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To B, Broeker C, Jhan JR, Garcia-Lerena J, Vusich J, Rempel R, Rennhack JP, Hollern D, Jackson L, Judah D, Swiatnicki M, Bylett E, Kubiak R, Honeysett J, Nevins J, Andrechek E. Insight into mammary gland development and tumor progression in an E2F5 conditional knockout mouse model. Oncogene 2024; 43:3402-3415. [PMID: 39341991 PMCID: PMC11554565 DOI: 10.1038/s41388-024-03172-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 08/23/2024] [Accepted: 09/16/2024] [Indexed: 10/01/2024]
Abstract
Development of breast cancer is linked to altered regulation of mammary gland developmental processes. A better understanding of normal mammary gland development can thus reveal possible mechanisms of how normal cells are re-programmed to become malignant. E2Fs 1-4 are part of the E2F transcription factor family with varied roles in mammary development, but little is known about the role of E2F5. A combination of scRNAseq and predictive signature tools demonstrated the presence of E2F5 in the mammary gland and showed changes in predicted activity during the various phases of mammary gland development. Testing the hypothesis that E2F5 regulates mammary function, we generated a mammary-specific E2F5 knockout mouse model, resulting in modest mammary gland development changes. However, after a prolonged latency the E2F5 conditional knockout mice developed highly metastatic mammary tumors. Whole genome sequencing revealed significant intertumor heterogeneity. RNAseq and protein analysis identified altered levels of Cyclin D1, with similarities to MMTV-Neu tumors, suggesting that E2F5 conditional knockout mammary glands and tumors may be dependent on Cyclin D1. Transplantation of the tumors revealed metastases to lymph nodes that were enriched through serial transplantation in immune competent recipients. Based on these findings, we propose that loss of E2F5 leads to altered regulation of Cyclin D1, which facilitates the development of metastatic mammary tumors after long latency. More importantly, this study demonstrates that conditional loss of E2F5 in the mammary gland leads to tumor formation, revealing its role as a transcription factor regulating a network of genes that normally result in a tumor suppressor function.
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Affiliation(s)
- Briana To
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Carson Broeker
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Jing-Ru Jhan
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | | | - John Vusich
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | | | | | | | - Lauren Jackson
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - David Judah
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Matt Swiatnicki
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Evan Bylett
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Rachel Kubiak
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Jordan Honeysett
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | | | - Eran Andrechek
- Department of Physiology, Michigan State University, East Lansing, MI, USA.
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2
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Fan Z, Kong M, Miao X, Guo Y, Ren H, Wang J, Wang S, Tang N, Shang L, Zhu Z, Liu H, Zhu W, Shi X. An E2F5-TFDP1-BRG1 Complex Mediates Transcriptional Activation of MYCN in Hepatocytes. Front Cell Dev Biol 2021; 9:742319. [PMID: 34746136 PMCID: PMC8569672 DOI: 10.3389/fcell.2021.742319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/04/2021] [Indexed: 12/22/2022] Open
Abstract
Liver regeneration is characterized by cell cycle reentrance of hepatocytes. N-Myc, encoded by MYCN, is a member of the Myc family of transcription factors. Elevation of MYCN expression has been noted in the course of liver regeneration whereas the underlying mechanism remains unclear. Here we describe that up-regulation of MYCN expression, as measured by quantitative PCR, Western blotting, and immunohistochemical staining, paralleled liver regeneration in animal and cell models. MYCN expression was up-regulated as a result of transcriptional activation. Ingenuity pathway analysis (IPA) revealed several up-stream transcriptional regulators for MYCN and RNA interference validated E2F5 and TFDP1 as essential for hepatocyte growth factor (HGF)-induced MYCN trans-activation. Further examination showed that deficiency of BRG1, a chromatin remodeling protein, attenuated MYCN induction during liver regeneration. BRG1 interacted with and was recruited by E2F5/TFDP1 to the MYCN promoter. Mechanistically, BRG1 might play a role regulating histone H3 acetylation and H3K4 trimethylation and facilitating/stabilizing the binding of RNA polymerase II surrounding the MYCN promoter. Over-expression of ectopic MYCN in BRG1-null hepatocytes overcame deficiency of proliferation. Importantly, a positive correlation between MYCN expression and BRG1/E2F5/TFDP1 expression was observed in human liver specimens. In conclusion, our data identify a novel epigenetic pathway where an E2F5-TFDP1-BRG1 complex regulates MYCN transcription to promote liver regeneration.
