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Wang Y, Ma C, Yang X, Gao J, Sun Z. ZNF217: An Oncogenic Transcription Factor and Potential Therapeutic Target for Multiple Human Cancers. Cancer Manag Res 2024; 16:49-62. [PMID: 38259608 PMCID: PMC10802126 DOI: 10.2147/cmar.s431135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Zinc finger protein 217 (ZNF217) is one of the well-researched members of the Krüppel-like factor transcription factor family. ZNF217 possesses a characteristic structure of zinc finger motifs and plays a crucial role in regulating the biological activities of cells. Recent findings have revealed that ZNF217 is strongly associated with multiple aspects of cancer progression, impacting patient prognosis. Notably, ZNF217 is subject to regulation by non-coding RNAs, suggesting the potential for targeted manipulation of such RNAs as a robust therapeutic avenue for managing cancer in the future. The main purpose of this article is to provide a detailed examination of the role of ZNF217 in human malignant tumors and the regulation of its expression, and to offer new perspectives for cancer treatment.
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Affiliation(s)
- Yepeng Wang
- Department of Neurosurgery, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, People’s Republic of China
| | - Chao Ma
- Department of Thoracic Surgery, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, People’s Republic of China
| | - Xuekun Yang
- Department of Neurology, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, People’s Republic of China
| | - Jun Gao
- Department of Neurosurgery, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, People’s Republic of China
| | - Zhigang Sun
- Department of Thoracic Surgery, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, People’s Republic of China
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Sharma T, Zhang Y, Zigrossi A, Cravatt BF, Kastrati I. Dimethyl fumarate inhibits ZNF217 and can be beneficial in a subset of estrogen receptor positive breast cancers. Breast Cancer Res Treat 2023; 201:561-570. [PMID: 37477798 DOI: 10.1007/s10549-023-07037-4] [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: 02/23/2023] [Accepted: 07/05/2023] [Indexed: 07/22/2023]
Abstract
PURPOSE The oncogenic factor ZNF217 promotes aggressive estrogen receptor (ER)+breast cancer disease suggesting that its inhibition may be useful in the clinic. Unfortunately, no direct pharmacological inhibitor is available. Dimethyl fumarate (DMF) exhibits anti-breast cancer activities, in vitro and in pre-clinical in vivo models. Its therapeutic benefits stem from covalent modification of cellular thiols such as protein cysteines, but the full profile of molecular targets mediating its anti-breast cancer effects remains to be determined. METHODS ER+breast cancer cells were treated with DMF followed by cysteine-directed proteomics. Cells with modulated ZNF217 levels were used to probe the efficacy of DMF. RESULTS Covalent modification of ZNF217 by DMF identified by proteomics was confirmed by using a DMF-chemical probe. Inhibition of ZNF217's transcriptional activity by DMF was evident on reported ZNF217-target genes. ZNF217 as an oncogene has been shown to enhance stem-like properties, survival, proliferation, and invasion. Consistent with ZNF217 inhibition, DMF was more effective at blocking these ZNF217-driven phenotypes in cells with elevated ZNF217 expression. Furthermore, partial knockdown of ZNF217 led to a reduction in DMF's efficacy. DMF's in vivo activity was evaluated in a xenograft model of MCF-7 HER2 cells that have elevated expression of ZNF217 and DMF treatment resulted in significant inhibition of tumor growth. CONCLUSION These data indicate that DMF's anti-breast cancer activities in the ER+HER2+models, at least in part, are due to inhibition of ZNF217. DMF is identified as a new covalent inhibitor of ZNF217.
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Affiliation(s)
- Tanu Sharma
- The Department of Cancer Biology, Loyola University Chicago, 2160 S 1St Avenue, Maywood, IL, 60153, USA
| | - Yuanjin Zhang
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Alexandra Zigrossi
- The Department of Cancer Biology, Loyola University Chicago, 2160 S 1St Avenue, Maywood, IL, 60153, USA
| | - Benjamin F Cravatt
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Irida Kastrati
- The Department of Cancer Biology, Loyola University Chicago, 2160 S 1St Avenue, Maywood, IL, 60153, USA.
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Costermans NGJ, Teerds KJ, Kemp B, Keijer J, Soede NM. Physiological and metabolic aspects of follicular developmental competence as affected by lactational body condition loss. Mol Reprod Dev 2023; 90:491-502. [PMID: 35775400 DOI: 10.1002/mrd.23628] [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: 01/24/2022] [Revised: 06/07/2022] [Accepted: 06/17/2022] [Indexed: 11/09/2022]
Abstract
Metabolic demands of modern hybrid sows have increased over the years, which increases the chance that sows enter a substantial negative energy balance (NEB) during lactation. This NEB can negatively impact reproductive outcome, which is especially evident in primiparous sows causing a reduced second parity reproductive performance. The negative effects of the lactational NEB on reproductive performance can be partly explained by the influence of the premating metabolic state, during and after lactation, on the development of follicles from which oocytes will give rise to the next litter. In addition, the degree and type of body tissue mobilization during lactation that is, adipose tissue or lean mass, highly influences follicular development. Research investigating relations between the premating metabolic state and follicular and oocyte competence in modern hybrid sows, which experience higher metabolic demands during lactation, is limited. In this review we summarize current knowledge of physiological relations between the metabolic state of modern hybrid sows and follicular developmental competence. In addition, we discuss potential implications of these relations for current sow management strategies.
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Affiliation(s)
- Natasja G J Costermans
- Human and Animal Physiology, Wageningen University and Research, Wageningen, The Netherlands
- Adaptation Physiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Katja J Teerds
- Human and Animal Physiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Bas Kemp
- Adaptation Physiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Nicoline M Soede
- Adaptation Physiology, Wageningen University and Research, Wageningen, The Netherlands
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The Intricate Interplay between the ZNF217 Oncogene and Epigenetic Processes Shapes Tumor Progression. Cancers (Basel) 2022; 14:cancers14246043. [PMID: 36551531 PMCID: PMC9776013 DOI: 10.3390/cancers14246043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
The oncogenic transcription factor ZNF217 orchestrates several molecular signaling networks to reprogram integrated circuits governing hallmark capabilities within cancer cells. High levels of ZNF217 expression provide advantages to a specific subset of cancer cells to reprogram tumor progression, drug resistance and cancer cell plasticity. ZNF217 expression level, thus, provides a powerful biomarker of poor prognosis and a predictive biomarker for anticancer therapies. Cancer epigenetic mechanisms are well known to support the acquisition of hallmark characteristics during oncogenesis. However, the complex interactions between ZNF217 and epigenetic processes have been poorly appreciated. Deregulated DNA methylation status at ZNF217 locus or an intricate cross-talk between ZNF217 and noncoding RNA networks could explain aberrant ZNF217 expression levels in a cancer cell context. On the other hand, the ZNF217 protein controls gene expression signatures and molecular signaling for tumor progression by tuning DNA methylation status at key promoters by interfering with noncoding RNAs or by refining the epitranscriptome. Altogether, this review focuses on the recent advances in the understanding of ZNF217 collaboration with epigenetics processes to orchestrate oncogenesis. We also discuss the exciting burgeoning translational medicine and candidate therapeutic strategies emerging from those recent findings connecting ZNF217 to epigenetic deregulation in cancer.
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Mantsou A, Pitou M, Papachristou E, Papi RM, Lamprou P, Choli-Papadopoulou T. Effect of a Bone Morphogenetic Protein-2-derived peptide on the expression of tumor marker ZNF217 in osteoblasts and MCF-7 cells. Bone Rep 2021; 15:101125. [PMID: 34632002 PMCID: PMC8487976 DOI: 10.1016/j.bonr.2021.101125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/27/2021] [Accepted: 09/01/2021] [Indexed: 11/24/2022] Open
Abstract
Zinc Finger Protein 217 (ZNF217), a transcription factor and oncogene product, has been found to dysregulate Bone Morphogenetic Protein (BMP) signaling and induce invasion in breast tumors. In this study, the effect of BMP-2 or an active BMP-2 peptide, AISMLYLDEN, on the expression of ZNF217, BMP4 and CDK-inhibitor p21 gene, CDKN1A, was investigated in MCF-7 breast cancer cells. In parallel, the entire protein (BMP-2) as well as the aforementioned peptide were investigated in hDPSCs during osteogenic differentiation. The treatment of MCF-7 cancer cells with different concentrations of peptide AISMLYLDEN showed that the addition of 22.6 ng/ml was more effective in comparison to the other used concentrations. In particular, 48 h after treatment, CDKN1A and BMP4 mRNA levels were substantially increased in contrast to ZNF217 mRNA levels which were decreased. These results are strongly supported by BrdU assay that clearly indicated inhibition of cancer cell proliferation. Taken together, these results open ways for a concurrent use, at appropriate concentrations, of the peptide AISMLYLDEN during conventional therapeutic treatment in breast tumors with a metastatic tendency to the bones. Regarding the effect of the entire protein as well as its peptide on hDPSCs differentiation into osteocytes, the mRNA levels of osteocalcin, an osteogenic marker, showed that the peptide enhanced osteogenesis at a higher degree in comparison to the entire BMP-2 without however altering ZNF217, CDKN1A and BMP4 expression levels, which remained as expected of non-cancer cells.
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Affiliation(s)
- Aglaia Mantsou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Maria Pitou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Eleni Papachristou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Rigini M Papi
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Paraskevas Lamprou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Theodora Choli-Papadopoulou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
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Li Y, Wu H, Wang Q, Xu S. ZNF217: the cerberus who fails to guard the gateway to lethal malignancy. Am J Cancer Res 2021; 11:3378-3405. [PMID: 34354851 PMCID: PMC8332857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 05/14/2021] [Indexed: 06/13/2023] Open
Abstract
The aberrant expression of the zinc finger protein 217 (ZNF217) promotes multiple malignant phenotypes, such as replicative immortality, maintenance of proliferation, malignant heterogeneity, metastasis, and cell death resistance, via diverse mechanisms, including transcriptional activation, mRNA N6-methyladenosine (m6A) regulation, and protein interactions. The induction of these cellular processes by ZNF217 leads to therapeutic resistance and patients' poor outcomes. However, few ZNF217 related clinical applications or trials, have been reported. Moreover, looming observations about ZNF217 roles in m6A regulation and cancer immune response triggered significant attention while lacking critical evidence. Thus, in this review, we revisit the literature about ZNF217 and emphasize its importance as a prognostic biomarker for early prevention and as a therapeutic target.
