Bim. Increased expression occurred after p53 activation, measured by its phosphorylation at serine 15, but prior to the conformational change of Bax at the mitochondria, cytochrome c (cyt c) release and apoptosis. Hence Noxa, Puma and Bim could potentially link p53 to Bax. We directly tested this hypothesis by the use of nullizygous mice. We show that Puma, but not Bim or Noxa, is a crucial mediator of DNA damage-induced neuronal apoptosis. Despite the powerful pro-apoptotic effects of overexpressed Puma in Bax-expressing neurons, Bax nullizygous neurons were resistant to Puma-induced death. Therefore, Puma provides the critical link between p53 and Bax, and is both necessary and sufficient to mediate DNA damage-induced apoptosis of sympathetic neurons.
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Affiliation(s)
- Andreas Wyttenbach
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
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45
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Furuta T, Hayward RL, Meng LH, Takemura H, Aune GJ, Bonner WM, Aladjem MI, Kohn KW, Pommier Y. p21CDKN1A allows the repair of replication-mediated DNA double-strand breaks induced by topoisomerase I and is inactivated by the checkpoint kinase inhibitor 7-hydroxystaurosporine. Oncogene 2006; 25:2839-49. [PMID: 16407843 DOI: 10.1038/sj.onc.1209313] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This study provides evidence for the importance of p21(CDKN1A) for the repair of replication-mediated DNA double-strand breaks (DSBs) induced by topoisomerase I. We report that defects of p21(CDKN1A) and p53 enhance camptothecin-induced histone H2AX phosphorylation (gammaH2AX), a marker for DNA DSBs. In human colon carcinoma HCT116 cells with wild-type (wt) p53, gammaH2AX reverses after camptothecin removal. By contrast, gammaH2AX increases after camptothecin removal in HCT116 cells deficient for p53 (p53-/-) or p21(CDKN1A) (p21-/-) as the cells reach the late-S and G2 phases. Since p21-/- cells exhibit similar S-phase arrest as wt cells in response to camptothecin and aphidicolin does not abrogate the enhanced gammaH2AX formation in p21-/- cells, we conclude that enhanced gammaH2AX formation in p21-/- cells is not due to re-replication. The cell cycle checkpoint abrogator and Chk1/Chk2 inhibitor 7-hydroxystaurosporine (UCN-01) also increases camptothecin-induced gammaH2AX formation and inhibits camptothecin-induced p21(CDKN1A) upregulation in HCT116 wt cells. TUNEL (terminal deoxynucleotidyl transferase (TdT)-mediated dUTP-biotin nick end labeling) assays demonstrate that gammaH2AX formation in late S and G2 cells following CPT treatment corresponds to DNA breaks. However, these breaks are not related to apoptotic DNA fragmentation. We propose that p21(CDKN1A) prevents the collapse of replication forks damaged by stabilized topoisomerase I cleavage complexes.
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Affiliation(s)
- T Furuta
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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46
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Lang F, Föller M, Lang KS, Lang PA, Ritter M, Gulbins E, Vereninov A, Huber SM. Ion channels in cell proliferation and apoptotic cell death. J Membr Biol 2006; 205:147-57. [PMID: 16362503 DOI: 10.1007/s00232-005-0780-5] [Citation(s) in RCA: 223] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Indexed: 12/11/2022]
Abstract
Cell proliferation and apoptosis are paralleled by altered regulation of ion channels that play an active part in the signaling of those fundamental cellular mechanisms. Cell proliferation must--at some time point--increase cell volume and apoptosis is typically paralleled by cell shrinkage. Cell volume changes require the participation of ion transport across the cell membrane, including appropriate activity of Cl- and K+ channels. Besides regulating cytosolic Cl- activity, osmolyte flux and, thus, cell volume, most Cl- channels allow HCO3- exit and cytosolic acidification, which inhibits cell proliferation and favors apoptosis. K+ exit through K+ channels may decrease intracellular K+ concentration, which in turn favors apoptotic cell death. K+ channel activity further maintains the cell membrane potential, a critical determinant of Ca2+ entry through Ca2+ channels. Cytosolic Ca2+ may trigger mechanisms required for cell proliferation and stimulate enzymes executing apoptosis. The switch between cell proliferation and apoptosis apparently depends on the magnitude and temporal organization of Ca2+ entry and on the functional state of the cell. Due to complex interaction with other signaling pathways, a given ion channel may play a dual role in both cell proliferation and apoptosis. Thus, specific ion channel blockers may abrogate both fundamental cellular mechanisms, depending on cell type, regulatory environment and condition of the cell. Clearly, considerable further experimental effort is required to fully understand the complex interplay between ion channels, cell proliferation and apoptosis.