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Affiliation(s)
- Zhiwen Fan
- Department of Hepatobiliary Surgery, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
- Hepatobiliary Institute, Nanjing University, Nanjing, China
| | - Ming Kong
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Translational Medicine, and Center for Experimental Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Xiulian Miao
- College of Life Sciences and Institute of Biomedical Research, Liaocheng University, Liaocheng, China
| | - Yan Guo
- College of Life Sciences and Institute of Biomedical Research, Liaocheng University, Liaocheng, China
| | - Haozhen Ren
- Department of Hepatobiliary Surgery, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
- Hepatobiliary Institute, Nanjing University, Nanjing, China
| | - Jinglin Wang
- Department of Hepatobiliary Surgery, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
- Hepatobiliary Institute, Nanjing University, Nanjing, China
| | - Shuai Wang
- Department of Hepatobiliary Surgery, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
- Hepatobiliary Institute, Nanjing University, Nanjing, China
| | - Ning Tang
- Department of Hepatobiliary Surgery, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
- Hepatobiliary Institute, Nanjing University, Nanjing, China
| | - Longcheng Shang
- Department of Hepatobiliary Surgery, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Zhengyi Zhu
- Department of Hepatobiliary Surgery, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Hanyi Liu
- Department of Hepatobiliary Surgery, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Wei Zhu
- Department of Anesthesiology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Xiaolei Shi
- Department of Hepatobiliary Surgery, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
- Hepatobiliary Institute, Nanjing University, Nanjing, China
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3
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Pham TH, Park HM, Kim J, Hong JT, Yoon DY. Interleukin-32θ Triggers Cellular Senescence and Reduces Sensitivity to Doxorubicin-Mediated Cytotoxicity in MDA-MB-231 Cells. Int J Mol Sci 2021; 22:ijms22094974. [PMID: 34067074 PMCID: PMC8124300 DOI: 10.3390/ijms22094974] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/26/2022] Open
Abstract
The recently discovered interleukin (IL)- 32 isoform IL-32θ exerts anti-metastatic effects in the breast tumor microenvironment. However, the involvement of IL-32θ in breast cancer cell proliferation is not yet fully understood; therefore, the current study aimed to determine how IL-32θ affects cancer cell growth and evaluated the responses of IL-32θ-expressing cells to other cancer therapy. We compared the functions of IL-32θ in triple-negative breast cancer MDA-MB-231 cells that stably express IL-32θ, with MDA-MB-231 cells transfected with a mock vector. Slower growth was observed in cells expressing IL-32θ than in control cells, and changes were noted in nuclear morphology, mitotic division, and nucleolar size between the two groups of cells. Interleukin-32θ significantly reduced the colony-forming ability of MDA-MB-231 cells and induced permanent cell cycle arrest at the G1 phase. Long-term IL-32θ accumulation triggered permanent senescence and chromosomal instability in MDA-MB-231 cells. Genotoxic drug doxorubicin (DR) reduced the viability of MDA-MB-231 cells not expressing IL-32θ more than in cells expressing IL-32θ. Overall, these findings suggest that IL-32θ exerts antiproliferative effects in breast cancer cells and initiates senescence, which may cause DR resistance. Therefore, targeting IL-32θ in combination with DR treatment may not be suitable for treating metastatic breast cancer.
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Affiliation(s)
- Thu-Huyen Pham
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea; (T.-H.P.); (H.-M.P.); (J.K.)
| | - Hyo-Min Park
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea; (T.-H.P.); (H.-M.P.); (J.K.)
| | - Jinju Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea; (T.-H.P.); (H.-M.P.); (J.K.)
| | - Jin-Tae Hong
- College of Pharmacy and Medical Research Center, Chungbuk National University, Chungbuk 28160, Korea;
| | - Do-Young Yoon
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea; (T.-H.P.); (H.-M.P.); (J.K.)