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Affiliation(s)
- Yingpu Li
- Department of Breast Surgery, Harbin Medical University Cancer HospitalHarbin, China
| | - Hao Wu
- Sino-Russian Medical Research Center, Harbin Medical University Cancer HospitalHarbin, China
- Heilongjiang Academy of Medical SciencesHarbin, China
| | - Qin Wang
- Department of Breast Surgery, Harbin Medical University Cancer HospitalHarbin, China
- Sino-Russian Medical Research Center, Harbin Medical University Cancer HospitalHarbin, China
- Heilongjiang Academy of Medical SciencesHarbin, China
| | - Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer HospitalHarbin, China
- Sino-Russian Medical Research Center, Harbin Medical University Cancer HospitalHarbin, China
- Heilongjiang Academy of Medical SciencesHarbin, China
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Zhang F, Yuan Y, Ma F. Function and Regulation of Nuclear DNA Sensors During Viral Infection and Tumorigenesis. Front Immunol 2021; 11:624556. [PMID: 33505405 PMCID: PMC7829187 DOI: 10.3389/fimmu.2020.624556] [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: 10/31/2020] [Accepted: 11/25/2020] [Indexed: 12/13/2022] Open
Abstract
IFI16, hnRNPA2B1, and nuclear cGAS are nuclear-located DNA sensors that play important roles in initiating host antiviral immunity and modulating tumorigenesis. IFI16 triggers innate antiviral immunity, inflammasome, and suppresses tumorigenesis by recognizing double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), damaged nuclear DNA, or cooperatively interacting with multiple tumor suppressors such as p53 and BRCA1. hnRNPA2B1 initiates interferon (IFN)-α/β production and enhances STING-dependent cytosolic antiviral signaling by directly binding viral dsDNA from invaded viruses and facilitating N6 -methyladenosine (m6A) modification of cGAS, IFI16, and STING mRNAs. Nuclear cGAS is recruited to double-stranded breaks (DSBs), suppresses DNA repair, and promotes tumorigenesis. This review briefly describes the nuclear functions of IFI16, hnRNPA2B1, and cGAS, and summarizes the transcriptional, post-transcriptional, and post-translational regulation of these nuclear DNA sensors.
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Affiliation(s)
- Fan Zhang
- Key Laboratory of Synthetic Biology Regulatory Elements, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Yi Yuan
- Key Laboratory of Synthetic Biology Regulatory Elements, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China.,Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine of Tongji University, Shanghai, China
| | - Feng Ma
- Key Laboratory of Synthetic Biology Regulatory Elements, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
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Sarparast M, Dattmore D, Alan J, Lee KSS. Cytochrome P450 Metabolism of Polyunsaturated Fatty Acids and Neurodegeneration. Nutrients 2020; 12:E3523. [PMID: 33207662 PMCID: PMC7696575 DOI: 10.3390/nu12113523] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 12/11/2022] Open
Abstract
Due to the aging population in the world, neurodegenerative diseases have become a serious public health issue that greatly impacts patients' quality of life and adds a huge economic burden. Even after decades of research, there is no effective curative treatment for neurodegenerative diseases. Polyunsaturated fatty acids (PUFAs) have become an emerging dietary medical intervention for health maintenance and treatment of diseases, including neurodegenerative diseases. Recent research demonstrated that the oxidized metabolites, particularly the cytochrome P450 (CYP) metabolites, of PUFAs are beneficial to several neurodegenerative diseases, including Alzheimer's disease and Parkinson's disease; however, their mechanism(s) remains unclear. The endogenous levels of CYP metabolites are greatly affected by our diet, endogenous synthesis, and the downstream metabolism. While the activity of omega-3 (ω-3) CYP PUFA metabolites and omega-6 (ω-6) CYP PUFA metabolites largely overlap, the ω-3 CYP PUFA metabolites are more active in general. In this review, we will briefly summarize recent findings regarding the biosynthesis and metabolism of CYP PUFA metabolites. We will also discuss the potential mechanism(s) of CYP PUFA metabolites in neurodegeneration, which will ultimately improve our understanding of how PUFAs affect neurodegeneration and may identify potential drug targets for neurodegenerative diseases.
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Affiliation(s)
- Morteza Sarparast
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA;
| | - Devon Dattmore
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA;
| | - Jamie Alan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA;
| | - Kin Sing Stephen Lee
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA;
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA;
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SOX10-regulated promoter use defines isoform-specific gene expression in Schwann cells. BMC Genomics 2020; 21:549. [PMID: 32770939 PMCID: PMC7430845 DOI: 10.1186/s12864-020-06963-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/29/2020] [Indexed: 01/12/2023] Open
Abstract
Background Multicellular organisms adopt various strategies to tailor gene expression to cellular contexts including the employment of multiple promoters (and the associated transcription start sites (TSSs)) at a single locus that encodes distinct gene isoforms. Schwann cells—the myelinating cells of the peripheral nervous system (PNS)—exhibit a specialized gene expression profile directed by the transcription factor SOX10, which is essential for PNS myelination. SOX10 regulates promoter elements associated with unique TSSs and gene isoforms at several target loci, implicating SOX10-mediated, isoform-specific gene expression in Schwann cell function. Here, we report on genome-wide efforts to identify SOX10-regulated promoters and TSSs in Schwann cells to prioritize genes and isoforms for further study. Results We performed global TSS analyses and mined previously reported ChIP-seq datasets to assess the activity of SOX10-bound promoters in three models: (i) an adult mammalian nerve; (ii) differentiating primary Schwann cells, and (iii) cultured Schwann cells with ablated SOX10 function. We explored specific characteristics of SOX10-dependent TSSs, which provides confidence in defining them as SOX10 targets. Finally, we performed functional studies to validate our findings at four previously unreported SOX10 target loci: ARPC1A, CHN2, DDR1, and GAS7. These findings suggest roles for the associated SOX10-regulated gene products in PNS myelination. Conclusions In sum, we provide comprehensive computational and functional assessments of SOX10-regulated TSS use in Schwann cells. The data presented in this study will stimulate functional studies on the specific mRNA and protein isoforms that SOX10 regulates, which will improve our understanding of myelination in the peripheral nerve.
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ARMCX Family Gene Expression Analysis and Potential Prognostic Biomarkers for Prediction of Clinical Outcome in Patients with Gastric Carcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3575038. [PMID: 32685472 PMCID: PMC7345962 DOI: 10.1155/2020/3575038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/20/2020] [Indexed: 01/04/2023]
Abstract
Armadillo gene subfamily members (ARMCX1-6) are well-known to regulate protein-protein interaction involved in nuclear transport, cellular connection, and transcription activation. Moreover, ARMCX signals on cell pathways also implicated in carcinogenesis and tumor progression. However, little is known about the associations of the ARMCX subfamily members with gastric carcinoma. This study investigated the prognostic value of ARMCX subfamily mRNA expression levels with the prognosis of gastric carcinoma (GC). We retrieved the data of a total of 351 GC patients from TCGA database. Survival and gene set enrichment analyses were employed to explore the predictive value and underlying mechanism of ARMCX genes in GC. The multivariate survival analysis revealed that individually low expressions of ARMCX1 (adjusted P = 0.006, HR = 0.620, CI = 0.440 - 0.874) and ARMCX2 (adjusted P = 0.005, HR = 0.610, 95%CI = 0.432-0.861) were related to preferable overall survival (OS). The joint-effects analysis shown that combinations of low level expression of ARMCX1 and ARMCX2 were correlated with favorable OS (adjusted P = 0.003, HR = 0.563, 95%CI = 0.384-0.825). ARMCX1 and ARMCX2 were implicated in WNT and NF-kappaB pathways, and biological processes including cell cycle, apoptosis, RNA modification, DNA replication, and damage response. Our results suggest that mRNA expression levels of ARMCX subfamily are potential prognostic markers of GC.
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Si W, Zhao Y, Zhou J, Zhang Q, Zhang Y. The coordination between ZNF217 and LSD1 contributes to hepatocellular carcinoma progress and is negatively regulated by miR-101. Exp Cell Res 2019; 379:1-10. [DOI: 10.1016/j.yexcr.2019.03.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/08/2019] [Accepted: 03/10/2019] [Indexed: 12/16/2022]
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Wang D, Xu Q, Yuan Q, Jia M, Niu H, Liu X, Zhang J, Young CY, Yuan H. Proteasome inhibition boosts autophagic degradation of ubiquitinated-AGR2 and enhances the antitumor efficiency of bevacizumab. Oncogene 2019; 38:3458-3474. [PMID: 30647455 PMCID: PMC6756021 DOI: 10.1038/s41388-019-0675-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/24/2018] [Accepted: 12/21/2018] [Indexed: 11/09/2022]
Abstract
Anterior gradient 2 (AGR2), a protein belonging to the protein disulfide isomerase (PDI) family, is overexpressed in multiple cancers and promotes angiogenesis to drive cancer progression. The mechanisms controlling AGR2 abundance in cancer remain largely unknown. Here, we observed that AGR2 expression is significantly suppressed by proteasome inhibitor MG132/bortezomib at mRNA and protein levels in lung cancer cells. MG132-mediated repression of AGR2 transcription was independent of ROS generation and ER stress induction, but partially resulted from the downregulated E2F1. Further investigation revealed that MG132 facilitated polyubiquitinated AGR2 degradation through activation of autophagy, as evidenced by predominant restoration of AGR2 level in cells genetic depletion of Atg5 and Atg7, or by autophagy inhibitors. Activation of autophagy by rapamycin noticeably reduced the AGR2 protein in cells and in the mouse tissue samples administrated with bortezomib. We also provided evidence identifying the K48-linked polyubiquitin chains conjugating onto K89 of AGR2 by an E3 ligase UBR5. In addition, an autophagy receptor NBR1 was demonstrated to be important in polyubiquitinated AGR2 clearance in response to MG132 or bortezomib. Importantly, downregulation of AGR2 by proteasome inhibition significantly enhanced antitumor activity of bevacizumab, highlighting the importance of AGR2 as a predictive marker for selection of subgroup patients in chemotherapy.
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Affiliation(s)
- Dawei Wang
- Key Laboratory of Experimental Teratology of the Ministry of Education, Institute of Medical Sciences, The Second Hospital of Shandong University, Jinan, China
| | - Qingqing Xu
- Key Laboratory of Experimental Teratology of the Ministry of Education, Institute of Medical Sciences, The Second Hospital of Shandong University, Jinan, China
| | - Quan Yuan
- Key Laboratory of Experimental Teratology of the Ministry of Education, Institute of Medical Sciences, The Second Hospital of Shandong University, Jinan, China
| | - Mengqi Jia
- Key Laboratory of Experimental Teratology of the Ministry of Education, Institute of Medical Sciences, The Second Hospital of Shandong University, Jinan, China
| | - Huanmin Niu
- Key Laboratory of Experimental Teratology of the Ministry of Education, Institute of Medical Sciences, The Second Hospital of Shandong University, Jinan, China
| | - Xiaofei Liu
- Key Laboratory of Experimental Teratology of the Ministry of Education, Institute of Medical Sciences, The Second Hospital of Shandong University, Jinan, China
| | - Jinsan Zhang
- Department of Urology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Charles Yf Young
- Department of Urology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Huiqing Yuan
- Key Laboratory of Experimental Teratology of the Ministry of Education, Institute of Medical Sciences, The Second Hospital of Shandong University, Jinan, China.
