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Yang T, Liu YL, Guo HL, Peng XF, Zhang B, Wang D, Yao HF, Zhang JF, Wang XY, Chen PC, Xu DP. Unveiling an anoikis-related risk model and the role of RAD9A in colon cancer. Int Immunopharmacol 2024; 140:112874. [PMID: 39116498 DOI: 10.1016/j.intimp.2024.112874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 07/23/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024]
Abstract
OBJECTIVE Colorectal cancer (CRC), specifically colon adenocarcinoma, is the third most prevalent and the second most lethal form of cancer. Anoikis is found to be specialized form of programmed cell death (PCD), which plays a pivotal role in tumor progression. This study aimed to investigate the role of the anoikis related genes (ARGs) in colon cancer. METHODS Consensus unsupervised clustering, differential expression analysis, tumor mutational burden analysis, and analysis of immune cell infiltration were utilized in the study. For the analysis of RNA sequences and clinical data of COAD patients, data from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) were obtained. A prognostic scoring system for overall survival (OS) prediction was developed using Cox regression and LASSO regression analysis. Furthermore, loss-of-function assay was utilized to explore the role of RAD9A played in the progression of colon cancer. RESULTS The prognostic value of a risk score composed of NTRK2, EPHA2, RAD9A, CDC25C, and SNAI1 genes was significant. Furthermore, these findings suggested potential mechanisms that may influence prognosis, supporting the development of individualized treatment plans and management of patient outcomes. Further experiments confirmed that RAD9A could promote proliferation and metastasis of colon cancer cells. These effects may be achieved by affecting the phosphorylation of AKT. CONCLUSION Differences in survival time and the tumor immune microenvironment (TIME) were observed between two gene clusters associated with ARGs. In addition, a prognostic risk model was established and confirmed as an independent risk factor. Furthermore, our data indicated that RAD9A promoted tumorigenicityby activating AKT in colon cancer.
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Affiliation(s)
- Ting Yang
- Shanghai Key Laboratory for Cancer Systems Regulation and Clinical Translation, Department of General Surgery, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai 201800, PR China
| | - Yan-Li Liu
- Department of Gastroenterology, Jiading District Central Hospital Affiliated Shanghai University of Medicine &Health Sciences, Shanghai 201800, PR China
| | - Hai-Long Guo
- Shanghai Key Laboratory for Cancer Systems Regulation and Clinical Translation, Department of General Surgery, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai 201800, PR China
| | - Xiao-Fei Peng
- Shanghai Key Laboratory for Cancer Systems Regulation and Clinical Translation, Department of General Surgery, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai 201800, PR China
| | - Bo Zhang
- Shanghai Key Laboratory for Cancer Systems Regulation and Clinical Translation, Department of General Surgery, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai 201800, PR China
| | - Dong Wang
- Shanghai Key Laboratory for Cancer Systems Regulation and Clinical Translation, Department of General Surgery, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai 201800, PR China
| | - Hong-Fei Yao
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PR China
| | - Jun-Feng Zhang
- Shanghai Key Laboratory for Cancer Systems Regulation and Clinical Translation, Department of General Surgery, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai 201800, PR China
| | - Xiao-Yun Wang
- Shanghai Key Laboratory for Cancer Systems Regulation and Clinical Translation, Department of General Surgery, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai 201800, PR China.
| | - Peng-Cheng Chen
- Shanghai Key Laboratory for Cancer Systems Regulation and Clinical Translation, Department of General Surgery, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai 201800, PR China.
| | - Da-Peng Xu
- Shanghai Key Laboratory for Cancer Systems Regulation and Clinical Translation, Department of General Surgery, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai 201800, PR China.