- Correspondence: ; Tel.: +82-2-450-4119; Fax: +82-2-444-4218
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4
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Karmakar D, Maity J, Mondal P, Shyam Chowdhury P, Sikdar N, Karmakar P, Das C, Sengupta S. E2F5 promotes prostate cancer cell migration and invasion through regulation of TFPI2, MMP-2 and MMP-9. Carcinogenesis 2020; 41:1767-1780. [PMID: 32386317 DOI: 10.1093/carcin/bgaa043] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/13/2022] Open
Abstract
Previously, our laboratory demonstrated that a deregulated E2F5/p38/SMAD3 axis was associated with uncontrolled cellular proliferation in prostate cancer (PCa). Here, we investigate the role of E2F5 in PCa in further details. RNAi-mediated E2F5 knockdown and pathway-focused gene expression profiling in PC3 cells identified TFPI2 as a downstream target of E2F5. Manipulation of E2F5 expression was also found to alter MMP-2 and MMP-9 levels as detected by Proteome Profiler array, western blot and reverse transcription coupled quantitative polymerase chain reaction Site-directed mutagenesis, dual-luciferase assays and chromatin immunoprecipitation with anti-E2F5-IgG coupled with qPCR confirmed recruitment of E2F5 on TFPI2, MMP-2 and MMP-9 promoters. RNAi-mediated knockdown of E2F5 expression in PC3 caused a significant alteration of cell migration while that of TFFI2 resulted in a modest change. Abrogation of E2F5 and TFPI2 expression was associated with significant changes in the gelatinolytic activity of active forms of MMP-2 and MMP-9. Moreover, E2F5, MMP-2 and MMP-9 levels were elevated in biopsies of PCa patients relative to that of benign hyperplasia, while TFPI2 expression was reduced. MMP-9 was coimmunoprecipitated with anti-TFPI2-IgG in PCa tissue samples suggesting a direct interaction between the proteins. Finally, artemisinin treatment in PC3 cells repressed E2F5 along with MMP-2/MMP-9 while triggering TFPI2 expression which alleviated PC3 aggressiveness possibly through inhibition of MMP activities. Together, our study reinstates an oncogenic role of E2F5 which operates as a dual-function transcription factor for its targets TFPI2, MMP-2 and MMP-9 and promotes cellular invasiveness. This study also indicates a therapeutic potential of artemisinin, a natural compound which acts by correcting dysfunctional E2F5/TFPI2/MMP axis in PCa.
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Affiliation(s)
- Deepmala Karmakar
- Department of Biochemistry, University of Calcutta, Kolkata, West Bengal, India
| | - Jyotirindra Maity
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, West Bengal, India
| | - Payel Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India
- Department of Life Sciences, Homi Bhaba National Institute (HBNI), BARC Training School Complex, Anushaktinagar, Mumbai, Maharashtra, India
| | - Puskar Shyam Chowdhury
- Department of Urology, K. P. C. Medical College and Hospital Campus, Jadavpur, Kolkata, West Bengal, India
| | - Nilabja Sikdar
- Human Genetics Unit, Biological Sciences Division, Indian Statistical Institute, Kolkata, West Bengal, India
| | - Parimal Karmakar
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, West Bengal, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India
- Department of Life Sciences, Homi Bhaba National Institute (HBNI), BARC Training School Complex, Anushaktinagar, Mumbai, Maharashtra, India
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Kumar A, Rathi E, Kini SG. Identification of E6 Inhibitors Employing Energetically Optimized Structure‐Based Pharmacophore Modelling, Ligand Docking and Molecular Dynamics Simulations Studies. ChemistrySelect 2019. [DOI: 10.1002/slct.201902105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Avinash Kumar
- Department of Pharmaceutical ChemistryManipal College of PharmaceuticalSsciences, MAHE. Madhav Nagar, Manipal Karnataka India- 576104
| | - Ekta Rathi
- Department of Pharmaceutical ChemistryManipal College of PharmaceuticalSsciences, MAHE. Madhav Nagar, Manipal Karnataka India- 576104
| | - Suvarna G. Kini