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Jiang X, Zhang C, Qi S, Guo S, Chen Y, Du E, Zhang H, Wang X, Liu R, Qiao B, Yang K, Zhang Z, Xu Y. Elevated expression of ZNF217 promotes prostate cancer growth by restraining ferroportin-conducted iron egress. Oncotarget 2018; 7:84893-84906. [PMID: 27768596 PMCID: PMC5356707 DOI: 10.18632/oncotarget.12753] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 10/05/2016] [Indexed: 01/09/2023] Open
Abstract
Although we and other studies indicated ZNF217 expression was increased in prostate cancer (PCa), the factors mediating its misregulated expression and their oncogenic activity remain largely unexplored. Recent evidence demonstrated that ferroportin (FPN) reduction lead to decreased iron export and increased intercellular iron that consequently aggravates the oncogenic effects of iron. In the present study, ZNF217 was identified as a transcriptional repressor that inhibits FPN expression. Increased of ZNF217 expression led to decreased FPN concentration, coupled with resultant intracellular iron retention, increased iron-related cellular activities and enhanced tumor cell growth. In contrast, decreased of ZNF217 expression restrained tumor cell growth by promoting FPN-driven iron egress. Mechanistic investigation manifested that ZNF217 facilitated the H3K27me3 levels of FPN promoter by interacting with EZH2. Besides, we also found that MAZ increased the transcription level of ZNF217, and subsequently inhibited the FPN expression and their iron–related activities. Strikingly, the expression of MAZ, EZH2 and ZNF217 were concurrently upregulated in PCa, leading to decreased expression of FPN, which induce disordered iron metabolism. Collectively, this study underscored that elevated expression of ZNF217 promotes prostate cancer growth by restraining FPN-conducted iron egress.
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Affiliation(s)
- Xingkang Jiang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Changwen Zhang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Shiyong Qi
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Shanqi Guo
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300112, China
| | - Yue Chen
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - E Du
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Hongtuan Zhang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Xiaoming Wang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Ranlu Liu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Baomin Qiao
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Kuo Yang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Zhihong Zhang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Yong Xu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
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Bellanger A, Donini CF, Vendrell JA, Lavaud J, Machuca-Gayet I, Ruel M, Vollaire J, Grisard E, Győrffy B, Bièche I, Peyruchaud O, Coll JL, Treilleux I, Maguer-Satta V, Josserand V, Cohen PA. The critical role of the ZNF217 oncogene in promoting breast cancer metastasis to the bone. J Pathol 2017; 242:73-89. [PMID: 28207159 DOI: 10.1002/path.4882] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 11/10/2016] [Accepted: 01/18/2017] [Indexed: 12/24/2022]
Abstract
Bone metastasis affects >70% of patients with advanced breast cancer. However, the molecular mechanisms underlying this process remain unclear. On the basis of analysis of clinical datasets, and in vitro and in vivo experiments, we report that the ZNF217 oncogene is a crucial mediator and indicator of bone metastasis. Patients with high ZNF217 mRNA expression levels in primary breast tumours had a higher risk of developing bone metastases. MDA-MB-231 breast cancer cells stably transfected with ZNF217 (MDA-MB-231-ZNF217) showed the dysregulated expression of a set of genes with bone-homing and metastasis characteristics, which overlapped with two previously described 'osteolytic bone metastasis' gene signatures, while also highlighting the bone morphogenetic protein (BMP) pathway. The latter was activated in MDA-MB-231-ZNF217 cells, and its silencing by inhibitors (Noggin and LDN-193189) was sufficient to rescue ZNF217-dependent cell migration, invasion or chemotaxis towards the bone environment. Finally, by using non-invasive multimodal in vivo imaging, we found that ZNF217 increases the metastatic growth rate in the bone and accelerates the development of severe osteolytic lesions. Altogether, the findings of this study highlight ZNF217 as an indicator of the emergence of breast cancer bone metastasis; future therapies targeting ZNF217 and/or the BMP signalling pathway may be beneficial by preventing the development of bone metastases. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Aurélie Bellanger
- Univ. Lyon, Université Claude Bernard Lyon 1, INSERM U1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Caterina F Donini
- Univ. Lyon, Université Claude Bernard Lyon 1, INSERM U1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Unité Cancer et Environnement, Centre Léon Bérard, Lyon, France
| | - Julie A Vendrell
- Univ. Lyon, Université Claude Bernard Lyon 1, INSERM U1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Jonathan Lavaud
- INSERM U1209, Institut Albert Bonniot, Grenoble, France.,Université Grenoble Alpes, Institut Albert Bonniot, Grenoble, France
| | - Irma Machuca-Gayet
- Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France.,INSERM, Unit 1033 (Faculté de Médecine Lyon Est), Lyon, France
| | - Maëva Ruel
- Univ. Lyon, Université Claude Bernard Lyon 1, INSERM U1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Julien Vollaire
- INSERM U1209, Institut Albert Bonniot, Grenoble, France.,Université Grenoble Alpes, Institut Albert Bonniot, Grenoble, France
| | - Evelyne Grisard
- Univ. Lyon, Université Claude Bernard Lyon 1, INSERM U1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Budapest, Hungary.,Second Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Ivan Bièche
- Unit of Pharmacogenetics, Department of Genetics, Institut Curie, Paris, France
| | - Olivier Peyruchaud
- Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France.,INSERM, Unit 1033 (Faculté de Médecine Lyon Est), Lyon, France
| | - Jean-Luc Coll
- INSERM U1209, Institut Albert Bonniot, Grenoble, France.,Université Grenoble Alpes, Institut Albert Bonniot, Grenoble, France
| | | | - Véronique Maguer-Satta
- Univ. Lyon, Université Claude Bernard Lyon 1, INSERM U1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Véronique Josserand
- INSERM U1209, Institut Albert Bonniot, Grenoble, France.,Université Grenoble Alpes, Institut Albert Bonniot, Grenoble, France
| | - Pascale A Cohen
- Univ. Lyon, Université Claude Bernard Lyon 1, INSERM U1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France
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15
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Cohen PA, Donini CF, Nguyen NT, Lincet H, Vendrell JA. The dark side of ZNF217, a key regulator of tumorigenesis with powerful biomarker value. Oncotarget 2016; 6:41566-81. [PMID: 26431164 PMCID: PMC4747174 DOI: 10.18632/oncotarget.5893] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/18/2015] [Indexed: 12/31/2022] Open
Abstract
The recently described oncogene ZNF217 belongs to a chromosomal region that is frequently amplified in human cancers. Recent findings have revealed that alternative mechanisms such as epigenetic regulation also govern the expression of the encoded ZNF217 protein. Newly discovered molecular functions of ZNF217 indicate that it orchestrates complex intracellular circuits as a new key regulator of tumorigenesis. In this review, we focus on recent research on ZNF217-driven molecular functions in human cancers, revisiting major hallmarks of cancer and highlighting the downstream molecular targets and signaling pathways of ZNF217. We also discuss the exciting translational medicine investigating ZNF217 expression levels as a new powerful biomarker, and ZNF217 as a candidate target for future anti-cancer therapies.
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Affiliation(s)
- Pascale A Cohen
- ISPB, Faculté de Pharmacie, Lyon, France.,Université Lyon 1, Lyon, France.,INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Caterina F Donini
- ISPB, Faculté de Pharmacie, Lyon, France.,Université Lyon 1, Lyon, France.,INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Nhan T Nguyen
- ISPB, Faculté de Pharmacie, Lyon, France.,Université Lyon 1, Lyon, France.,INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Hubert Lincet
- ISPB, Faculté de Pharmacie, Lyon, France.,Université Lyon 1, Lyon, France.,INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Julie A Vendrell
- ISPB, Faculté de Pharmacie, Lyon, France.,Université Lyon 1, Lyon, France.,INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
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16
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Lee DF, Walsh MJ, Aguiló F. ZNF217/ZFP217 Meets Chromatin and RNA. Trends Biochem Sci 2016; 41:986-988. [PMID: 27519282 DOI: 10.1016/j.tibs.2016.07.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/22/2016] [Accepted: 07/27/2016] [Indexed: 10/21/2022]
Abstract
The Kruppel-like transcription factor zinc finger protein (ZNF)217 (mouse homolog ZFP217) contributes to tumorigenesis by dysregulating gene expression programs. The newly discovered molecular function of ZFP217 in controlling N6-methyladenosine (m6A) deposition in embryonic stem cells (ESCs) sheds new light on the role of this transcription factor in tumor development.
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Affiliation(s)
- Dung-Fang Lee
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA
| | - Martin J Walsh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Francesca Aguiló
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Current address: Wallenberg Centre for Molecular Medicine, Department of Medical Biosciences, Umeå University, SE-901 85 Umeå, Sweden.
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17
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Mantsou A, Koutsogiannouli E, Haitoglou C, Papavassiliou AG, Papanikolaou NA. Regulation of expression of the p21 CIP1 gene by the transcription factor ZNF217 and MDM2. Biochem Cell Biol 2016; 94:560-568. [PMID: 27792410 DOI: 10.1139/bcb-2016-0026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Using mouse double minute 2 (MDM2) protein-specific affinity chromatography and mass spectrometry, we have isolated the protein product of the oncogene znf217, which is a transcription factor and a component of a Hela-S-derived HDAC1 complex, as a novel MDM2-interacting protein. When co-expressed in cultured cancer cells, ZNF217 forms a complex with MDM2 and its ectopic over-expression reduces the steady-state levels of acetylated p53 in cell lines, suppressing its ability to activate the expression of a p21 promoter construct. In-silico analysis of the p21 promoter revealed the presence of several ZNF217-binding sites. These findings suggest that MDM2 controls p21 expression by at least 2 mechanisms: through ZNF217-mediated recruitment of HDAC1/MDM2 activity, which inhibits p53 acetylation; and through direct interaction with its binding site(s) on the p21 promoter.