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Affiliation(s)
- F Lang
- Department of Physiology, University of Tübingen, Germany.
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47
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Pommier Y, Barcelo J, Rao VA, Sordet O, Jobson AG, Thibaut L, Miao Z, Seiler J, Zhang H, Marchand C, Agama K, Redon C. Repair of topoisomerase I-mediated DNA damage. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2006; 81:179-229. [PMID: 16891172 PMCID: PMC2576451 DOI: 10.1016/s0079-6603(06)81005-6] [Citation(s) in RCA: 225] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Topoisomerase I (Top1) is an abundant and essential enzyme. Top1 is the selective target of camptothecins, which are effective anticancer agents. Top1-DNA cleavage complexes can also be trapped by various endogenous and exogenous DNA lesions including mismatches, abasic sites and carcinogenic adducts. Tyrosyl-DNA phosphodiesterase (Tdp1) is one of the repair enzymes for Top1-DNA covalent complexes. Tdp1 forms a multiprotein complex that includes poly(ADP) ribose polymerase (PARP). PARP-deficient cells are hypersensitive to camptothecins and functionally deficient for Tdp1. We will review recent developments in several pathways involved in the repair of Top1 cleavage complexes and the role of Chk1 and Chk2 checkpoint kinases in the cellular responses to Top1 inhibitors. The genes conferring camptothecin hypersensitivity are compiled for humans, budding yeast and fission yeast.
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Affiliation(s)
- Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Juana Barcelo
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - V. Ashutosh Rao
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Olivier Sordet
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Andrew G. Jobson
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Laurent Thibaut
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Zheyong Miao
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Jennifer Seiler
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Hongliang Zhang
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Christophe Marchand
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Keli Agama
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Christophe Redon
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
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48
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Chang NS, Doherty J, Ensign A, Schultz L, Hsu LJ, Hong Q. WOX1 Is Essential for Tumor Necrosis Factor-, UV Light-, Staurosporine-, and p53-mediated Cell Death, and Its Tyrosine 33-phosphorylated Form Binds and Stabilizes Serine 46-phosphorylated p53. J Biol Chem 2005; 280:43100-8. [PMID: 16219768 DOI: 10.1074/jbc.m505590200] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
WW domain-containing oxidoreductase WOX1, also named WWOX or FOR, undergoes Tyr33 phosphorylation at its first N-terminal WW domain and subsequent nuclear translocation in response to sex steroid hormones and stress stimuli. The activated WOX1 binds tumor suppressor p53, and both proteins may induce apoptosis synergistically. Functional suppression of WOX1 by antisense mRNA or a dominant negative abolishes p53-mediated apoptosis. Here, we determined that UV light, anisomycin, etoposide, and hypoxic stress rapidly induced phosphorylation of p53 at Ser46 and WOX1 at Tyr33 (phospho-WOX1) and their binding interactions in several tested cancer cells. Mapping by yeast two-hybrid analysis and co-immunoprecipitation showed that phospho-WOX1 physically interacted with Ser46-phosphorylated p53. Knockdown of WOX1 protein expression by small interfering RNA resulted in L929 fibroblast resistance to apoptosis by tumor necrosis factor, staurosporine, UV light, and ectopic p53, indicating an essential role of WOX1 in stress stimuli-induced apoptosis. Notably, UV light could not induce p53 protein expression in these WOX1 knockdown cells, although p53 mRNA levels were not reduced. Suppression of WOX1 by dominant negative WOX1 (to block Tyr33 phosphorylation) also abolished UV light-induced p53 protein expression. Time course analysis showed that the stability of ectopic wild type p53, tagged with DsRed, was decreased in WOX1 knockdown cells. Inhibition of MDM2 by nutlin-3 increased the binding of p53 and WOX1 and stability of p53. Together, our data show that WOX1 plays a critical role in conferring cellular sensitivity to apoptotic stress and that Tyr33 phosphorylation in WOX1 is essential for binding and stabilizing Ser46-phosphorylated p53.