- Department of Pharmaceutical ChemistryManipal College of PharmaceuticalSsciences, MAHE. Madhav Nagar, Manipal Karnataka India- 576104
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6
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Drug repurposing approach for the identification and designing of potential E6 inhibitors against cervical cancer: an in silico investigation. Struct Chem 2019. [DOI: 10.1007/s11224-019-01378-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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7
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Trapp-Fragnet L, Bencherit D, Chabanne-Vautherot D, Le Vern Y, Remy S, Boutet-Robinet E, Mirey G, Vautherot JF, Denesvre C. Cell cycle modulation by Marek's disease virus: the tegument protein VP22 triggers S-phase arrest and DNA damage in proliferating cells. PLoS One 2014; 9:e100004. [PMID: 24945933 PMCID: PMC4063868 DOI: 10.1371/journal.pone.0100004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 05/21/2014] [Indexed: 01/22/2023] Open
Abstract
Marek's disease is one of the most common viral diseases of poultry affecting chicken flocks worldwide. The disease is caused by an alphaherpesvirus, the Marek's disease virus (MDV), and is characterized by the rapid onset of multifocal aggressive T-cell lymphoma in the chicken host. Although several viral oncogenes have been identified, the detailed mechanisms underlying MDV-induced lymphomagenesis are still poorly understood. Many viruses modulate cell cycle progression to enhance their replication and persistence in the host cell, in the case of some oncogenic viruses ultimately leading to cellular transformation and oncogenesis. In the present study, we found that MDV, like other viruses, is able to subvert the cell cycle progression by triggering the proliferation of low proliferating chicken cells and a subsequent delay of the cell cycle progression into S-phase. We further identified the tegument protein VP22 (pUL49) as a major MDV-encoded cell cycle regulator, as its vector-driven overexpression in cells lead to a dramatic cell cycle arrest in S-phase. This striking functional feature of VP22 appears to depend on its ability to associate with histones in the nucleus. Finally, we established that VP22 expression triggers the induction of massive and severe DNA damages in cells, which might cause the observed intra S-phase arrest. Taken together, our results provide the first evidence for a hitherto unknown function of the VP22 tegument protein in herpesviral reprogramming of the cell cycle of the host cell and its potential implication in the generation of DNA damages.
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Affiliation(s)
- Laëtitia Trapp-Fragnet
- INRA, UMR1282 Infectiologie et Santé Publique, Equipe Biologie des Virus Aviaires, Nouzilly, France
- * E-mail:
| | - Djihad Bencherit
- INRA, UMR1282 Infectiologie et Santé Publique, Equipe Biologie des Virus Aviaires, Nouzilly, France
| | | | - Yves Le Vern
- INRA, UMR1282 Infectiologie et Santé Publique, Laboratoire de Cytométrie, Nouzilly, France
| | - Sylvie Remy
- INRA, UMR1282 Infectiologie et Santé Publique, Equipe Biologie des Virus Aviaires, Nouzilly, France
| | - Elisa Boutet-Robinet
- INRA, UMR 1331, Toxalim, Research Centre in Food Toxicology, Toulouse, France
- University of Toulouse, UPS, UMR1331, Toxalim, Toulouse, France
| | - Gladys Mirey
- INRA, UMR 1331, Toxalim, Research Centre in Food Toxicology, Toulouse, France
- University of Toulouse, UPS, UMR1331, Toxalim, Toulouse, France
| | - Jean-François Vautherot
- INRA, UMR1282 Infectiologie et Santé Publique, Equipe Biologie des Virus Aviaires, Nouzilly, France
| | - Caroline Denesvre
- INRA, UMR1282 Infectiologie et Santé Publique, Equipe Biologie des Virus Aviaires, Nouzilly, France
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8
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HAM SUNYOUNG, KIM KIHONG, KWON TAEHO, BAK YESOL, LEE DONGHUN, SONG YONGSEOK, PARK SUHO, PARK YUNSUN, KIM MANSUB, KANG JEONGWOO, HONG JINTAE, YOON DOYOUNG. Luteolin induces intrinsic apoptosis via inhibition of E6/E7 oncogenes and activation of extrinsic and intrinsic signaling pathways in HPV-18-associated cells. Oncol Rep 2014; 31:2683-91. [DOI: 10.3892/or.2014.3157] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 03/25/2014] [Indexed: 11/05/2022] Open