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Affiliation(s)
- Aglaia Mantsou
- a Laboratory of Biological Chemistry, Division of Biological Sciences and Preventive Medicine, Faculty of Medicine, Aristotle University of Thessaloniki, University Campus Bldg 16a, 54124 Thessaloniki, Greece
| | - Evangelia Koutsogiannouli
- a Laboratory of Biological Chemistry, Division of Biological Sciences and Preventive Medicine, Faculty of Medicine, Aristotle University of Thessaloniki, University Campus Bldg 16a, 54124 Thessaloniki, Greece
| | - Costas Haitoglou
- a Laboratory of Biological Chemistry, Division of Biological Sciences and Preventive Medicine, Faculty of Medicine, Aristotle University of Thessaloniki, University Campus Bldg 16a, 54124 Thessaloniki, Greece
| | - Athanasios G Papavassiliou
- b Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street, 11527 Athens, Greece
| | - Nikolaos A Papanikolaou
- a Laboratory of Biological Chemistry, Division of Biological Sciences and Preventive Medicine, Faculty of Medicine, Aristotle University of Thessaloniki, University Campus Bldg 16a, 54124 Thessaloniki, Greece
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18
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Aguilo F, Zhang F, Sancho A, Fidalgo M, Di Cecilia S, Vashisht A, Lee DF, Chen CH, Rengasamy M, Andino B, Jahouh F, Roman A, Krig SR, Wang R, Zhang W, Wohlschlegel JA, Wang J, Walsh MJ. Coordination of m(6)A mRNA Methylation and Gene Transcription by ZFP217 Regulates Pluripotency and Reprogramming. Cell Stem Cell 2015; 17:689-704. [PMID: 26526723 DOI: 10.1016/j.stem.2015.09.005] [Citation(s) in RCA: 231] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 06/24/2015] [Accepted: 09/11/2015] [Indexed: 12/15/2022]
Abstract
Epigenetic and epitranscriptomic networks have important functions in maintaining the pluripotency of embryonic stem cells (ESCs) and somatic cell reprogramming. However, the mechanisms integrating the actions of these distinct networks are only partially understood. Here we show that the chromatin-associated zinc finger protein 217 (ZFP217) coordinates epigenetic and epitranscriptomic regulation. ZFP217 interacts with several epigenetic regulators, activates the transcription of key pluripotency genes, and modulates N6-methyladenosine (m(6)A) deposition on their transcripts by sequestering the enzyme m(6)A methyltransferase-like 3 (METTL3). Consistently, Zfp217 depletion compromises ESC self-renewal and somatic cell reprogramming, globally increases m(6)A RNA levels, and enhances m(6)A modification of the Nanog, Sox2, Klf4, and c-Myc mRNAs, promoting their degradation. ZFP217 binds its own target gene mRNAs, which are also METTL3 associated, and is enriched at promoters of m(6)A-modified transcripts. Collectively, these findings shed light on how a transcription factor can tightly couple gene transcription to m(6)A RNA modification to ensure ESC identity.
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Affiliation(s)
- Francesca Aguilo
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Fan Zhang
- Bioinformatics Laboratory, Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana Sancho
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miguel Fidalgo
- Department of Developmental and Regenerative Biology and The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Serena Di Cecilia
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ajay Vashisht
- Department of Biological Chemistry and Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dung-Fang Lee
- Department of Developmental and Regenerative Biology and The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chih-Hung Chen
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Madhumitha Rengasamy
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Blanca Andino
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Farid Jahouh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Angel Roman
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid 28002, Spain
| | - Sheryl R Krig
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Sacramento, CA 95817, USA
| | - Rong Wang
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weijia Zhang
- Bioinformatics Laboratory, Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry and Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jianlong Wang
- Department of Developmental and Regenerative Biology and The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Martin J Walsh
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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19
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Ramasubramanyan S, Osborn K, Al-Mohammad R, Naranjo Perez-Fernandez IB, Zuo J, Balan N, Godfrey A, Patel H, Peters G, Rowe M, Jenner RG, Sinclair AJ. Epstein-Barr virus transcription factor Zta acts through distal regulatory elements to directly control cellular gene expression. Nucleic Acids Res 2015; 43:3563-77. [PMID: 25779048 PMCID: PMC4402532 DOI: 10.1093/nar/gkv212] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 03/01/2015] [Indexed: 12/13/2022] Open
Abstract
Lytic replication of the human gamma herpes virus Epstein-Barr virus (EBV) is an essential prerequisite for the spread of the virus. Differential regulation of a limited number of cellular genes has been reported in B-cells during the viral lytic replication cycle. We asked whether a viral bZIP transcription factor, Zta (BZLF1, ZEBRA, EB1), drives some of these changes. Using genome-wide chromatin immunoprecipitation coupled to next-generation DNA sequencing (ChIP-seq) we established a map of Zta interactions across the human genome. Using sensitive transcriptome analyses we identified 2263 cellular genes whose expression is significantly changed during the EBV lytic replication cycle. Zta binds 278 of the regulated genes and the distribution of binding sites shows that Zta binds mostly to sites that are distal to transcription start sites. This differs from the prevailing view that Zta activates viral genes by binding exclusively at promoter elements. We show that a synthetic Zta binding element confers Zta regulation at a distance and that distal Zta binding sites from cellular genes can confer Zta-mediated regulation on a heterologous promoter. This leads us to propose that Zta directly reprograms the expression of cellular genes through distal elements.
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Affiliation(s)
| | - Kay Osborn
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | | | | | - Jianmin Zuo
- School of Cancer Sciences, The University of Birmingham, Birmingham B15 2TT, UK
| | - Nicolae Balan
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - Anja Godfrey
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - Harshil Patel
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Gordon Peters
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Martin Rowe
- School of Cancer Sciences, The University of Birmingham, Birmingham B15 2TT, UK
| | - Richard G Jenner
- UCL Cancer Institute and MRC Centre for Medical Molecular Virology, Paul O'Gorman Building, University College London, London W1CE 6BT, UK
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20
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Li Z, Du L, Dong Z, Yang Y, Zhang X, Wang L, Li J, Zheng G, Qu A, Wang C. MiR-203 suppresses ZNF217 upregulation in colorectal cancer and its oncogenicity. PLoS One 2015; 10:e0116170. [PMID: 25621839 PMCID: PMC4306553 DOI: 10.1371/journal.pone.0116170] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/03/2014] [Indexed: 12/11/2022] Open
Abstract
Zinc finger protein 217 (ZNF217) is essential for cell proliferation and has been implicated in tumorigenesis. However, its expression and exact roles in colorectal cancer (CRC) remain unclear. In this study, we demonstrated that ZNF217 expression was aberrantly upregulated in CRC tissues and associated with poor overall survival of CRC patients. In addition, we found that ZNF217 was a putative target of microRNA (miR)-203 using bioinformatics analysis and confirmed that using luciferase reporter assay. Moreover, in vitro knockdown of ZNF217 or enforced expression of miR-203 attenuated CRC cell proliferation, invasion and migration. Furthermore, combined treatment of ZNF217 siRNA and miR-203 exhibited synergistic inhibitory effects. Taken together, our results provide new evidences that ZNF217 has an oncogenic role in CRC and is regulated by miR-203, and open up the possibility of ZNF217- and miR-203-targeted therapy for CRC.
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Affiliation(s)
- Zewu Li
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong Province, China
| | - Lutao Du
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong Province, China
| | - Zhaogang Dong
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong Province, China
| | - Yongmei Yang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong Province, China
| | - Xin Zhang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong Province, China
| | - Lili Wang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong Province, China
| | - Juan Li
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong Province, China
| | - Guixi Zheng
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong Province, China
| | - Ailin Qu
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong Province, China
| | - Chuanxin Wang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong Province, China
- * E-mail:
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21
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Yoo S, Bieda MC. Differences among brain tumor stem cell types and fetal neural stem cells in focal regions of histone modifications and DNA methylation, broad regions of modifications, and bivalent promoters. BMC Genomics 2014; 15:724. [PMID: 25163646 PMCID: PMC4155105 DOI: 10.1186/1471-2164-15-724] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 08/04/2014] [Indexed: 12/15/2022] Open
Abstract
Background Aberrational epigenetic marks are believed to play a major role in establishing the abnormal features of cancer cells. Rational use and development of drugs aimed at epigenetic processes requires an understanding of the range, extent, and roles of epigenetic reprogramming in cancer cells. Using ChIP-chip and MeDIP-chip approaches, we localized well-established and prevalent epigenetic marks (H3K27me3, H3K4me3, H3K9me3, DNA methylation) on a genome scale in several lines of putative glioma stem cells (brain tumor stem cells, BTSCs) and, for comparison, normal human fetal neural stem cells (fNSCs). Results We determined a substantial “core” set of promoters possessing each mark in every surveyed BTSC cell type, which largely overlapped the corresponding fNSC sets. However, there was substantial diversity among cell types in mark localization. We observed large differences among cell types in total number of H3K9me3+ positive promoters and peaks and in broad modifications (defined as >50 kb peak length) for H3K27me3 and, to a lesser extent, H3K9me3. We verified that a change in a broad modification affected gene expression of CACNG7. We detected large numbers of bivalent promoters, but most bivalent promoters did not display direct overlap of contrasting epigenetic marks, but rather occupied nearby regions of the proximal promoter. There were significant differences in the sets of promoters bearing bivalent marks in the different cell types and few consistent differences between fNSCs and BTSCs. Conclusions Overall, our “core set” data establishes sets of potential therapeutic targets, but the diversity in sets of sites and broad modifications among cell types underscores the need to carefully consider BTSC subtype variation in epigenetic therapy. Our results point toward substantial differences among cell types in the activity of the production/maintenance systems for H3K9me3 and for broad regions of modification (H3K27me3 or H3K9me3). Finally, the unexpected diversity in bivalent promoter sets among these multipotent cells indicates that bivalent promoters may play complex roles in the overall biology of these cells. These results provide key information for forming the basis for future rational drug therapy aimed at epigenetic processes in these cells. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-724) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Mark C Bieda
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada.
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22
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Frietze S, O'Geen H, Littlepage LE, Simion C, Sweeney CA, Farnham PJ, Krig SR. Global analysis of ZNF217 chromatin occupancy in the breast cancer cell genome reveals an association with ERalpha. BMC Genomics 2014; 15:520. [PMID: 24962896 PMCID: PMC4082627 DOI: 10.1186/1471-2164-15-520] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 06/18/2014] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The ZNF217 gene, encoding a C2H2 zinc finger protein, is located at 20q13 and found amplified and overexpressed in greater than 20% of breast tumors. Current studies indicate ZNF217 drives tumorigenesis, yet the regulatory mechanisms of ZNF217 are largely unknown. Because ZNF217 associates with chromatin modifying enzymes, we postulate that ZNF217 functions to regulate specific gene signaling networks. Here, we present a large-scale functional genomic analysis of ZNF217, which provides insights into the regulatory role of ZNF217 in MCF7 breast cancer cells. RESULTS ChIP-seq analysis reveals that the majority of ZNF217 binding sites are located at distal regulatory regions associated with the chromatin marks H3K27ac and H3K4me1. Analysis of ChIP-seq transcription factor binding sites shows clustering of ZNF217 with FOXA1, GATA3 and ERalpha binding sites, supported by the enrichment of corresponding motifs for the ERalpha-associated cis-regulatory sequences. ERalpha expression highly correlates with ZNF217 in lysates from breast tumors (n = 15), and ERalpha co-precipitates ZNF217 and its binding partner CtBP2 from nuclear extracts. Transcriptome profiling following ZNF217 depletion identifies differentially expressed genes co-bound by ZNF217 and ERalpha; gene ontology suggests a role for ZNF217-ERalpha in expression programs associated with ER+ breast cancer studies found in the Molecular Signature Database. Data-mining of expression data from breast cancer patients correlates ZNF217 with reduced overall survival. CONCLUSIONS Our genome-wide ZNF217 data suggests a functional role for ZNF217 at ERalpha target genes. Future studies will investigate whether ZNF217 expression contributes to aberrant ERalpha regulatory events in ER+ breast cancer and hormone resistance.