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Affiliation(s)
- Nan-Shan Chang
- Guthrie Research Institute, Laboratory of Molecular Immunology, Sayre, Pennsylvania 18840, USA. chang@
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49
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Tabakin-Fix Y, Azran I, Schavinky-Khrapunsky Y, Levy O, Aboud M. Functional inactivation of p53 by human T-cell leukemia virus type 1 Tax protein: mechanisms and clinical implications. Carcinogenesis 2005; 27:673-81. [PMID: 16308315 DOI: 10.1093/carcin/bgi274] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-I) has been implicated with the etiology of adult T-cell leukemia (ATL) and certain other clinical disorders. Although the leukemogenic mechanism of HTLV-1 is not fully understood yet, the viral Tax protein is widely regarded as a key factor in this mechanism. Tax can modulate the synthesis or function of many regulatory factors which control a wide range of normal and oncogenic cellular processes and therefore, it acts as a potent oncoprotein. In the last few years, special attention has been attracted to Tax interference with the transactivation function of p53, a tumor-suppressor protein that is involved in regulation of the cell-cycle and apoptosis and in maintaining the cellular genome integrity. p53 is mutated in approximately 60% of all human tumors. In contrast, mutant p53 is found in only small percentage of ATL patients. Nevertheless, p53 is inactive in the leukemic cells of most ATL patients and in most HTLV-1 transformed cells. By inactivating p53, Tax can immortalize the HTLV-1-infected cells and destabilize their genome. Consequently, such cells can progress toward the ultimate leukemic state by a stepwise accumulation of oncogenic mutations and other types of chromosomal aberrations. Furthermore, since p53 exists in most ATL patients in its wild-type form, its reactivation by therapeutic drugs might be an effective approach for ATL therapy. Several mechanisms have been proposed so far for Tax-induced p53 inactivation. Understanding the exact mechanism of this Tax effect is essential for designing effective means for this therapeutic approach. In this review article, we discuss the various mechanisms proposed for Tax interference with p53 functions and their clinical and therapeutic implications.
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Affiliation(s)
- Yulia Tabakin-Fix
- Department of Microbiology and Immunology, Cancer Research Center, Faculty of Health Sciences and Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
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50
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Cookson S, Ostroff N, Pang WL, Volfson D, Hasty J. Monitoring dynamics of single-cell gene expression over multiple cell cycles. Mol Syst Biol 2005; 1:2005.0024. [PMID: 16729059 PMCID: PMC1681470 DOI: 10.1038/msb4100032] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Accepted: 10/27/2005] [Indexed: 01/20/2023] Open
Abstract
Recent progress in reconstructing gene regulatory networks has established a framework for a quantitative description of the dynamics of many important cellular processes. Such a description will require novel experimental techniques that enable the generation of time-series data for the governing regulatory proteins in a large number of individual living cells. Here, we utilize microfabrication to construct a Tesla microchemostat that permits single-cell fluorescence imaging of gene expression over many cellular generations. The device is used to capture and constrain asymmetrically dividing or motile cells within a trapping region and to deliver nutrients and regulate the cellular population within this region. We illustrate the operation of the microchemostat with Saccharomyces cerevisiae and explore the evolution of single-cell gene expression and cycle time as a function of generation. Our findings highlight the importance of novel assays for quantifying the dynamics of gene expression and cellular growth, and establish a methodology for exploring the effects of gene expression on long-term processes such as cellular aging.
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Affiliation(s)
- Scott Cookson
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA
| | - Natalie Ostroff
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA
| | - Wyming Lee Pang
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA
| | - Dmitri Volfson
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA
- Institute for Nonlinear Science, University of California at San Diego, La Jolla, CA, USA
| | - Jeff Hasty
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA
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