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9
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A functional interaction of E7 with B-Myb-MuvB complex promotes acute cooperative transcriptional activation of both S- and M-phase genes. (129 c). Oncogene 2013; 33:4039-49. [PMID: 24141769 DOI: 10.1038/onc.2013.426] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/13/2013] [Accepted: 08/15/2013] [Indexed: 12/11/2022]
Abstract
High-risk human papillomaviruses are causative agents of cervical cancer. Viral protein E7 is required to establish and maintain the pro-oncogenic phenotype in infected cells, but the molecular mechanisms by which E7 promotes carcinogenesis are only partially understood. Our transcriptome analyses in primary human fibroblasts transduced with the viral protein revealed that E7 activates a group of mitotic genes via the activator B-Myb-MuvB complex. We show that E7 interacts with the B-Myb, FoxM1 and LIN9 components of this activator complex, leading to cooperative transcriptional activation of mitotic genes in primary cells and E7 recruitment to the corresponding promoters. E7 interaction with LIN9 and FoxM1 depended on the LXCXE motif, which is also required for pocket protein interaction and degradation. Using E7 mutants for the degradation of pocket proteins but intact for the LXCXE motif, we demonstrate that E7 functional interaction with the B-Myb-MuvB complex and pocket protein degradation are two discrete functions of the viral protein that cooperate to promote acute transcriptional activation of mitotic genes. Transcriptional level of E7 in patient's cervical lesions at different stages of progression was shown to correlate with those of B-Myb and FoxM1 as well as other mitotic gene transcripts, thereby linking E7 with cellular proliferation and progression in cervical cancer in vivo. E7 thus can directly activate the transcriptional levels of cell cycle genes independently of pocket protein stability.
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Di Fiore R, D'Anneo A, Tesoriere G, Vento R. RB1 in cancer: different mechanisms of RB1 inactivation and alterations of pRb pathway in tumorigenesis. J Cell Physiol 2013; 228:1676-87. [PMID: 23359405 DOI: 10.1002/jcp.24329] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 01/15/2013] [Indexed: 12/14/2022]
Abstract
Loss of RB1 gene is considered either a causal or an accelerating event in retinoblastoma. A variety of mechanisms inactivates RB1 gene, including intragenic mutations, loss of expression by methylation and chromosomal deletions, with effects which are species-and cell type-specific. RB1 deletion can even lead to aneuploidy thus greatly increasing cancer risk. The RB1gene is part of a larger gene family that includes RBL1 and RBL2, each of the three encoding structurally related proteins indicated as pRb, p107, and p130, respectively. The great interest in these genes and proteins springs from their ability to slow down neoplastic growth. pRb can associate with various proteins by which it can regulate a great number of cellular activities. In particular, its association with the E2F transcription factor family allows the control of the main pRb functions, while the loss of these interactions greatly enhances cancer development. As RB1 gene, also pRb can be functionally inactivated through disparate mechanisms which are often tissue specific and dependent on the scenario of the involved tumor suppressors and oncogenes. The critical role of the context is complicated by the different functions played by the RB proteins and the E2F family members. In this review, we want to emphasize the importance of the mechanisms of RB1/pRb inactivation in inducing cancer cell development. The review is divided in three chapters describing in succession the mechanisms of RB1 inactivation in cancer cells, the alterations of pRb pathway in tumorigenesis and the RB protein and E2F family in cancer.