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2
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Chen J, Huang Y, Tang Z, Li M, Ling X, Liao J, Zhou X, Fang S, Zhao H, Zhong W, Yuan X. Genome-Scale CRISPR-Cas9 Transcriptional Activation Screening in Metformin Resistance Related Gene of Prostate Cancer. Front Cell Dev Biol 2021; 8:616332. [PMID: 33575255 PMCID: PMC7870801 DOI: 10.3389/fcell.2020.616332] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/09/2020] [Indexed: 01/01/2023] Open
Abstract
Metformin is a classic type II diabetes drug which possesses anti-tumor properties for various cancers. However, different cancers do not respond to metformin with the same effectiveness or acquire resistance. Thus, searching for vulnerabilities of metformin-resistant prostate cancer is a promising strategy to improve the therapeutic efficiency of the drug. A genome-scale CRISPR-Cas9 activation library search targeting 23,430 genes was conducted to identify the genes that confer resistance to metformin in prostate cancer cells. Candidate genes were selected by total reads of sgRNA and sgRNA diversity, and then a CCK8 assay was used to verify their resistance to metformin. Interestingly, we discovered that the activation of ECE1, ABCA12, BPY2, EEF1A1, RAD9A, and NIPSNAP1 contributed to in vitro resistance to metformin in DU145 and PC3 cell lines. Notably, a high level of RAD9A, with poor prognosis in PCa, was the most significant gene in the CCK8 assay. Furthermore, we discerned the tumor immune microenvironment with RAD9A expression by CIBERSORT. These results suggested that a high level of RAD9A may upregulate regulatory T cells to counterbalance metformin in the tumor immune microenvironment.
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Affiliation(s)
- Jiahong Chen
- Department of Urology, Huizhou Municipal Central Hospital, Huizhou, China
| | - Yaqiang Huang
- Department of Urology, Zhongshan City People's Hospital, Zhongshan, China
| | - Zhenfeng Tang
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, Guangzhou Urology Research Institute, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Maozhang Li
- Department of Urology, Huizhou Municipal Central Hospital, Huizhou, China
| | - Xiaohui Ling
- Reproductive Medicine Centre, Huizhou Central People's Hospital, Guangdong Medical University, Huizhou, China
| | - Jinxian Liao
- Department of Urology, Huizhou Municipal Central Hospital, Huizhou, China
| | - Xiaobo Zhou
- Department of Urology, Huizhou Municipal Central Hospital, Huizhou, China
| | - Shumin Fang
- Department of Urology, Huizhou Municipal Central Hospital, Huizhou, China
| | - Haibo Zhao
- Guangdong Provincial Institute of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Weide Zhong
- Department of Urology, Huizhou Municipal Central Hospital, Huizhou, China.,Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Department of Urology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Xia Yuan
- Department of Urology, Huizhou Municipal Central Hospital, Huizhou, China
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3
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Cell Cycle-Dependent Control and Roles of DNA Topoisomerase II. Genes (Basel) 2019; 10:genes10110859. [PMID: 31671531 PMCID: PMC6896119 DOI: 10.3390/genes10110859] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 12/13/2022] Open
Abstract
Type II topoisomerases are ubiquitous enzymes in all branches of life that can alter DNA superhelicity and unlink double-stranded DNA segments during processes such as replication and transcription. In cells, type II topoisomerases are particularly useful for their ability to disentangle newly-replicated sister chromosomes. Growing lines of evidence indicate that eukaryotic topoisomerase II (topo II) activity is monitored and regulated throughout the cell cycle. Here, we discuss the various roles of topo II throughout the cell cycle, as well as mechanisms that have been found to govern and/or respond to topo II function and dysfunction. Knowledge of how topo II activity is controlled during cell cycle progression is important for understanding how its misregulation can contribute to genetic instability and how modulatory pathways may be exploited to advance chemotherapeutic development.
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4
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Permissiveness to form pluripotent stem cells may be an evolutionarily derived characteristic in Mus musculus. Sci Rep 2018; 8:14706. [PMID: 30279419 PMCID: PMC6168588 DOI: 10.1038/s41598-018-32116-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 09/03/2018] [Indexed: 01/06/2023] Open
Abstract
Mus musculus is the only known species from which embryonic stem cells (ESC) can be isolated under conditions requiring only leukemia inhibitory factor (LIF). Other species are non-permissive in LIF media, and form developmentally primed epiblast stem cells (EpiSC) similar to cells derived from post-implantation, egg cylinders. To evaluate whether non-permissiveness extends to induced pluripotent stem cells (iPSC), we derived iPSC from the eight founder strains of the mouse Collaborative Cross. Two strains, NOD/ShiLtJ and the WSB/EiJ, were non-permissive, consistent with the previous classification of NOD/ShiLtJ as non-permissive to ESC derivation. We determined non-permissiveness is recessive, and that non-permissive genomes do not compliment. We overcame iPSC non-permissiveness by using GSK3B and MEK inhibitors with serum, a technique we termed 2iS reprogramming. Although used for ESC derivation, GSK3B and MEK inhibitors have not been used during iPSC reprogramming because they inhibit survival of progenitor differentiated cells. iPSC derived in 2iS are more transcriptionally similar to ESC than EpiSC, indicating that 2iS reprogramming acts to overcome genetic background constraints. Finally, of species tested for ESC or iPSC derivation, only some M. musculus strains are permissive under LIF culture conditions suggesting that this is an evolutionarily derived characteristic in the M. musculus lineage.