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Affiliation(s)
- Seth Frietze
- School of Biological Sciences, University of Northern Colorado, Greeley, CO 80639, USA.
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23
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A functional interplay between ZNF217 and estrogen receptor alpha exists in luminal breast cancers. Mol Oncol 2014; 8:1441-57. [PMID: 24973012 DOI: 10.1016/j.molonc.2014.05.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 05/26/2014] [Accepted: 05/26/2014] [Indexed: 01/15/2023] Open
Abstract
We aimed at highlighting the role of ZNF217, a Krüppel-like finger protein, in Estrogen Receptor-α (ERα)-positive (ER+) and luminal breast cancers. Here we report for the first time that ZNF217 and ERα proteins bind to each other in both breast cancer cells and breast tumour samples, via the ERα hinge domain and the ZNF217 C-terminal domain. ZNF217 enhances the recruitment of ERα to its estrogen response elements (ERE) and the ERα-dependent transcription of the GREB1 estrogen-regulated gene. The prognostic power of ZNF217 mRNA expression levels is most discriminatory in breast cancers classified with a "good prognosis", particularly the Luminal-A subclass. A new immunohistochemistry ZNF217 index, based on nuclear and cytoplasmic ZNF217 staining, also allowed the identification of intermediate/poor relapse-free survivors in the Luminal-A subgroup. ZNF217 confers tamoxifen resistance in ER+ breast cancer cells and is a predictor of relapse under endocrine therapy in patients with ER+ breast cancer. ZNF217 thus allows the re-stratification of patients with ER+ breast cancers considered as cancers with good prognosis where no other biomarkers are currently available and widely used. Here we propose a model in ER+ breast cancer where ZNF217-driven aggressiveness incorporates ZNF217 as a positive enhancer of ERα direct genomic activity and where ZNF217 possesses its highest discriminatory prognostic value.
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Cusanovich DA, Pavlovic B, Pritchard JK, Gilad Y. The functional consequences of variation in transcription factor binding. PLoS Genet 2014; 10:e1004226. [PMID: 24603674 PMCID: PMC3945204 DOI: 10.1371/journal.pgen.1004226] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/22/2014] [Indexed: 01/24/2023] Open
Abstract
One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the gene expression data with transcription factor binding data (based on ChIP-seq and DNase-seq) within 10 kb of the transcription start sites of expressed genes. This combination of data allowed us to infer functional TF binding. Using this approach, we found that only a small subset of genes bound by a factor were differentially expressed following the knockdown of that factor, suggesting that most interactions between TF and chromatin do not result in measurable changes in gene expression levels of putative target genes. We found that functional TF binding is enriched in regulatory elements that harbor a large number of TF binding sites, at sites with predicted higher binding affinity, and at sites that are enriched in genomic regions annotated as “active enhancers.” An important question in genomics is to understand how a class of proteins called “transcription factors” controls the expression level of other genes in the genome in a cell-type-specific manner – a process that is essential to human development. One major approach to this problem is to study where these transcription factors bind in the genome, but this does not tell us about the effect of that binding on gene expression levels and it is generally accepted that much of the binding does not strongly influence gene expression. To address this issue, we artificially reduced the concentration of 59 different transcription factors in the cell and then examined which genes were impacted by the reduced transcription factor level. Our results implicate some attributes that might influence what binding is functional, but they also suggest that a simple model of functional vs. non-functional binding may not suffice.
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Affiliation(s)
- Darren A Cusanovich
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Bryan Pavlovic
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America; Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, United States of America
| | - Jonathan K Pritchard
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America; Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, United States of America; Departments of Genetics and Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California, United States of America
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
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Diakos C, Xiao Y, Zheng S, Kager L, Dworzak M, Wiemels JL. Direct and indirect targets of the E2A-PBX1 leukemia-specific fusion protein. PLoS One 2014; 9:e87602. [PMID: 24503810 PMCID: PMC3913655 DOI: 10.1371/journal.pone.0087602] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 12/20/2013] [Indexed: 01/04/2023] Open
Abstract
E2A-PBX1 is expressed as a result of the t(1;19) chromosomal translocation in nearly 5% of cases of childhood acute lymphoblastic leukemia. The E2A-PBX1 chimeric transcription factor contains the N-terminal transactivation domain of E2A (TCF3) fused to the C-terminal DNA-binding homeodomain of PBX1. While there is no doubt of its oncogenic potential, the mechanisms of E2A-PBX1-mediated pre-B cell transformation and the nature of direct E2A-PBX1 target genes and pathways remain largely unknown. Herein we used chromatin immunoprecipitation assays (ChIP-chip) to identify direct targets of E2A-PBX1, and we used gene expression arrays of siRNA E2A-PBX1-silenced cells to evaluate changes in expression induced by the fusion protein. Combined ChIP-chip and expression data analysis gave rise to direct and functional targets of E2A-PBX1. Further we observe that the set of ChIP-chip identified E2A-PBX1 targets show a collective down-regulation trend in the E2A-PBX1 silenced samples compared to controls suggesting an activating role of this fusion transcription factor. Our data suggest that the expression of the E2A-PBX1 fusion gene interferes with key regulatory pathways and functions of hematopoietic biology. Among these are members of the WNT and apoptosis/cell cycle control pathways, and thus may comprise an essential driving force for the propagation and maintenance of the leukemic phenotype. These findings may also provide evidence of potentially attractive therapeutic targets.
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Affiliation(s)
- Christofer Diakos
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
- Department of Pediatrics, St Anna Children’s Hospital, Medical University of Vienna, Vienna, Austria
| | - Yuanyuan Xiao
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Shichun Zheng
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
- Department of Neurosurgery, University of California San Francisco, San Francisco, California, United States of America
| | - Leo Kager
- Department of Pediatrics, St Anna Children’s Hospital, Medical University of Vienna, Vienna, Austria
| | - Michael Dworzak
- Department of Pediatrics, St Anna Children’s Hospital, Medical University of Vienna, Vienna, Austria
- Children’s Cancer Research Institute, St Anna Kinderkrebsforschung, Vienna, Austria
| | - Joseph L. Wiemels
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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Organista-Nava J, Gómez-Gómez Y, Gariglio P. Embryonic stem cell-specific signature in cervical cancer. Tumour Biol 2013; 35:1727-38. [PMID: 24163107 DOI: 10.1007/s13277-013-1321-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/14/2013] [Indexed: 10/26/2022] Open
Abstract
The wide range of invasive and noninvasive lesion phenotypes associated with high-risk human papillomavirus (HR-HPV) infection in cervical cancer (CC) indicates that not only the virus but also specific cervical epithelial cells in the transformation zone (TZ), such as stem cells (SCs), play an important part in the development of cervical neoplasia. In this review, we focused in an expression signature that is specific to embryonic SCs and to poorly differentiated cervical malignant tumors and we hypothesize that this expression signature may play an important role to promote cell growth, survival, colony formation, lack of adhesion, as well as cell invasion and migration in CC.
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Affiliation(s)
- Jorge Organista-Nava
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), México, DF, México,
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27
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Mao XG, Song SJ, Xue XY, Yan M, Wang L, Lin W, Guo G, Zhang X. LGR5 is a proneural factor and is regulated by OLIG2 in glioma stem-like cells. Cell Mol Neurobiol 2013; 33:851-65. [PMID: 23793848 DOI: 10.1007/s10571-013-9951-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 06/13/2013] [Indexed: 01/10/2023]
Abstract
The biological functional roles of LGR5 (leucine-rich repeat containing G protein-coupled receptor 5, also known as GPR49), a novel potential marker for stem-like cells in glioblastoma (GSCs), is poorly acknowledged. Here, we demonstrated that LGR5 was detected in glioblastoma tissues and GSCs. Bioinformatics analysis revealed that LGR5 is closely related to neurogenesis and neuronal functions, and preferentially expressed in Proneural subtype of GBMs. Furthermore, LGR5 is regulated by Proneural factor OLIG2, which is important for both neurogenesis and GSC maintenance. Biological experiments in GSC cells validated the bioinformatics analysis results and revealed that LGR5 regulated the tumor sphere formation capacity, an important stem cell property for GSCs. Therefore, LGR5 expression may be functionally correlated with the neurogenic competence, and be regulated by OLIG2 in GSCs.
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Affiliation(s)
- Xing-Gang Mao
- Department of Neurosurgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi Province, China
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Prestat E, de Morais SR, Vendrell JA, Thollet A, Gautier C, Cohen PA, Aussem A. Learning the local Bayesian network structure around the ZNF217 oncogene in breast tumours. Comput Biol Med 2013; 43:334-41. [PMID: 23375235 DOI: 10.1016/j.compbiomed.2012.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 07/23/2012] [Accepted: 12/07/2012] [Indexed: 01/18/2023]
Abstract
In this study, we discuss and apply a novel and efficient algorithm for learning a local Bayesian network model in the vicinity of the ZNF217 oncogene from breast cancer microarray data without having to decide in advance which genes have to be included in the learning process. ZNF217 is a candidate oncogene located at 20q13, a chromosomal region frequently amplified in breast and ovarian cancer, and correlated with shorter patient survival in these cancers. To properly address the difficulties in managing complex gene interactions given our limited sample, statistical significance of edge strengths was evaluated using bootstrapping and the less reliable edges were pruned to increase the network robustness. We found that 13 out of the 35 genes associated with deregulated ZNF217 expression in breast tumours have been previously associated with survival and/or prognosis in cancers. Identifying genes involved in lipid metabolism opens new fields of investigation to decipher the molecular mechanisms driven by the ZNF217 oncogene. Moreover, nine of the 13 genes have already been identified as putative ZNF217 targets by independent biological studies. We therefore suggest that the algorithms for inferring local BNs are valuable data mining tools for unraveling complex mechanisms of biological pathways from expression data. The source code is available at http://www710.univ-lyon1.fr/∼aaussem/Software.html.