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Affiliation(s)
- Riccardo Di Fiore
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Polyclinic, University of Palermo, Palermo, Italy
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11
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Bhinder B, Antczak C, Ramirez CN, Shum D, Liu-Sullivan N, Radu C, Frattini MG, Djaballah H. An arrayed genome-scale lentiviral-enabled short hairpin RNA screen identifies lethal and rescuer gene candidates. Assay Drug Dev Technol 2012. [PMID: 23198867 DOI: 10.1089/adt.2012.475] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RNA interference technology is becoming an integral tool for target discovery and validation.; With perhaps the exception of only few studies published using arrayed short hairpin RNA (shRNA) libraries, most of the reports have been either against pooled siRNA or shRNA, or arrayed siRNA libraries. For this purpose, we have developed a workflow and performed an arrayed genome-scale shRNA lethality screen against the TRC1 library in HeLa cells. The resulting targets would be a valuable resource of candidates toward a better understanding of cellular homeostasis. Using a high-stringency hit nomination method encompassing criteria of at least three active hairpins per gene and filtered for potential off-target effects (OTEs), referred to as the Bhinder-Djaballah analysis method, we identified 1,252 lethal and 6 rescuer gene candidates, knockdown of which resulted in severe cell death or enhanced growth, respectively. Cross referencing individual hairpins with the TRC1 validated clone database, 239 of the 1,252 candidates were deemed independently validated with at least three validated clones. Through our systematic OTE analysis, we have identified 31 microRNAs (miRNAs) in lethal and 2 in rescuer genes; all having a seed heptamer mimic in the corresponding shRNA hairpins and likely cause of the OTE observed in our screen, perhaps unraveling a previously unknown plausible essentiality of these miRNAs in cellular viability. Taken together, we report on a methodology for performing large-scale arrayed shRNA screens, a comprehensive analysis method to nominate high-confidence hits, and a performance assessment of the TRC1 library highlighting the intracellular inefficiencies of shRNA processing in general.
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Affiliation(s)
- Bhavneet Bhinder
- High-Throughput Screening Core Facility, Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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12
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Lung MSY, Zhang N, Murray V. Site-directed mutagenesis of human papillomavirus 18 promoter elements and tissue-specific expression in cervical carcinoma cells. Virus Genes 2012; 44:395-402. [DOI: 10.1007/s11262-012-0723-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 01/31/2012] [Indexed: 10/28/2022]
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13
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The use of a human papillomavirus 18 promoter for tissue-specific expression in cervical carcinoma cells. Cell Mol Biol Lett 2011; 16:477-92. [PMID: 21786035 PMCID: PMC6275744 DOI: 10.2478/s11658-011-0018-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 06/29/2011] [Indexed: 11/25/2022] Open
Abstract
The use of tissue-specific promoter elements in the treatment of cervical cancer has been explored in this paper. The P105 promoter of human papillomavirus 18 (HPV18) was utilised to direct tissue-specific expression in a number of cell types. Expression was examined in three cervical carcinoma cell lines: HeLa (HPV18 positive), SiHa (HPV16 positive), and C33A cells (HPV negative); the epithelial cell line, H1299; and the foetal fibroblast cell line, MRC5, utilising a luciferase expression vector. Expression was highest in the cervical cell lines by a factor of at least 80. The effect of a number of mutations in the P105 promoter on expression levels was examined. Three deletion constructs of the long control region (LCR) were investigated: an 800 bp fragment (LCR800), a 400 bp fragment (LCR400), and a 200 bp fragment (LCR200), as well as the full length product LCR of HPV18 (LCR1000). The LCR800 construct of the HPV18 P105 promoter had the highest level of expression in the cervical cell lines and was also highest in the HPV18-positive HeLa cell line. Site-directed mutagenesis was then employed on the LCR800 construct to create four further constructs that each had inactivating mutations in one of the four E2 binding sites (E2BSs). Overall, this study indicated that the LCR800 construct of the HPV18 P105 promoter could be utilised as a tissuerestricted promoter in cervical cancer cells.
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