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5
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Brown A, Geiger H. Chromosome integrity checkpoints in stem and progenitor cells: transitions upon differentiation, pathogenesis, and aging. Cell Mol Life Sci 2018; 75:3771-3779. [PMID: 30066086 PMCID: PMC6154040 DOI: 10.1007/s00018-018-2891-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 07/22/2018] [Accepted: 07/25/2018] [Indexed: 01/30/2023]
Abstract
Loss of chromosome integrity is a major contributor to cancer. Checkpoints within the cell division cycle that facilitate the accuracy and outcome of chromosome segregation are thus critical pathways for preserving chromosome integrity and preventing chromosomal instability. The spindle assembly checkpoint, the decatenation checkpoint and the post-mitotic tetraploidy checkpoint ensure the appropriate establishment of the spindle apparatus, block mitotic entry upon entanglement of chromosomes or prevent further progression of post-mitotic cells that display massive spindle defects. Most of our knowledge on these mechanisms originates from studies conducted in yeast, cancer cell lines and differentiated cells. Considering that in many instances cancer derives from transformed stem and progenitor cells, our knowledge on these checkpoints in these cells just started to emerge. With this review, we provide a general overview of the current knowledge of these checkpoints in embryonic as well as in adult stem and progenitor cells with a focus on the hematopoietic system and outline common mis-regulations of their function associated with cancer and leukemia. Most cancers are aging-associated diseases. We will thus also discuss changes in the function and outcome of these checkpoints upon aging of stem and progenitor cells.
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Affiliation(s)
- Andreas Brown
- Institute of Molecular Medicine, Ulm University, Life Science Building N27, James Franck-Ring/Meyerhofstrasse, 89081, Ulm, Germany
| | - Hartmut Geiger
- Institute of Molecular Medicine, Ulm University, Life Science Building N27, James Franck-Ring/Meyerhofstrasse, 89081, Ulm, Germany.
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229, USA.
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6
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Michlits G, Hubmann M, Wu SH, Vainorius G, Budusan E, Zhuk S, Burkard TR, Novatchkova M, Aichinger M, Lu Y, Reece-Hoyes J, Nitsch R, Schramek D, Hoepfner D, Elling U. CRISPR-UMI: single-cell lineage tracing of pooled CRISPR-Cas9 screens. Nat Methods 2017; 14:1191-1197. [PMID: 29039415 DOI: 10.1038/nmeth.4466] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/11/2017] [Indexed: 12/12/2022]
Abstract
Pooled CRISPR screens are a powerful tool for assessments of gene function. However, conventional analysis is based exclusively on the relative abundance of integrated single guide RNAs (sgRNAs) between populations, which does not discern distinct phenotypes and editing outcomes generated by identical sgRNAs. Here we present CRISPR-UMI, a single-cell lineage-tracing methodology for pooled screening to account for cell heterogeneity. We generated complex sgRNA libraries with unique molecular identifiers (UMIs) that allowed for screening of clonally expanded, individually tagged cells. A proof-of-principle CRISPR-UMI negative-selection screen provided increased sensitivity and robustness compared with conventional analysis by accounting for underlying cellular and editing-outcome heterogeneity and detection of outlier clones. Furthermore, a CRISPR-UMI positive-selection screen uncovered new roadblocks in reprogramming mouse embryonic fibroblasts as pluripotent stem cells, distinguishing reprogramming frequency and speed (i.e., effect size and probability). CRISPR-UMI boosts the predictive power, sensitivity, and information content of pooled CRISPR screens.