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29
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Vadnais C, Awan AA, Harada R, Clermont PL, Leduy L, Bérubé G, Nepveu A. Long-range transcriptional regulation by the p110 CUX1 homeodomain protein on the ENCODE array. BMC Genomics 2013; 14:258. [PMID: 23590133 PMCID: PMC3770232 DOI: 10.1186/1471-2164-14-258] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 03/26/2013] [Indexed: 01/19/2023] Open
Abstract
Background Overexpression of the Cut homeobox 1 gene, CUX1, inversely
correlates with patient survival in breast cancers. Cell-based assays and
molecular studies have revealed that transcriptional regulation by
CUX1 involves mostly the proteolytically processed p110
isoform. As there is no antibody specific to p110 CUX1 only, an alternate
strategy must be employed to identify its targets. Results We expressed physiological levels of a tagged-p110 CUX1 protein and performed
chromatin affinity purification followed by hybridization on ENCODE and
promoter arrays. Targets were validated by chromatin immunoprecipitation and
transcriptional regulation by CUX1 was analyzed in expression profiling and
RT-qPCR assays following CUX1 knockdown or p110 CUX1 overexpression.
Approximately 47% and 14% of CUX1 binding sites were respectively mapped
less than 4 Kbp, or more than 40 Kbp, away from a transcription start site.
More genes exhibited changes in expression following CUX1 knockdown than
p110 CUX1 overexpression. CUX1 directly activated or repressed 7.4% and 8.4%
of putative targets identified on the ENCODE and promoter arrays
respectively. This proportion increased to 11.2% for targets with 2 binding
sites or more. Transcriptional repression was observed in a slightly higher
proportion of target genes. The CUX1 consensus binding motif, ATCRAT, was
found at 47.2% of the CUX1 binding sites, yet only 8.3% of the CUX1
consensus motifs present on the array were bound in vivo. The
presence of a consensus binding motif did not have an impact on whether a
target gene was repressed or activated. Interestingly, the distance between
a binding site and a transcription start site did not significantly reduced
the ability of CUX1 to regulate a target gene. Moreover, CUX1 not only was
able to regulate the next adjacent gene, but also regulated the gene located
beyond this one as well as the gene located further away in the opposite
direction. Conclusion Our results demonstrate that p110 CUX1 can activate or repress transcription
when bound at a distance and can regulate more than one gene on certain
genomic loci.
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Affiliation(s)
- Charles Vadnais
- Goodman Cancer Centre, McGill University, 1160 Pine avenue West, Montreal, Quebec H3A 1A3, Canada
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30
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Montero-Conde C, Ruiz-Llorente S, Dominguez JM, Knauf JA, Viale A, Sherman EJ, Ryder M, Ghossein RA, Rosen N, Fagin JA. Relief of feedback inhibition of HER3 transcription by RAF and MEK inhibitors attenuates their antitumor effects in BRAF-mutant thyroid carcinomas. Cancer Discov 2013; 3:520-33. [PMID: 23365119 DOI: 10.1158/2159-8290.cd-12-0531] [Citation(s) in RCA: 299] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The RAF inhibitor vemurafenib (PLX4032) increases survival in patients with BRAF-mutant metastatic melanoma, but has limited efficacy in patients with colorectal cancers. Thyroid cancer cells are also comparatively refractory to RAF inhibitors. In contrast to melanomas, inhibition of mitogen-activated protein kinase (MAPK) signaling by PLX4032 is transient in thyroid and colorectal cancer cells. The rebound in extracellular signal-regulated kinase (ERK) in thyroid cells is accompanied by increased HER3 signaling caused by induction of ERBB3 (HER3) transcription through decreased promoter occupancy by the transcriptional repressors C-terminal binding protein 1 and 2 and by autocrine secretion of neuregulin-1 (NRG1). The HER kinase inhibitor lapatinib prevents MAPK rebound and sensitizes BRAF-mutant thyroid cancer cells to RAF or MAP-ERK kinase inhibitors. This provides a rationale for combining ERK pathway antagonists with inhibitors of feedback-reactivated HER signaling in this disease. The determinants of primary resistance to MAPK inhibitors vary between cancer types, due to preferential upregulation of specific receptor tyrosine kinases, and the abundance of their respective ligands.
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Affiliation(s)
- Cristina Montero-Conde
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 2013; 22:1813-31. [PMID: 22955991 PMCID: PMC3431496 DOI: 10.1101/gr.136184.111] [Citation(s) in RCA: 1290] [Impact Index Per Article: 117.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in living cells. Despite its widespread use, there are considerable differences in how these experiments are conducted, how the results are scored and evaluated for quality, and how the data and metadata are archived for public use. These practices affect the quality and utility of any global ChIP experiment. Through our experience in performing ChIP-seq experiments, the ENCODE and modENCODE consortia have developed a set of working standards and guidelines for ChIP experiments that are updated routinely. The current guidelines address antibody validation, experimental replication, sequencing depth, data and metadata reporting, and data quality assessment. We discuss how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data. All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE (http://encodeproject.org/ENCODE/) and modENCODE (http://www.modencode.org/) portals.
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Affiliation(s)
- Stephen G Landt
- Department of Genetics, Stanford University, Stanford, California 94305, USA
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Lord CC, Thomas G, Brown JM. Mammalian alpha beta hydrolase domain (ABHD) proteins: Lipid metabolizing enzymes at the interface of cell signaling and energy metabolism. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1831:792-802. [PMID: 23328280 DOI: 10.1016/j.bbalip.2013.01.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 12/07/2012] [Accepted: 01/02/2013] [Indexed: 11/16/2022]
Abstract
Dysregulation of lipid metabolism underlies many chronic diseases such as obesity, diabetes, cardiovascular disease, and cancer. Therefore, understanding enzymatic mechanisms controlling lipid synthesis and degradation is imperative for successful drug discovery for these human diseases. Genes encoding α/β hydrolase fold domain (ABHD) proteins are present in virtually all reported genomes, and conserved structural motifs shared by these proteins predict common roles in lipid synthesis and degradation. However, the physiological substrates and products for these lipid metabolizing enzymes and their broader role in metabolic pathways remain largely uncharacterized. Recently, mutations in several members of the ABHD protein family have been implicated in inherited inborn errors of lipid metabolism. Furthermore, studies in cell and animal models have revealed important roles for ABHD proteins in lipid metabolism, lipid signal transduction, and metabolic disease. The purpose of this review is to provide a comprehensive summary surrounding the current state of knowledge regarding mammalian ABHD protein family members. In particular, we will discuss how ABHD proteins are ideally suited to act at the interface of lipid metabolism and signal transduction. Although, the current state of knowledge regarding mammalian ABHD proteins is still in its infancy, this review highlights the potential for the ABHD enzymes as being attractive targets for novel therapies targeting metabolic disease.
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Affiliation(s)
- Caleb C Lord
- Department of Pathology, Section on Lipid Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Gwynneth Thomas
- Department of Pathology, Section on Lipid Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - J Mark Brown
- Department of Pathology, Section on Lipid Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
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Emerging roles for the pro-oncogenic anterior gradient-2 in cancer development. Oncogene 2012; 32:2499-509. [PMID: 22945652 DOI: 10.1038/onc.2012.346] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Clinical studies have defined the core 'genetic blueprint' of a cancer cell, but this information does not necessarily predict the cancer phenotype. Signalling hubs that mediate such phenotype have been identified largely using OMICS platforms that measure dynamic molecular changes within the cancer cell landscape. The pro-oncogenic protein anterior gradient 2 (AGR2) is a case in point; AGR2 has been shown using a range of expression platforms to be involved in asthma, inflammatory bowel disease, cell transformation, cancer drug resistance and metastatic growth. AGR2 protein is also highly overexpressed in a diverse range of human cancers and can be secreted and detected in extracellular fluids, thus representing a compelling pro-oncogenic signalling intermediate in human cancer. AGR2 belongs to the protein disulphide isomerase family with all the key features of an endoplasmic reticulum-resident protein-this gives clues into how it might function as an oncoprotein through the regulation of protein folding, maturation and secretion that can drive metastatic cell growth. In this review, we will describe the known aspects of AGR2 molecular biology, including gene structure and regulation, emerging protein interaction networks and how its subcellular localization mediates its biological functions. We will finally review the cases of AGR2 expression in human cancers, the pathophysiological consequences of AGR2 overexpression, its potential role as a tumour biomarker that predicts the response to therapy and how the AGR2 pathway might form the basis for drug discovery programmes aimed at targeting protein folding/maturation pathways that mediate secretion and metastasis.
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Barisone GA, Ngo T, Tran M, Cortes D, Shahi MH, Nguyen TV, Perez-Lanza D, Matayasuwan W, Díaz E. Role of MXD3 in proliferation of DAOY human medulloblastoma cells. PLoS One 2012; 7:e38508. [PMID: 22808009 PMCID: PMC3393725 DOI: 10.1371/journal.pone.0038508] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 05/07/2012] [Indexed: 11/18/2022] Open
Abstract
A subset of medulloblastomas, the most common brain tumor in children, is hypothesized to originate from granule neuron precursors (GNPs) in which the sonic hedgehog (SHH) pathway is over-activated. MXD3, a basic helix-look-helix zipper transcription factor of the MAD family, has been reported to be upregulated during postnatal cerebellar development and to promote GNP proliferation and MYCN expression. Mxd3 is upregulated in mouse models of medulloblastoma as well as in human medulloblastomas. Therefore, we hypothesize that MXD3 plays a role in the cellular events that lead to medulloblastoma biogenesis. In agreement with its proliferative role in GNPs, MXD3 knock-down in DAOY cells resulted in decreased proliferation. Sustained overexpression of MXD3 resulted in decreased cell numbers due to increased apoptosis and cell cycle arrest. Structure-function analysis revealed that the Sin3 interacting domain, the basic domain, and binding to E-boxes are essential for this activity. Microarray-based expression analysis indicated up-regulation of 84 genes and down-regulation of 47 genes. Potential direct MXD3 target genes were identified by ChIP-chip. Our results suggest that MXD3 is necessary for DAOY medulloblastoma cell proliferation. However, increased level and/or duration of MXD3 expression ultimately reduces cell numbers via increased cell death and cell cycle arrest.