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Affiliation(s)
- Georg Michlits
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Maria Hubmann
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Szu-Hsien Wu
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Gintautas Vainorius
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Elena Budusan
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Sergei Zhuk
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC),Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC),Vienna, Austria
| | - Martin Aichinger
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC),Vienna, Austria
| | - Yiqing Lu
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - John Reece-Hoyes
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Roberto Nitsch
- Discovery Sciences RAD, AstraZeneca R&D, Gothenburg, Sweden
| | - Daniel Schramek
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
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7
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Tong HL, Jiang RY, Zhang WW, Yan YQ. MiR-2425-5p targets RAD9A and MYOG to regulate the proliferation and differentiation of bovine skeletal muscle-derived satellite cells. Sci Rep 2017; 7:418. [PMID: 28341832 PMCID: PMC5428422 DOI: 10.1038/s41598-017-00470-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 02/28/2017] [Indexed: 12/18/2022] Open
Abstract
Our group previously identified miR-2425-5p, a unique bovine miRNA; however, its biological function and regulation in muscle-derived satellite cells (MDSCs) remain unclear. Herein, stem-loop RT-PCR results showed that miR-2425-5p increased during MDSCs proliferation, but decreased during differentiation. Cell proliferation was examined using EdU assays, cyclin B1 (CCNB1) and proliferating cell nuclear antigen (PCNA) western blot (WB) and flow cytometry analysis. These results showed that miR-2425-5p mimics (miR-2425-M) enhanced MDSCs proliferation, whereas, miR-2425-5p inhibitor (miR-2425-I) had opposite effect. Conversely, cell differentiation studies by desmin (DES) immunofluorescence, myotubes formation, and myosin heavy chain 3 (MYH3) WB analyses revealed that miR-2425-M and miR-2425-I blocked and promoted MDSCs differentiation, respectively. Moreover, luciferase reporter, RT-PCR, and WB assays showed that miR-2425-5p directly targeted the 3′-UTR of RAD9 homolog A (RAD9A) and myogenin (MYOG) to regulate their expression. Rescue experiment showed RAD9A inhibited the proliferation of MDSCs through miR-2425-5p. In addition, we found that miR-2425-5p expression was regulated by its host gene NCK associated protein 5-like (NCKAP5L) rather than being transcribed independently as a separate small RNA. Collectively, these data indicate that miR-2425-5p is a novel regulator of bovine MDSCs proliferation and differentiation and provides further insight into the biological functions of miRNA in this species.
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Affiliation(s)
- Hui Li Tong
- The Laboratory of Cell and Developmental Biology, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Run Ying Jiang
- The Laboratory of Cell and Developmental Biology, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Wei Wei Zhang
- College of Life Sciences and Agriculture & Forestry, Qiqihar University, Qiqihar, Heilongjiang, 161006, China
| | - Yun Qin Yan
- The Laboratory of Cell and Developmental Biology, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China.
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8
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Williamson CT, Miller R, Pemberton HN, Jones SE, Campbell J, Konde A, Badham N, Rafiq R, Brough R, Gulati A, Ryan CJ, Francis J, Vermulen PB, Reynolds AR, Reaper PM, Pollard JR, Ashworth A, Lord CJ. ATR inhibitors as a synthetic lethal therapy for tumours deficient in ARID1A. Nat Commun 2016; 7:13837. [PMID: 27958275 PMCID: PMC5159945 DOI: 10.1038/ncomms13837] [Citation(s) in RCA: 251] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/03/2016] [Indexed: 01/01/2023] Open
Abstract
Identifying genetic biomarkers of synthetic lethal drug sensitivity effects provides one approach to the development of targeted cancer therapies. Mutations in ARID1A represent one of the most common molecular alterations in human cancer, but therapeutic approaches that target these defects are not yet clinically available. We demonstrate that defects in ARID1A sensitize tumour cells to clinical inhibitors of the DNA damage checkpoint kinase, ATR, both in vitro and in vivo. Mechanistically, ARID1A deficiency results in topoisomerase 2A and cell cycle defects, which cause an increased reliance on ATR checkpoint activity. In ARID1A mutant tumour cells, inhibition of ATR triggers premature mitotic entry, genomic instability and apoptosis. The data presented here provide the pre-clinical and mechanistic rationale for assessing ARID1A defects as a biomarker of single-agent ATR inhibitor response and represents a novel synthetic lethal approach to targeting tumour cells.
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Affiliation(s)
- Chris T. Williamson
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London
SW3 6JB, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London
SW3 6JB, UK
| | - Rowan Miller
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London
SW3 6JB, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London
SW3 6JB, UK
| | - Helen N. Pemberton
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London
SW3 6JB, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London
SW3 6JB, UK
| | - Samuel E. Jones
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London
SW3 6JB, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London
SW3 6JB, UK
| | - James Campbell
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London
SW3 6JB, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London
SW3 6JB, UK
| | - Asha Konde
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London
SW3 6JB, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London
SW3 6JB, UK
| | - Nicholas Badham
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London
SW3 6JB, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London
SW3 6JB, UK
| | - Rumana Rafiq
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London
SW3 6JB, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London
SW3 6JB, UK
| | - Rachel Brough
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London
SW3 6JB, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London
SW3 6JB, UK
| | - Aditi Gulati
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London
SW3 6JB, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London
SW3 6JB, UK
| | - Colm J. Ryan
- Systems Biology Ireland, University College Dublin, Dublin
4, Ireland
| | - Jeff Francis
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London
SW3 6JB, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London
SW3 6JB, UK
| | - Peter B. Vermulen
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London
SW3 6JB, UK
- GZA Hospitals Sint-Augustinus, Wilrijk, Belgium and Center for Oncological Research, University of Antwerp, Oosterveldlaan 24, Wilrijk Antwerp
2610, Belgium
| | - Andrew R. Reynolds
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London
SW3 6JB, UK
| | - Philip M. Reaper
- Vertex Pharmaceuticals (Europe) Limited, Milton Park, Abingdon, Oxfordshire
OX14 4RY, UK
| | - John R. Pollard
- Vertex Pharmaceuticals (Europe) Limited, Milton Park, Abingdon, Oxfordshire
OX14 4RY, UK
| | - Alan Ashworth
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London
SW3 6JB, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London
SW3 6JB, UK
| | - Christopher J. Lord
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London
SW3 6JB, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London
SW3 6JB, UK
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9
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van der Stok EP, Smid M, Sieuwerts AM, Vermeulen PB, Sleijfer S, Ayez N, Grünhagen DJ, Martens JWM, Verhoef C. mRNA expression profiles of colorectal liver metastases as a novel biomarker for early recurrence after partial hepatectomy. Mol Oncol 2016; 10:1542-1550. [PMID: 27692894 DOI: 10.1016/j.molonc.2016.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/31/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Identification of specific risk groups for recurrence after surgery for isolated colorectal liver metastases (CRLM) remains challenging due to the heterogeneity of the disease. Classical clinicopathologic parameters have limited prognostic value. The aim of this study was to identify a gene expression signature measured in CRLM discriminating early from late recurrence after partial hepatectomy. METHODS CRLM from two patient groups were collected: I) with recurrent disease ≤12 months after surgery (N = 33), and II) without recurrences and disease free for ≥36 months (N = 30). The patients were clinically homogeneous; all had a low clinical risk score (0-2) and did not receive (neo-) adjuvant chemotherapy. Total RNA was hybridised to Illumina arrays, and processed for analysis. A leave-one-out cross validation (LOOCV) analysis was performed to identify a prognostic gene expression signature. RESULTS LOOCV yielded an 11-gene profile with prognostic value in relation to recurrent disease ≤12 months after partial hepatectomy. This signature had a sensitivity of 81.8%, with a specificity of 66.7% for predicting recurrences (≤12 months) versus no recurrences for at least 36 months after surgery (X2 P < 0.0001). CONCLUSION The current study yielded an 11-gene signature at mRNA level in CRLM discriminating early from late or no relapse after partial hepatectomy.