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Affiliation(s)
- Gustavo A. Barisone
- Department of Pharmacology, University of California Davis School of Medicine, Davis, California, United States of America
| | - Tin Ngo
- Department of Pharmacology, University of California Davis School of Medicine, Davis, California, United States of America
| | - Martin Tran
- Department of Pharmacology, University of California Davis School of Medicine, Davis, California, United States of America
| | - Daniel Cortes
- Department of Pharmacology, University of California Davis School of Medicine, Davis, California, United States of America
| | - Mehdi H. Shahi
- Department of Pharmacology, University of California Davis School of Medicine, Davis, California, United States of America
| | - Tuong-Vi Nguyen
- Department of Pharmacology, University of California Davis School of Medicine, Davis, California, United States of America
| | - Daniel Perez-Lanza
- Department of Pharmacology, University of California Davis School of Medicine, Davis, California, United States of America
| | - Wanna Matayasuwan
- Department of Pharmacology, University of California Davis School of Medicine, Davis, California, United States of America
| | - Elva Díaz
- Department of Pharmacology, University of California Davis School of Medicine, Davis, California, United States of America
- * E-mail:
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35
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Vendrell JA, Thollet A, Nguyen NT, Ghayad SE, Vinot S, Bièche I, Grisard E, Josserand V, Coll JL, Roux P, Corbo L, Treilleux I, Rimokh R, Cohen PA. ZNF217 Is a Marker of Poor Prognosis in Breast Cancer That Drives Epithelial–Mesenchymal Transition and Invasion. Cancer Res 2012; 72:3593-606. [DOI: 10.1158/0008-5472.can-11-3095] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Littlepage LE, Adler AS, Kouros-Mehr H, Huang G, Chou J, Krig SR, Griffith OL, Korkola JE, Qu K, Lawson DA, Xue Q, Sternlicht MD, Dijkgraaf GJP, Yaswen P, Rugo HS, Sweeney CA, Collins CC, Gray JW, Chang HY, Werb Z. The transcription factor ZNF217 is a prognostic biomarker and therapeutic target during breast cancer progression. Cancer Discov 2012; 2:638-51. [PMID: 22728437 DOI: 10.1158/2159-8290.cd-12-0093] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
UNLABELLED The transcription factor ZNF217 is a candidate oncogene in the amplicon on chromosome 20q13 that occurs in 20% to 30% of primary human breast cancers and that correlates with poor prognosis. We show that Znf217 overexpression drives aberrant differentiation and signaling events, promotes increased self-renewal capacity, mesenchymal marker expression, motility, and metastasis, and represses an adult tissue stem cell gene signature downregulated in cancers. By in silico screening, we identified candidate therapeutics that at low concentrations inhibit growth of cancer cells expressing high ZNF217. We show that the nucleoside analogue triciribine inhibits ZNF217-induced tumor growth and chemotherapy resistance and inhibits signaling events [e.g., phospho-AKT, phospho-mitogen-activated protein kinase (MAPK)] in vivo. Our data suggest that ZNF217 is a biomarker of poor prognosis and a therapeutic target in patients with breast cancer and that triciribine may be part of a personalized treatment strategy in patients overexpressing ZNF217. Because ZNF217 is amplified in numerous cancers, these results have implications for other cancers. SIGNIFICANCE This study finds that ZNF217 is a poor prognostic indicator and therapeutic target in patients with breast cancer and may be a strong biomarker of triciribine treatment efficacy in patients. Because previous clinical trials for triciribine did not include biomarkers of treatment efficacy, this study provides a rationale for revisiting triciribine in the clinical setting as a therapy for patients with breast cancer who overexpress ZNF217.
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Affiliation(s)
- Laurie E Littlepage
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
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Thillainadesan G, Chitilian JM, Isovic M, Ablack JNG, Mymryk JS, Tini M, Torchia J. TGF-β-dependent active demethylation and expression of the p15ink4b tumor suppressor are impaired by the ZNF217/CoREST complex. Mol Cell 2012; 46:636-49. [PMID: 22560925 DOI: 10.1016/j.molcel.2012.03.027] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 01/30/2012] [Accepted: 03/29/2012] [Indexed: 12/13/2022]
Abstract
In this study we examine the mechanisms of dynamic DNA methylation of the p15(ink4b) tumor suppressor gene. Using conventional ChIP and ChiPseq, we identify the p15(ink4b) promoter as a target for the ZNF217 oncogene, the CoREST complex, and DNMT3A. Treatment of cells with TGF-β triggers active demethylation involving loss of ZNF217/CoREST/DNMT3A and the corecruitment of SMAD2/3, CBP, and the DNA glycosylase TDG. Knockdown of TDG, or its functional homolog MBD4, prevents TGF-β-dependent demethylation of p15(ink4b). DNA immunoprecipitation of 5mC and 5hmC indicates that 5mC undergoes conversion to 5hmC prior to activation of p15(ink4b). Remarkably, overexpression of ZNF217 inhibits active demethylation and expression of the p15(ink4b) gene by preventing recruitment of SMAD2/3 and TDG. These findings suggest that active demethylation is essential for regulating a subset of TGF-β-dependent genes. Importantly, disruption of active demethylation by the ZNF217 oncogene may be a paradigm for other oncogenic signals on DNA methylation dynamics.
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Affiliation(s)
- Gobi Thillainadesan
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
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Zambelli F, Pesole G, Pavesi G. Motif discovery and transcription factor binding sites before and after the next-generation sequencing era. Brief Bioinform 2012; 14:225-37. [PMID: 22517426 PMCID: PMC3603212 DOI: 10.1093/bib/bbs016] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Motif discovery has been one of the most widely studied problems in bioinformatics ever since genomic and protein sequences have been available. In particular, its application to the de novo prediction of putative over-represented transcription factor binding sites in nucleotide sequences has been, and still is, one of the most challenging flavors of the problem. Recently, novel experimental techniques like chromatin immunoprecipitation (ChIP) have been introduced, permitting the genome-wide identification of protein-DNA interactions. ChIP, applied to transcription factors and coupled with genome tiling arrays (ChIP on Chip) or next-generation sequencing technologies (ChIP-Seq) has opened new avenues in research, as well as posed new challenges to bioinformaticians developing algorithms and methods for motif discovery.
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Chen Z, Wang L, Wang Q, Li W. Histone modifications and chromatin organization in prostate cancer. Epigenomics 2012; 2:551-60. [PMID: 21318127 DOI: 10.2217/epi.10.31] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Epigenetic mechanisms, including histone modifications, nucleosomal remodeling and chromosomal looping, contribute to the onset and progression of prostate cancer. Recent technical advances significantly increase our understanding of the genome-wide epigenetic regulation of gene expression in prostate cancer. Aberrant genomic distribution and global level of histone modifications, nucleosome repositioning at the gene promoter and enhancer regions, as well as androgen receptor-mediated chromosomal looping may lead to the silencing of tumor suppressor genes and the activation of proto-oncogenes. In addition, androgen receptor-induced chromosomal looping facilitates recurrent gene fusion in prostate cancer. Studies in epigenetic regulation have translational implications in the identification of new biomarkers and the development of new therapies in prostate cancer.
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Affiliation(s)
- Zhong Chen
- Department of Molecular & Cellular Biochemistry & Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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41
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Abstract
The Rb/E2F pathway is deregulated in virtually all human tumors. It is clear that, in addition to Rb itself, essential cofactors required for transcriptional repression and silencing of E2F target genes are mutated or lost in cancer. To identify novel cofactors required for Rb/E2F-mediated inhibition of cell proliferation, we performed a genome-wide short hairpin RNA screen. In addition to several known Rb cofactors, the screen identified components of the Mediator complex, a large multiprotein coactivator required for RNA polymerase II transcription. We show that the Mediator complex subunit MED13L is required for Rb/E2F control of cell growth, the complete repression of cell cycle target genes, and cell cycle inhibition.
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Rahman MT, Nakayama K, Rahman M, Nakayama N, Ishikawa M, Katagiri A, Iida K, Nakayama S, Otsuki Y, Shih IM, Miyazaki K. Prognostic and therapeutic impact of the chromosome 20q13.2 ZNF217 locus amplification in ovarian clear cell carcinoma. Cancer 2011; 118:2846-57. [DOI: 10.1002/cncr.26598] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2011] [Revised: 07/13/2011] [Accepted: 08/15/2011] [Indexed: 12/22/2022]
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Nunez N, Clifton MMK, Funnell APW, Artuz C, Hallal S, Quinlan KGR, Font J, Vandevenne M, Setiyaputra S, Pearson RCM, Mackay JP, Crossley M. The multi-zinc finger protein ZNF217 contacts DNA through a two-finger domain. J Biol Chem 2011; 286:38190-38201. [PMID: 21908891 DOI: 10.1074/jbc.m111.301234] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Classical C2H2 zinc finger proteins are among the most abundant transcription factors found in eukaryotes, and the mechanisms through which they recognize their target genes have been extensively investigated. In general, a tandem array of three fingers separated by characteristic TGERP links is required for sequence-specific DNA recognition. Nevertheless, a significant number of zinc finger proteins do not contain a hallmark three-finger array of this type, raising the question of whether and how they contact DNA. We have examined the multi-finger protein ZNF217, which contains eight classical zinc fingers. ZNF217 is implicated as an oncogene and in repressing the E-cadherin gene. We show that two of its zinc fingers, 6 and 7, can mediate contacts with DNA. We examine its putative recognition site in the E-cadherin promoter and demonstrate that this is a suboptimal site. NMR analysis and mutagenesis is used to define the DNA binding surface of ZNF217, and we examine the specificity of the DNA binding activity using fluorescence anisotropy titrations. Finally, sequence analysis reveals that a variety of multi-finger proteins also contain two-finger units, and our data support the idea that these may constitute a distinct subclass of DNA recognition motif.
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Affiliation(s)
- Noelia Nunez
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Molly M K Clifton
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Alister P W Funnell
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales 2052, Australia
| | - Crisbel Artuz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales 2052, Australia
| | - Samantha Hallal
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Kate G R Quinlan
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Josep Font
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Marylène Vandevenne
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Surya Setiyaputra
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Richard C M Pearson
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales 2052, Australia
| | - Joel P Mackay
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Merlin Crossley
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales 2052, Australia.
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Mao XG, Yan M, Xue XY, Zhang X, Ren HG, Guo G, Wang P, Zhang W, Huo JL. Overexpression of ZNF217 in glioblastoma contributes to the maintenance of glioma stem cells regulated by hypoxia-inducible factors. J Transl Med 2011; 91:1068-78. [PMID: 21483406 DOI: 10.1038/labinvest.2011.56] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Glioblastoma multiforme (GBM) is the most aggressive and common kind of primary brain tumor in adults, and is thought to be driven by a subpopulation of glioma stem cells (GSCs). GSCs reside in a specialized hypoxic niche, which can regulate the tumorigenic capacity of GSCs primarily through the hypoxia-inducible factors (HIFs), HIF1α and HIF2α. ZNF217 is an oncogene frequently amplified in many kinds of tumors. It is associated with aggressive tumor behavior and poor clinical prognosis, but its role in gliomas is poorly known. Gene expression and copy number analysis from TCGA data reveal that ZNF217 is amplified in 32% and overexpressed in 71.2% of GBMs. Quantitative RT-PCR and western blotting of a cohort of glioma samples showed that ZNF217 was highly expressed in gliomas and increased with tumor grade. Analysis of a molecular database demonstrated that ZNF217 expression correlated with poor survival of glioma patients. Investigation of ZNF217 expression in GSCs, non-GSCs and normal neural stem cells (NSCs) indicated that ZNF217 was more highly expressed in GSCs than in non-GSCs and NSCs. Knockdown of ZNF217 in GSCs by small-interfering RNA (siRNA) inhibited their growth and promoted their differentiation. Interestingly, ZNF217 was upregulated in GSCs and the GBM cell line U87 when exposed to the hypoxic environment of 1% oxygen. Knockdown of either HIF1α or HIF2α, which has a central role in the hypoxia-induced responses of these cells, inhibited ZNF217 expression. In addition, ZNF217 upregulation was compromised under hypoxia in U87 and GSCs when either HIF1α or HIF2α was targeted by siRNA. HIF2α knockdown inhibited ZNF217 expression more efficiently in both normoxia and hypoxia than HIF1α knockdown. Therefore, ZNF217 is overexpressed in GBMs and contributes to the maintenance of GSCs, which is regulated by HIFs released by the hypoxic environment of the tumor.