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Affiliation(s)
- E P van der Stok
- Department of Surgical Oncology, Erasmus MC Cancer Institute, Groene Hilledijk 301, 3075 EA Rotterdam, The Netherlands.
| | - M Smid
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - A M Sieuwerts
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - P B Vermeulen
- Translational Cancer Research Group, Sint-Augustinus (GZA Hospitals) & CORE (Antwerp University), Oosterveldlaan 24, 2610 Wilrijk-Antwerp, Belgium
| | - S Sleijfer
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - N Ayez
- Department of Surgical Oncology, Erasmus MC Cancer Institute, Groene Hilledijk 301, 3075 EA Rotterdam, The Netherlands
| | - D J Grünhagen
- Department of Surgical Oncology, Erasmus MC Cancer Institute, Groene Hilledijk 301, 3075 EA Rotterdam, The Netherlands
| | - J W M Martens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - C Verhoef
- Department of Surgical Oncology, Erasmus MC Cancer Institute, Groene Hilledijk 301, 3075 EA Rotterdam, The Netherlands
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10
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Chk1 Activation Protects Rad9A from Degradation as Part of a Positive Feedback Loop during Checkpoint Signalling. PLoS One 2015; 10:e0144434. [PMID: 26658951 PMCID: PMC4676731 DOI: 10.1371/journal.pone.0144434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/18/2015] [Indexed: 11/19/2022] Open
Abstract
Phosphorylation of Rad9A at S387 is critical for establishing a physical interaction with TopBP1, and to downstream activation of Chk1 for checkpoint activation. We have previously demonstrated a phosphorylation of Rad9A that occurs at late time points in cells exposed to genotoxic agents, which is eliminated by either Rad9A overexpression, or conversion of S387 to a non-phosphorylatable analogue. Based on this, we hypothesized that this late Rad9A phosphorylation is part of a feedback loop regulating the checkpoint. Here, we show that Rad9A is hyperphosphorylated and accumulates in cells exposed to bleomycin. Following the removal of bleomycin, Rad9A is polyubiquitinated, and Rad9A protein levels drop, indicating an active degradation process for Rad9A. Chk1 inhibition by UCN-01 or siRNA reduces Rad9A levels in cells synchronized in S-phase or exposed to DNA damage, indicating that Chk1 activation is required for Rad9A stabilization in S-phase and during checkpoint activation. Together, these results demonstrate a positive feedback loop involving Rad9A-dependend activation of Chk1, coupled with Chk1-dependent stabilization of Rad9A that is critical for checkpoint regulation.
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Zhao B, Zhang WD, Duan YL, Lu YQ, Cun YX, Li CH, Guo K, Nie WH, Li L, Zhang R, Zheng P. Filia Is an ESC-Specific Regulator of DNA Damage Response and Safeguards Genomic Stability. Cell Stem Cell 2015; 16:684-98. [PMID: 25936915 DOI: 10.1016/j.stem.2015.03.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 02/16/2015] [Accepted: 03/22/2015] [Indexed: 12/20/2022]
Abstract
Pluripotent stem cells (PSCs) hold great promise in cell-based therapy, but the genomic instability seen in culture hampers their full application. A greater understanding of the factors that regulate genomic stability in PSCs could help address this issue. Here we describe the identification of Filia as a specific regulator of genomic stability in mouse embryonic stem cells (ESCs). Filia expression is induced by genotoxic stress. Filia promotes centrosome integrity and regulates the DNA damage response (DDR) through multiple pathways, including DDR signaling, cell-cycle checkpoints and damage repair, ESC differentiation, and apoptosis. Filia depletion causes ESC genomic instability, induces resistance to apoptosis, and promotes malignant transformation. As part of its role in DDR, Filia interacts with PARP1 and stimulates its enzymatic activity. Filia also constitutively resides on centrosomes and translocates to DNA damage sites and mitochondria, consistent with its multifaceted roles in regulating centrosome integrity, damage repair, and apoptosis.
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Affiliation(s)
- Bo Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wei-Dao Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Ying-Liang Duan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yong-Qing Lu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yi-Xian Cun
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Chao-Hui Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Kun Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Wen-Hui Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Lei Li
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rugang Zhang
- Gene Expression and Regulation Program, The Wistar Institute Cancer Center, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
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12
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Jain CK, Roychoudhury S, Majumder HK. Selective killing of G2 decatenation checkpoint defective colon cancer cells by catalytic topoisomerase II inhibitor. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1195-204. [PMID: 25746763 DOI: 10.1016/j.bbamcr.2015.02.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 02/09/2015] [Accepted: 02/25/2015] [Indexed: 12/16/2022]
Abstract
Cancer cells with defective DNA decatenation checkpoint can be selectively targeted by the catalytic inhibitors of DNA topoisomerase IIα (topo IIα) enzyme. Upon treatment with catalytic topo IIα inhibitors, cells with defective decatenation checkpoint fail to arrest their cell cycle in G2 phase and enter into M phase with catenated and under-condensed chromosomes resulting into impaired mitosis and eventually cell death. In the present work we analyzed decatenation checkpoint in five different colon cancer cell lines (HCT116, HT-29, Caco2, COLO 205 and SW480) and in one non-cancerous cell line (HEK293T). Four out of the five colon cancer cell lines i.e. HCT116, HT-29, Caco2, and COLO 205 were found to be compromised for the decatenation checkpoint function at different extents, whereas SW480 and HEK293T cell lines were found to be proficient for the checkpoint function. Upon treatment with ICRF193, decatenation checkpoint defective cell lines failed to arrest the cell cycle in G2 phase and entered into M phase without proper chromosomal decatenation, resulting into the formation of tangled mass of catenated and under-condensed chromosomes. Such cells underwent mitotic catastrophe and rapid apoptosis like cell death and showed higher sensitivity for ICRF193. Our study suggests that catalytic inhibitors of topoisomerase IIα are promising therapeutic agents for the treatment of colon cancers with defective DNA decatenation checkpoint.
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Affiliation(s)
- Chetan Kumar Jain
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India; Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Susanta Roychoudhury
- Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India.
| | - Hemanta Kumar Majumder
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India.
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13
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Bruck T, Yanuka O, Benvenisty N. Human pluripotent stem cells with distinct X inactivation status show molecular and cellular differences controlled by the X-Linked ELK-1 gene. Cell Rep 2013; 4:262-70. [PMID: 23871667 DOI: 10.1016/j.celrep.2013.06.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 06/02/2013] [Accepted: 06/24/2013] [Indexed: 10/26/2022] Open
Abstract
Female human pluripotent stem cells show vast heterogeneity regarding the status of X chromosome inactivation. By comparing the gene expression profile of cells with two active X chromosomes (XaXa cells) to that of cells with only one active X chromosome (XaXi cells), a set of autosomal genes was shown to be overexpressed in the XaXa cells. Among these genes, we found significant enrichment for genes regulated by the X-linked transcription factor ELK-1. Comparison of the phenotype of XaXa and XaXi cells demonstrated differences in programmed cell death and differentiation, implying some growth disadvantage of the XaXa cells. Interestingly, ELK-1-overexpressing cells mimicked the phenotype of XaXa cells, whereas knockdown of ELK-1 with small hairpin RNA mimicked the phenotype of XaXi cells. When cultured at low oxygen levels, these cellular differences were considerably weakened. Our analysis implies a role of ELK-1 in the differences between pluripotent stem cells with distinct X chromosome inactivation statuses.
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Affiliation(s)
- Tal Bruck
- Stem Cell Unit, Department of Genetics, Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
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Pastor N, Domínguez I, Orta ML, Campanella C, Mateos S, Cortés F. The DNA topoisomerase II catalytic inhibitor merbarone is genotoxic and induces endoreduplication. Mutat Res 2012; 738-739:45-51. [PMID: 22921906 DOI: 10.1016/j.mrfmmm.2012.07.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 07/03/2012] [Accepted: 07/19/2012] [Indexed: 06/01/2023]
Abstract
In the last years a number of reports have shown that the so-called topoisomerase II (topo II) catalytic inhibitors are able to induce DNA and chromosome damage, an unexpected result taking into account that they do not stabilize topo II-DNA cleavable complexes, a feature of topo II poisons such as etoposide and amsacrine. Merbarone inhibits the catalytic activity of topo II by blocking DNA cleavage by the enzyme. While it was first reported that merbarone does not induce genotoxic effects in mammalian cells, this has been challenged by reports showing that the topo II inhibitor induces efficiently chromosome and DNA damage, and the question as to a possible behavior as a topo II poison has been put forward. Given these contradictory results, and the as yet incomplete knowledge of the molecular mechanism of action of merbarone, in the present study we have tried to further characterize the mechanism of action of merbarone on cell proliferation, cell cycle, as well as chromosome and DNA damage in cultured CHO cells. Merbarone was cytotoxic as well as genotoxic, inhibited topo II catalytic activity, and induced endoreduplication. We have also shown that merbarone-induced DNA damage depends upon ongoing DNA synthesis. Supporting this, inhibition of DNA synthesis causes reduction of DNA damage and increased cell survival.