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Affiliation(s)
- Xing-gang Mao
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
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Abstract
There is increasing evidence that miRNA and transcription factors interact in an instructive fashion in normal and malignant hematopoiesis. We explored the impact of TEL-AML1 (ETV6-RUNX1), the most common fusion protein in childhood leukemia, on miRNA expression and the leukemic phenotype. Using RNA interference, miRNA expression arrays, and quantitative polymerase chain reaction, we identified miRNA-494 and miRNA-320a to be up-regulated upon TEL-AML1 silencing independently of TEL expression. Chromatin immunoprecipitation analysis identified miRNA-494 as a direct miRNA target of the fusion protein TEL-AML1. Using bioinformatic analysis as well as functional luciferase experiments, we demonstrate that survivin is a target of the 2 miRNAs. miRNA-494 and miRNA-320a were introduced to the cells by transfection and survivin expression determined by Western blot analysis. These miRNAs blocked survivin expression and resulted in apoptosis in a similar manner as TEL-AML1 silencing by itself; this silencing was also shown to be Dicer-dependent. miRNAs-494 and -320a are expressed at lower levels in TEL-AML1+ leukemias compared with immunophenotype-matched nonTEL-AML1 acute lymphoblastic leukemia subtypes, and within TEL-AML1+ leukemias their expression is correlated to survivin levels. In summary our data suggest that TEL-AML1 might exert its antiapoptotic action at least in part by suppressing miRNA-494 and miRNA-320a, lowering their expression causing enhanced survivin expression.
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ZNF217, a candidate breast cancer oncogene amplified at 20q13, regulates expression of the ErbB3 receptor tyrosine kinase in breast cancer cells. Oncogene 2010; 29:5500-10. [PMID: 20661224 PMCID: PMC4256946 DOI: 10.1038/onc.2010.289] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Understanding the mechanisms underlying ErbB3 overexpression in breast cancer will facilitate the rational design of therapies to disrupt ErbB2-ErbB3 oncogenic function. Although ErbB3 overexpression is frequently observed in breast cancer, the factors mediating its aberrant expression are poorly understood. In particular, the ErbB3 gene is not significantly amplified, raising the question as to how ErbB3 overexpression is achieved. In this study we showed that the ZNF217 transcription factor, amplified at 20q13 in ∼20% of breast tumors, regulates ErbB3 expression. Analysis of a panel of human breast cancer cell lines (n = 50) and primary human breast tumors (n = 15) showed a strong positive correlation between ZNF217 and ErbB3 expression. Ectopic expression of ZNF217 in human mammary epithelial cells induced ErbB3 expression, whereas ZNF217 silencing in breast cancer cells resulted in decreased ErbB3 expression. Although ZNF217 has previously been linked with transcriptional repression because of its close association with C-terminal-binding protein (CtBP)1/2 repressor complexes, our results show that ZNF217 also activates gene expression. We showed that ZNF217 recruitment to the ErbB3 promoter is CtBP1/2-independent and that ZNF217 and CtBP1/2 have opposite roles in regulating ErbB3 expression. In addition, we identify ErbB3 as one of the mechanisms by which ZNF217 augments PI-3K/Akt signaling.
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Abu-Helo A, Simonin F. Identification and biological significance of G protein-coupled receptor associated sorting proteins (GASPs). Pharmacol Ther 2010; 126:244-50. [PMID: 20394773 DOI: 10.1016/j.pharmthera.2010.03.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 03/23/2010] [Indexed: 12/25/2022]
Abstract
G protein-coupled receptors (GPCRs) represent one of the most abundant protein families encoded by the human genome. They are involved in the modulation of numerous physiological functions and represent major drug targets. Their activity is tightly controlled by a vast array of interacting partners that modulate their membrane targeting, intracellular trafficking and signalling properties. Among them, several proteins from the same family, G protein-coupled receptor associated sorting proteins (GASP), have been shown to display a broad spectrum of interactions with GPCRs. In addition to their postulated role in the modulation of the post-endocytic sorting of these receptors, recent data indicate that several GASPs may modulate the transcriptional activity of the cell through their interaction with transcription factors. However, no clear molecular function has been assigned yet to this protein family. In this review, we describe the discovery of GASPs, their major features, interacting partners, functions and possible involvement in pathological situations including neurodegenerative diseases and cancer.
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Affiliation(s)
- Alaa Abu-Helo
- Institut de Recherche de l'ESBS, CNRS - Université de Strasbourg, FRE3211, Bld Sébastien Brant, 67412 Illkirch, France
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Kusama Y, Takayanagi S, Tategu M, Yoshida K. Expression and tissue distribution of human X-linked armadillo repeat containing-6. Exp Ther Med 2010; 1:395-399. [PMID: 22993554 DOI: 10.3892/etm_00000062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Accepted: 01/29/2010] [Indexed: 11/06/2022] Open
Abstract
The armadillo family of proteins has been implicated in embryogenesis and tumorigenesis. Armadillo repeat containing X-linked (ARMCX)1-6 and its most closely related protein, ARMC10, share an uncharacterized domain in their carboxyl-terminal region and thereby constitute a unique subfamily. We previously detected an elevated ARMCX6 mRNA level in human cervical carcinoma (HeLa) cells in which the cyclin-dependent kinase inhibitor 2A products (p16INK4A and p14ARF) were silenced by RNA interference; however, the function of the ARMCX6 gene has yet to be determined. In the present study, we demonstrated that ARMCX6 tagged with green fluorescent protein was localized in the cytoplasm of HeLa cells. ARMCX6 mRNA was highly detected in the pancreas and spleen, indicating a tissue-specific expression pattern in human tissues. Taken together, these results suggest that ARMCX6 may be uniquely involved in a specific cellular function of certain tissues.
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Affiliation(s)
- Yusuke Kusama
- Department of Life Sciences, Faculty of Agriculture, Meiji University, Kanagawa 214-8571, Japan
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Kojima T, Hashimoto Y, Kato M, Kobayashi T, Nakano H. High-throughput screening of DNA binding sites for transcription factor AmyR from Aspergillus nidulans using DNA beads display system. J Biosci Bioeng 2010; 109:519-25. [PMID: 20471587 DOI: 10.1016/j.jbiosc.2009.11.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 11/22/2009] [Accepted: 11/29/2009] [Indexed: 11/17/2022]
Abstract
We established a high-throughput screening method for the DNA binding sequence of a eukaryotic transcription factor by using the bead display system with emulsion PCR and flow cytometry and applied it for identifying a eukaryotic transcriptional activator AmyR, which is known to regulate amylolytic gene expression in Aspergillus species. Segmented parts of the binding site of AmyR were randomized to make a DNA library on beads, onto which MalE-tagged AmyR protein and fluorescent anti-MalE tag antibody were bound, followed by selection with a flow cytometer. From a library replacing well-conserved six nucleotides (CGG-CGG) to random ones, the consensus sequence was recovered at a high frequency, demonstrating the reliability of the screening system. Interestingly, similar analysis for another library having randomized intermediate eight nucleotides between the conserved triplets revealed that the selected intermediate sequence had a strong preference for the T nucleotide. Moreover, exactly the same sequence with the upstream region of amyB, a typical AmyR-regulated gene, was found in the selection. These results suggest that this screening system will be a powerful tool for high-throughput analysis of the eukaryotic transcriptome.
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Affiliation(s)
- Takaaki Kojima
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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50
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Murphy DM, Buckley PG, Bryan K, Das S, Alcock L, Foley NH, Prenter S, Bray I, Watters KM, Higgins D, Stallings RL. Global MYCN transcription factor binding analysis in neuroblastoma reveals association with distinct E-box motifs and regions of DNA hypermethylation. PLoS One 2009; 4:e8154. [PMID: 19997598 PMCID: PMC2781550 DOI: 10.1371/journal.pone.0008154] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 11/09/2009] [Indexed: 01/19/2023] Open
Abstract
Background Neuroblastoma, a cancer derived from precursor cells of the sympathetic nervous system, is a major cause of childhood cancer related deaths. The single most important prognostic indicator of poor clinical outcome in this disease is genomic amplification of MYCN, a member of a family of oncogenic transcription factors. Methodology We applied MYCN chromatin immunoprecipitation to microarrays (ChIP-chip) using MYCN amplified/non-amplified cell lines as well as a conditional knockdown cell line to determine the distribution of MYCN binding sites within all annotated promoter regions. Conclusion Assessment of E-box usage within consistently positive MYCN binding sites revealed a predominance for the CATGTG motif (p<0.0016), with significant enrichment of additional motifs CATTTG, CATCTG, CAACTG in the MYCN amplified state. For cell lines over-expressing MYCN, gene ontology analysis revealed enrichment for the binding of MYCN at promoter regions of numerous molecular functional groups including DNA helicases and mRNA transcriptional regulation. In order to evaluate MYCN binding with respect to other genomic features, we determined the methylation status of all annotated CpG islands and promoter sequences using methylated DNA immunoprecipitation (MeDIP). The integration of MYCN ChIP-chip and MeDIP data revealed a highly significant positive correlation between MYCN binding and DNA hypermethylation. This association was also detected in regions of hemizygous loss, indicating that the observed association occurs on the same homologue. In summary, these findings suggest that MYCN binding occurs more commonly at CATGTG as opposed to the classic CACGTG E-box motif, and that disease associated over expression of MYCN leads to aberrant binding to additional weaker affinity E-box motifs in neuroblastoma. The co-localization of MYCN binding and DNA hypermethylation further supports the dual role of MYCN, namely that of a classical transcription factor affecting the activity of individual genes, and that of a mediator of global chromatin structure.
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Affiliation(s)
- Derek M. Murphy
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
| | - Patrick G. Buckley
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
| | - Kenneth Bryan
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
| | - Sudipto Das
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
| | - Leah Alcock
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
| | - Niamh H. Foley
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
| | - Suzanne Prenter
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
| | - Isabella Bray
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
| | - Karen M. Watters
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
| | - Desmond Higgins
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Raymond L. Stallings
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
- * E-mail:
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