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Affiliation(s)
- Nuria Pastor
- Department of Cell Biology, University of Seville, Spain
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15
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Zhan Z, He K, Zhu D, Jiang D, Huang YH, Li Y, Sun C, Jin YH. Phosphorylation of Rad9 at serine 328 by cyclin A-Cdk2 triggers apoptosis via interfering Bcl-xL. PLoS One 2012; 7:e44923. [PMID: 23028682 PMCID: PMC3441668 DOI: 10.1371/journal.pone.0044923] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 08/09/2012] [Indexed: 11/18/2022] Open
Abstract
Cyclin A-Cdk2, a cell cycle regulated Ser/Thr kinase, plays important roles in a variety of apoptoticprocesses. However, the mechanism of cyclin A-Cdk2 regulated apoptosis remains unclear. Here, we demonstrated that Rad9, a member of the BH3-only subfamily of Bcl-2 proteins, could be phosphorylated by cyclin A-Cdk2 in vitro and in vivo. Cyclin A-Cdk2 catalyzed the phosphorylation of Rad9 at serine 328 in HeLa cells during apoptosis induced by etoposide, an inhibitor of topoisomeraseII. The phosphorylation of Rad9 resulted in its translocation from the nucleus to the mitochondria and its interaction with Bcl-xL. The forced activation of cyclin A-Cdk2 in these cells by the overexpression of cyclin A,triggered Rad9 phosphorylation at serine 328 and thereby promoted the interaction of Rad9 with Bcl-xL and the subsequent initiation of the apoptotic program. The pro-apoptotic effects regulated by the cyclin A-Cdk2 complex were significantly lower in cells transfected with Rad9S328A, an expression vector that encodes a Rad9 mutant that is resistant to cyclin A-Cdk2 phosphorylation. These findings suggest that cyclin A-Cdk2 regulates apoptosis through a mechanism that involves Rad9phosphorylation.
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Affiliation(s)
- Zhuo Zhan
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun, China
- State Key Laboratory of Supramolecular Structure & Materials, Jilin University, Changchun, China
| | - Kan He
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun, China
| | - Dan Zhu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun, China
| | - Dan Jiang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun, China
| | - Ying-Hui Huang
- Cancer Center, China-Japan Union Hospital, Jilin University, Changchun, China
| | - Yang Li
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun, China
| | - Chao Sun
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun, China
| | - Ying-Hua Jin
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun, China
- State Key Laboratory of Supramolecular Structure & Materials, Jilin University, Changchun, China
- * E-mail:
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16
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Lieberman HB, Bernstock JD, Broustas CG, Hopkins KM, Leloup C, Zhu A. The role of RAD9 in tumorigenesis. J Mol Cell Biol 2011; 3:39-43. [PMID: 21278450 DOI: 10.1093/jmcb/mjq039] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
RAD9 regulates multiple cellular processes that influence genomic integrity, and for at least some of its functions the protein acts as part of a heterotrimeric complex bound to HUS1 and RAD1 proteins. RAD9 participates in DNA repair, including base excision repair, homologous recombination repair and mismatch repair, multiple cell cycle phase checkpoints and apoptosis. In addition, functions including the transactivation of downstream target genes, immunoglobulin class switch recombination, as well as 3'-5' exonuclease activity have been reported. Aberrant RAD9 expression has been linked to breast, lung, thyroid, skin and prostate tumorigenesis, and a cause-effect relationship has been demonstrated for the latter two. Interestingly, human RAD9 overproduction correlates with prostate cancer whereas deletion of Mrad9, the corresponding mouse gene, in keratinocytes leads to skin cancer. These results reveal that RAD9 protein can function as an oncogene or tumor suppressor, and aberrantly high or low levels can have deleterious health consequences. It is not clear which of the many functions of RAD9 is critical for carcinogenesis, but several alternatives are considered herein and implications for the development of novel cancer therapies based on these findings are examined.
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Affiliation(s)
- Howard B Lieberman
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, 630 W 168th St, New York, NY 10032, USA.
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